1
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Kohashi H, Nagata R, Tamenori Y, Amatani T, Ueda Y, Mori Y, Kasahara Y, Obika S, Shimojo M. A novel transient receptor potential C3/C6 selective activator induces the cellular uptake of antisense oligonucleotides. Nucleic Acids Res 2024; 52:4784-4798. [PMID: 38621757 PMCID: PMC11109983 DOI: 10.1093/nar/gkae245] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2023] [Revised: 03/12/2024] [Accepted: 03/27/2024] [Indexed: 04/17/2024] Open
Abstract
Antisense oligonucleotide (ASO) therapy is a novel therapeutic approach in which ASO specifically binds target mRNA, resulting in mRNA degradation; however, cellular uptake of ASOs remains critically low, warranting improvement. Transient receptor potential canonical (TRPC) channels regulate Ca2+ influx and are activated upon stimulation by phospholipase C-generated diacylglycerol. Herein, we report that a novel TRPC3/C6/C7 activator, L687, can induce cellular ASO uptake. L687-induced ASO uptake was enhanced in a dose- and incubation-time-dependent manner. L687 enhanced the knockdown activity of various ASOs both in vitro and in vivo. Notably, suppression of TRPC3/C6 by specific siRNAs reduced ASO uptake in A549 cells. Application of BAPTA-AM, a Ca2+ chelator, and SKF96365, a TRPC3/C6 inhibitor, suppressed Ca2+ influx via TRPC3/C6, resulting in reduced ASO uptake, thereby suggesting that Ca2+ influx via TRPC3/C6 is critical for L687-mediated increased ASO uptake. L687 also induced dextran uptake, indicating that L687 increased endocytosis. Adding ASO to L687 resulted in endosome accumulation; however, the endosomal membrane disruptor UNC7938 facilitated endosomal escape and enhanced knockdown activity. We discovered a new function for TRPC activators regarding ASO trafficking in target cells. Our findings provide an opportunity to formulate an innovative drug delivery system for the therapeutic development of ASO.
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Affiliation(s)
- Hiroto Kohashi
- Graduate School of Pharmaceutical Sciences, Osaka University, Osaka 565-0871, Japan
| | - Ryu Nagata
- Graduate School of Pharmaceutical Sciences, Osaka University, Osaka 565-0871, Japan
| | - Yusuke Tamenori
- School of Pharmaceutical Sciences, Osaka University, Osaka 565-0871, Japan
| | - Tomorrow Amatani
- Graduate School of Engineering, Kyoto University, Kyoto 615-8510, Japan
| | - Yoshifumi Ueda
- Graduate School of Engineering, Kyoto University, Kyoto 615-8510, Japan
| | - Yasuo Mori
- Graduate School of Engineering, Kyoto University, Kyoto 615-8510, Japan
| | - Yuuya Kasahara
- National Institutes of Biomedical Innovation, Health and Nutrition, Osaka 567-0085, Japan
| | - Satoshi Obika
- Graduate School of Pharmaceutical Sciences, Osaka University, Osaka 565-0871, Japan
- Institute for Open and Transdisciplinary Research Initiatives (OTRI), Osaka University, Osaka 565-0871, Japan
| | - Masahito Shimojo
- Graduate School of Pharmaceutical Sciences, Osaka University, Osaka 565-0871, Japan
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2
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Hayashi J, Ochi Y, Senpuku K, Wada SI, Wada F, Harada-Shiba M, Urata H. Rational design of prodrug-type apoB-targeted siRNA for nuclease resistance improvement without compromising gene silencing potency. Bioorg Med Chem 2024; 104:117693. [PMID: 38552598 DOI: 10.1016/j.bmc.2024.117693] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2024] [Revised: 03/12/2024] [Accepted: 03/15/2024] [Indexed: 04/20/2024]
Abstract
Synthetic siRNA molecules without chemical modifications are easily degraded in the body, and 2'-O-modifications are frequently introduced to enhance stability. However, such chemical modifications tend to impact the gene knockdown potency of siRNA negatively. To circumvent this problem, we previously developed a prodrug-type siRNA bearing 2'-O-methyldithiomethyl (MDTM) groups, which can be converted into unmodified siRNA under the reductive environment in cells. In this study, we developed a nuclease-resistant prodrug-type 2'-O-MDTM siRNA for deployment in future animal experiments. To rationally design siRNA modified with a minimal number of 2'-O-MDTM nucleotide residues, we identified the sites susceptible to nuclease digestion and tolerant to 2'-O-methyl (2'-OMe) modification in the antisense strand of apolipoprotein B-targeted siRNA. Subsequently, we optimized the positions where the 2'-OMe and 2'-O-MDTM groups should be incorporated. siRNA bearing the 2'-O-MDTM and 2'-OMe groups at their respective optimized positions exhibited efficient knockdown potency in vitro and enhanced stability in serum.
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Affiliation(s)
- Junsuke Hayashi
- Department of Bioorganic Chemistry, Faculty of Pharmacy, Osaka Medical and Pharmaceutical University, 4-20-1 Nasahara, Takatsuki, Osaka 569-1094, Japan.
| | - Yosuke Ochi
- Department of Bioorganic Chemistry, Faculty of Pharmacy, Osaka Medical and Pharmaceutical University, 4-20-1 Nasahara, Takatsuki, Osaka 569-1094, Japan
| | - Kota Senpuku
- Department of Bioorganic Chemistry, Faculty of Pharmacy, Osaka Medical and Pharmaceutical University, 4-20-1 Nasahara, Takatsuki, Osaka 569-1094, Japan
| | - Shun-Ichi Wada
- Department of Bioorganic Chemistry, Faculty of Pharmacy, Osaka Medical and Pharmaceutical University, 4-20-1 Nasahara, Takatsuki, Osaka 569-1094, Japan
| | - Fumito Wada
- National Cerebral & Cardiovascular Center Research Institute, 6-1 Kishibe-shinmachi, Suita, Osaka 564-8565, Japan
| | - Mariko Harada-Shiba
- National Cerebral & Cardiovascular Center Research Institute, 6-1 Kishibe-shinmachi, Suita, Osaka 564-8565, Japan
| | - Hidehito Urata
- Department of Bioorganic Chemistry, Faculty of Pharmacy, Osaka Medical and Pharmaceutical University, 4-20-1 Nasahara, Takatsuki, Osaka 569-1094, Japan.
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3
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Sugimoto N, Hayashi J, Funaki R, Wada SI, Wada F, Harada-Shiba M, Urata H. Prodrug-Type Phosphotriester Oligonucleotides with Linear Disulfide Promoieties Responsive to Reducing Environment. Chembiochem 2023; 24:e202300526. [PMID: 37840006 DOI: 10.1002/cbic.202300526] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Revised: 10/12/2023] [Accepted: 10/14/2023] [Indexed: 10/17/2023]
Abstract
Various chemical modifications have been developed to create new antisense oligonucleotides (AONs) for clinical applications. Our previously designed prodrug-type phosphotriester-modified oligonucleotide with cyclic disulfides (cyclic SS PTE ON) can be converted into unmodified ON in an intracellular-mimetic reducing environment. However, the conversion rate of the cyclic SS PTE ON was very low, and the AON with cyclic SS PTE modifications showed much weaker antisense activity than corresponding to the fully phosphorothioate-modified AON. In this study, we synthesized several types of PTE ONs containing linear disulfides (linear SS PTE ONs) and evaluated their conversion rates under reducing conditions. From the results, the structural requirements for the conversion of the synthesized linear SS PTE ONs were elucidated. Linear SS PTE ON with promising promoieties showed a nuclease resistance up to 4.8-fold compared to unmodified ON and a cellular uptake by endocytosis without any transfection reagent. In addition, although the knockdown activity of the linear SS PTE gapmer AON is weaker than that of the fully phosphorothioate-modified gapmer AON, the knockdown activity is slightly stronger than that of the cyclic SS PTE gapmer AON. These results suggest that the conversion rates may be related to the expression of the antisense activity.
