1
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Mejzini R, Caruthers MH, Schafer B, Kostov O, Sudheendran K, Ciba M, Danielsen M, Wilton S, Akkari PA, Flynn LL. Allele-Selective Thiomorpholino Antisense Oligonucleotides as a Therapeutic Approach for Fused-in-Sarcoma Amyotrophic Lateral Sclerosis. Int J Mol Sci 2024; 25:8495. [PMID: 39126066 PMCID: PMC11312655 DOI: 10.3390/ijms25158495] [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: 06/28/2024] [Revised: 07/31/2024] [Accepted: 07/31/2024] [Indexed: 08/12/2024] Open
Abstract
Pathogenic variations in the fused in sarcoma (FUS) gene are associated with rare and aggressive forms of amyotrophic lateral sclerosis (ALS). As FUS-ALS is a dominant disease, a targeted, allele-selective approach to FUS knockdown is most suitable. Antisense oligonucleotides (AOs) are a promising therapeutic platform for treating such diseases. In this study, we have explored the potential for allele-selective knockdown of FUS. Gapmer-type AOs targeted to two common neutral polymorphisms in FUS were designed and evaluated in human fibroblasts. AOs had either methoxyethyl (MOE) or thiomorpholino (TMO) modifications. We found that the TMO modification improved allele selectivity and efficacy for the lead sequences when compared to the MOE counterparts. After TMO-modified gapmer knockdown of the target allele, up to 93% of FUS transcripts detected were from the non-target allele. Compared to MOE-modified AOs, the TMO-modified AOs also demonstrated reduced formation of structured nuclear inclusions and SFPQ aggregation that can be triggered by phosphorothioate-containing AOs. How overall length and gap length of the TMO-modified AOs affected allele selectivity, efficiency and off-target gene knockdown was also evaluated. We have shown that allele-selective knockdown of FUS may be a viable therapeutic strategy for treating FUS-ALS and demonstrated the benefits of the TMO modification for allele-selective applications.
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Affiliation(s)
- Rita Mejzini
- Centre for Molecular Medicine and Innovative Therapeutics, Health Futures Institute, Murdoch University, Murdoch, WA 6150, Australia; (S.W.); (P.A.A.); (L.L.F.)
- The Perron Institute for Neurological and Translational Science, Nedlands, WA 6009, Australia
| | - Marvin H. Caruthers
- Department of Biochemistry, University of Colorado, Boulder, CO 80309, USA; (M.H.C.); (B.S.); (O.K.); (K.S.); (M.C.); (M.D.)
| | - Balazs Schafer
- Department of Biochemistry, University of Colorado, Boulder, CO 80309, USA; (M.H.C.); (B.S.); (O.K.); (K.S.); (M.C.); (M.D.)
| | - Ondrej Kostov
- Department of Biochemistry, University of Colorado, Boulder, CO 80309, USA; (M.H.C.); (B.S.); (O.K.); (K.S.); (M.C.); (M.D.)
| | - Kavitha Sudheendran
- Department of Biochemistry, University of Colorado, Boulder, CO 80309, USA; (M.H.C.); (B.S.); (O.K.); (K.S.); (M.C.); (M.D.)
| | - Marija Ciba
- Department of Biochemistry, University of Colorado, Boulder, CO 80309, USA; (M.H.C.); (B.S.); (O.K.); (K.S.); (M.C.); (M.D.)
| | - Mathias Danielsen
- Department of Biochemistry, University of Colorado, Boulder, CO 80309, USA; (M.H.C.); (B.S.); (O.K.); (K.S.); (M.C.); (M.D.)
| | - Steve Wilton
- Centre for Molecular Medicine and Innovative Therapeutics, Health Futures Institute, Murdoch University, Murdoch, WA 6150, Australia; (S.W.); (P.A.A.); (L.L.F.)
- The Perron Institute for Neurological and Translational Science, Nedlands, WA 6009, Australia
- Centre for Neuromuscular and Neurological Disorders, University of Western Australia, Crawley, WA 6009, Australia
| | - Patrick Anthony Akkari
- Centre for Molecular Medicine and Innovative Therapeutics, Health Futures Institute, Murdoch University, Murdoch, WA 6150, Australia; (S.W.); (P.A.A.); (L.L.F.)
- The Perron Institute for Neurological and Translational Science, Nedlands, WA 6009, Australia
- Black Swan Pharmaceuticals, Wake Forest, NC 27587, USA
- Department of Neurology, Duke University, Durham, NC 27708, USA
| | - Loren L. Flynn
- Centre for Molecular Medicine and Innovative Therapeutics, Health Futures Institute, Murdoch University, Murdoch, WA 6150, Australia; (S.W.); (P.A.A.); (L.L.F.)
- The Perron Institute for Neurological and Translational Science, Nedlands, WA 6009, Australia
- Centre for Neuromuscular and Neurological Disorders, University of Western Australia, Crawley, WA 6009, Australia
- Black Swan Pharmaceuticals, Wake Forest, NC 27587, USA
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2
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Matsubayashi T, Yoshioka K, Lei Mon SS, Katsuyama M, Jia C, Yamaguchi T, Hara RI, Nagata T, Nakagawa O, Obika S, Yokota T. Favorable efficacy and reduced acute neurotoxicity by antisense oligonucleotides with 2',4'-BNA/LNA with 9-(aminoethoxy)phenoxazine. MOLECULAR THERAPY. NUCLEIC ACIDS 2024; 35:102161. [PMID: 38978695 PMCID: PMC11229412 DOI: 10.1016/j.omtn.2024.102161] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/14/2023] [Accepted: 02/28/2024] [Indexed: 07/10/2024]
Abstract
An increasing number of antisense oligonucleotides (ASOs) have been approved for clinical use. However, improvements of both efficacy and safety in the central nervous system (CNS) are crucial for the treatment with CNS diseases. We aimed to overcome the crucial issues by our development of various gapmer ASOs with a novel nucleoside derivative including a 2',4'-BNA/LNA with 9-(aminoethoxy)phenoxazine (BNAP-AEO). The various gapmer ASOs with BNAP-AEO were evaluated for thermal stability, in vitro and in vivo efficacy, and acute CNS toxicity. Thermal stability analysis of the duplexes with their complementary RNAs showed that ASOs with BNAP-AEO had a higher binding affinity than those without BNAP-AEO. In vitro assays, when transfected into neuroblastoma cell lines, demonstrated that ASOs with BNAP-AEO, had a more efficient gene silencing effect than those without BNAP-AEO. In vivo assays, involving intracerebroventricular injections into mice, revealed ASOs with BNAP-AEO potently suppressed gene expression in the brain. Surprisingly, the acute CNS toxicity in mice, as assessed through open field tests and scoring systems, was significantly lower for ASOs with BNAP-AEO than for those without BNAP-AEO. This study underscores the efficient gene-silencing effect and low acute CNS toxicity of ASOs incorporating BNAP-AEO, indicating the potential for future therapeutic applications.
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Affiliation(s)
- Taiki Matsubayashi
- Department of Neurology and Neurological Science, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, 1-5-45 Yushima, Bunkyo-Ku, Tokyo 113-8519, Japan
| | - Kotaro Yoshioka
- Department of Neurology and Neurological Science, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, 1-5-45 Yushima, Bunkyo-Ku, Tokyo 113-8519, Japan
| | - Su Su Lei Mon
- Department of Neurology and Neurological Science, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, 1-5-45 Yushima, Bunkyo-Ku, Tokyo 113-8519, Japan
| | - Maho Katsuyama
- Department of Neurology and Neurological Science, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, 1-5-45 Yushima, Bunkyo-Ku, Tokyo 113-8519, Japan
| | - Chunyan Jia
- Department of Neurology and Neurological Science, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, 1-5-45 Yushima, Bunkyo-Ku, Tokyo 113-8519, Japan
| | - Takao Yamaguchi
- Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka Suita, Osaka 565-0871, Japan
| | - Rintaro Iwata Hara
- Department of Neurology and Neurological Science, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, 1-5-45 Yushima, Bunkyo-Ku, Tokyo 113-8519, Japan
| | - Tetsuya Nagata
- Department of Neurology and Neurological Science, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, 1-5-45 Yushima, Bunkyo-Ku, Tokyo 113-8519, Japan
| | - Osamu Nakagawa
- Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka Suita, Osaka 565-0871, Japan
- Faculty of Pharmaceutical Sciences, Tokushima Bunri University, 180 Nishihamahoji, Yamashiro-cho, Tokushima 770-8514, Japan
| | - Satoshi Obika
- Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka Suita, Osaka 565-0871, Japan
| | - Takanori Yokota
- Department of Neurology and Neurological Science, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, 1-5-45 Yushima, Bunkyo-Ku, Tokyo 113-8519, Japan
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3
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Story S, Bhaduri S, Ganguly S, Dakarapu R, Wicks SL, Bhadra J, Kwange S, Arya DP. Understanding Antisense Oligonucleotide Efficiency in Inhibiting Prokaryotic Gene Expression. ACS Infect Dis 2024; 10:971-987. [PMID: 38385613 DOI: 10.1021/acsinfecdis.3c00645] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/23/2024]
Abstract
Oligonucleotides offer a unique opportunity for sequence specific regulation of gene expression in bacteria. A fundamental question to address is the choice of oligonucleotide, given the large number of options available. Different modifications varying in RNA binding affinities and cellular uptake are available but no comprehensive comparisons have been performed. Herein, the efficiency of blocking expression of β-galactosidase (β-Gal) in E. coli was evaluated utilizing different antisense oligomers (ASOs). Fluorescein (FAM)-labeled oligomers were used to understand their differences in bacterial uptake. Flow cytometry analysis revealed significant differences in uptake, with high fluorescence seen in cells treated with FAM-labeled peptidic nucleic acid (PNA), phosphorodiamidate morpholino oligonucleotide (PMO) and phosphorothioate (PS) oligomers, and low fluorescence observed in cells treated with phosphodiester (PO) oligomers. Thermal denaturation (Tm) of oligomer:RNA duplexes and isothermal titration calorimetry (ITC) studies reveal that ASO binding to target RNA demonstrates a good correlation between Tm and Kd values. There was no correlation between Kd values and reduction of β-Gal activity in bacterial cells. However, cell-free translation assays demonstrated a direct relationship between Kd values and inhibition of gene expression by antisense oligomers, with tight binding oligomers such as LNA being the most efficient. Membrane active compounds such as polymyxin B and A22 further improved the cellular uptake of FAM-PNA and FAM-PS oligomers in wild-type E. coli cells. PNA and PMO were most effective in cellular uptake and reducing β-Gal activity as compared to oligomers with PS or those with PO linkages. Overall, cell uptake of the oligomers is shown as the key determinant in predicting their differences in bacterial antisense inhibition, and the RNA affinity is the key determinant in inhibition of gene expression in cell free systems.
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Affiliation(s)
- Sandra Story
- NUBAD, LLC, Greenville, South Carolina 29605, United States
| | | | - Sudakshina Ganguly
- Laboratory of Medicinal Chemistry, Department of Chemistry, Clemson University, Clemson, South Carolina 29634, United States
| | | | - Sarah L Wicks
- NUBAD, LLC, Greenville, South Carolina 29605, United States
| | - Jhuma Bhadra
- Laboratory of Medicinal Chemistry, Department of Chemistry, Clemson University, Clemson, South Carolina 29634, United States
| | - Simeon Kwange
- NUBAD, LLC, Greenville, South Carolina 29605, United States
| | - Dev P Arya
- Laboratory of Medicinal Chemistry, Department of Chemistry, Clemson University, Clemson, South Carolina 29634, United States
- NUBAD, LLC, Greenville, South Carolina 29605, United States
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4
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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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5
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Yamaji R, Nakagawa O, Kishimoto Y, Fujii A, Matsumura T, Nakayama T, Kamada H, Osawa T, Yamaguchi T, Obika S. Synthesis and physical and biological properties of 1,3-diaza-2-oxophenoxazine-conjugated oligonucleotides. Bioorg Med Chem 2022; 72:116972. [DOI: 10.1016/j.bmc.2022.116972] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2022] [Revised: 08/18/2022] [Accepted: 08/19/2022] [Indexed: 11/26/2022]
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6
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Helm J, Schöls L, Hauser S. Towards Personalized Allele-Specific Antisense Oligonucleotide Therapies for Toxic Gain-of-Function Neurodegenerative Diseases. Pharmaceutics 2022; 14:pharmaceutics14081708. [PMID: 36015334 PMCID: PMC9416334 DOI: 10.3390/pharmaceutics14081708] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2022] [Revised: 08/11/2022] [Accepted: 08/12/2022] [Indexed: 11/29/2022] Open
Abstract
Antisense oligonucleotides (ASOs) are single-stranded nucleic acid strings that can be used to selectively modify protein synthesis by binding complementary (pre-)mRNA sequences. By specific arrangements of DNA and RNA into a chain of nucleic acids and additional modifications of the backbone, sugar, and base, the specificity and functionality of the designed ASOs can be adjusted. Thereby cellular uptake, toxicity, and nuclease resistance, as well as binding affinity and specificity to its target (pre-)mRNA, can be modified. Several neurodegenerative diseases are caused by autosomal dominant toxic gain-of-function mutations, which lead to toxic protein products driving disease progression. ASOs targeting such mutations—or even more comprehensively, associated variants, such as single nucleotide polymorphisms (SNPs)—promise a selective degradation of the mutant (pre-)mRNA while sparing the wild type allele. By this approach, protein expression from the wild type strand is preserved, and side effects from an unselective knockdown of both alleles can be prevented. This makes allele-specific targeting strategies a focus for future personalized therapies. Here, we provide an overview of current strategies to develop personalized, allele-specific ASO therapies for the treatment of neurodegenerative diseases, such Huntington’s disease (HD) and spinocerebellar ataxia type 3 (SCA3/MJD).
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Affiliation(s)
- Jacob Helm
- German Center for Neurodegenerative Diseases (DZNE), 72076 Tübingen, Germany
- Hertie Institute for Clinical Brain Research and Department of Neurology, University of Tübingen, 72076 Tübingen, Germany
- Graduate School of Cellular and Molecular Neuroscience, University of Tübingen, 72076 Tübingen, Germany
| | - Ludger Schöls
- German Center for Neurodegenerative Diseases (DZNE), 72076 Tübingen, Germany
- Hertie Institute for Clinical Brain Research and Department of Neurology, University of Tübingen, 72076 Tübingen, Germany
| | - Stefan Hauser
- German Center for Neurodegenerative Diseases (DZNE), 72076 Tübingen, Germany
- Hertie Institute for Clinical Brain Research and Department of Neurology, University of Tübingen, 72076 Tübingen, Germany
- Correspondence:
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7
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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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8
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Deprey K, Batistatou N, Debets MF, Godfrey J, VanderWall KB, Miles RR, Shehaj L, Guo J, Andreucci A, Kandasamy P, Lu G, Shimizu M, Vargeese C, Kritzer JA. Quantitative Measurement of Cytosolic and Nuclear Penetration of Oligonucleotide Therapeutics. ACS Chem Biol 2022; 17:348-360. [PMID: 35034446 PMCID: PMC9252293 DOI: 10.1021/acschembio.1c00830] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A major obstacle in the development of effective oligonucleotide therapeutics is a lack of understanding about their cytosolic and nuclear penetration. To address this problem, we have applied the chloroalkane penetration assay (CAPA) to oligonucleotide therapeutics. CAPA was used to quantitate cytosolic delivery of antisense oligonucleotides (ASOs) and siRNAs and to explore the effects of a wide variety of commonly used chemical modifications and their patterning. We evaluated potential artifacts by exploring the effects of serum, comparing activity data and CAPA data, and assessing the impact of the chloroalkane tag and its linker chemistry. We also used viral transduction to expand CAPA to the nuclear compartment in epithelial and neuronal cell lines. Using this enhanced method, we measured a 48-h time course of nuclear penetration for a panel of chemically diverse modified RNAs. Moving forward, CAPA will be a useful tool for deconvoluting the complex processes of endosomal uptake, escape into the cytosol, and subcellular trafficking of oligonucleotide therapeutics in therapeutically relevant cell types.