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Affiliation(s)
- Norihito Sugimoto
- Department of Bioorganic Chemistry, Faculty of Pharmacy, Osaka Medical and Pharmaceutical University, 4-20-1 Nasahara, Takatsuki, Osaka, 569-1094, Japan
| | - Junsuke Hayashi
- Department of Bioorganic Chemistry, Faculty of Pharmacy, Osaka Medical and Pharmaceutical University, 4-20-1 Nasahara, Takatsuki, Osaka, 569-1094, Japan
| | - Ryohei Funaki
- Department of Bioorganic Chemistry, Faculty of Pharmacy, Osaka Medical and Pharmaceutical University, 4-20-1 Nasahara, Takatsuki, Osaka, 569-1094, Japan
| | - Shun-Ichi Wada
- Department of Bioorganic Chemistry, Faculty of Pharmacy, Osaka Medical and Pharmaceutical University, 4-20-1 Nasahara, Takatsuki, Osaka, 569-1094, Japan
| | - Fumito Wada
- National Cerebral & Cardiovascular Center Research Institute, 6-1 Kishibe-shinmachi, Suita, Osaka, 564-8565, Japan
- Present address: Liid Pharmaceuticals, Inc.21001 Open Innovation Center, National Cerebral & Cardiovascular Center, 6-1 Kishibe-shinmachi, Suita, Osaka, 564-8565, Japan
| | - Mariko Harada-Shiba
- National Cerebral & Cardiovascular Center Research Institute, 6-1 Kishibe-shinmachi, Suita, Osaka, 564-8565, Japan
| | - Hidehito Urata
- Department of Bioorganic Chemistry, Faculty of Pharmacy, Osaka Medical and Pharmaceutical University, 4-20-1 Nasahara, Takatsuki, Osaka, 569-1094, Japan
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4
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Terada C, Oh K, Tsubaki R, Chan B, Aibara N, Ohyama K, Shibata MA, Wada T, Harada-Shiba M, Yamayoshi A, Yamamoto T. Dynamic and static control of the off-target interactions of antisense oligonucleotides using toehold chemistry. Nat Commun 2023; 14:7972. [PMID: 38042877 PMCID: PMC10693639 DOI: 10.1038/s41467-023-43714-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2023] [Accepted: 11/17/2023] [Indexed: 12/04/2023] Open
Abstract
Off-target interactions between antisense oligonucleotides (ASOs) with state-of-the-art modifications and biological components still pose clinical safety liabilities. To mitigate a broad spectrum of off-target interactions and enhance the safety profile of ASO drugs, we here devise a nanoarchitecture named BRace On a THERapeutic aSo (BROTHERS or BRO), which is composed of a standard gapmer ASO paired with a partially complementary peptide nucleic acid (PNA) strand. We show that these non-canonical ASO/PNA hybrids have reduced non-specific protein-binding capacity. The optimization of the structural and thermodynamic characteristics of this duplex system enables the operation of an in vivo toehold-mediated strand displacement (TMSD) reaction, effectively reducing hybridization with RNA off-targets. The optimized BROs dramatically mitigate hepatotoxicity while maintaining the on-target knockdown activity of their parent ASOs in vivo. This technique not only introduces a BRO class of drugs that could have a transformative impact on the extrahepatic delivery of ASOs, but can also help uncover the toxicity mechanism of ASOs.
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Affiliation(s)
- Chisato Terada
- Department of Chemistry of Biofunctional Molecules, Graduate School of Biomedical Sciences, Nagasaki University, Nagasaki, Japan
- JSPS Research Fellow (DC1), Japan Society for the Promotion of Science, Tokyo, Japan
| | - Kaho Oh
- Department of Chemistry of Biofunctional Molecules, Graduate School of Biomedical Sciences, Nagasaki University, Nagasaki, Japan
| | - Ryutaro Tsubaki
- Department of Chemistry of Biofunctional Molecules, Graduate School of Biomedical Sciences, Nagasaki University, Nagasaki, Japan
| | - Bun Chan
- Graduate School of Engineering, Nagasaki University, Nagasaki, Japan
| | - Nozomi Aibara
- Department of Pharmacy Practice, Graduate School of Biomedical Sciences, Nagasaki University, Nagasaki, Japan
| | - Kaname Ohyama
- Department of Molecular Pathochemistry, Graduate School of Biomedical Sciences, Nagasaki University, Nagasaki, Japan
| | - Masa-Aki Shibata
- Department of Anatomy and Cell Biology, Faculty of Medicine, Osaka Medical and Pharmaceutical University, Takatsuki, Japan
| | - Takehiko Wada
- Institute of Multidisciplinary Research for Advanced Materials (IMRAM), Tohoku University, Sendai, Miyagi, Japan
| | - Mariko Harada-Shiba
- Department of Molecular Innovation in Lipidology, National Cerebral and Cardiovascular Center Research Institute, Suita, Japan
- Cardiovascular Center, Osaka Medical and Pharmaceutical University, Takatsuki, Japan
| | - Asako Yamayoshi
- Department of Chemistry of Biofunctional Molecules, Graduate School of Biomedical Sciences, Nagasaki University, Nagasaki, Japan
| | - Tsuyoshi Yamamoto
- Department of Chemistry of Biofunctional Molecules, Graduate School of Biomedical Sciences, Nagasaki University, Nagasaki, Japan.
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5
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Periyasamy K, Maloverjan M, Biswas A, Remm A, Pook M, Rebane A, Pooga M. PepFect14 mediates the delivery of mRNA into human primary keratinocytes and in vivo. Front Pharmacol 2023; 14:1219761. [PMID: 37521463 PMCID: PMC10374019 DOI: 10.3389/fphar.2023.1219761] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2023] [Accepted: 07/03/2023] [Indexed: 08/01/2023] Open
Abstract
mRNA-based vaccines and candidate therapeutics have great potential in various medical fields. For the delivery of mRNA into target cells and tissues, lipid formulations are often employed. However, this approach could cause the activation of immune responses, making it unsuitable for the treatment of inflammatory conditions. Therefore, alternative delivery systems are highly demanded. In this study, we evaluated the transport efficiency and characteristics of cell-penetrating peptide PepFect14 (PF14) and mRNA nanoparticles in the presence of different additives. Our results show that all PF14-mRNA formulations entered cultured cells, while calcium chloride enhanced the transport and production of the encoded protein in HeLa and HaCaT cell lines, and polysorbate 80 did so in primary human keratinocytes. All formulations had similar physical properties and did not remarkably affect cell viability. By selectively blocking endocytosis pathways, we show that PF14-mRNA nanoparticles primarily entered HeLa cells via macropinocytosis and HaCaT cells via both macropinocytosis and clathrin-mediated endocytosis, while none of the blockers significantly affected the delivery into primary keratinocytes. Finally, subcutaneous injection of PF14-mRNA nanoparticles before inducing mouse irritant contact dermatitis resulted in the expression of a reporter protein without provoking harmful immune responses in the skin. Together, our findings suggest that PF14-mRNA nanoparticles have the potential for developing mRNA-based therapeutics for treating inflammatory skin conditions.
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Affiliation(s)
- Kapilraj Periyasamy
- Institute of Biomedicine and Translational Medicine, University of Tartu, Tartu, Estonia
| | | | - Abhijit Biswas
- Institute of Technology, University of Tartu, Tartu, Estonia
| | - Anu Remm
- Institute of Biomedicine and Translational Medicine, University of Tartu, Tartu, Estonia
| | - Martin Pook
- Institute of Biomedicine and Translational Medicine, University of Tartu, Tartu, Estonia
| | - Ana Rebane
- Institute of Biomedicine and Translational Medicine, University of Tartu, Tartu, Estonia
| | - Margus Pooga
- Institute of Technology, University of Tartu, Tartu, Estonia
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6
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Choosing an Optimal Solvent Is Crucial for Obtaining Cell-Penetrating Peptide Nanoparticles with Desired Properties and High Activity in Nucleic Acid Delivery. Pharmaceutics 2023; 15:pharmaceutics15020396. [PMID: 36839718 PMCID: PMC9963036 DOI: 10.3390/pharmaceutics15020396] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2023] [Revised: 01/16/2023] [Accepted: 01/19/2023] [Indexed: 01/27/2023] Open
Abstract
Cell-penetrating peptides (CPPs) are highly promising transfection agents that can deliver various compounds into living cells, including nucleic acids (NAs). Positively charged CPPs can form non-covalent complexes with negatively charged NAs, enabling simple and time-efficient nanoparticle preparation. However, as CPPs have substantially different chemical and physical properties, their complexation with the cargo and characteristics of the resulting nanoparticles largely depends on the properties of the surrounding environment, i.e., solution. Here, we show that the solvent used for the initial dissolving of a CPP determines the properties of the resulting CPP particles formed in an aqueous solution, including the activity and toxicity of the CPP-NA complexes. Using different biophysical methods such as dynamic light scattering (DLS), atomic force microscopy (AFM), transmission and scanning electron microscopy (TEM and SEM), we show that PepFect14 (PF14), a cationic amphipathic CPP, forms spherical particles of uniform size when dissolved in organic solvents, such as ethanol and DMSO. Water-dissolved PF14, however, tends to form micelles and non-uniform aggregates. When dissolved in organic solvents, PF14 retains its α-helical conformation and biological activity in cell culture conditions without any increase in cytotoxicity. Altogether, our results indicate that by using a solvent that matches the chemical nature of the CPP, the properties of the peptide-cargo particles can be tuned in the desired way. This can be of critical importance for in vivo applications, where CPP particles that are too large, non-uniform, or prone to aggregation may induce severe consequences.
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7
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Goossens R, Verwey N, Ariyurek Y, Schnell F, Aartsma-Rus A. DMD antisense oligonucleotide mediated exon skipping efficiency correlates with flanking intron retention time and target position within the exon. RNA Biol 2023; 20:693-702. [PMID: 37667454 PMCID: PMC10481881 DOI: 10.1080/15476286.2023.2254041] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Revised: 08/25/2023] [Accepted: 08/28/2023] [Indexed: 09/06/2023] Open
Abstract
Mutations in the DMD gene are causative for Duchenne muscular dystrophy (DMD). Antisense oligonucleotide (AON) mediated exon skipping to restore disrupted dystrophin reading frame is a therapeutic approach that allows production of a shorter but functional protein. As DMD causing mutations can affect most of the 79 exons encoding dystrophin, a wide variety of AONs are needed to treat the patient population. Design of AONs is largely guided by trial-and-error, and it is yet unclear what defines the skippability of an exon. Here, we use a library of phosphorodiamidate morpholino oligomer (PMOs) AONs of similar physical properties to test the skippability of a large number of DMD exons. The DMD transcript is non-sequentially spliced, meaning that certain introns are retained longer in the transcript than downstream introns. We tested whether the relative intron retention time has a significant effect on AON efficiency, and found that targeting an out-of-frame exon flanked at its 5'-end by an intron that is retained in the transcript longer ('slow' intron) leads to overall higher exon skipping efficiency than when the 5'-end flanking intron is 'fast'. Regardless of splicing speed of flanking introns, we find that positioning an AON closer to the 5'-end of the target exon leads to higher exon skipping efficiency opposed to targeting an exons 3'-end. The data enclosed herein can be of use to guide future target selection and preferential AON binding sites for both DMD and other disease amenable by exon skipping therapies.
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Affiliation(s)
- Remko Goossens
- Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | - Nisha Verwey
- Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | - Yavuz Ariyurek
- Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands
- Leiden Genome Technology Center, Leiden University Medical Center, Leiden, The Netherlands
| | | | - Annemieke Aartsma-Rus
- Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands
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8
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Williams LA, Gerber DJ, Elder A, Tseng WC, Baru V, Delaney-Busch N, Ambrosi C, Mahimkar G, Joshi V, Shah H, Harikrishnan K, Upadhyay H, Rajendran SH, Dhandapani A, Meier J, Ryan SJ, Lewarch C, Black L, Douville J, Cinquino S, Legakis H, Nalbach K, Behrends C, Sato A, Galluzzi L, Yu TW, Brown D, Agrawal S, Margulies D, Kopin A, Dempsey GT. Developing antisense oligonucleotides for a TECPR2 mutation-induced, ultra-rare neurological disorder using patient-derived cellular models. MOLECULAR THERAPY. NUCLEIC ACIDS 2022; 29:189-203. [PMID: 35860385 PMCID: PMC9287140 DOI: 10.1016/j.omtn.2022.06.015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Accepted: 06/17/2022] [Indexed: 11/16/2022]
Abstract
Mutations in the TECPR2 gene are the cause of an ultra-rare neurological disorder characterized by intellectual disability, impaired speech, motor delay, and hypotonia evolving to spasticity, central sleep apnea, and premature death (SPG49 or HSAN9; OMIM: 615031). Little is known about the biological function of TECPR2, and there are currently no available disease-modifying therapies for this disease. Here we describe implementation of an antisense oligonucleotide (ASO) exon-skipping strategy targeting TECPR2 c.1319delT (p.Leu440Argfs∗19), a pathogenic variant that results in a premature stop codon within TECPR2 exon 8. We used patient-derived fibroblasts and induced pluripotent stem cell (iPSC)-derived neurons homozygous for the p.Leu440Argfs∗19 mutation to model the disease in vitro. Both patient-derived fibroblasts and neurons showed lack of TECPR2 protein expression. We designed and screened ASOs targeting sequences across the TECPR2 exon 8 region to identify molecules that induce exon 8 skipping and thereby remove the premature stop signal. TECPR2 exon 8 skipping restored in-frame expression of a TECPR2 protein variant (TECPR2ΔEx8) containing 1,300 of 1,411 amino acids. Optimization of ASO sequences generated a lead candidate (ASO-005-02) with ∼27 nM potency in patient-derived fibroblasts. To examine potential functional rescue induced by ASO-005-02, we used iPSC-derived neurons to analyze the neuronal localization of TECPR2ΔEx8 and showed that this form of TECPR2 retains the distinct, punctate neuronal expression pattern of full-length TECPR2. Finally, ASO-005-02 had an acceptable tolerability profile in vivo following a single 20-mg intrathecal dose in cynomolgus monkeys, showing some transient non-adverse behavioral effects with no correlating histopathology. Broad distribution of ASO-005-02 and induction of TECPR2 exon 8 skipping was detected in multiple central nervous system (CNS) tissues, supporting the potential utility of this therapeutic strategy for a subset of patients suffering from this rare disease.