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Affiliation(s)
- Kirsten Deprey
- Department of Chemistry, Tufts University, Medford, Massachusetts 02155, United States
| | - Nefeli Batistatou
- Department of Chemistry, Tufts University, Medford, Massachusetts 02155, United States
| | - Marjoke F. Debets
- Lilly Research Laboratories, Eli Lilly and Company, Indianapolis, Indiana 46285, United States
| | - Jack Godfrey
- Wave Life Sciences, Cambridge, Massachusetts 02138, United States
| | - Kirstin B. VanderWall
- Lilly Research Laboratories, Eli Lilly and Company, Indianapolis, Indiana 46285, United States
| | - Rebecca R. Miles
- Lilly Research Laboratories, Eli Lilly and Company, Indianapolis, Indiana 46285, United States
| | - Livia Shehaj
- Department of Chemistry, Tufts University, Medford, Massachusetts 02155, United States
| | - Jiaxing Guo
- Department of Chemistry, Tufts University, Medford, Massachusetts 02155, United States
| | - Amy Andreucci
- Wave Life Sciences, Cambridge, Massachusetts 02138, United States
| | | | - Genliang Lu
- Wave Life Sciences, Cambridge, Massachusetts 02138, United States
| | - Mamoru Shimizu
- Wave Life Sciences, Cambridge, Massachusetts 02138, United States
| | - Chandra Vargeese
- Wave Life Sciences, Cambridge, Massachusetts 02138, United States
| | - Joshua A. Kritzer
- Department of Chemistry, Tufts University, Medford, Massachusetts 02155, United States,corresponding author:
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9
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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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10
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García-Garrido E, Cordani M, Somoza Á. Modified Gold Nanoparticles to Overcome the Chemoresistance to Gemcitabine in Mutant p53 Cancer Cells. Pharmaceutics 2021; 13:2067. [PMID: 34959348 PMCID: PMC8703659 DOI: 10.3390/pharmaceutics13122067] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Revised: 11/27/2021] [Accepted: 11/28/2021] [Indexed: 12/29/2022] Open
Abstract
Mutant p53 proteins result from missense mutations in the TP53 gene, the most mutated in human cancer, and have been described to contribute to cancer initiation and progression. Therapeutic strategies for targeting mutant p53 proteins in cancer cells are limited and have proved unsuitable for clinical application due to problems related to drug delivery and toxicity to healthy tissues. Therefore, the discovery of efficient and safe therapeutic strategies that specifically target mutant p53 remains challenging. In this study, we generated gold nanoparticles (AuNPs) chemically modified with low molecular branched polyethylenimine (bPEI) for the efficient delivery of gapmers targeting p53 mutant protein. The AuNPs formulation consists of a combination of polymeric mixed layer of polyethylene glycol (PEG) and PEI, and layer-by-layer assembly of bPEI through a sensitive linker. These nanoparticles can bind oligonucleotides through electrostatic interactions and release them in the presence of a reducing agent as glutathione. The nanostructures generated here provide a non-toxic and powerful system for the delivery of gapmers in cancer cells, which significantly downregulated mutant p53 proteins and altered molecular markers related to cell growth and apoptosis, thus overcoming chemoresistance to gemcitabine.
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Affiliation(s)
- Eduardo García-Garrido
- Instituto Madrileño de Estudios Avanzados en Nanociencia (IMDEA Nanociencia), Faraday 9, 28049 Madrid, Spain
| | - Marco Cordani
- Instituto Madrileño de Estudios Avanzados en Nanociencia (IMDEA Nanociencia), Faraday 9, 28049 Madrid, Spain
| | - Álvaro Somoza
- Instituto Madrileño de Estudios Avanzados en Nanociencia (IMDEA Nanociencia), Faraday 9, 28049 Madrid, Spain
- Unidad Asociada al Centro Nacional de Biotecnología (CSIC), Darwin 3, 28049 Madrid, Spain
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11
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Søgaard PP, Lind M, Christiansen CR, Petersson K, Clauss A, Caffarel-Salvador E. Future Perspectives of Oral Delivery of Next Generation Therapies for Treatment of Skin Diseases. Pharmaceutics 2021; 13:1722. [PMID: 34684016 PMCID: PMC8537019 DOI: 10.3390/pharmaceutics13101722] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2021] [Revised: 10/08/2021] [Accepted: 10/08/2021] [Indexed: 12/12/2022] Open
Abstract
Gene therapies have conspicuously bloomed in recent years as evidenced by the increasing number of cell-, gene-, and oligo-based approved therapies. These therapies hold great promise for dermatological disorders with high unmet need, for example, epidermolysis bullosa or pachyonychia congenita. Furthermore, the recent clinical success of clustered regularly interspaced short palindromic repeats (CRISPR) for genome editing in humans will undoubtedly contribute to defining a new wave of therapies. Like biologics, naked nucleic acids are denatured inside the gastrointestinal tract and need to be administered via injections. For a treatment to be effective, a sufficient amount of a given regimen needs to reach systemic circulation. Multiple companies are racing to develop novel oral drug delivery approaches to circumvent the proteolytic and acidic milieu of the gastrointestinal tract. In this review, we provide an overview of the evolution of the gene therapy landscape, with a deep focus on gene and oligonucleotide therapies in clinical trials aimed at treating skin diseases. We then examine the progress made in drug delivery, with particular attention on the peptide field and drug-device combinations that deliver macromolecules into the gastrointestinal tract. Such novel devices could potentially be applied to administer other therapeutics including genes and CRISPR-based systems.
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Affiliation(s)
- Pia Pernille Søgaard
- Regenerative Medicine Department, LEO Pharma A/S, Industriparken 55, 2750 Ballerup, Denmark; (P.P.S.); (C.R.C.); (A.C.)
| | - Marianne Lind
- Explorative Formulation and Technologies, LEO Pharma A/S, Industriparken 55, 2750 Ballerup, Denmark; (M.L.); (K.P.)
| | | | - Karsten Petersson
- Explorative Formulation and Technologies, LEO Pharma A/S, Industriparken 55, 2750 Ballerup, Denmark; (M.L.); (K.P.)
| | - Adam Clauss
- Regenerative Medicine Department, LEO Pharma A/S, Industriparken 55, 2750 Ballerup, Denmark; (P.P.S.); (C.R.C.); (A.C.)
| | - Ester Caffarel-Salvador
- Regenerative Medicine Department, LEO Pharma A/S, Industriparken 55, 2750 Ballerup, Denmark; (P.P.S.); (C.R.C.); (A.C.)
- LEO Science & Tech Hub, One Broadway, Cambridge, MA 02142, USA
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12
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Kishimoto Y, Fujii A, Nakagawa O, Obika S. Enhanced duplex- and triplex-forming ability and enzymatic resistance of oligodeoxynucleotides modified by a tricyclic thymine derivative. Org Biomol Chem 2021; 19:8063-8074. [PMID: 34494641 DOI: 10.1039/d1ob01462e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We designed and synthesized an artificial nucleic acid, [3-(1,2-dihydro-2-oxobenzo[b][1,8]naphthyridine)]-2'-deoxy-D-ribofuranose (OBN), with a tricyclic structure in a nucleobase as a thymidine analog. Oligodeoxynucleotides (ODNs) containing consecutive OBN displayed improved duplex-forming ability with complementary single-stranded (ss) RNA and triplex-forming ability with double-stranded DNA in comparison with ODNs composed of natural thymidine. OBN-modified ODNs also displayed enhanced enzymatic resistance compared with ODNs with natural thymidine and phosphorothioate modification, respectively, due to the structural steric hindrance of the nucleobase. The fluorescence spectra of OBN-modified ODNs showed sufficient fluorescence intensity with ssDNA and ssRNA, which is an advantageous feature for fluorescence imaging techniques of nucleic acids with longer emission wavelengths than bicyclic thymine (bT).
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Affiliation(s)
- Yuki Kishimoto
- Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka 565-0871, Japan.
- Core Research for Evolutional Science and Technology (CREST), Japan Sciences and Technology Agency (JST), 7 Gobancho, Chiyoda-ku, Tokyo 102-0076, Japan
| | - Akane Fujii
- Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka 565-0871, Japan.
- Core Research for Evolutional Science and Technology (CREST), Japan Sciences and Technology Agency (JST), 7 Gobancho, Chiyoda-ku, Tokyo 102-0076, Japan
| | - Osamu Nakagawa
- Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka 565-0871, Japan.
- Core Research for Evolutional Science and Technology (CREST), Japan Sciences and Technology Agency (JST), 7 Gobancho, Chiyoda-ku, Tokyo 102-0076, Japan
- Faculty of Pharmaceutical Sciences, Tokushima Bunri University, 180 Nishihamahoji, Yamashiro-cho, Tokushima 770-8514, Japan.
| | - Satoshi Obika
- Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka 565-0871, Japan.
- Core Research for Evolutional Science and Technology (CREST), Japan Sciences and Technology Agency (JST), 7 Gobancho, Chiyoda-ku, Tokyo 102-0076, Japan
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13
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Bibby G, Krasniqi B, Reddy I, Sekar D, Ross K. Capturing the RNA castle: Exploiting MicroRNA inhibition for wound healing. FEBS J 2021; 289:5137-5151. [PMID: 34403569 DOI: 10.1111/febs.16160] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Revised: 07/14/2021] [Accepted: 08/16/2021] [Indexed: 02/06/2023]
Abstract
The growing pipelines of RNA-based therapies herald new opportunities to deliver better patient outcomes for complex disorders such as chronic nonhealing wounds associated with diabetes. Members of the microRNA (miRNA) family of small noncoding RNAs have emerged as targets for diverse elements of cutaneous wound repair, and both miRNA enhancement with mimics or inhibition with antisense oligonucleotides represent tractable approaches for miRNA-directed wound healing. In this review, we focus on miRNA inhibition strategies to stimulate skin repair given advances in chemical modifications to enhance the performance of antisense miRNA (anti-miRs). We first explore miRNAs whose inhibition in keratinocytes promotes keratinocyte migration, an essential part of re-epithelialisation during wound repair. We then focus on miRNAs that can be targeted for inhibition in endothelial cells to promote neovascularisation for wound healing in the context of diabetic mouse models. The picture that emerges is that direct comparisons of different anti-miRNAs modifications are required to establish the most translationally viable options in the chronic wound environment, that direct comparisons of the impact of inhibition of different miRNAs are needed to quantify and rank their relative efficacies in promoting wound repair, and that a standardised human ex vivo model of the diabetic wound is needed to reduce reliance on mouse models that do not necessarily enhance mechanistic understanding of miRNA-targeted wound healing.
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Affiliation(s)
- George Bibby
- School of Pharmacy and Biomolecular Sciences, Liverpool John Moores University, UK
| | - Blerta Krasniqi
- School of Pharmacy and Biomolecular Sciences, Liverpool John Moores University, UK
| | - Izaak Reddy
- School of Pharmacy and Biomolecular Sciences, Liverpool John Moores University, UK
| | - Durairaj Sekar
- Dental Research Cell and Biomedical Research Unit (DRC-BRULAC), Saveetha Dental College and Hospitals, Saveetha Institute of Medical and Technical Science (SIMATS), Saveetha University, Chennai, India
| | - Kehinde Ross
- School of Pharmacy and Biomolecular Sciences, Liverpool John Moores University, UK
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14
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Nieskens TTG, Magnusson O, Andersson P, Söderberg M, Persson M, Sjögren AK. Nephrotoxic antisense oligonucleotide SPC5001 induces kidney injury biomarkers in a proximal tubule-on-a-chip. Arch Toxicol 2021; 95:2123-2136. [PMID: 33961089 DOI: 10.1007/s00204-021-03062-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Accepted: 04/28/2021] [Indexed: 01/02/2023]
Abstract
Antisense oligonucleotides (ASOs) are a promising therapeutic modality. However, failure to predict acute kidney injury induced by SPC5001 ASO observed in a clinical trial suggests the need for additional preclinical models to complement the preceding animal toxicity studies. To explore the utility of in vitro systems in this space, we evaluated the induction of nephrotoxicity and kidney injury biomarkers by SPC5001 in human renal proximal tubule epithelial cells (HRPTEC), cultured in 2D, and in a recently developed kidney proximal tubule-on-a-chip. 2D HRPTEC cultures were exposed to the nephrotoxic ASO SPC5001 or the safe control ASO 556089 (0.16-40 µM) for up to 72 h, targeting PCSK9 and MALAT1, respectively. Both ASOs induced a concentration-dependent downregulation of their respective mRNA targets but cytotoxicity (determined by LDH activity) was not observed at any concentration. Next, chip-cultured HRPTEC were exposed to SPC5001 (0.5 and 5 µM) and 556089 (1 and 10 µM) for 48 h to confirm downregulation of their respective target transcripts, with 74.1 ± 5.2% for SPC5001 (5 µM) and 79.4 ± 0.8% for 556089 (10 µM). During extended exposure for up to 20 consecutive days, only SPC5001 induced cytotoxicity (at the higher concentration; 5 µM), as evaluated by LDH in the perfusate medium. Moreover, perfusate levels of biomarkers KIM-1, NGAL, clusterin, osteopontin and VEGF increased 2.5 ± 0.2-fold, 3.9 ± 0.9-fold, 2.3 ± 0.6-fold, 3.9 ± 1.7-fold and 1.9 ± 0.4-fold respectively, in response to SPC5001, generating distinct time-dependent profiles. In conclusion, target downregulation, cytotoxicity and kidney injury biomarkers were induced by the clinically nephrotoxic ASO SPC5001, demonstrating the translational potential of this kidney on-a-chip.
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Affiliation(s)
- Tom T G Nieskens
- CVRM Safety, Clinical Pharmacology and Safety Sciences, R&D, AstraZeneca, Gothenburg, Pepparedsleden 1, 43150, Mölndal, Sweden
| | - Otto Magnusson
- CVRM Safety, Clinical Pharmacology and Safety Sciences, R&D, AstraZeneca, Gothenburg, Pepparedsleden 1, 43150, Mölndal, Sweden
| | - Patrik Andersson
- R&I Safety, Clinical Pharmacology and Safety Sciences, R&D, AstraZeneca, Gothenburg, Sweden
| | - Magnus Söderberg
- CVRM Safety, Clinical Pharmacology and Safety Sciences, R&D, AstraZeneca, Gothenburg, Pepparedsleden 1, 43150, Mölndal, Sweden
| | - Mikael Persson
- CVRM Safety, Clinical Pharmacology and Safety Sciences, R&D, AstraZeneca, Gothenburg, Pepparedsleden 1, 43150, Mölndal, Sweden
| | - Anna-Karin Sjögren
- CVRM Safety, Clinical Pharmacology and Safety Sciences, R&D, AstraZeneca, Gothenburg, Pepparedsleden 1, 43150, Mölndal, Sweden.