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Affiliation(s)
- Luis A Williams
- Q-State Biosciences, 179 Sidney Street, Cambridge, MA 02139, USA
| | - David J Gerber
- Q-State Biosciences, 179 Sidney Street, Cambridge, MA 02139, USA
| | - Amy Elder
- Q-State Biosciences, 179 Sidney Street, Cambridge, MA 02139, USA
| | - Wei Chou Tseng
- Q-State Biosciences, 179 Sidney Street, Cambridge, MA 02139, USA
| | - Valeriya Baru
- Q-State Biosciences, 179 Sidney Street, Cambridge, MA 02139, USA
| | | | | | - Gauri Mahimkar
- Q-State Biosciences, 179 Sidney Street, Cambridge, MA 02139, USA
| | - Vaibhav Joshi
- Q-State Biosciences, 179 Sidney Street, Cambridge, MA 02139, USA
| | - Himali Shah
- Q-State Biosciences, 179 Sidney Street, Cambridge, MA 02139, USA
| | | | - Hansini Upadhyay
- Q-State Biosciences, 179 Sidney Street, Cambridge, MA 02139, USA
| | | | | | - Joshua Meier
- Q-State Biosciences, 179 Sidney Street, Cambridge, MA 02139, USA
| | - Steven J Ryan
- Q-State Biosciences, 179 Sidney Street, Cambridge, MA 02139, USA
| | - Caitlin Lewarch
- Q-State Biosciences, 179 Sidney Street, Cambridge, MA 02139, USA
| | - Lauren Black
- Charles River Laboratories, Montreal, QC, Canada
| | | | | | | | - Karsten Nalbach
- Munich Cluster for Systems Neurology, Ludwig-Maximilians-Universität München, Germany
| | - Christian Behrends
- Munich Cluster for Systems Neurology, Ludwig-Maximilians-Universität München, Germany
| | - Ai Sato
- Department of Radiation Oncology, Weill Cornell Medical College, New York, NY, USA
| | - Lorenzo Galluzzi
- Department of Radiation Oncology, Weill Cornell Medical College, New York, NY, USA
| | - Timothy W Yu
- Boston Children's Hospital, 300 Longwood Avenue, Boston, MA 02115, USA
| | - Duncan Brown
- Q-State Biosciences, 179 Sidney Street, Cambridge, MA 02139, USA
| | - Sudhir Agrawal
- University of Massachusetts Medical School, Department of Medicine, Worcester, MA 01655, USA.,Arnay Sciences LLC, Shrewsbury, MA 01545, USA
| | - David Margulies
- Q-State Biosciences, 179 Sidney Street, Cambridge, MA 02139, USA
| | - Alan Kopin
- Tufts University School of Medicine, Boston, MA, USA.,Luke Heller TECPR2 Foundation, Swampscott, MA, USA
| | - Graham T Dempsey
- Q-State Biosciences, 179 Sidney Street, Cambridge, MA 02139, USA
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9
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Honcharenko D, Rocha CSJ, Lundin KE, Maity J, Milton S, Tedebark U, Murtola M, Honcharenko M, Slaitas A, Smith CIE, Zain R, Strömberg R. 2'- O-( N-(Aminoethyl)carbamoyl)methyl Modification Allows for Lower Phosphorothioate Content in Splice-Switching Oligonucleotides with Retained Activity. Nucleic Acid Ther 2022; 32:221-233. [PMID: 35238623 PMCID: PMC9221157 DOI: 10.1089/nat.2021.0086] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
2′-O-(N-(Aminoethyl)carbamoyl)methyl (2′-O-AECM)-modified oligonucleotides (ONs) and their mixmers with 2′-O-methyl oligonucleotides (2′-OMe ONs) with phosphodiester linkers as well as with partial and full phosphorothioate (PS) inclusion were synthesized and functionally evaluated as splice-switching oligonucleotides in several different reporter cell lines originating from different tissues. This was enabled by first preparing the AECM-modified A, C, G and U, which required a different strategy for each building block. The AECM modification has previously been shown to provide high resistance to enzymatic degradation, even without PS linkages. It is therefore particularly interesting and unprecedented that the 2′-O-AECM ONs are shown to have efficient splice-switching activity even without inclusion of PS linkages and found to be as effective as 2′-OMe PS ONs. Importantly, the PS linkages can be partially included, without any significant reduction in splice-switching efficacy. This suggests that AECM modification has the potential to be used in balancing the PS content of ONs. Furthermore, conjugation of 2′-O-AECM ONs to an endosomal escape peptide significantly increased splice-switching suggesting that this effect could possibly be due to an increase in uptake of ON to the site of action.
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Affiliation(s)
- Dmytro Honcharenko
- Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge, Sweden
| | - Cristina S J Rocha
- Department of Laboratory Medicine, Clinical Research Center, Karolinska Institutet, Karolinska University Hospital, Huddinge, Sweden
| | - Karin E Lundin
- Department of Laboratory Medicine, Clinical Research Center, Karolinska Institutet, Karolinska University Hospital, Huddinge, Sweden
| | - Jyotirmoy Maity
- Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge, Sweden
| | - Stefan Milton
- Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge, Sweden
| | - Ulf Tedebark
- Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge, Sweden
| | - Merita Murtola
- Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge, Sweden
| | | | | | - C I Edvard Smith
- Department of Laboratory Medicine, Clinical Research Center, Karolinska Institutet, Karolinska University Hospital, Huddinge, Sweden
| | - Rula Zain
- Department of Laboratory Medicine, Clinical Research Center, Karolinska Institutet, Karolinska University Hospital, Huddinge, Sweden.,Department of Clinical Genetics, Center for Rare Diseases, Karolinska University Hospital, Stockholm, Sweden
| | - Roger Strömberg
- Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge, Sweden
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10
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Kobayashi Y, Chhoeu C, Li J, Price KS, Kiedrowski LA, Hutchins JL, Hardin AI, Wei Z, Hong F, Bahcall M, Gokhale PC, Jänne PA. Silent mutations reveal therapeutic vulnerability in RAS Q61 cancers. Nature 2022; 603:335-342. [PMID: 35236983 DOI: 10.1038/s41586-022-04451-4] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Accepted: 01/20/2022] [Indexed: 12/26/2022]
Abstract
RAS family members are the most frequently mutated oncogenes in human cancers. Although KRAS(G12C)-specific inhibitors show clinical activity in patients with cancer1-3, there are no direct inhibitors of NRAS, HRAS or non-G12C KRAS variants. Here we uncover the requirement of the silent KRASG60G mutation for cells to produce a functional KRAS(Q61K). In the absence of this G60G mutation in KRASQ61K, a cryptic splice donor site is formed, promoting alternative splicing and premature protein termination. A G60G silent mutation eliminates the splice donor site, yielding a functional KRAS(Q61K) variant. We detected a concordance of KRASQ61K and a G60G/A59A silent mutation in three independent pan-cancer cohorts. The region around RAS Q61 is enriched in exonic splicing enhancer (ESE) motifs and we designed mutant-specific oligonucleotides to interfere with ESE-mediated splicing, rendering the RAS(Q61) protein non-functional in a mutant-selective manner. The induction of aberrant splicing by antisense oligonucleotides demonstrated therapeutic effects in vitro and in vivo. By studying the splicing necessary for a functional KRAS(Q61K), we uncover a mutant-selective treatment strategy for RASQ61 cancer and expose a mutant-specific vulnerability, which could potentially be exploited for therapy in other genetic contexts.
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Affiliation(s)
- Yoshihisa Kobayashi
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA. .,Department of Medicine, Harvard Medical School, Boston, MA, USA. .,Division of Molecular Pathology, National Cancer Center Research Institute, Tokyo, Japan.
| | - Chhayheng Chhoeu
- Experimental Therapeutics Core, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Jiaqi Li
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Kristin S Price
- Department of Medical Affairs, Guardant Health, Redwood City, CA, USA
| | | | - Jamie L Hutchins
- Department of Medical Affairs, Guardant Health, Redwood City, CA, USA
| | - Aaron I Hardin
- Department of Medical Affairs, Guardant Health, Redwood City, CA, USA
| | - Zihan Wei
- Department of Data Science, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Fangxin Hong
- Department of Data Science, Dana-Farber Cancer Institute, Boston, MA, USA.,Harvard T. H. Chan School of Public Health, Boston, MA, USA
| | - Magda Bahcall
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA.,Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Prafulla C Gokhale
- Experimental Therapeutics Core, Dana-Farber Cancer Institute, Boston, MA, USA.,Belfer Center for Applied Cancer Science, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Pasi A Jänne
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA. .,Department of Medicine, Harvard Medical School, Boston, MA, USA. .,Belfer Center for Applied Cancer Science, Dana-Farber Cancer Institute, Boston, MA, USA. .,Lowe Center for Thoracic Oncology, Dana-Farber Cancer Institute, Boston, MA, USA.
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11
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Maloverjan M, Padari K, Abroi A, Rebane A, Pooga M. Divalent Metal Ions Boost Effect of Nucleic Acids Delivered by Cell-Penetrating Peptides. Cells 2022; 11:cells11040756. [PMID: 35203400 PMCID: PMC8870069 DOI: 10.3390/cells11040756] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2022] [Revised: 02/11/2022] [Accepted: 02/19/2022] [Indexed: 12/01/2022] Open
Abstract
Cell-penetrating peptides (CPPs) are promising tools for the transfection of various substances, including nucleic acids, into cells. The aim of the current work was to search for novel safe and effective approaches for enhancing transfection efficiency of nanoparticles formed from CPP and splice-correcting oligonucleotide (SCO) without increasing the concentration of peptide. We analyzed the effect of inclusion of calcium and magnesium ions into nanoparticles on CPP-mediated transfection in cell culture. We also studied the mechanism of such transfection as well as its efficiency, applicability in case of different cell lines, nucleic acid types and peptides, and possible limitations. We discovered a strong positive effect of these ions on transfection efficiency of SCO, that translated to enhanced synthesis of functional reporter protein. We observed significant changes in intracellular distribution and trafficking of nanoparticles formed by the addition of the ions, without increasing cytotoxicity. We propose a novel strategy for preparing CPP-oligonucleotide nanoparticles with enhanced efficiency and, thus, higher therapeutic potential. Our discovery may be translated to primary cell cultures and, possibly, in vivo studies, with the aim of increasing CPP-mediated transfection efficiency and the likelihood of using CPPs in clinics.
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Affiliation(s)
- Maria Maloverjan
- Institute of Technology, University of Tartu, 1 Nooruse Street, 50411 Tartu, Estonia; (M.M.); (A.A.)
| | - Kärt Padari
- Institute of Molecular and Cell Biology, University of Tartu, 23b Riia Street, 51010 Tartu, Estonia;
| | - Aare Abroi
- Institute of Technology, University of Tartu, 1 Nooruse Street, 50411 Tartu, Estonia; (M.M.); (A.A.)
| | - Ana Rebane
- Institute of Biomedicine and Translational Medicine, University of Tartu, 14b Ravila Street, 50411 Tartu, Estonia;
| | - Margus Pooga
- Institute of Technology, University of Tartu, 1 Nooruse Street, 50411 Tartu, Estonia; (M.M.); (A.A.)
- Correspondence: ; Tel.: +372-737-4836
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12
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Abstract
Antisense oligonucleotides (AONs) are small synthetic molecules of therapeutic interest for a variety of human disease. Their ability to bind mRNA and affect its splicing gives AONs potential use for exon skipping therapies aimed at restoring the dystrophin transcript reading frame for Duchenne muscular dystrophy (DMD) patients. The neutrally charged phosphorodiamidate morpholino oligomers (PMOs) are a stable and relatively nontoxic AON modification. To assess exon skipping efficiency in vitro, it is important to deliver them to target cells. Here, we describe a method for the delivery of PMOs to myoblasts by electroporation. The described protocol for the Amaxa 4D X unit nucleofector system allows efficient processing of 16 samples in one nucleocuvette strip, aiding in high-throughput PMO efficacy screens.
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Affiliation(s)
- Remko Goossens
- Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands.
| | - Annemieke Aartsma-Rus
- Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands
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13
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Wada F, Yamamoto T, Kobayashi T, Tachibana K, Ito KR, Hamasaki M, Kayaba Y, Terada C, Yamayoshi A, Obika S, Harada-Shiba M. Drug discovery and development scheme for liver-targeting bridged nucleic acid antisense oligonucleotides. MOLECULAR THERAPY-NUCLEIC ACIDS 2021; 26:957-969. [PMID: 34760338 PMCID: PMC8560717 DOI: 10.1016/j.omtn.2021.10.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/05/2021] [Revised: 08/15/2021] [Accepted: 10/06/2021] [Indexed: 11/21/2022]
Abstract
Antisense oligonucleotides (ASOs) containing bridged nucleic acids (BNAs) have been proven to be very powerful. However, ensuring a reliable discovery and translational development scheme for this class of ASOs with wider therapeutic windows remains a fundamental challenge. We here demonstrate the robustness of our scheme in the context of the selection of ASOs having two different BNA chemistries (2,′4′-BNA/locked nucleic acid [LNA] and amido-bridged nucleic acid [AmNA]) targeting human proprotein convertase subtilisin/kexin type 9 (PCSK9). The scheme features a two-step process, including (1) a unique and sensitive in vitro screening approach, called Ca2+ enrichment of medium (CEM) transfection, and (2) a ligand-targeted drug delivery approach to better reach target tissues, averting unintended accumulation of ASOs. Using CEM screening, we identified a candidate ASO that shows >70% cholesterol-lowering action in monkeys. An N-acetylgalactosamine (GalNAc) ligand then was appended to the candidate ASO to further broaden the therapeutic margin by altering the molecule’s pharmacokinetics. The GalNAc conjugate, HsPCSK9-1811-LNA, was found to be at least ten times more potent in non-human primates (compared with the unconjugated counterpart), with reduced nephrotoxicity in rats. Overall, we successfully showed that our drug development scheme is better suited for selecting clinically relevant BNA-based ASOs, especially for the treatment of liver-associated diseases.