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15
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Tanaka H, Takata N, Sakurai Y, Yoshida T, Inoue T, Tamagawa S, Nakai Y, Tange K, Yoshioka H, Maeki M, Tokeshi M, Akita H. Delivery of Oligonucleotides Using a Self-Degradable Lipid-Like Material. Pharmaceutics 2021; 13:pharmaceutics13040544. [PMID: 33924589 PMCID: PMC8070490 DOI: 10.3390/pharmaceutics13040544] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Revised: 04/05/2021] [Accepted: 04/05/2021] [Indexed: 11/16/2022] Open
Abstract
The world-first success of lipid nanoparticle (LNP)-based siRNA therapeutics (ONPATTRO®) promises to accelerate developments in siRNA therapeutics/gene therapy using LNP-type drug delivery systems (DDS). In this study, we explore the optimal composition of an LNP containing a self-degradable material (ssPalmO-Phe) for the delivery of oligonucleotides. siRNA or antisense oligonucleotides (ASO) were encapsulated in LNP with different lipid compositions. The hepatic knockdown efficiency of the target genes and liver toxicity were evaluated. The optimal compositions for the siRNA were different from those for ASO, and different from those for mRNA that were reported in a previous study. Extracellular stability, endosomal escape and cellular uptake appear to be the key processes for the successful delivery of mRNA, siRNA and ASO, respectively. Moreover, the compositions of the LNPs likely contribute to their toxicity. The lipid composition of the LNP needs to be optimized depending on the type of nucleic acids under consideration if the applications of LNPs are to be further expanded.
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Affiliation(s)
- Hiroki Tanaka
- Laboratory of DDS Design and Drug Disposition, Graduate School of Pharmaceutical Sciences, Chiba University, 1-8-1 Inohana, Chuo-ku, Chiba City, Chiba 260-0856, Japan; (H.T.); (N.T.); (Y.S.)
| | - Nae Takata
- Laboratory of DDS Design and Drug Disposition, Graduate School of Pharmaceutical Sciences, Chiba University, 1-8-1 Inohana, Chuo-ku, Chiba City, Chiba 260-0856, Japan; (H.T.); (N.T.); (Y.S.)
| | - Yu Sakurai
- Laboratory of DDS Design and Drug Disposition, Graduate School of Pharmaceutical Sciences, Chiba University, 1-8-1 Inohana, Chuo-ku, Chiba City, Chiba 260-0856, Japan; (H.T.); (N.T.); (Y.S.)
| | - Tokuyuki Yoshida
- Division of Molecular Target and Gene Therapy Products, National Institute of Health Sciences, 3-25-26 Tonomachi, Kawasaki-ku, Kawasaki, Kanagawa 210-9501, Japan; (T.Y.); (T.I.)
| | - Takao Inoue
- Division of Molecular Target and Gene Therapy Products, National Institute of Health Sciences, 3-25-26 Tonomachi, Kawasaki-ku, Kawasaki, Kanagawa 210-9501, Japan; (T.Y.); (T.I.)
| | - Shinya Tamagawa
- DDS Research Laboratory, NOF CORPORATION, 3-3 Chidori-cho, Kawasaki-ku, Kawasaki City, Kanagawa 210-0865, Japan; (S.T.); (Y.N.); (K.T.); (H.Y.)
| | - Yuta Nakai
- DDS Research Laboratory, NOF CORPORATION, 3-3 Chidori-cho, Kawasaki-ku, Kawasaki City, Kanagawa 210-0865, Japan; (S.T.); (Y.N.); (K.T.); (H.Y.)
| | - Kota Tange
- DDS Research Laboratory, NOF CORPORATION, 3-3 Chidori-cho, Kawasaki-ku, Kawasaki City, Kanagawa 210-0865, Japan; (S.T.); (Y.N.); (K.T.); (H.Y.)
| | - Hiroki Yoshioka
- DDS Research Laboratory, NOF CORPORATION, 3-3 Chidori-cho, Kawasaki-ku, Kawasaki City, Kanagawa 210-0865, Japan; (S.T.); (Y.N.); (K.T.); (H.Y.)
| | - Masatoshi Maeki
- Division of Applied Chemistry, Faculty of Engineering, Hokkaido University, Kita 13, Nishi 8, Kita-ku, Sapporo, Hokkaido 060-8628, Japan; (M.M.); (M.T.)
| | - Manabu Tokeshi
- Division of Applied Chemistry, Faculty of Engineering, Hokkaido University, Kita 13, Nishi 8, Kita-ku, Sapporo, Hokkaido 060-8628, Japan; (M.M.); (M.T.)
| | - Hidetaka Akita
- Laboratory of DDS Design and Drug Disposition, Graduate School of Pharmaceutical Sciences, Chiba University, 1-8-1 Inohana, Chuo-ku, Chiba City, Chiba 260-0856, Japan; (H.T.); (N.T.); (Y.S.)
- Correspondence: ; Tel.: +81-43-226-2893
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16
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Hofmans M, Lammens T, Depreter B, Wu Y, Erlacher M, Caye A, Cavé H, Flotho C, de Haas V, Niemeyer CM, Stary J, Van Nieuwerburgh F, Deforce D, Van Loocke W, Van Vlierberghe P, Philippé J, De Moerloose B. Long non-coding RNAs as novel therapeutic targets in juvenile myelomonocytic leukemia. Sci Rep 2021; 11:2801. [PMID: 33531590 PMCID: PMC7854679 DOI: 10.1038/s41598-021-82509-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2020] [Accepted: 01/20/2021] [Indexed: 12/15/2022] Open
Abstract
Juvenile myelomonocytic leukemia (JMML) treatment primarily relies on hematopoietic stem cell transplantation and results in long-term overall survival of 50-60%, demonstrating a need to develop novel treatments. Dysregulation of the non-coding RNA transcriptome has been demonstrated before in this rare and unique disorder of early childhood. In this study, we investigated the therapeutic potential of targeting overexpressed long non-coding RNAs (lncRNAs) in JMML. Total RNA sequencing of bone marrow and peripheral blood mononuclear cell preparations from 19 untreated JMML patients and three healthy children revealed 185 differentially expressed lncRNA genes (131 up- and 54 downregulated). LNA GapmeRs were designed for 10 overexpressed and validated lncRNAs. Molecular knockdown (≥ 70% compared to mock control) after 24 h of incubation was observed with two or more independent GapmeRs in 6 of them. For three lncRNAs (lnc-THADA-4, lnc-ACOT9-1 and NRIR) knockdown resulted in a significant decrease of cell viability after 72 h of incubation in primary cultures of JMML mononuclear cells, respectively. Importantly, the extent of cellular damage correlated with the expression level of the lncRNA of interest. In conclusion, we demonstrated in primary JMML cell cultures that knockdown of overexpressed lncRNAs such as lnc-THADA-4, lnc-ACOT9-1 and NRIR may be a feasible therapeutic strategy.
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Affiliation(s)
- Mattias Hofmans
- Department of Pediatric Hematology-Oncology and Stem Cell Transplantation, Ghent University Hospital, Ghent, Belgium. .,Department of Diagnostic Sciences, Ghent University Hospital, Corneel Heymanslaan 10, Ghent, 9000, Belgium.
| | - Tim Lammens
- Department of Pediatric Hematology-Oncology and Stem Cell Transplantation, Ghent University Hospital, Ghent, Belgium.,Cancer Research Institute Ghent, Ghent University, Ghent, Belgium
| | - Barbara Depreter
- Department of Laboratory Medicine Hematology, University Hospital Brussels, Brussels, Belgium
| | - Ying Wu
- Faculty of Biology, University of Freiburg, Freiburg, Germany.,Division of Pediatric Hematology and Oncology, Department of Pediatrics and Adolescent Medicine, University Medical Center Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Miriam Erlacher
- Division of Pediatric Hematology and Oncology, Department of Pediatrics and Adolescent Medicine, University Medical Center Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany.,German Cancer Consortium, Partner Site Freiburg, German Cancer Research Center, Heidelberg, Germany
| | - Aurélie Caye
- Department of Genetics, University Hospital of Robert Debré (APHP) and INSERM U1131, Institut de Recherche Saint-Louis, Université de Paris, Paris, France
| | - Hélène Cavé
- Department of Genetics, University Hospital of Robert Debré (APHP) and INSERM U1131, Institut de Recherche Saint-Louis, Université de Paris, Paris, France
| | - Christian Flotho
- Division of Pediatric Hematology and Oncology, Department of Pediatrics and Adolescent Medicine, University Medical Center Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany.,German Cancer Consortium, Partner Site Freiburg, German Cancer Research Center, Heidelberg, Germany
| | - Valerie de Haas
- Princess Máxima Center for Pediatric Oncology, Utrecht, The Netherlands.,Dutch Childhood Oncology Group, The Hague, The Netherlands
| | - Charlotte M Niemeyer
- Division of Pediatric Hematology and Oncology, Department of Pediatrics and Adolescent Medicine, University Medical Center Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany.,German Cancer Consortium, Partner Site Freiburg, German Cancer Research Center, Heidelberg, Germany
| | - Jan Stary
- Department of Pediatric Hematology/Oncology, Charles University and University Hospital Motol, Prague, Czech Republic
| | - Filip Van Nieuwerburgh
- Laboratory for Pharmaceutical Biotechnology, Faculty of Pharmaceutical Sciences, Ghent University, Ghent, Belgium
| | - Dieter Deforce
- Laboratory for Pharmaceutical Biotechnology, Faculty of Pharmaceutical Sciences, Ghent University, Ghent, Belgium
| | - Wouter Van Loocke
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
| | - Pieter Van Vlierberghe
- Cancer Research Institute Ghent, Ghent University, Ghent, Belgium.,Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
| | - Jan Philippé
- Department of Diagnostic Sciences, Ghent University Hospital, Corneel Heymanslaan 10, Ghent, 9000, Belgium.,Cancer Research Institute Ghent, Ghent University, Ghent, Belgium
| | - Barbara De Moerloose
- Department of Pediatric Hematology-Oncology and Stem Cell Transplantation, Ghent University Hospital, Ghent, Belgium.,Cancer Research Institute Ghent, Ghent University, Ghent, Belgium
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17
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Kishimoto Y, Nakagawa O, Fujii A, Yoshioka K, Nagata T, Yokota T, Hari Y, Obika S. 2',4'-BNA/LNA with 9-(2-Aminoethoxy)-1,3-diaza-2-oxophenoxazine Efficiently Forms Duplexes and Has Enhanced Enzymatic Resistance*. Chemistry 2021; 27:2427-2438. [PMID: 33280173 PMCID: PMC7898338 DOI: 10.1002/chem.202003982] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Indexed: 11/28/2022]
Abstract
Artificial nucleic acids are widely used in various technologies, such as nucleic acid therapeutics and DNA nanotechnologies requiring excellent duplex-forming abilities and enhanced nuclease resistance. 2'-O,4'-C-Methylene-bridged nucleic acid/locked nucleic acid (2',4'-BNA/LNA) with 1,3-diaza-2-oxophenoxazine (BNAP (BH )) was previously reported. Herein, a novel BH analogue, 2',4'-BNA/LNA with 9-(2-aminoethoxy)-1,3-diaza-2-oxophenoxazine (G-clamp), named BNAP-AEO (BAEO ), was designed. The BAEO nucleoside was successfully synthesized and incorporated into oligodeoxynucleotides (ODNs). ODNs containing BAEO possessed up to 104 -, 152-, and 11-fold higher binding affinities for complementary (c) RNA than those of ODNs containing 2'-deoxycytidine (C), 2',4'-BNA/LNA with 5-methylcytosine (L), or 2'-deoxyribonucleoside with G-clamp (PAEO ), respectively. Moreover, duplexes formed by ODN bearing BAEO with cDNA and cRNA were thermally stable, even under molecular crowding conditions induced by the addition of polyethylene glycol. Furthermore, ODN bearing BAEO was more resistant to 3'-exonuclease than ODNs with phosphorothioate linkages.
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Affiliation(s)
- Yuki Kishimoto
- Graduate School of Pharmaceutical SciencesOsaka University1–6 Yamadaoka SuitaOsaka565-0871Japan
- Core Research for Evolutional Science and Technology (CREST), (Japan) Sciences and Technology Agency (JST)7 GobanchoChiyoda-kuTokyo102-0076Japan
| | - Osamu Nakagawa
- Graduate School of Pharmaceutical SciencesOsaka University1–6 Yamadaoka SuitaOsaka565-0871Japan
- Core Research for Evolutional Science and Technology (CREST), (Japan) Sciences and Technology Agency (JST)7 GobanchoChiyoda-kuTokyo102-0076Japan
- Faculty of Pharmaceutical SciencesTokushima Bunri University180 Nishihamahoji, Yamashiro-choTokushima770-8514Japan
| | - Akane Fujii
- Graduate School of Pharmaceutical SciencesOsaka University1–6 Yamadaoka SuitaOsaka565-0871Japan
- Core Research for Evolutional Science and Technology (CREST), (Japan) Sciences and Technology Agency (JST)7 GobanchoChiyoda-kuTokyo102-0076Japan
| | - Kotaro Yoshioka
- Core Research for Evolutional Science and Technology (CREST), (Japan) Sciences and Technology Agency (JST)7 GobanchoChiyoda-kuTokyo102-0076Japan
- Department of Neurology and Neurological ScienceGraduate School of Medical and Dental SciencesTokyo Medical and Dental University1-5-45 Yushima, Bunkyo-kuTokyo113-8519Japan
| | - Tetsuya Nagata
- Core Research for Evolutional Science and Technology (CREST), (Japan) Sciences and Technology Agency (JST)7 GobanchoChiyoda-kuTokyo102-0076Japan
- Department of Neurology and Neurological ScienceGraduate School of Medical and Dental SciencesTokyo Medical and Dental University1-5-45 Yushima, Bunkyo-kuTokyo113-8519Japan
| | - Takanori Yokota
- Core Research for Evolutional Science and Technology (CREST), (Japan) Sciences and Technology Agency (JST)7 GobanchoChiyoda-kuTokyo102-0076Japan
- Department of Neurology and Neurological ScienceGraduate School of Medical and Dental SciencesTokyo Medical and Dental University1-5-45 Yushima, Bunkyo-kuTokyo113-8519Japan
| | - Yoshiyuki Hari
- Faculty of Pharmaceutical SciencesTokushima Bunri University180 Nishihamahoji, Yamashiro-choTokushima770-8514Japan
| | - Satoshi Obika
- Graduate School of Pharmaceutical SciencesOsaka University1–6 Yamadaoka SuitaOsaka565-0871Japan
- Core Research for Evolutional Science and Technology (CREST), (Japan) Sciences and Technology Agency (JST)7 GobanchoChiyoda-kuTokyo102-0076Japan
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18
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Chen S, Sbuh N, Veedu RN. Antisense Oligonucleotides as Potential Therapeutics for Type 2 Diabetes. Nucleic Acid Ther 2020; 31:39-57. [PMID: 33026966 DOI: 10.1089/nat.2020.0891] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Type 2 diabetes (T2D) is a chronic metabolic disorder characterized by persistent hyperglycemia resulting from inefficient signaling and insufficient production of insulin. Conventional management of T2D has largely relied on small molecule-based oral hypoglycemic medicines, which do not halt the progression of the disease due to limited efficacy and induce adverse effects as well. To this end, antisense oligonucleotide has attracted immense attention in developing antidiabetic agents because of their ability to downregulate the expression of disease-causing genes at the RNA and protein level. To date, seven antisense agents have been approved by the United States Food and Drug Administration for therapies of a variety of human maladies, including genetic disorders. Herein, we provide a comprehensive review of antisense molecules developed for suppressing the causative genes believed to be responsible for insulin resistance and hyperglycemia toward preventing and treating T2D.