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Affiliation(s)
- Fumito Wada
- Department of Molecular Innovation in Lipidology, National Cerebral and Cardiovascular Center Research Institute, 6-1 Kishibe-shinmachi, Suita, Osaka 564-8565, Japan.,Department of Molecular Pathogenesis, National Cerebral and Cardiovascular Center Research Institute, 6-1 Kishibe-shinmachi, Suita, Osaka 564-8565, Japan.,Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Tsuyoshi Yamamoto
- Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka 565-0871, Japan.,Graduate School of Biomedical Sciences, Nagasaki University, 1-14 Bunkyo-machi, Nagasaki 852-8131, Japan
| | - Tadayuki Kobayashi
- Department of Molecular Innovation in Lipidology, National Cerebral and Cardiovascular Center Research Institute, 6-1 Kishibe-shinmachi, Suita, Osaka 564-8565, Japan.,Department of Molecular Pathogenesis, National Cerebral and Cardiovascular Center Research Institute, 6-1 Kishibe-shinmachi, Suita, Osaka 564-8565, Japan.,Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Keisuke Tachibana
- Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Kosuke Ramon Ito
- Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Mayumi Hamasaki
- Department of Molecular Pathogenesis, National Cerebral and Cardiovascular Center Research Institute, 6-1 Kishibe-shinmachi, Suita, Osaka 564-8565, Japan
| | - Yukina Kayaba
- Graduate School of Biomedical Sciences, Nagasaki University, 1-14 Bunkyo-machi, Nagasaki 852-8131, Japan
| | - Chisato Terada
- Graduate School of Biomedical Sciences, Nagasaki University, 1-14 Bunkyo-machi, Nagasaki 852-8131, Japan
| | - Asako Yamayoshi
- Graduate School of Biomedical Sciences, Nagasaki University, 1-14 Bunkyo-machi, Nagasaki 852-8131, Japan
| | - Satoshi Obika
- Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Mariko Harada-Shiba
- Department of Molecular Innovation in Lipidology, National Cerebral and Cardiovascular Center Research Institute, 6-1 Kishibe-shinmachi, Suita, Osaka 564-8565, Japan.,Department of Molecular Pathogenesis, National Cerebral and Cardiovascular Center Research Institute, 6-1 Kishibe-shinmachi, Suita, Osaka 564-8565, Japan
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14
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Wada F, Hori SI, Obika S, Yamamoto T. Calcium-Mediated In Vitro Transfection Technique of Oligonucleotides with Broad Chemical Modification Compatibility. Methods Mol Biol 2021; 2176:141-154. [PMID: 32865788 DOI: 10.1007/978-1-0716-0771-8_10] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
Oligonucleotide drugs (ODs) have gained increasing attention owing to their promising therapeutic potential. One major obstacle that ODs have been facing is the lack of appropriate in vitro validation systems that can predict in vivo activity and toxicity. We have devised a transfection method called CEM (Ca2+-enrichment method), where the simple enrichment of calcium ion with calcium chloride in culture medium potentiates the activity of various types of naked oligonucleotides including gapmers, siRNA, and phosphorodiamidate morpholino antisense oligonucleotides (PMO) in many cultured cell lines with limited cytotoxicity. We here describe a precise procedure of the method. Besides the benefit of the CEM's predictive power to accurately estimate in vivo activity of ODs of your interest in drug discovery and development settings, this cost-efficient, easy-to-access method can be a robust laboratory technique to modulate gene expressions with ODs with a variety of mechanisms of action.
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Affiliation(s)
- Fumito Wada
- Graduate School of Pharmaceutical Sciences, Osaka University, Osaka, Japan.,Department of Molecular Innovation in Lipidology, National Cerebral and Cardiovascular Center Research Institute, Osaka, Japan
| | - Shin-Ichiro Hori
- Graduate School of Pharmaceutical Sciences, Osaka University, Osaka, Japan.,Medicinal Chemistry Research Laboratory for Medium Molecular Drug Discovery, Shionogi & Co., Ltd., Osaka, Japan
| | - Satoshi Obika
- Graduate School of Pharmaceutical Sciences, Osaka University, Osaka, Japan
| | - Tsuyoshi Yamamoto
- Graduate School of Pharmaceutical Sciences, Osaka University, Osaka, Japan. .,Graduate School of Biomedical Sciences, Nagasaki University, Nagasaki, Japan.
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15
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Fumoto S, Yamamoto T, Okami K, Maemura Y, Terada C, Yamayoshi A, Nishida K. Understanding In Vivo Fate of Nucleic Acid and Gene Medicines for the Rational Design of Drugs. Pharmaceutics 2021; 13:pharmaceutics13020159. [PMID: 33530309 PMCID: PMC7911509 DOI: 10.3390/pharmaceutics13020159] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2020] [Revised: 01/21/2021] [Accepted: 01/22/2021] [Indexed: 02/07/2023] Open
Abstract
Nucleic acid and genetic medicines are increasingly being developed, owing to their potential to treat a variety of intractable diseases. A comprehensive understanding of the in vivo fate of these agents is vital for the rational design, discovery, and fast and straightforward development of the drugs. In case of intravascular administration of nucleic acids and genetic medicines, interaction with blood components, especially plasma proteins, is unavoidable. However, on the flip side, such interaction can be utilized wisely to manipulate the pharmacokinetics of the agents. In other words, plasma protein binding can help in suppressing the elimination of nucleic acids from the blood stream and deliver naked oligonucleotides and gene carriers into target cells. To control the distribution of these agents in the body, the ligand conjugation method is widely applied. It is also important to understand intracellular localization. In this context, endocytosis pathway, endosomal escape, and nuclear transport should be considered and discussed. Encapsulated nucleic acids and genes must be dissociated from the carriers to exert their activity. In this review, we summarize the in vivo fate of nucleic acid and gene medicines and provide guidelines for the rational design of drugs.
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16
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Amido-Bridged Nucleic Acid-Modified Antisense Oligonucleotides Targeting SYT13 to Treat Peritoneal Metastasis of Gastric Cancer. MOLECULAR THERAPY-NUCLEIC ACIDS 2020; 22:791-802. [PMID: 33230476 PMCID: PMC7644579 DOI: 10.1016/j.omtn.2020.10.001] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/25/2020] [Accepted: 10/01/2020] [Indexed: 02/06/2023]
Abstract
Patients with peritoneal metastasis of gastric cancer have dismal prognosis, mainly because of inefficient systemic delivery of drugs to peritoneal tumors. We aimed to develop an intraperitoneal treatment strategy using amido-bridged nucleic acid (AmNA)-modified antisense oligonucleotides (ASOs) targeting synaptotagmin XIII (SYT13) and to identify the function of SYT13 in gastric cancer cells. We screened 71 candidate oligonucleotide sequences according to SYT13-knockdown efficacy, in vitro activity, and off-target effects. We evaluated the effects of SYT13 knockdown on cellular functions and signaling pathways, as well as the effects of intraperitoneal administration to mice of AmNA-modified anti-SYT13 ASOs. We selected the ASOs (designated hSYT13-4378 and hSYT13-4733) with the highest knockdown efficiencies and lowest off-target effects and determined their abilities to inhibit cellular functions associated with the metastatic potential of gastric cancer cells. We found that SYT13 interfered with focal adhesion kinase (FAK)-mediated intracellular signals. Intraperitoneal administration of hSYT13-4378 and hSYT13-4733 in a mouse xenograft model of metastasis inhibited the formation of peritoneal nodules and significantly increased survival. Reversible, dose- and sequence-dependent liver damage was induced by ASO treatment without causing abnormal morphological and histological changes in the brain. Intra-abdominal administration of AmNA-modified anti-SYT13 ASOs represents a promising strategy for treating peritoneal metastasis of gastric cancer.
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17
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Zhang X, Castanotto D, Liu X, Shemi A, Stein CA. Ammonium and arsenic trioxide are potent facilitators of oligonucleotide function when delivered by gymnosis. Nucleic Acids Res 2019. [PMID: 29522198 DOI: 10.1093/nar/gky150] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Oligonucleotide (ON) concentrations employed for therapeutic applications vary widely, but in general are high enough to raise significant concerns for off target effects and cellular toxicity. However, lowering ON concentrations reduces the chances of a therapeutic response, since typically relatively small amounts of ON are taken up by targeted cells in tissue culture. It is therefore imperative to identify new strategies to improve the concentration dependence of ON function. In this work, we have identified ammonium ion (NH4+) as a non-toxic potent enhancer of ON activity in the nucleus and cytoplasm following delivery by gymnosis. NH4+ is a metabolite that has been extensively employed as diuretic, expectorant, for the treatment of renal calculi and in a variety of other diseases. Enhancement of function can be found in attached and suspension cells, including in difficult-to-transfect Jurkat T and CEM T cells. We have also demonstrated that NH4+ can synergistically interact with arsenic trioxide (arsenite) to further promote ON function without producing any apparent increased cellular toxicity. These small, inexpensive, widely distributed molecules could be useful not only in laboratory experiments but potentially in therapeutic ON-based combinatorial strategy for clinical applications.
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Affiliation(s)
- Xiaowei Zhang
- Department of Medical Oncology and Experimental Therapeutics, City of Hope, 1500 E. Duarte Rd., Duarte, CA 91010, USA
| | - Daniela Castanotto
- Department of Medical Oncology and Experimental Therapeutics, City of Hope, 1500 E. Duarte Rd., Duarte, CA 91010, USA
| | - Xueli Liu
- Department of Information Science, City of Hope, 1500 E. Duarte Rd., Duarte, CA 91010, USA
| | - Amotz Shemi
- Silenseed, 2 HaMa'ayan Street, Modi'in Technology Park, Modi'in 7177871, Israel
| | - Cy A Stein
- Department of Medical Oncology and Experimental Therapeutics, City of Hope, 1500 E. Duarte Rd., Duarte, CA 91010, USA
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18
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Hande M, Saher O, Lundin KE, Smith CIE, Zain R, Lönnberg T. Oligonucleotide⁻Palladacycle Conjugates as Splice-Correcting Agents. Molecules 2019; 24:E1180. [PMID: 30917503 PMCID: PMC6470670 DOI: 10.3390/molecules24061180] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2019] [Revised: 03/14/2019] [Accepted: 03/25/2019] [Indexed: 12/15/2022] Open
Abstract
2'-O-Methylribo phosphorothioate oligonucleotides incorporating cyclopalladated benzylamine conjugate groups at their 5'-termini have been prepared and their ability to hybridize with a designated target sequence was assessed by conventional UV melting experiments. The oligonucleotides were further examined in splice-switching experiments in human cervical cancer (HeLa Luc/705), human liver (HuH7_705), and human osteosarcoma (U-2 OS_705) reporter cell lines. Melting temperatures of duplexes formed by the modified oligonucleotides were approximately 5 °C lower than melting temperatures of the respective unmodified duplexes. The cyclopalladated oligonucleotides functioned as splice-correcting agents in the HeLa Luc/705 cell line somewhat more efficiently than their unmodified counterparts. Furthermore, the introduction of this chemical modification did not induce toxicity in cells. These results demonstrate the feasibility of using covalently metalated oligonucleotides as therapeutic agents.
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Affiliation(s)
- Madhuri Hande
- Department of Chemistry, University of Turku, Vatselankatu 2, FIN-20014 Turku, Finland.
- Department of Laboratory Medicine, Clinical Research Center, Karolinska Institutet, Karolinska University Hospital Huddinge, SE-141 86 Huddinge, Sweden.
| | - Osama Saher
- Department of Laboratory Medicine, Clinical Research Center, Karolinska Institutet, Karolinska University Hospital Huddinge, SE-141 86 Huddinge, Sweden.
- Department of Pharmaceutics and Industrial Pharmacy, Cairo University, Cairo 11562, Egypt.
| | - Karin E Lundin
- Department of Laboratory Medicine, Clinical Research Center, Karolinska Institutet, Karolinska University Hospital Huddinge, SE-141 86 Huddinge, Sweden.
| | - C I Edvard Smith
- Department of Laboratory Medicine, Clinical Research Center, Karolinska Institutet, Karolinska University Hospital Huddinge, SE-141 86 Huddinge, Sweden.
| | - Rula Zain
- Department of Laboratory Medicine, Clinical Research Center, Karolinska Institutet, Karolinska University Hospital Huddinge, SE-141 86 Huddinge, Sweden.
- Department of Clinical Genetics, Centre for Rare Diseases, Karolinska University Hospital, SE-171 76 Stockholm, Sweden.
| | - Tuomas Lönnberg
- Department of Chemistry, University of Turku, Vatselankatu 2, FIN-20014 Turku, Finland.
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19
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Hayashi J, Nishigaki M, Ochi Y, Wada SI, Wada F, Nakagawa O, Obika S, Harada-Shiba M, Urata H. Effective gene silencing activity of prodrug-type 2′-O-methyldithiomethyl siRNA compared with non-prodrug-type 2′-O-methyl siRNA. Bioorg Med Chem Lett 2018; 28:2171-2174. [DOI: 10.1016/j.bmcl.2018.05.016] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2018] [Revised: 05/01/2018] [Accepted: 05/07/2018] [Indexed: 11/15/2022]
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20
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Sin Y, Makimura F, Saijo M, Obika S. Generation of splice switching oligonucleotides targeting the Cockayne syndrome group B gene product in order to change the diseased cell state. Biochem Biophys Res Commun 2018; 500:163-169. [PMID: 29625109 DOI: 10.1016/j.bbrc.2018.04.015] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2018] [Accepted: 04/03/2018] [Indexed: 12/31/2022]
Abstract
Cockayne syndrome (CS) is a severe disorder with no effective treatment. The Cockayne syndrome group B (CSB) gene is one gene responsible for CS and also causes UV sensitive syndrome (UVSS), a disorder that causes mild symptoms. How the CSB gene determines a patient's fate is unknown, but one intriguing point is that in UVSS patient cell, there are nonsense mutations in both alleles at the same position in each upstream region of the PiggyBac transposable element derived 3 (PGBD3) inserted region. In contrast, in CS patient cells, there is at least one allele with several mutations downstream of the PGBD3 inserted region, or there are homozygous mutations in exon 1. Here, we designed and synthesized 24 splice switching oligonucleotides (SSOs) to skip exon 3 in CSB mRNA. Use of these SSOs induced a frame shift in order to generate an alternative stop codon at the upstream region of the PGBD3 invasion site. As a result, a reduction of mitochondrial membrane potential following H2O2 treatment in CS cell was recovered. It was demonstrated that up-regulation of several gene expression brought about by SSOs are related to mitochondrial dysfunction in CS cells.
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Affiliation(s)
- Yooksil Sin
- National Institutes of Biomedical Innovation, Health and Nutrition (NIBIOHN), 7-6-8 Saito-Asagi, Ibaraki, Osaka, 567-0085, Japan.
| | - Futaba Makimura
- National Institutes of Biomedical Innovation, Health and Nutrition (NIBIOHN), 7-6-8 Saito-Asagi, Ibaraki, Osaka, 567-0085, Japan
| | - Masafumi Saijo
- Graduate School of Frontier Biosciences, Osaka University, 1-3 Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Satoshi Obika
- National Institutes of Biomedical Innovation, Health and Nutrition (NIBIOHN), 7-6-8 Saito-Asagi, Ibaraki, Osaka, 567-0085, Japan; Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka, 565-0871, Japan
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21
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Mori S, Morihiro K, Okuda T, Kasahara Y, Obika S. Hydrogen peroxide-triggered gene silencing in mammalian cells through boronated antisense oligonucleotides. Chem Sci 2018; 9:1112-1118. [PMID: 29629168 PMCID: PMC5875086 DOI: 10.1039/c7sc04318j] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2017] [Accepted: 11/21/2017] [Indexed: 12/16/2022] Open
Abstract
Hydrogen peroxide (H2O2) is a reactive oxygen species (ROS) involved in various diseases, including neurodegeneration, diabetes, and cancer. Here, we introduce a new approach to use H2O2 to modulate specific gene expression in mammalian cells. H2O2-responsive nucleoside analogues, in which the Watson-Crick faces of the nucleobases are caged by arylboronate moieties, were synthesized. One of these analogues, boronated thymidine (dTB ), was incorporated into oligodeoxynucleotides (ODNs) using an automated DNA synthesizer. The hybridization ability of this boronated ODN to complementary RNA was clearly switched in the off-to-on direction upon H2O2 addition. Furthermore, we demonstrated H2O2-triggered gene silencing in mammalian cells using antisense oligonucleotides (ASOs) modified with dTB . Our approach can be used for the regulation of any gene of interest by the sequence design of boronated ASOs and will contribute to the development of targeted disease therapeutics.