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Affiliation(s)
- Suxiang Chen
- Centre for Molecular Medicine and Innovative Therapeutics, Murdoch University, Perth, Australia.,Perron Institute for Neurological and Translational Science, Perth, Australia
| | - Nabayet Sbuh
- Centre for Molecular Medicine and Innovative Therapeutics, Murdoch University, Perth, Australia.,Perron Institute for Neurological and Translational Science, Perth, Australia
| | - Rakesh N Veedu
- Centre for Molecular Medicine and Innovative Therapeutics, Murdoch University, Perth, Australia.,Perron Institute for Neurological and Translational Science, Perth, Australia
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19
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Hagiwara K, Honma M, Harumoto T, Harada K, Sawada T, Yamamoto J, Shinohara F. Development of Prodrug Type Circular siRNA for In Vivo Knockdown by Systemic Administration. Nucleic Acid Ther 2020; 30:346-364. [PMID: 33016851 DOI: 10.1089/nat.2020.0894] [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: 12/13/2022] Open
Abstract
siRNAs are being developed as a novel therapeutic modality; however, problems impeding their application in extrahepatic tissues persist, including inadequate stability in biological environments and inefficient drug delivery system to target tissues. Thus, technological improvements that enable robust silencing of target messenger RNA (mRNA) in extrahepatic tissues are necessary. We developed prodrug type covalently closed siRNA (circular siRNA) as a novel nucleic acid agent to knockdown target genes in extrahepatic tissues by systemic administration without drug delivery components. Circular siRNA, which is chemically synthesizable, can assume optimal structures for efficient knockdown using its cleavable linker; namely, circular and linear structure in extracellular and intracellular environment, respectively. In this study, we investigated circular siRNA physicochemical properties, knockdown mechanism, and characteristics in vitro, as well as pharmacokinetics, accumulation, knockdown activity, and safety in vivo. Our circular siRNA exhibited higher stability against serum and exonucleases, increased cellular uptake, and stronger knockdown activity without transfection reagent in vitro than linear siRNA. Furthermore, after systemic administration to mice, circular siRNA showed prolonged circulation and improved knockdown activity in the liver, kidney, and muscle, without causing adverse effects. Circular siRNA may represent an additional platform for RNAi therapeutics, providing alternate solutions for disease treatment.
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Affiliation(s)
- Kenji Hagiwara
- Nucleic Acid Medicine Research Laboratories and Research Functions Unit, R&D Division, Kyowa Kirin Co., Ltd., Tokyo, Japan
| | - Masakazu Honma
- Nucleic Acid Medicine Research Laboratories and Research Functions Unit, R&D Division, Kyowa Kirin Co., Ltd., Tokyo, Japan
| | - Toshimasa Harumoto
- Nucleic Acid Medicine Research Laboratories and Research Functions Unit, R&D Division, Kyowa Kirin Co., Ltd., Tokyo, Japan
| | - Kenji Harada
- Management Office, Research Functions Unit, R&D Division, Kyowa Kirin Co., Ltd., Tokyo, Japan
| | - Takashi Sawada
- Nucleic Acid Medicine Research Laboratories and Research Functions Unit, R&D Division, Kyowa Kirin Co., Ltd., Tokyo, Japan
| | - Junichiro Yamamoto
- Nucleic Acid Medicine Research Laboratories and Research Functions Unit, R&D Division, Kyowa Kirin Co., Ltd., Tokyo, Japan
| | - Fumikazu Shinohara
- Management Office, Research Functions Unit, R&D Division, Kyowa Kirin Co., Ltd., Tokyo, Japan
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20
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Deprey K, Batistatou N, Kritzer JA. A critical analysis of methods used to investigate the cellular uptake and subcellular localization of RNA therapeutics. Nucleic Acids Res 2020; 48:7623-7639. [PMID: 32644123 PMCID: PMC7430645 DOI: 10.1093/nar/gkaa576] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2020] [Revised: 06/17/2020] [Accepted: 06/24/2020] [Indexed: 12/21/2022] Open
Abstract
RNA therapeutics are a promising strategy to treat genetic diseases caused by the overexpression or aberrant splicing of a specific protein. The field has seen major strides in the clinical efficacy of this class of molecules, largely due to chemical modifications and delivery strategies that improve nuclease resistance and enhance cell penetration. However, a major obstacle in the development of RNA therapeutics continues to be the imprecise, difficult, and often problematic nature of most methods used to measure cell penetration. Here, we review these methods and clearly distinguish between those that measure total cellular uptake of RNA therapeutics, which includes both productive and non-productive uptake, and those that measure cytosolic/nuclear penetration, which represents only productive uptake. We critically analyze the benefits and drawbacks of each method. Finally, we use key examples to illustrate how, despite rigorous experimentation and proper controls, our understanding of the mechanism of gymnotic uptake of RNA therapeutics remains limited by the methods commonly used to analyze RNA delivery.
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Affiliation(s)
- Kirsten Deprey
- Department of Chemistry, Tufts University, 62 Talbot Ave, Medford, MA 02155, USA
| | - Nefeli Batistatou
- Department of Chemistry, Tufts University, 62 Talbot Ave, Medford, MA 02155, USA
| | - Joshua A Kritzer
- Department of Chemistry, Tufts University, 62 Talbot Ave, Medford, MA 02155, USA
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21
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Baldassarre A, Paolini A, Bruno SP, Felli C, Tozzi AE, Masotti A. Potential use of noncoding RNAs and innovative therapeutic strategies to target the 5'UTR of SARS-CoV-2. Epigenomics 2020; 12:1349-1361. [PMID: 32875809 PMCID: PMC7466951 DOI: 10.2217/epi-2020-0162] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
After the increasing number of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infections all over the world, researchers and clinicians are struggling to find a vaccine or innovative therapeutic strategies to treat this viral infection. The severe acute respiratory syndrome coronavirus infection that occurred in 2002, Middle East respiratory syndrome (MERS) and other more common infectious diseases such as hepatitis C virus, led to the discovery of many RNA-based drugs. Among them, siRNAs and antisense locked nucleic acids have been demonstrated to have effective antiviral effects both in animal models and humans. Owing to the high genomic homology of SARS-CoV-2 and severe acute respiratory syndrome coronavirus (80–82%) the use of these molecules could be employed successfully also to target this emerging coronavirus. Trying to translate this approach to treat COVID-19, we analyzed the common structural features of viral 5’UTR regions that can be targeted by noncoding RNAs and we also identified miRNAs binding sites suitable for designing RNA-based drugs to be employed successfully against SARS-CoV-2.
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Affiliation(s)
- Antonella Baldassarre
- Children's Hospital Bambino Gesù-IRCCS, Research Laboratories; Multifactorial & Complex Phenotype Research Area, V.le di San Paolo 15, Rome 00146, Italy
| | - Alessandro Paolini
- Children's Hospital Bambino Gesù-IRCCS, Research Laboratories; Multifactorial & Complex Phenotype Research Area, V.le di San Paolo 15, Rome 00146, Italy
| | - Stefania Paola Bruno
- Children's Hospital Bambino Gesù-IRCCS, Research Laboratories; Multifactorial & Complex Phenotype Research Area, V.le di San Paolo 15, Rome 00146, Italy
| | - Cristina Felli
- Children's Hospital Bambino Gesù-IRCCS, Research Laboratories; Multifactorial & Complex Phenotype Research Area, V.le di San Paolo 15, Rome 00146, Italy
| | - Alberto Eugenio Tozzi
- Children's Hospital Bambino Gesù-IRCCS, Research Laboratories; Multifactorial & Complex Phenotype Research Area, V.le di San Paolo 15, Rome 00146, Italy
| | - Andrea Masotti
- Children's Hospital Bambino Gesù-IRCCS, Research Laboratories; Multifactorial & Complex Phenotype Research Area, V.le di San Paolo 15, Rome 00146, Italy
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22
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Li D, Mastaglia FL, Fletcher S, Wilton SD. Progress in the molecular pathogenesis and nucleic acid therapeutics for Parkinson's disease in the precision medicine era. Med Res Rev 2020; 40:2650-2681. [PMID: 32767426 PMCID: PMC7589267 DOI: 10.1002/med.21718] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2020] [Revised: 07/02/2020] [Accepted: 07/25/2020] [Indexed: 12/16/2022]
Abstract
Parkinson's disease (PD) is one of the most common neurodegenerative disorders that manifest various motor and nonmotor symptoms. Although currently available therapies can alleviate some of the symptoms, the disease continues to progress, leading eventually to severe motor and cognitive decline and reduced life expectancy. The past two decades have witnessed rapid progress in our understanding of the molecular and genetic pathogenesis of the disease, paving the way for the development of new therapeutic approaches to arrest or delay the neurodegenerative process. As a result of these advances, biomarker‐driven subtyping is making it possible to stratify PD patients into more homogeneous subgroups that may better respond to potential genetic‐molecular pathway targeted disease‐modifying therapies. Therapeutic nucleic acid oligomers can bind to target gene sequences with very high specificity in a base‐pairing manner and precisely modulate downstream molecular events. Recently, nucleic acid therapeutics have proven effective in the treatment of a number of severe neurological and neuromuscular disorders, drawing increasing attention to the possibility of developing novel molecular therapies for PD. In this review, we update the molecular pathogenesis of PD and discuss progress in the use of antisense oligonucleotides, small interfering RNAs, short hairpin RNAs, aptamers, and microRNA‐based therapeutics to target critical elements in the pathogenesis of PD that could have the potential to modify disease progression. In addition, recent advances in the delivery of nucleic acid compounds across the blood–brain barrier and challenges facing PD clinical trials are also reviewed.
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Affiliation(s)
- Dunhui Li
- Centre for Molecular Medicine and Innovative Therapeutics, Murdoch University, Murdoch, Western Australia, Australia.,Perron Institute for Neurological and Translational Science, University of Western Australia, Nedlands, Western Australia, Australia
| | - Frank L Mastaglia
- Perron Institute for Neurological and Translational Science, University of Western Australia, Nedlands, Western Australia, Australia
| | - Sue Fletcher
- Centre for Molecular Medicine and Innovative Therapeutics, Murdoch University, Murdoch, Western Australia, Australia.,Perron Institute for Neurological and Translational Science, University of Western Australia, Nedlands, Western Australia, Australia
| | - Steve D Wilton
- Centre for Molecular Medicine and Innovative Therapeutics, Murdoch University, Murdoch, Western Australia, Australia.,Perron Institute for Neurological and Translational Science, University of Western Australia, Nedlands, Western Australia, Australia
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23
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Hyjek-Składanowska M, Vickers TA, Napiórkowska A, Anderson BA, Tanowitz M, Crooke ST, Liang XH, Seth PP, Nowotny M. Origins of the Increased Affinity of Phosphorothioate-Modified Therapeutic Nucleic Acids for Proteins. J Am Chem Soc 2020; 142:7456-7468. [PMID: 32202774 DOI: 10.1021/jacs.9b13524] [Citation(s) in RCA: 55] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
The phosphorothioate backbone modification (PS) is one of the most widely used chemical modifications for enhancing the drug-like properties of nucleic acid-based drugs, including antisense oligonucleotides (ASOs). PS-modified nucleic acid therapeutics show improved metabolic stability from nuclease-mediated degradation and exhibit enhanced interactions with plasma, cell-surface, and intracellular proteins, which facilitates their tissue distribution and cellular uptake in animals. However, little is known about the structural basis of the interactions of PS nucleic acids with proteins. Here, we report a crystal structure of the DNA-binding domain of a model ASO-binding protein PC4, in complex with a full PS 2'-OMe DNA gapmer ASO. To our knowledge this is the first structure of a complex between a protein and fully PS nucleic acid. Each PC4 dimer comprises two DNA-binding interfaces. In the structure one interface binds the 5'-terminal 2'-OMe PS flank of the ASO, while the other interface binds the regular PS DNA central part in the opposite polarity. As a result, the ASO forms a hairpin-like structure. ASO binding also induces the formation of a dimer of dimers of PC4, which is stabilized by base pairing between homologous regions of the ASOs bound by each dimer of PC4. The protein interacts with the PS nucleic acid through a network of electrostatic and hydrophobic interactions, which provides insights into the origins for the enhanced affinity of PS for proteins. The importance of these contacts was further confirmed in a NanoBRET binding assay using a Nano luciferase tagged PC4 acting as the BRET donor, to a fluorescently conjugated ASO acting as the BRET acceptor. Overall, our results provide insights into the molecular forces that govern the interactions of PS ASOs with cellular proteins and provide a potential model for how these interactions can template protein-protein interactions causative of cellular toxicity.
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Affiliation(s)
- Malwina Hyjek-Składanowska
- Structural Biology Center, International Institute of Molecular and Cell Biology, 4 Trojdena St., 02-109 Warsaw, Poland.,Laboratory of Protein Structure, International Institute of Molecular and Cell Biology, 4 Trojdena Street, 02-109 Warsaw, Poland
| | - Timothy A Vickers
- Ionis Pharmaceuticals, Inc., 2855 Gazelle Court, Carlsbad, California 92010, United States
| | - Agnieszka Napiórkowska
- Structural Biology Center, International Institute of Molecular and Cell Biology, 4 Trojdena St., 02-109 Warsaw, Poland.,Laboratory of Protein Structure, International Institute of Molecular and Cell Biology, 4 Trojdena Street, 02-109 Warsaw, Poland
| | - Brooke A Anderson
- Ionis Pharmaceuticals, Inc., 2855 Gazelle Court, Carlsbad, California 92010, United States
| | - Michael Tanowitz
- Ionis Pharmaceuticals, Inc., 2855 Gazelle Court, Carlsbad, California 92010, United States
| | - Stanley T Crooke
- Ionis Pharmaceuticals, Inc., 2855 Gazelle Court, Carlsbad, California 92010, United States
| | - Xue-Hai Liang
- Ionis Pharmaceuticals, Inc., 2855 Gazelle Court, Carlsbad, California 92010, United States
| | - Punit P Seth
- Ionis Pharmaceuticals, Inc., 2855 Gazelle Court, Carlsbad, California 92010, United States
| | - Marcin Nowotny
- Structural Biology Center, International Institute of Molecular and Cell Biology, 4 Trojdena St., 02-109 Warsaw, Poland.,Laboratory of Protein Structure, International Institute of Molecular and Cell Biology, 4 Trojdena Street, 02-109 Warsaw, Poland
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24
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Sewing S, Minz T, Boess F. In Vitro Assessment of the Hepatotoxicity Potential of Therapeutic Oligonucleotides. Methods Mol Biol 2020; 2036:249-259. [PMID: 31410802 DOI: 10.1007/978-1-4939-9670-4_15] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
The mechanisms of antisense oligonucleotide-induced liver toxicity are still poorly understood. Assessment of the hepatic safety profile is currently mostly investigated directly in rodent studies. A predictive preclinical in vitro model that is capturing liver liabilities of antisense oligonucleotides can be of great help to be used as a first filter in the screening process of therapeutic oligonucleotides. We describe here an in vitro cytotoxicity assay using freshly isolated mouse hepatocytes or cryopreserved human hepatocytes that recapitulates the hepatotoxic profile of antisense oligonucleotides previously observed in rodents and can be used for the prioritization of molecules prior to in vivo testing.
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Affiliation(s)
- Sabine Sewing
- Roche Pharma Research and Early Development, Pharmaceutical Sciences (PS), Roche Innovation Center Basel, Basel, Switzerland.
| | - Tanja Minz
- Roche Pharma Research and Early Development, Pharmaceutical Sciences (PS), Roche Innovation Center Basel, Basel, Switzerland
| | - Franziska Boess
- Roche Pharma Research and Early Development, Pharmaceutical Sciences (PS), Roche Innovation Center Basel, Basel, Switzerland
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25
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Pedersen L, Hagedorn PH, Koch T. Identifying Suitable Target Regions and Analyzing Off-Target Effects of Therapeutic Oligonucleotides. Methods Mol Biol 2020; 2036:261-282. [PMID: 31410803 DOI: 10.1007/978-1-4939-9670-4_16] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Antisense oligonucleotides (AONs) that promote degradation of complementary RNA are being developed as therapeutics. Here, we describe a simple computational workflow for identification of the regions on an RNA that are suitable for targeting with such AONs. The workflow is based on the statistical programming language R, and the calculations and data processing can be carried out on a desktop computer. Our workflow integrates well-established data resources and RNA structure-prediction tools and can be modified easily and expanded as new resources become available.
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Affiliation(s)
- Lykke Pedersen
- Therapeutic Modalities, Roche Pharma Research and Early Development, Roche Innovation Center Copenhagen, Hørsholm, Denmark.
| | - Peter H Hagedorn
- Therapeutic Modalities, Roche Pharma Research and Early Development, Roche Innovation Center Copenhagen, Hørsholm, Denmark
| | - Troels Koch
- Therapeutic Modalities, Roche Pharma Research and Early Development, Roche Innovation Center Copenhagen, Hørsholm, Denmark
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26
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Christou M, Wengel J, Sokratous K, Kyriacou K, Nikolaou G, Phylactou LA, Mastroyiannopoulos NP. Systemic Evaluation of Chimeric LNA/2'-O-Methyl Steric Blockers for Myotonic Dystrophy Type 1 Therapy. Nucleic Acid Ther 2019; 30:80-93. [PMID: 31873063 PMCID: PMC7133450 DOI: 10.1089/nat.2019.0811] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Myotonic dystrophy type 1 (DM1) is a dominantly inherited, multisystemic disorder characterized clinically by delayed muscle relaxation and weakness. The disease is caused by a CTG repeat expansion in the 3′ untranslated region (3′ UTR) of the DMPK gene, which leads to the expression of a toxic gain-of-function mRNA. The expanded CUG repeat mRNA sequesters the MBNL1 splicing regulator in nuclear-retained foci structures, resulting in loss of protein function and disruption of alternative splicing homeostasis. In this study, we used CAG repeat antisense oligonucleotides (ASOs), composed of locked nucleic acid (LNA)- and 2′-O-methyl (2′OMe)-modified bases in a chimeric design, to alleviate CUGexpanded-mediated toxicity. Chimeric 14–18mer LNA/2′OMe oligonucleotides, exhibiting an LNA incorporation of ∼33%, significantly ameliorated the misregulated alternative splicing of Mbnl1-dependent exons in primary DM1 mouse myoblasts and tibialis anterior muscles of DM1 mice. Subcutaneous delivery of 14mer and 18mer LNA/2′OMe chimeras in DM1 mice resulted in high levels of accumulation in all tested skeletal muscles, as well as in the diaphragm and heart tissue. Despite the efficient delivery, chimeric LNA/2′OMe oligonucleotides were not able, even at a high-dosage regimen (400 mg/kg/week), to correct the misregulated splicing of Serca1 exon 22 in skeletal muscles. Nevertheless, oligonucleotide doses were well-tolerated as determined by histological and plasma biochemistry analyses. Our results provide proof of concept that inhibition of MBNL1 sequestration by systemic delivery of a steric-blocking ASO is extremely challenging, considering the large number of target sites that need to be occupied per RNA molecule. Although not suitable for DM1 therapy, chimeric LNA/2′OMe oligonucleotides could prove to be highly beneficial for other diseases, such as Duchenne muscular dystrophy, that require inhibition of a single target site per RNA molecule.
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Affiliation(s)
- Melina Christou
- Department of Molecular Genetics, Function & Therapy, The Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus.,The Cyprus School of Molecular Medicine, The Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus
| | - Jesper Wengel
- Department of Physics, Chemistry and Pharmacy, Biomolecular Nanoscale Engineering Center, University of Southern Denmark, Odense M, Denmark
| | - Kleitos Sokratous
- Department of Electron Microscopy and Molecular Pathology, The Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus.,Bioinformatics Group, The Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus
| | - Kyriacos Kyriacou
- The Cyprus School of Molecular Medicine, The Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus.,Department of Electron Microscopy and Molecular Pathology, The Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus
| | - Georgios Nikolaou
- Veterinary Diagnostic Laboratory, Vet Ex Machina Ltd, Nicosia, Cyprus
| | - Leonidas A Phylactou
- Department of Molecular Genetics, Function & Therapy, The Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus.,The Cyprus School of Molecular Medicine, The Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus
| | - Nikolaos P Mastroyiannopoulos
- Department of Molecular Genetics, Function & Therapy, The Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus.,The Cyprus School of Molecular Medicine, The Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus
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27
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Chemical Diversity of Locked Nucleic Acid-Modified Antisense Oligonucleotides Allows Optimization of Pharmaceutical Properties. MOLECULAR THERAPY-NUCLEIC ACIDS 2019; 19:706-717. [PMID: 31951854 PMCID: PMC6965521 DOI: 10.1016/j.omtn.2019.12.011] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/08/2019] [Revised: 12/10/2019] [Accepted: 12/10/2019] [Indexed: 01/21/2023]
Abstract
The identification of molecules that can modulate RNA or protein function and the subsequent chemical and structural optimization to refine such molecules into drugs is a key activity in drug discovery. Here, we explored the extent to which chemical and structural differences in antisense oligonucleotides, designed as gapmers and capable of recruiting RNase H for target RNA cleavage, can affect their functional properties. To facilitate structure-activity learning, we analyzed two sets of iso-sequential locked nucleic acid (LNA)-modified gapmers, where we systematically varied the number and positions of LNA modifications in the flanks. In total, we evaluated 768 different and architecturally diverse gapmers in HeLa cells for target knockdown activity and cytotoxic potential and found widespread differences in both of these properties. Binding affinity between gapmer and RNA target, as well as the presence of certain short sequence motifs in the gap region, can explain these differences, and we propose statistical and machine-learning models that can be used to predict region-specific, optimal LNA-modification architectures. Once accessible regions in the target of interest have been identified, our results show how to refine and optimize LNA gapmers with improved pharmacological profiles targeting such regions.
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28
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Yoshioka K, Kunieda T, Asami Y, Guo H, Miyata H, Yoshida-Tanaka K, Sujino Y, Piao W, Kuwahara H, Nishina K, Hara RI, Nagata T, Wada T, Obika S, Yokota T. Highly efficient silencing of microRNA by heteroduplex oligonucleotides. Nucleic Acids Res 2019; 47:7321-7332. [PMID: 31214713 PMCID: PMC6698647 DOI: 10.1093/nar/gkz492] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2018] [Revised: 05/21/2019] [Accepted: 05/28/2019] [Indexed: 12/11/2022] Open
Abstract
AntimiR is an antisense oligonucleotide that has been developed to silence microRNA (miRNA) for the treatment of intractable diseases. Enhancement of its in vivo efficacy and improvement of its toxicity are highly desirable but remain challenging. We here design heteroduplex oligonucleotide (HDO)-antimiR as a new technology comprising an antimiR and its complementary RNA. HDO-antimiR binds targeted miRNA in vivo more efficiently by 12-fold than the parent single-stranded antimiR. HDO-antimiR also produced enhanced phenotypic effects in mice with upregulated expression of miRNA-targeting messenger RNAs. In addition, we demonstrated that the enhanced potency of HDO-antimiR was not explained by its bio-stability or delivery to the targeted cell, but reflected an improved intracellular potency. Our findings provide new insights into biology of miRNA silencing by double-stranded oligonucleotides and support the in vivo potential of this technology based on a new class of for the treatment of miRNA-related diseases.
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Affiliation(s)
- Kotaro Yoshioka
- Department of Neurology and Neurological Science, Graduate School of Medical and Dental Sciences and Center for Brain Integration Research, Tokyo Medical and Dental University (TMDU), 1-5-45 Yushima, Bunkyo-Ku, Tokyo, 113-8519, Japan.,Section of Molecular Technology, Core Research for Evolutional Science and Technology (CREST), Japan Science and Technology Agency (JST), 4-1-8 Honcho, Kawaguchi-shi, Saitama 332-0012, Japan
| | - Taiki Kunieda
- Department of Neurology and Neurological Science, Graduate School of Medical and Dental Sciences and Center for Brain Integration Research, Tokyo Medical and Dental University (TMDU), 1-5-45 Yushima, Bunkyo-Ku, Tokyo, 113-8519, Japan.,Section of Molecular Technology, Core Research for Evolutional Science and Technology (CREST), Japan Science and Technology Agency (JST), 4-1-8 Honcho, Kawaguchi-shi, Saitama 332-0012, Japan
| | - Yutaro Asami
- Department of Neurology and Neurological Science, Graduate School of Medical and Dental Sciences and Center for Brain Integration Research, Tokyo Medical and Dental University (TMDU), 1-5-45 Yushima, Bunkyo-Ku, Tokyo, 113-8519, Japan.,Section of Molecular Technology, Core Research for Evolutional Science and Technology (CREST), Japan Science and Technology Agency (JST), 4-1-8 Honcho, Kawaguchi-shi, Saitama 332-0012, Japan
| | - Huijia Guo
- Department of Neurology and Neurological Science, Graduate School of Medical and Dental Sciences and Center for Brain Integration Research, Tokyo Medical and Dental University (TMDU), 1-5-45 Yushima, Bunkyo-Ku, Tokyo, 113-8519, Japan
| | - Haruka Miyata
- Department of Neurology and Neurological Science, Graduate School of Medical and Dental Sciences and Center for Brain Integration Research, Tokyo Medical and Dental University (TMDU), 1-5-45 Yushima, Bunkyo-Ku, Tokyo, 113-8519, Japan.,Section of Molecular Technology, Core Research for Evolutional Science and Technology (CREST), Japan Science and Technology Agency (JST), 4-1-8 Honcho, Kawaguchi-shi, Saitama 332-0012, Japan
| | - Kie Yoshida-Tanaka
- Department of Neurology and Neurological Science, Graduate School of Medical and Dental Sciences and Center for Brain Integration Research, Tokyo Medical and Dental University (TMDU), 1-5-45 Yushima, Bunkyo-Ku, Tokyo, 113-8519, Japan.,Section of Molecular Technology, Core Research for Evolutional Science and Technology (CREST), Japan Science and Technology Agency (JST), 4-1-8 Honcho, Kawaguchi-shi, Saitama 332-0012, Japan
| | - Yumiko Sujino
- Department of Neurology and Neurological Science, Graduate School of Medical and Dental Sciences and Center for Brain Integration Research, Tokyo Medical and Dental University (TMDU), 1-5-45 Yushima, Bunkyo-Ku, Tokyo, 113-8519, Japan.,Section of Molecular Technology, Core Research for Evolutional Science and Technology (CREST), Japan Science and Technology Agency (JST), 4-1-8 Honcho, Kawaguchi-shi, Saitama 332-0012, Japan
| | - Wenying Piao
- Department of Neurology and Neurological Science, Graduate School of Medical and Dental Sciences and Center for Brain Integration Research, Tokyo Medical and Dental University (TMDU), 1-5-45 Yushima, Bunkyo-Ku, Tokyo, 113-8519, Japan.,Section of Molecular Technology, Core Research for Evolutional Science and Technology (CREST), Japan Science and Technology Agency (JST), 4-1-8 Honcho, Kawaguchi-shi, Saitama 332-0012, Japan
| | - Hiroya Kuwahara
- Department of Neurology and Neurological Science, Graduate School of Medical and Dental Sciences and Center for Brain Integration Research, Tokyo Medical and Dental University (TMDU), 1-5-45 Yushima, Bunkyo-Ku, Tokyo, 113-8519, Japan.,Section of Molecular Technology, Core Research for Evolutional Science and Technology (CREST), Japan Science and Technology Agency (JST), 4-1-8 Honcho, Kawaguchi-shi, Saitama 332-0012, Japan
| | - Kazutaka Nishina
- Department of Neurology and Neurological Science, Graduate School of Medical and Dental Sciences and Center for Brain Integration Research, Tokyo Medical and Dental University (TMDU), 1-5-45 Yushima, Bunkyo-Ku, Tokyo, 113-8519, Japan.,Section of Molecular Technology, Core Research for Evolutional Science and Technology (CREST), Japan Science and Technology Agency (JST), 4-1-8 Honcho, Kawaguchi-shi, Saitama 332-0012, Japan
| | - Rintaro Iwata Hara
- Section of Molecular Technology, Core Research for Evolutional Science and Technology (CREST), Japan Science and Technology Agency (JST), 4-1-8 Honcho, Kawaguchi-shi, Saitama 332-0012, Japan.,Faculty of Pharmaceutical Sciences, Tokyo University of Science, 2641 Yamazaki, Noda, Chiba, 278-8510, Japan
| | - Tetsuya Nagata
- Department of Neurology and Neurological Science, Graduate School of Medical and Dental Sciences and Center for Brain Integration Research, Tokyo Medical and Dental University (TMDU), 1-5-45 Yushima, Bunkyo-Ku, Tokyo, 113-8519, Japan.,Section of Molecular Technology, Core Research for Evolutional Science and Technology (CREST), Japan Science and Technology Agency (JST), 4-1-8 Honcho, Kawaguchi-shi, Saitama 332-0012, Japan
| | - Takeshi Wada
- Section of Molecular Technology, Core Research for Evolutional Science and Technology (CREST), Japan Science and Technology Agency (JST), 4-1-8 Honcho, Kawaguchi-shi, Saitama 332-0012, Japan.,Faculty of Pharmaceutical Sciences, Tokyo University of Science, 2641 Yamazaki, Noda, Chiba, 278-8510, Japan
| | - Satoshi Obika
- Section of Molecular Technology, Core Research for Evolutional Science and Technology (CREST), Japan Science and Technology Agency (JST), 4-1-8 Honcho, Kawaguchi-shi, Saitama 332-0012, Japan.,Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Takanori Yokota
- Department of Neurology and Neurological Science, Graduate School of Medical and Dental Sciences and Center for Brain Integration Research, Tokyo Medical and Dental University (TMDU), 1-5-45 Yushima, Bunkyo-Ku, Tokyo, 113-8519, Japan.,Section of Molecular Technology, Core Research for Evolutional Science and Technology (CREST), Japan Science and Technology Agency (JST), 4-1-8 Honcho, Kawaguchi-shi, Saitama 332-0012, Japan
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29
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Fujii A, Nakagawa O, Kishimoto Y, Nakatsuji Y, Nozaki N, Obika S. Oligonucleotides Containing Phenoxazine Artificial Nucleobases: Triplex-Forming Abilities and Fluorescence Properties. Chembiochem 2019; 21:860-864. [PMID: 31568630 DOI: 10.1002/cbic.201900536] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2019] [Indexed: 11/11/2022]
Abstract
1,3-Diaza-2-oxophenoxazine ("phenoxazine"), a tricyclic cytosine analogue, can strongly bind to guanine moieties and improve π-π stacking effects with adjacent bases in a duplex. Phenoxazine has been widely used for improving duplex-forming abilities. In this study, we have investigated whether phenoxazine and its analogue, 1,3,9-triaza-2-oxophenoxazine (9-TAP), could improve triplex-forming abilities. A triplex-forming oligonucleotide (TFO) incorporating a phenoxazine component was found to show considerably decreased binding affinity with homopurine/homopyrimidine double-stranded DNA, so the phenoxazine system was considered not to function as either a protonated cytosine or thymine analogue. Alternatively, a 9-TAP-containing artificial nucleobase developed by us earlier as a new phenoxazine analogue functioned as a thymine analogue with respect to AT base pairs in a parallel triplex DNA motif. The fluorescence of the 9-TAP moiety was maintained even in triplex (9-TAP:AT) formation, so 9-TAP might be useful as an imaging tool for various oligonucleotide nanotechnologies requiring triplex formation.