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Affiliation(s)
- Shohei Mori
- Graduate School of Pharmaceutical Sciences , Osaka University , 1-6 Yamadaoka , Suita , Osaka 565-0871 , Japan . ;
| | - Kunihiko Morihiro
- Graduate School of Pharmaceutical Sciences , Osaka University , 1-6 Yamadaoka , Suita , Osaka 565-0871 , Japan . ;
- National Institutes of Biomedical Innovation, Health and Nutrition (NIBIOHN) , 7-6-8 Saito-Asagi , Ibaraki , Osaka 567-0085 , Japan
| | - Takumi Okuda
- Graduate School of Pharmaceutical Sciences , Osaka University , 1-6 Yamadaoka , Suita , Osaka 565-0871 , Japan . ;
| | - Yuuya Kasahara
- Graduate School of Pharmaceutical Sciences , Osaka University , 1-6 Yamadaoka , Suita , Osaka 565-0871 , Japan . ;
- National Institutes of Biomedical Innovation, Health and Nutrition (NIBIOHN) , 7-6-8 Saito-Asagi , Ibaraki , Osaka 567-0085 , 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 (NIBIOHN) , 7-6-8 Saito-Asagi , Ibaraki , Osaka 567-0085 , Japan
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22
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Hayashi J, Samezawa Y, Ochi Y, Wada SI, Urata H. Syntheses of prodrug-type phosphotriester oligonucleotides responsive to intracellular reducing environment for improvement of cell membrane permeability and nuclease resistance. Bioorg Med Chem Lett 2017; 27:3135-3138. [PMID: 28532670 DOI: 10.1016/j.bmcl.2017.05.031] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2017] [Revised: 05/08/2017] [Accepted: 05/10/2017] [Indexed: 02/07/2023]
Abstract
We synthesized prodrug-type phosphotriester (PTE) oligonucleotides containing the six-membered cyclic disulfide moiety by using phosphoramidite chemistry. Prodrug-type oligonucleotides named "Reducing-Environment-Dependent Uncatalyzed Chemical Transforming (REDUCT) PTE oligonucleotides" were converted into natural oligonucleotides under cytosol-mimetic reductive condition. Furthermore, the REDUCT PTE oligonucleotides were robust to nuclease digestion and exhibited good cell membrane permeability.
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Affiliation(s)
- Junsuke Hayashi
- Laboratory of Bioorganic Chemistry, Osaka University of Pharmaceutical Sciences, 4-20-1 Nasahara, Takatsuki, Osaka 569-1094, Japan
| | - Yusuke Samezawa
- Laboratory of Bioorganic Chemistry, Osaka University of Pharmaceutical Sciences, 4-20-1 Nasahara, Takatsuki, Osaka 569-1094, Japan
| | - Yosuke Ochi
- Laboratory of Bioorganic Chemistry, Osaka University of Pharmaceutical Sciences, 4-20-1 Nasahara, Takatsuki, Osaka 569-1094, Japan
| | - Shun-Ichi Wada
- Laboratory of Bioorganic Chemistry, Osaka University of Pharmaceutical Sciences, 4-20-1 Nasahara, Takatsuki, Osaka 569-1094, Japan
| | - Hidehito Urata
- Laboratory of Bioorganic Chemistry, Osaka University of Pharmaceutical Sciences, 4-20-1 Nasahara, Takatsuki, Osaka 569-1094, Japan.
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23
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Rocha CSJ, Lundin KE, Behlke MA, Zain R, El Andaloussi S, Smith CIE. Four Novel Splice-Switch Reporter Cell Lines: Distinct Impact of Oligonucleotide Chemistry and Delivery Vector on Biological Activity. Nucleic Acid Ther 2016; 26:381-391. [PMID: 27629437 DOI: 10.1089/nat.2016.0631] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
New advances in oligonucleotide (ON) chemistry emerge continuously, and over the last few years, several aspects of ON delivery have been improved. However, clear knowledge regarding how certain chemistries behave alone, or in combination with various delivery vectors, is limited. Moreover, characterization is frequently limited to a single reporter cell line and, when different cell types are studied, experiments are commonly not carried out under similar conditions, hampering comparative analysis. To address this, we have developed a small "tissue" library of new, stable, pLuc/705 splice-switching reporter cell lines (named HuH7_705, U-2 OS_705, C2C12_705, and Neuro-2a_705). Our data show that, indeed, the cell type used in activity screenings influences the efficiency of ONs of different chemistry (phosphorothioate with locked nucleic acid or 2'-O-methyl with or without N,N-diethyl-4-(4-nitronaphthalen-1-ylazo)-phenylamine). Likewise, the delivery method, Lipofectamine® 2000, PepFect14 nanoparticles, or "naked" uptake, also demonstrates cell-type-dependent outcomes. Taken together, these cell lines can potentially become useful tools for future in vitro evaluation of new nucleic acid-based oligomers as well as delivery compounds for splice-switching approaches and cell-specific therapies.
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Affiliation(s)
- Cristina S J Rocha
- 1 Department of Laboratory Medicine, Clinical Research Center, Karolinska Institutet, Karolinska University Hospital , Huddinge, Sweden
| | - Karin E Lundin
- 1 Department of Laboratory Medicine, Clinical Research Center, Karolinska Institutet, Karolinska University Hospital , Huddinge, Sweden
| | - Mark A Behlke
- 2 Integrated DNA Technologies, Inc. , Coralville, Iowa
| | - Rula Zain
- 1 Department of Laboratory Medicine, Clinical Research Center, Karolinska Institutet, Karolinska University Hospital , Huddinge, Sweden .,3 Department of Clinical Genetics, Centre for Rare Diseases, Karolinska University Hospital , Stockholm, Sweden
| | - Samir El Andaloussi
- 1 Department of Laboratory Medicine, Clinical Research Center, Karolinska Institutet, Karolinska University Hospital , Huddinge, Sweden .,4 Department of Physiology, Anatomy and Genetics, University of Oxford , Oxford, United Kingdom
| | - C I Edvard Smith
- 1 Department of Laboratory Medicine, Clinical Research Center, Karolinska Institutet, Karolinska University Hospital , Huddinge, Sweden
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Yamamoto T, Wada F, Harada-Shiba M. Development of Antisense Drugs for Dyslipidemia. J Atheroscler Thromb 2016; 23:1011-25. [PMID: 27466159 PMCID: PMC5090806 DOI: 10.5551/jat.rv16001] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Abnormal elevation of low-density lipoprotein (LDL) and triglyceride-rich lipoproteins in plasma as well as dysfunction of anti-atherogenic high-density lipoprotein (HDL) have both been recognized as essential components of the pathogenesis of atherosclerosis and are classified as dyslipidemia. This review describes the arc of development of antisense oligonucleotides for the treatment of dyslipidemia. Chemically-armed antisense candidates can act on various kinds of transcripts, including mRNA and miRNA, via several different endogenous antisense mechanisms, and have exhibited potent systemic anti-dyslipidemic effects. Here, we present specific cutting-edge technologies have recently been brought into antisense strategies, and describe how they have improved the potency of antisense drugs in regard to pharmacokinetics and pharmacodynamics. In addition, we discuss perspectives for the use of armed antisense oligonucleotides as new clinical options for dyslipidemia, in the light of outcomes of recent clinical trials and safety concerns indicated by several clinical and preclinical studies.
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