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Affiliation(s)
- Akane Fujii
- Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka Suita, Osaka, 565-0871, Japan
| | - Osamu Nakagawa
- Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka Suita, Osaka, 565-0871, Japan
| | - Yuki Kishimoto
- Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka Suita, Osaka, 565-0871, Japan
| | - Yusuke Nakatsuji
- Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka Suita, Osaka, 565-0871, Japan
| | - Natsumi Nozaki
- Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka Suita, Osaka, 565-0871, Japan
| | - Satoshi Obika
- Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka Suita, Osaka, 565-0871, Japan
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30
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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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31
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Xu S, Hazlett LD. MicroRNAs in Ocular Infection. Microorganisms 2019; 7:microorganisms7090359. [PMID: 31533211 PMCID: PMC6780979 DOI: 10.3390/microorganisms7090359] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2019] [Revised: 09/13/2019] [Accepted: 09/16/2019] [Indexed: 12/12/2022] Open
Abstract
MicroRNAs (miRNAs) are small, non-coding, regulatory RNA molecules and constitute a newly recognized, important layer of gene-expression regulation at post-transcriptional levels. miRNAs quantitatively fine tune the expression of their downstream genes in a cell type- and developmental stage-specific fashion. miRNAs have been proven to play important roles in the normal development and function as well as in the pathogenesis of diseases in all tissues and organ systems. miRNAs have emerged as new therapeutic targets and biomarkers for treatment and diagnosis of various diseases. Although miRNA research in ocular infection remains in its early stages, a handful of pioneering studies have provided insight into the roles of miRNAs in the pathogenesis of parasitic, fungal, bacterial, and viral ocular infections. Here, we review the current status of research in miRNAs in several major ocular infectious diseases. We predict that the field of miRNAs in ocular infection will greatly expand with the discovery of novel miRNA-involved molecular mechanisms that will inform development of new therapies and identify novel diagnostic biomarkers.
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Affiliation(s)
- Shunbin Xu
- Department of Ophthalmology, Visual and Anatomical Sciences, Wayne State University, School of Medicine, Detroit, MI 48201, USA.
| | - Linda D Hazlett
- Department of Ophthalmology, Visual and Anatomical Sciences, Wayne State University, School of Medicine, Detroit, MI 48201, USA.
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32
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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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33
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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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34
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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: 120] [Impact Index Per Article: 24.0] [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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35
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Raichur S, Brunner B, Bielohuby M, Hansen G, Pfenninger A, Wang B, Bruning JC, Larsen PJ, Tennagels N. The role of C16:0 ceramide in the development of obesity and type 2 diabetes: CerS6 inhibition as a novel therapeutic approach. Mol Metab 2019; 21:36-50. [PMID: 30655217 PMCID: PMC6407366 DOI: 10.1016/j.molmet.2018.12.008] [Citation(s) in RCA: 126] [Impact Index Per Article: 25.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/10/2018] [Revised: 12/20/2018] [Accepted: 12/21/2018] [Indexed: 12/12/2022] Open
Abstract
OBJECTIVE Ectopic fat deposition is associated with increased tissue production of ceramides. Recent genetic mouse studies suggest that specific sphingolipid C16:0 ceramide produced by ceramide synthase 6 (CerS6) plays an important role in the development of insulin resistance. However, the therapeutic potential of CerS6 inhibition not been demonstrated. Therefore, we pharmacologically investigated the selective ablation of CerS6 using antisense oligonucleotides (ASO) in obese insulin resistance animal models. METHODS We utilized ASO as therapeutic modality, CerS6 ASO molecules designed and synthesized were initially screened for in-vitro knock-down (KD) potency and cytotoxicity. ASOs with >85% inhibition of CerS6 mRNA were selected for further investigations. Most promising ASOs verified for in-vivo KD efficacy in healthy mice. CerS6 ASO (AAGATGAGCCGCACC) was found most active with hepatic reduction of CerS6 mRNA expression. Prior to longitudinal metabolic studies, we performed a dose titration target engagement analysis with CerS6 ASO in healthy mice to select the optimal dose. Next, we utilized leptin deficiency ob/ob and high fat diet (HFD) induced obese mouse models for pharmacological efficacy study. RESULTS CerS6 expression were significantly elevated in the liver and brown adipose, this was correlated with significantly elevated C16:0 ceramide concentrations in plasma and liver. Treatment with CerS6 ASO selectively reduced CerS6 expression by ∼90% predominantly in the liver and this CerS6 KD resulted in a significant reduction of C16:0 ceramide by about 50% in both liver and plasma. CerS6 KD resulted in lower body weight gain and accompanied by a significant reduction in whole body fat and fed/fasted blood glucose levels (1% reduction in HbA1c). Moreover, ASO-mediated CerS6 KD significantly improved oral glucose tolerance (during oGTT) and mice displayed improved insulin sensitivity. Thus, CerS6 appear to play an important role in the development of obesity and insulin resistance. CONCLUSIONS Our investigations identified specific and selective therapeutic valid ASO for CerS6 ablation in in-vivo. CerS6 should specifically be targeted for the reduction of C16:0 ceramides, that results in amelioration of insulin resistance, hyperglycemia and obesity. CerS6 mediated C16:0 ceramide reduction could be a potentially attractive target for the treatment of insulin resistance, obesity and type 2 diabetes.
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Affiliation(s)
| | - Bodo Brunner
- Sanofi-Aventis Deutschland GmbH, TA Diabetes, Industriepark Höchst, D-65926 Frankfurt am Main, Germany
| | - Maximilian Bielohuby
- Sanofi-Aventis Deutschland GmbH, TA Diabetes, Industriepark Höchst, D-65926 Frankfurt am Main, Germany
| | - Gitte Hansen
- Gubra ApS, Hørsholm Kongevej 11B, 2970 Hørsholm, Denmark
| | - Anja Pfenninger
- Sanofi-Aventis Deutschland GmbH, TA Diabetes, Industriepark Höchst, D-65926 Frankfurt am Main, Germany
| | - Bing Wang
- Analytical Research & Development US Predevelopment Sciences, Sanofi, 153 Second Avenue, Waltham, MA 02451, USA
| | - Jens C Bruning
- Max Planck Institute for Metabolic Research, Gleueler Str. 50, D-50931 Cologne, Germany
| | | | - Norbert Tennagels
- Sanofi-Aventis Deutschland GmbH, TA Diabetes, Industriepark Höchst, D-65926 Frankfurt am Main, Germany.
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36
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Seth PP, Swayze EE. The Medicinal Chemistry of RNase H-activating Antisense Oligonucleotides. ADVANCES IN NUCLEIC ACID THERAPEUTICS 2019. [DOI: 10.1039/9781788015714-00032] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
This review focuses on the properties that an RNase H-activating antisense oligonucleotide (ASO) drug must have to function effectively in animals, as well as on medicinal chemistry strategies to achieve these properties. The biochemistry and structural requirements for activating RNase H are briefly summarized, as well as chemical modifications that can effect activation of RNase H when an ASO is bound to target RNA. The key modifications available to the medicinal chemist to engineer desired properties of the ASO are briefly reviewed, as are ASO design strategies to achieve optimal activity in animal systems. Lastly, the interactions of ASOs with proteins and strategies to control these interactions to improve the profile of ASOs are discussed.
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Affiliation(s)
- Punit P. Seth
- Ionis Pharmaceuticals 2855 Gazelle Court Carlsbad CA 92010 USA
| | - Eric E. Swayze
- Ionis Pharmaceuticals 2855 Gazelle Court Carlsbad CA 92010 USA
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37
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Frei S, Istrate A, Leumann CJ. 6'-Fluoro[4.3.0]bicyclo nucleic acid: synthesis, biophysical properties and molecular dynamics simulations. Beilstein J Org Chem 2018; 14:3088-3097. [PMID: 30643586 PMCID: PMC6317435 DOI: 10.3762/bjoc.14.288] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2018] [Accepted: 11/29/2018] [Indexed: 12/31/2022] Open
Abstract
Here we report on the synthesis, biophysical properties and molecular modeling of oligonucleotides containing unsaturated 6'-fluoro[4.3.0]bicyclo nucleotides (6'F-bc4,3-DNA). Two 6'F-bc4,3 phosphoramidite building blocks (T and C) were synthesized starting from a previously described [3.3.0]bicyclic sugar. The conversion of this sugar to a gem-difluorinated tricyclic intermediate via difluorocarbene addition followed either by a NIS-mediated or Vorbrüggen nucleosidation yielded in both cases the β-tricyclic nucleoside as major anomer. Subsequent desilylation and cyclopropane ring opening of these tricyclic intermediates afforded the unsaturated 6'F-bc4,3 nucleosides. The successful incorporation of the corresponding phosphoramidite building blocks into oligonucleotides was achieved with tert-butyl hydroperoxide as oxidation agent. Thermal melting experiments of the modified duplexes disclosed a destabilizing effect versus DNA and RNA complements, but with a lesser degree of destabilization versus complementary DNA (ΔT m/mod = -1.5 to -3.7 °C). Molecular dynamics simulation on the nucleoside and oligonucleotide level revealed the preference of the C1'-exo/C2'-endo alignment of the furanose ring. Moreover, the simulation of duplexes with complementary RNA disclosed a DNA/RNA-type duplex structure suggesting that this modification might be a substrate for RNase H.
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Affiliation(s)
- Sibylle Frei
- Department of Chemistry and Biochemistry, University of Bern, Freiestrasse 3, 3012 Bern, Switzerland
| | - Andrei Istrate
- Department of Chemistry and Biochemistry, University of Bern, Freiestrasse 3, 3012 Bern, Switzerland
| | - Christian J Leumann
- Department of Chemistry and Biochemistry, University of Bern, Freiestrasse 3, 3012 Bern, Switzerland
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38
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Garcia JP, Stein J, Cai Y, Riemers F, Wexselblatt E, Wengel J, Tryfonidou M, Yayon A, Howard KA, Creemers LB. Fibrin-hyaluronic acid hydrogel-based delivery of antisense oligonucleotides for ADAMTS5 inhibition in co-delivered and resident joint cells in osteoarthritis. J Control Release 2018; 294:247-258. [PMID: 30572032 DOI: 10.1016/j.jconrel.2018.12.030] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2018] [Accepted: 12/16/2018] [Indexed: 02/06/2023]
Abstract
To date no disease-modifying drugs for osteoarthritis (OA) are available, with treatment limited to the use of pain killers and prosthetic replacement. The ADAMTS (A Disintegrin and Metallo Proteinase with Thrombospondin Motifs) enzyme family is thought to be instrumental in the loss of proteoglycans during cartilage degeneration in OA, and their inhibition was shown to reverse osteoarthritic cartilage degeneration. Locked Nucleic Acid (LNA)-modified antisense oligonucleotides (gapmers) released from biomaterial scaffolds for specific and prolonged ADAMTS inhibition in co-delivered and resident chondrocytes, is an attractive therapeutic strategy. Here, a gapmer sequence identified from a gapmer screen showed 90% ADAMTS5 silencing in a monolayer culture of human OA chondrocytes. Incorporation of the gapmer in a fibrin-hyaluronic acid hydrogel exhibited a sustained release profile up to 14 days. Gapmers loaded in hydrogels were able to transfect both co-embedded chondrocytes and chondrocytes in a neighboring gapmer-free hydrogel, as demonstrated by flow cytometry and confocal microscopy. Efficient knockdown of ADAMTS5 was shown up to 14 days in both cell populations, i.e. the gapmer-loaded and gapmer-free hydrogel. This work demonstrates the use applicability of a hydrogel as a platform for combined local delivery of chondrocytes and an ADAMTS-targeting gapmer for catabolic gene modulation in OA.
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Affiliation(s)
- João Pedro Garcia
- Department of Orthopedics, University Medical Center Utrecht, the Netherlands
| | - Jeroen Stein
- Department of Orthopedics, University Medical Center Utrecht, the Netherlands
| | - Yunpeng Cai
- Interdisciplinary Nanoscience Center (iNANO), Department of Molecular Biology and Genetics, Aarhus University, Denmark
| | - Frank Riemers
- Department of Clinical Sciences of Companion Animals, Faculty of Veterinary Medicine, Utrecht University, the Netherlands
| | | | - Jesper Wengel
- Nucleic Acid Center, University of Southern Denmark, Denmark
| | - Marianna Tryfonidou
- Department of Clinical Sciences of Companion Animals, Faculty of Veterinary Medicine, Utrecht University, the Netherlands
| | | | - Kenneth A Howard
- Interdisciplinary Nanoscience Center (iNANO), Department of Molecular Biology and Genetics, Aarhus University, Denmark
| | - Laura B Creemers
- Department of Orthopedics, University Medical Center Utrecht, the Netherlands.
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39
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Janas MM, Harbison CE, Perry VK, Carito B, Sutherland JE, Vaishnaw AK, Keirstead ND, Warner G. The Nonclinical Safety Profile of GalNAc-conjugated RNAi Therapeutics in Subacute Studies. Toxicol Pathol 2018; 46:735-745. [PMID: 30139307 PMCID: PMC6249674 DOI: 10.1177/0192623318792537] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Short interfering RNAs (siRNAs) and antisense oligonucleotides (ASOs) are the most clinically advanced oligonucleotide-based platforms. A number of N-acetylgalactosamine (GalNAc)-conjugated siRNAs (GalNAc-siRNAs), also referred to as RNA interference (RNAi) therapeutics, are currently in various stages of development, though none is yet approved. While the safety of ASOs has been the subject of extensive review, the nonclinical safety profiles of GalNAc-siRNAs have not been reported. With the exception of sequence differences that confer target RNA specificity, GalNAc-siRNAs are largely chemically uniform, containing limited number of phosphorothioate linkages, and 2’-O-methyl and 2’-deoxy-2’-fluoro ribose modifications. Here, we present the outcomes of short-term (3–5 week) rat and monkey weekly repeat-dose toxicology studies of six Enhanced Stabilization Chemistry GalNAc-siRNAs currently in clinical development. In nonclinical studies at supratherapeutic doses, these molecules share similar safety signals, with histologic findings in the organ of pharmacodynamic effect (liver), the organ of elimination (kidney), and the reticuloendothelial system (lymph nodes). The majority of these changes are nonadverse, partially to completely reversible, correlate well with pharmacokinetic parameters and tissue distribution, and often reflect drug accumulation. Furthermore, all GalNAc-siRNAs tested to date have been negative in genotoxicity and safety pharmacology studies.
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Affiliation(s)
- Maja M Janas
- 1 Alnylam Pharmaceuticals, Cambridge, Massachusetts, USA.,Authors contributed equally to this work
| | - Carole E Harbison
- 1 Alnylam Pharmaceuticals, Cambridge, Massachusetts, USA.,Authors contributed equally to this work
| | | | - Brenda Carito
- 1 Alnylam Pharmaceuticals, Cambridge, Massachusetts, USA
| | | | | | | | - Garvin Warner
- 1 Alnylam Pharmaceuticals, Cambridge, Massachusetts, USA
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40
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Kasuya T, Kugimiya A. Role of Computationally Evaluated Target Specificity in the Hepatotoxicity of Gapmer Antisense Oligonucleotides. Nucleic Acid Ther 2018; 28:312-317. [PMID: 30095329 DOI: 10.1089/nat.2018.0724] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Gapmer antisense oligonucleotides (gapmers) sometimes cleave nontarget pre-mRNAs by recognizing target-like intronic/exonic portions. This off-target RNA cleavage could be a major cause of the hepatotoxicity that is induced by gapmers. In line with these findings, we hypothesized that gapmers with higher specificity have less hepatotoxicity, and that those with lower specificity have greater toxicity. To examine this concept, we investigated various Malat1-targeting gapmers with various computationally evaluated target specificities. We had expected that higher specificity gapmers would have lower hepatotoxicity, but these factors were not significantly related. In silico analysis of gapmer sequences does not always contribute to mitigating the risk of hepatotoxicity. Transcriptome analysis indicated that nontoxic gapmers do not cleave off-target RNAs, although they have many target-like RNA sequences. The present results shed light on the mechanism of the hepatotoxicity of gapmers.
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Affiliation(s)
- Takeshi Kasuya
- Discovery Research and Disease Research Laboratory, Shionogi & Co., Ltd. , Osaka, Japan
| | - Akira Kugimiya
- Discovery Research and Disease Research Laboratory, Shionogi & Co., Ltd. , Osaka, Japan
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41
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Cai Y, Makarova AM, Wengel J, Howard KA. Palmitoylated phosphodiester gapmer designs with albumin binding capacity and maintained in vitro gene silencing activity. J Gene Med 2018; 20:e3025. [PMID: 29800498 DOI: 10.1002/jgm.3025] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2018] [Revised: 05/09/2018] [Accepted: 05/16/2018] [Indexed: 01/18/2023] Open
Abstract
BACKGROUND Antisense gapmer oligonucleotide drugs require delivery and biodistribution enabling technologies to increase in vivo efficacy. An attractive approach is their binding and consequent transport by the endogenous human serum albumin pool as mediated by fatty acid incorporation into the gapmer design. METHODS The present study investigated the effect of palmitoyl modification and position on albumin-binding, cellular uptake and in vitro gene silencing of gapmers with either a phosphorothioate (PS) or phosphodiester (PO) backbone. RESULTS Two palmitoyls positioned exclusively at the 5' end, or a single palmitoyl at both the 3' and 5' positions, showed similar binding to human serum albumin as demonstrated by a gel-shift assay. Decreased cellular uptake determined by flow cytometry (27% compared to nonpalmitoyl gapmers) was observed for palmitoylated Cy5.5 labelled gapmers. However, HER3 (human epidermal growth factor receptor 3) gene silencing was exhibited by the palmitoylated gapmers with transfection agent in PC-3 and Caco-2 cells (68% and 62%, respectively), which was comparable to nonpalmitoyl gapmers (68% and 82%, respectively). Importantly, PO gapmers with a single palmitoyl positioned at both the 3' and 5' positions showed high silencing efficiencies (68% and 66% in PC-3 and Caco-2 cells, respectively) similar to those of PS nonpalmitoylated gapmers (67% and 66% in PC-3 and Caco-2 cells, respectively) in the absence of a transfection agent. CONCLUSIONS The present study defines phosphodiester gapmer design criteria exhibiting high gene silencing activity and albumin binding that may be utilized with potentially less in vivo toxicity that can be associated with phosphorothioate gapmer designs.
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Affiliation(s)
- Yunpeng Cai
- The Interdisciplinary Nanoscience Center (iNANO), Department of Molecular Biology and Genetics, Aarhus University, Aarhus C, Denmark
| | | | - Jesper Wengel
- Nucleic Acid Center, Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Odense, Denmark
| | - Kenneth A Howard
- The Interdisciplinary Nanoscience Center (iNANO), Department of Molecular Biology and Genetics, Aarhus University, Aarhus C, Denmark
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42
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Oberemok VV, Laikova KV, Repetskaya AI, Kenyo IM, Gorlov MV, Kasich IN, Krasnodubets AM, Gal'chinsky NV, Fomochkina II, Zaitsev AS, Bekirova VV, Seidosmanova EE, Dydik KI, Meshcheryakova AO, Nazarov SA, Smagliy NN, Chelengerova EL, Kulanova AA, Deri K, Subbotkin MV, Useinov RZ, Shumskykh MN, Kubyshkin AV. A Half-Century History of Applications of Antisense Oligonucleotides in Medicine, Agriculture and Forestry: We Should Continue the Journey. Molecules 2018; 23:E1302. [PMID: 29844255 PMCID: PMC6099785 DOI: 10.3390/molecules23061302] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2018] [Revised: 05/25/2018] [Accepted: 05/27/2018] [Indexed: 02/07/2023] Open
Abstract
Antisense oligonucleotides (ASO), short single-stranded polymers based on DNA or RNA chemistries and synthesized in vitro, regulate gene expression by binding in a sequence-specific manner to an RNA target. The functional activity and selectivity in the action of ASOs largely depends on the combination of nitrogenous bases in a target sequence. This simple and natural property of nucleic acids provides an attractive route by which scientists can create different ASO-based techniques. Over the last 50 years, planned and realized applications in the field of antisense and nucleic acid nanotechnologies have produced astonishing results and posed new challenges for further developments, exemplifying the essence of the post-genomic era. Today the majority of ASOs are chemically modified and/or incorporated within nanoparticles to enhance their stability and cellular uptake. This review critically analyzes some successful cases using the antisense approach in medicine to address severe diseases, such as Duchenne muscular dystrophy and spinal muscular atrophy, and suggests some prospective directions for future research. We also examine in detail the elaboration of unmodified insect-specific DNA insecticides and RNA preparations in the areas of agriculture and forestry, a relatively new branch of ASO that allows circumvention of the use of non-selective chemical insecticides. When considering the variety of successful ASO modifications with an efficient signal-to-noise ratio of action, coupled with the affordability of in vitro oligonucleotide synthesis and post-synthesis procedures, we predict that the next half-century will produce a fruitful yield of tools created from effective ASO-based end products.
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MESH Headings
- Agriculture/methods
- Animals
- Biological Control Agents/chemical synthesis
- Biological Control Agents/history
- Biological Control Agents/pharmacology
- DNA/antagonists & inhibitors
- DNA/genetics
- DNA/metabolism
- Forestry/methods
- Gene Expression Regulation/drug effects
- History, 20th Century
- History, 21st Century
- Humans
- Larva/drug effects
- Larva/genetics
- Larva/metabolism
- Moths/drug effects
- Moths/genetics
- Moths/growth & development
- Moths/metabolism
- Muscular Atrophy, Spinal/genetics
- Muscular Atrophy, Spinal/metabolism
- Muscular Atrophy, Spinal/pathology
- Muscular Atrophy, Spinal/therapy
- Muscular Dystrophy, Duchenne/genetics
- Muscular Dystrophy, Duchenne/metabolism
- Muscular Dystrophy, Duchenne/pathology
- Muscular Dystrophy, Duchenne/therapy
- Nanoparticles/administration & dosage
- Nanoparticles/chemistry
- Neuromuscular Agents/chemical synthesis
- Neuromuscular Agents/history
- Neuromuscular Agents/therapeutic use
- Oligonucleotides, Antisense/chemical synthesis
- Oligonucleotides, Antisense/genetics
- Oligonucleotides, Antisense/metabolism
- RNA, Messenger/antagonists & inhibitors
- RNA, Messenger/genetics
- RNA, Messenger/metabolism
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Affiliation(s)
- Volodymyr V Oberemok
- Taurida Academy, V.I. Vernadsky Crimean Federal University, Vernadsky Avenue 4, 295007 Simferopol, Crimea.
| | - Kateryna V Laikova
- Medical Academy named after S.I. Georgievsky, V.I. Vernadsky Crimean Federal University, Lenin Avenue 5/7, 295051 Simferopol, Crimea.
| | - Anna I Repetskaya
- Botanical Garden named after N.V. Bagrov, V.I. Vernadsky Crimean Federal University, Vernadsky Avenue 4, 29500 Simferopol, Crimea.
| | - Igor M Kenyo
- Academy of Bioresources and Environmental Management of V.I. Vernadsky Crimean Federal University, 95492 Agrarnoye, Crimea.
| | - Mikhail V Gorlov
- D. Mendeleev University of Chemical Technology of Russia, Miusskaya sq. 9, 125047 Moscow, Russia.
| | - Igor N Kasich
- Rostov State Medical University, Nakhchivan Lane 29, 344022 Rostov-on-Don, Russia.
| | - Alisa M Krasnodubets
- Taurida Academy, V.I. Vernadsky Crimean Federal University, Vernadsky Avenue 4, 295007 Simferopol, Crimea.
| | - Nikita V Gal'chinsky
- Taurida Academy, V.I. Vernadsky Crimean Federal University, Vernadsky Avenue 4, 295007 Simferopol, Crimea.
| | - Iryna I Fomochkina
- Medical Academy named after S.I. Georgievsky, V.I. Vernadsky Crimean Federal University, Lenin Avenue 5/7, 295051 Simferopol, Crimea.
| | - Aleksei S Zaitsev
- Taurida Academy, V.I. Vernadsky Crimean Federal University, Vernadsky Avenue 4, 295007 Simferopol, Crimea.
| | - Viktoriya V Bekirova
- Taurida Academy, V.I. Vernadsky Crimean Federal University, Vernadsky Avenue 4, 295007 Simferopol, Crimea.
| | - Eleonora E Seidosmanova
- Taurida Academy, V.I. Vernadsky Crimean Federal University, Vernadsky Avenue 4, 295007 Simferopol, Crimea.
| | - Ksenia I Dydik
- Taurida Academy, V.I. Vernadsky Crimean Federal University, Vernadsky Avenue 4, 295007 Simferopol, Crimea.
| | - Anna O Meshcheryakova
- Taurida Academy, V.I. Vernadsky Crimean Federal University, Vernadsky Avenue 4, 295007 Simferopol, Crimea.
| | - Sergey A Nazarov
- Taurida Academy, V.I. Vernadsky Crimean Federal University, Vernadsky Avenue 4, 295007 Simferopol, Crimea.
| | - Natalya N Smagliy
- Taurida Academy, V.I. Vernadsky Crimean Federal University, Vernadsky Avenue 4, 295007 Simferopol, Crimea.
| | - Edie L Chelengerova
- Taurida Academy, V.I. Vernadsky Crimean Federal University, Vernadsky Avenue 4, 295007 Simferopol, Crimea.
| | - Alina A Kulanova
- Medical Academy named after S.I. Georgievsky, V.I. Vernadsky Crimean Federal University, Lenin Avenue 5/7, 295051 Simferopol, Crimea.
| | - Karim Deri
- Medical Academy named after S.I. Georgievsky, V.I. Vernadsky Crimean Federal University, Lenin Avenue 5/7, 295051 Simferopol, Crimea.
| | - Mikhail V Subbotkin
- Medical Academy named after S.I. Georgievsky, V.I. Vernadsky Crimean Federal University, Lenin Avenue 5/7, 295051 Simferopol, Crimea.
| | - Refat Z Useinov
- Taurida Academy, V.I. Vernadsky Crimean Federal University, Vernadsky Avenue 4, 295007 Simferopol, Crimea.
| | - Maksym N Shumskykh
- Taurida Academy, V.I. Vernadsky Crimean Federal University, Vernadsky Avenue 4, 295007 Simferopol, Crimea.
| | - Anatoly V Kubyshkin
- Medical Academy named after S.I. Georgievsky, V.I. Vernadsky Crimean Federal University, Lenin Avenue 5/7, 295051 Simferopol, Crimea.
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43
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Kishimoto Y, Fujii A, Nakagawa O, Nagata T, Yokota T, Hari Y, Obika S. Synthesis and thermal stabilities of oligonucleotides containing 2'-O,4'-C-methylene bridged nucleic acid with a phenoxazine base. Org Biomol Chem 2018; 15:8145-8152. [PMID: 28920119 DOI: 10.1039/c7ob01874f] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
We designed and synthesized a novel artificial 2'-O,4'-C-methylene bridged nucleic acid (2',4'-BNA/LNA) with a phenoxazine nucleobase and named this compound BNAP. Oligodeoxynucleotide (ODN) containing BNAP showed higher binding affinities toward complementary DNA and RNA as compared to ODNs bearing 2',4'-BNA/LNA with 5-methylcytosine or 2'-deoxyribonucleoside with phenoxazine. Thermodynamic analysis revealed that BNAP exhibits properties associated with the phenoxazine moiety in DNA/DNA duplexes and characteristics associated with the 2',4'-BNA/LNA moiety in DNA/RNA duplexes.
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Affiliation(s)
- Yuki Kishimoto
- Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka 565-0871, Japan.
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44
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Moreno PMD, Ferreira AR, Salvador D, Rodrigues MT, Torrado M, Carvalho ED, Tedebark U, Sousa MM, Amaral IF, Wengel J, Pêgo AP. Hydrogel-Assisted Antisense LNA Gapmer Delivery for In Situ Gene Silencing in Spinal Cord Injury. MOLECULAR THERAPY. NUCLEIC ACIDS 2018; 11:393-406. [PMID: 29858074 PMCID: PMC5992461 DOI: 10.1016/j.omtn.2018.03.009] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/09/2017] [Revised: 03/04/2018] [Accepted: 03/15/2018] [Indexed: 12/16/2022]
Abstract
After spinal cord injury (SCI), nerve regeneration is severely hampered due to the establishment of a highly inhibitory microenvironment at the injury site, through the contribution of multiple factors. The potential of antisense oligonucleotides (AONs) to modify gene expression at different levels, allowing the regulation of cell survival and cell function, together with the availability of chemically modified nucleic acids with favorable biopharmaceutical properties, make AONs an attractive tool for novel SCI therapy developments. In this work, we explored the potential of locked nucleic acid (LNA)-modified AON gapmers in combination with a fibrin hydrogel bridging material to induce gene silencing in situ at a SCI lesion site. LNA gapmers were effectively developed against two promising gene targets aiming at enhancing axonal regeneration-RhoA and GSK3β. The fibrin-matrix-assisted AON delivery system mediated potent RNA knockdown in vitro in a dorsal root ganglion explant culture system and in vivo at a SCI lesion site, achieving around 75% downregulation 5 days after hydrogel injection. Our results show that local implantation of a AON-gapmer-loaded hydrogel matrix mediated efficient gene silencing in the lesioned spinal cord and is an innovative platform that can potentially combine gene regulation with regenerative permissive substrates aiming at SCI therapeutics and nerve regeneration.
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Affiliation(s)
- Pedro M D Moreno
- i3S - Instituto de Investigação e Inovação em Saúde, Universidade do Porto, 4200-135 Porto, Portugal; INEB - Instituto de Engenharia Biomédica, Universidade do Porto, 4200-135 Porto, Portugal
| | - Ana R Ferreira
- i3S - Instituto de Investigação e Inovação em Saúde, Universidade do Porto, 4200-135 Porto, Portugal; INEB - Instituto de Engenharia Biomédica, Universidade do Porto, 4200-135 Porto, Portugal
| | - Daniela Salvador
- i3S - Instituto de Investigação e Inovação em Saúde, Universidade do Porto, 4200-135 Porto, Portugal; INEB - Instituto de Engenharia Biomédica, Universidade do Porto, 4200-135 Porto, Portugal
| | - Maria T Rodrigues
- i3S - Instituto de Investigação e Inovação em Saúde, Universidade do Porto, 4200-135 Porto, Portugal; INEB - Instituto de Engenharia Biomédica, Universidade do Porto, 4200-135 Porto, Portugal
| | - Marília Torrado
- i3S - Instituto de Investigação e Inovação em Saúde, Universidade do Porto, 4200-135 Porto, Portugal; INEB - Instituto de Engenharia Biomédica, Universidade do Porto, 4200-135 Porto, Portugal
| | - Eva D Carvalho
- i3S - Instituto de Investigação e Inovação em Saúde, Universidade do Porto, 4200-135 Porto, Portugal; INEB - Instituto de Engenharia Biomédica, Universidade do Porto, 4200-135 Porto, Portugal
| | - Ulf Tedebark
- GE Healthcare Bio-Sciences AB, 75184 Uppsala, Sweden; SynMer AB, 17568 Järfälla, Sweden
| | - Mónica M Sousa
- i3S - Instituto de Investigação e Inovação em Saúde, Universidade do Porto, 4200-135 Porto, Portugal; IBMC - Instituto de Biologia Molecular e Celular, Nerve Regeneration Group, Universidade do Porto, 4200-135 Porto, Portugal
| | - Isabel F Amaral
- i3S - Instituto de Investigação e Inovação em Saúde, Universidade do Porto, 4200-135 Porto, Portugal; INEB - Instituto de Engenharia Biomédica, Universidade do Porto, 4200-135 Porto, Portugal
| | - Jesper Wengel
- Nucleic Acid Center, Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, 5230 Odense, Denmark
| | - Ana P Pêgo
- i3S - Instituto de Investigação e Inovação em Saúde, Universidade do Porto, 4200-135 Porto, Portugal; INEB - Instituto de Engenharia Biomédica, Universidade do Porto, 4200-135 Porto, Portugal; Faculdade de Engenharia da Universidade do Porto, 4200-465 Porto, Portugal; Instituto de Ciências Biomédicas Abel Salazar (ICBAS), Universidade do Porto, 4050-313 Porto, Portugal.
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45
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Roux BT, Lindsay MA, Heward JA. Knockdown of Nuclear-Located Enhancer RNAs and Long ncRNAs Using Locked Nucleic Acid GapmeRs. Methods Mol Biol 2018; 1468:11-8. [PMID: 27662866 DOI: 10.1007/978-1-4939-4035-6_2] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
The human genome is widely transcribed outside of protein-coding genes, producing thousands of noncoding RNAs from different subfamilies including enhancer RNAs. Functional studies to determine the role of individual genes are challenging with noncoding RNAs appearing to be more difficult to knockdown than mRNAs. One factor that may have hindered progress is that the majority of noncoding RNAs are thought to be located within the nucleus, where the efficiency of traditional RNA interference techniques is debatable. Here we present an alternative RNA interference technique utilizing Locked Nucleic Acids, which is able to efficiently knockdown noncoding RNAs irrespective of intracellular location.
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Affiliation(s)
- Benoit T Roux
- Department of Pharmacy and Pharmacology, University of Bath, Claverton Down, Bath, BA2 7AY, UK
| | - Mark A Lindsay
- Department of Pharmacy and Pharmacology, University of Bath, Claverton Down, Bath, BA2 7AY, UK
| | - James A Heward
- Department of Pharmacy and Pharmacology, University of Bath, Claverton Down, Bath, BA2 7AY, UK.
- Centre for Haemato-Oncology, Barts Cancer Institute, Charterhouse Square, London, EC1M 6BQ, UK.
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46
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Hagiwara K, Kurihara K, Honma M, Yamamoto J, Shinohara F. PEG-modification on the endo-position of an antisense oligonucleotide increases tumor accumulation via the EPR effect. JOURNAL OF BIOMATERIALS SCIENCE-POLYMER EDITION 2018; 29:448-459. [PMID: 29318941 DOI: 10.1080/09205063.2017.1422853] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
Nucleic acid medicine is the next-generation therapeutic modality for refractory diseases with its unique mode of action as an alternative to traditional therapies. A nucleic acid delivery system targeted to liver was validated clinically; however, the delivery system of nucleic acids targeting solid tumors following systemic administration is not efficient enough for clinical use. In this study, we first utilized an antisense oligonucleotide (ASO) and polyethylene glycol (PEG) in one-to-one conjugation (PEG-ASO) at the endo-position of the ASO (endo-PEG-ASO). The effects of ASO modification position, PEG structure and molecular weight, and PEG-ASO tumor accumulation were evaluated in vivo. The endo-PEG-ASO showed prolonged pharmacokinetics and enhanced tumor accumulation compared with the conventional ASO and the PEG-ASO modified at the ASO exo-position (exo-PEG-ASO), indicating that the modification position of PEG is crucial for targeting tumors. We also observed that the endo-PEG-ASO indicated possibility of enhanced permeability inside the tumor. Further research is needed to optimize the linker in the endo-PEG-ASO for clinical application as a novel and promising therapeutic format for targeting solid tumors.
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Affiliation(s)
- Kenji Hagiwara
- a Innovative Technology Laboratories, Research Functions Unit, R&D Division , Kyowa Hakko Kirin Co., Ltd , Tokyo , Japan
| | - Kana Kurihara
- b Research Core Function Laboratories, Research Functions Unit, R&D Division , Kyowa Hakko Kirin Co., Ltd , Tokyo , Japan
| | - Masakazu Honma
- a Innovative Technology Laboratories, Research Functions Unit, R&D Division , Kyowa Hakko Kirin Co., Ltd , Tokyo , Japan
| | - Junichiro Yamamoto
- a Innovative Technology Laboratories, Research Functions Unit, R&D Division , Kyowa Hakko Kirin Co., Ltd , Tokyo , Japan
| | - Fumikazu Shinohara
- a Innovative Technology Laboratories, Research Functions Unit, R&D Division , Kyowa Hakko Kirin Co., Ltd , Tokyo , Japan
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47
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Godfrey C, Desviat LR, Smedsrød B, Piétri-Rouxel F, Denti MA, Disterer P, Lorain S, Nogales-Gadea G, Sardone V, Anwar R, El Andaloussi S, Lehto T, Khoo B, Brolin C, van Roon-Mom WM, Goyenvalle A, Aartsma-Rus A, Arechavala-Gomeza V. Delivery is key: lessons learnt from developing splice-switching antisense therapies. EMBO Mol Med 2017; 9:545-557. [PMID: 28289078 PMCID: PMC5412803 DOI: 10.15252/emmm.201607199] [Citation(s) in RCA: 103] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
The use of splice‐switching antisense therapy is highly promising, with a wealth of pre‐clinical data and numerous clinical trials ongoing. Nevertheless, its potential to treat a variety of disorders has yet to be realized. The main obstacle impeding the clinical translation of this approach is the relatively poor delivery of antisense oligonucleotides to target tissues after systemic delivery. We are a group of researchers closely involved in the development of these therapies and would like to communicate our discussions concerning the validity of standard methodologies currently used in their pre‐clinical development, the gaps in current knowledge and the pertinent challenges facing the field. We therefore make recommendations in order to focus future research efforts and facilitate a wider application of therapeutic antisense oligonucleotides.
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Affiliation(s)
- Caroline Godfrey
- Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford, UK
| | - Lourdes R Desviat
- Centro de Biología Molecular Severo Ochoa UAM-CSIC, CIBERER, IdiPaz, Universidad Autónoma de Madrid, Madrid, Spain
| | - Bård Smedsrød
- Department of Medical Biology, University of Tromsø, Tromsø, Norway
| | | | - Michela A Denti
- Centre for Integrative Biology, University of Trento, Trento, Italy
| | - Petra Disterer
- Centre for Amyloidosis and Acute Phase Proteins, Division of Medicine, University College London, London, UK
| | - Stéphanie Lorain
- UPMC, INSERM, UMRS 974, CNRS FRE 3617, Institut de Myologie, Paris, France
| | - Gisela Nogales-Gadea
- Grup d'Investigació en Malalties Neuromusculars i Neuropediatriques, Institut d' Investigació en Ciències de la Salut Germans Trias i Pujol, Badalona Barcelona, Spain
| | - Valentina Sardone
- Dubowitz Neuromuscular Centre and Developmental Neuroscience Programme, Institute of Child Health, University College London, London, UK
| | - Rayan Anwar
- Drug Discovery Informatics Lab, Qasemi-Research Center, Al-Qasemi Academic College, Baka El-Garbiah, Israel.,Drug Discovery and Development Laboratory, Institute of Applied Research, Galilee Society, Shefa-Amr, Israel
| | - Samir El Andaloussi
- Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford, UK.,Department of Laboratory Medicine, Karolinska Institute, Stockholm, Sweden
| | - Taavi Lehto
- Department of Laboratory Medicine, Karolinska Institute, Stockholm, Sweden.,Institute of Technology, University of Tartu, Tartu, Estonia
| | - Bernard Khoo
- Centre for Neuroendocrinology, Division of Medicine, University College London, London, UK
| | - Camilla Brolin
- Department of Cellular and Molecular Medicine, University of Copenhagen, Copenhagen, Denmark
| | | | - Aurélie Goyenvalle
- INSERM U1179, UFR des sciences de la santé, Université Versailles Saint Quentin, Montigny-le-Bretonneux, France
| | - Annemieke Aartsma-Rus
- Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands
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48
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Dieckmann A, Hagedorn PH, Burki Y, Brügmann C, Berrera M, Ebeling M, Singer T, Schuler F. A Sensitive In Vitro Approach to Assess the Hybridization-Dependent Toxic Potential of High Affinity Gapmer Oligonucleotides. MOLECULAR THERAPY-NUCLEIC ACIDS 2017; 10:45-54. [PMID: 29499955 PMCID: PMC5725219 DOI: 10.1016/j.omtn.2017.11.004] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/05/2017] [Revised: 11/10/2017] [Accepted: 11/11/2017] [Indexed: 10/29/2022]
Abstract
The successful development of high-affinity gapmer antisense oligonucleotide (ASO) therapeutics containing locked nucleic acid (LNA) or constrained ethyl (cEt) substitutions has been hampered by the risk of hepatotoxicity. Here, we present an in vitro approach using transfected mouse fibroblasts to predict the potential hepatic liabilities of LNA-modified ASOs (LNA-ASOs), validated by assessing 236 different LNA-ASOs with known hepatotoxic potential. This in vitro assay accurately reflects in vivo findings and relates hepatotoxicity to RNase H1 activity, off-target RNA downregulation, and LNA-ASO-binding affinity. We further demonstrate that the hybridization-dependent toxic potential of LNA-ASOs is also evident in different cell types from different species, which indicates probable translatability of the in vitro results to humans. Additionally, we show that the melting temperature (Tm) of LNA-ASOs maintained below a threshold level of about 55°C greatly diminished the hepatotoxic potential. In summary, we have established a sensitive in vitro screening approach for assessing the hybridization-dependent toxic potential of LNA-ASOs, enabling prioritization of candidate molecules in drug discovery and early development.
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Affiliation(s)
- Andreas Dieckmann
- Roche Pharma Research and Early Development, Roche Innovation Center Basel, 4070 Basel, Switzerland.
| | - Peter H Hagedorn
- Roche Pharma Research and Early Development, Roche Innovation Center Copenhagen, 2970 Hørsholm, Denmark
| | - Yvonne Burki
- Roche Pharma Research and Early Development, Roche Innovation Center Basel, 4070 Basel, Switzerland
| | - Christine Brügmann
- Roche Pharma Research and Early Development, Roche Innovation Center Basel, 4070 Basel, Switzerland
| | - Marco Berrera
- Roche Pharma Research and Early Development, Roche Innovation Center Basel, 4070 Basel, Switzerland
| | - Martin Ebeling
- Roche Pharma Research and Early Development, Roche Innovation Center Basel, 4070 Basel, Switzerland
| | - Thomas Singer
- Roche Pharma Research and Early Development, Roche Innovation Center Basel, 4070 Basel, Switzerland
| | - Franz Schuler
- Roche Pharma Research and Early Development, Roche Innovation Center Basel, 4070 Basel, Switzerland
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49
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Bailey JK, Shen W, Liang XH, Crooke ST. Nucleic acid binding proteins affect the subcellular distribution of phosphorothioate antisense oligonucleotides. Nucleic Acids Res 2017; 45:10649-10671. [PMID: 28977508 PMCID: PMC5737868 DOI: 10.1093/nar/gkx709] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2017] [Accepted: 08/04/2017] [Indexed: 12/15/2022] Open
Abstract
Antisense oligonucleotides (ASOs) are versatile tools that can regulate multiple steps of RNA biogenesis in cells and living organisms. Significant improvements in delivery, potency, and stability have been achieved through modifications within the oligonucleotide backbone, sugar and heterocycles. However, these modifications can profoundly affect interactions between ASOs and intracellular proteins in ways that are only beginning to be understood. Here, we report that ASOs with specific backbone and sugar modifications can become localized to cytoplasmic ribonucleoprotein granules such as stress granules and those seeded by the aggregation of specific ASO-binding proteins such as FUS/TLS (FUS) and PSF/SFPQ (PSF). Further investigation into the basis for ASO-FUS binding illustrated the importance of ASO backbone and hydrophobic 2' sugar modifications and revealed that the C-terminal region of FUS is sufficient to retain ASOs in cellular foci. Taken together, the results of this study demonstrate that affinities of various nucleic acid binding domains for ASO depend on chemical modifications and further demonstrate how ASO-protein interactions influence the localization of ASOs.
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Affiliation(s)
- Jeffrey K Bailey
- Department of Core Antisense Research, Ionis Pharmaceuticals, Inc. 2855 Gazelle Court, Carlsbad, CA 92010, USA
| | - Wen Shen
- 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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50
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Hagedorn PH, Persson R, Funder ED, Albæk N, Diemer SL, Hansen DJ, Møller MR, Papargyri N, Christiansen H, Hansen BR, Hansen HF, Jensen MA, Koch T. Locked nucleic acid: modality, diversity, and drug discovery. Drug Discov Today 2017; 23:101-114. [PMID: 28988994 DOI: 10.1016/j.drudis.2017.09.018] [Citation(s) in RCA: 149] [Impact Index Per Article: 21.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2017] [Revised: 09/01/2017] [Accepted: 09/27/2017] [Indexed: 01/05/2023]
Abstract
Over the past 20 years, the field of RNA-targeted therapeutics has advanced based on discoveries of modified oligonucleotide chemistries, and an ever-increasing understanding of how to apply cellular assays to identify oligonucleotides with improved pharmacological properties in vivo. Locked nucleic acid (LNA), which exhibits high binding affinity and potency, is widely used for this purpose. Our understanding of RNA biology has also expanded tremendously, resulting in new approaches to engage RNA as a therapeutic target. Recent observations indicate that each oligonucleotide is a unique entity, and small structural differences between oligonucleotides can often lead to substantial differences in their pharmacological properties. Here, we outline new principles for drug discovery exploiting oligonucleotide diversity to identify rare molecules with unique pharmacological properties.
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Affiliation(s)
- Peter H Hagedorn
- Therapeutic Modalities, Roche Pharma Research and Early Development, Roche Innovation Center Copenhagen, 2970 Hørsholm, Denmark
| | - Robert Persson
- Pharmaceutical Sciences, Roche Pharma Research and Early Development, Roche Innovation Center Copenhagen, 2970 Hørsholm, Denmark
| | - Erik D Funder
- Therapeutic Modalities, Roche Pharma Research and Early Development, Roche Innovation Center Copenhagen, 2970 Hørsholm, Denmark
| | - Nanna Albæk
- Therapeutic Modalities, Roche Pharma Research and Early Development, Roche Innovation Center Copenhagen, 2970 Hørsholm, Denmark
| | - Sanna L Diemer
- Therapeutic Modalities, Roche Pharma Research and Early Development, Roche Innovation Center Copenhagen, 2970 Hørsholm, Denmark
| | - Dennis J Hansen
- Therapeutic Modalities, Roche Pharma Research and Early Development, Roche Innovation Center Copenhagen, 2970 Hørsholm, Denmark
| | - Marianne R Møller
- Therapeutic Modalities, Roche Pharma Research and Early Development, Roche Innovation Center Copenhagen, 2970 Hørsholm, Denmark
| | - Natalia Papargyri
- Department of Biotechnology and Biomedicine, Technical University of Denmark, 2800 Kgs. Lyngby, Denmark
| | - Helle Christiansen
- Therapeutic Modalities, Roche Pharma Research and Early Development, Roche Innovation Center Copenhagen, 2970 Hørsholm, Denmark
| | - Bo R Hansen
- Therapeutic Modalities, Roche Pharma Research and Early Development, Roche Innovation Center Copenhagen, 2970 Hørsholm, Denmark
| | - Henrik F Hansen
- Therapeutic Modalities, Roche Pharma Research and Early Development, Roche Innovation Center Copenhagen, 2970 Hørsholm, Denmark
| | - Mads A Jensen
- Therapeutic Modalities, Roche Pharma Research and Early Development, Roche Innovation Center Copenhagen, 2970 Hørsholm, Denmark
| | - Troels Koch
- Therapeutic Modalities, Roche Pharma Research and Early Development, Roche Innovation Center Copenhagen, 2970 Hørsholm, Denmark.
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