1
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Lincy-Bianchi L, Häfner M, Becquart C, Tängemo C, Kurczy ME, Munier CC, Knerr L. Incorporation of Intracellular NanoSIMS Tracers to Oligonucleotide Conjugates via Strain Promoted Sydnone-Alkyne Cycloaddition. Bioconjug Chem 2024. [PMID: 38860868 DOI: 10.1021/acs.bioconjchem.4c00068] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/12/2024]
Abstract
Extensive efforts have been dedicated to developing cell-specific targeting ligands that can be conjugated to therapeutic cargo, offering a promising yet still challenging strategy to deliver oligonucleotide therapeutics beyond the liver. Indeed, while the cargo and the ligand are crucial, the third component, the linker, is integral but is often overlooked. Here, we present strain-promoted sydnone-alkyne cycloaddition as a versatile linker chemistry for oligonucleotide synthesis, expanding the choices for bioconjugation of therapeutics while enabling subcellular detection of the linker and payload using nanoscale secondary ion mass spectrometry (NanoSIMS) imaging. This strategy was successfully applied to peptide and lipid ligands and profiled using the well characterized N-acetylgalactosamine (GalNAc) targeting ligand. The linker did not affect the expected activity of the conjugate and was detectable and distinguishable from the labeled cargo. Finally, this work not only offers a practical bioconjugation method but also enables the assessment of the linker's subcellular behavior, facilitating NanoSIMS imaging to monitor the three key components of therapeutic conjugates.
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Affiliation(s)
- Loujahine Lincy-Bianchi
- Medicinal Chemistry, Research and Development, Early Cardiovascular, Renal and Metabolism, Biopharmaceuticals R&D, AstraZeneca, SE-431 83 Gothenburg, Sweden
| | - Maximilian Häfner
- Medicinal Chemistry, Research and Development, Early Cardiovascular, Renal and Metabolism, Biopharmaceuticals R&D, AstraZeneca, SE-431 83 Gothenburg, Sweden
| | - Cécile Becquart
- DMPK, Early Cardiovascular, Renal and Metabolism, BioPharmaceuticals R&D, AstraZeneca, SE-431 83 Gothenburg, Sweden
| | - Carolina Tängemo
- Discovery Biology, Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, SE-431 83 Gothenburg, Sweden
| | - Michael E Kurczy
- DMPK, Early Cardiovascular, Renal and Metabolism, BioPharmaceuticals R&D, AstraZeneca, SE-431 83 Gothenburg, Sweden
| | - Claire C Munier
- Medicinal Chemistry, Research and Development, Early Cardiovascular, Renal and Metabolism, Biopharmaceuticals R&D, AstraZeneca, SE-431 83 Gothenburg, Sweden
| | - Laurent Knerr
- Medicinal Chemistry, Research and Development, Early Cardiovascular, Renal and Metabolism, Biopharmaceuticals R&D, AstraZeneca, SE-431 83 Gothenburg, Sweden
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2
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Chaiyawat P, Sangkhathat S, Chiangjong W, Wongtrakoongate P, Hongeng S, Pruksakorn D, Chutipongtanate S. Targeting pediatric solid tumors in the new era of RNA therapeutics. Crit Rev Oncol Hematol 2024; 200:104406. [PMID: 38834094 DOI: 10.1016/j.critrevonc.2024.104406] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Revised: 04/26/2024] [Accepted: 05/29/2024] [Indexed: 06/06/2024] Open
Abstract
Despite substantial progress in pediatric cancer treatment, poor prognosis remained for patients with recurrent or metastatic disease, given the limitations of approved targeted treatments and immunotherapies. RNA therapeutics offer significant potential for addressing a broad spectrum of diseases, including cancer. Advances in manufacturing and delivery systems are paving the way for the rapid development of therapeutic RNAs for clinical applications. This review summarizes therapeutic RNA classifications and the mechanisms of action, highlighting their potential in manipulating major cancer-related pathways and biological effects. We also focus on the pre-clinical investigation of RNA molecules with efficient delivery systems for their therapeutic potential targeting pediatric solid tumors.
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Affiliation(s)
- Parunya Chaiyawat
- Musculoskeletal Science and Translational Research Center, Department of Orthopedics, Faculty of Medicine, Chiang Mai University, Chiang Mai 50200, Thailand; Center of Multidisciplinary Technology for Advanced Medicine (CMUTEAM), Faculty of Medicine, Chiang Mai University, Chiang Mai 50200, Thailand; Extracellular Vesicle Working Group, University of Cincinnati College of Medicine, Cincinnati, OH 45267, USA
| | - Surasak Sangkhathat
- Department of Biomedical Science, Faculty of Medicine, Prince of Songkla University, Songkhla, Thailand; Department of Surgery, Faculty of Medicine, Prince of Songkla University, Songkhla, Thailand; Extracellular Vesicle Working Group, University of Cincinnati College of Medicine, Cincinnati, OH 45267, USA
| | - Wararat Chiangjong
- Pediatric Translational Research Unit, Department of Pediatrics, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Bangkok 10400, Thailand; Extracellular Vesicle Working Group, University of Cincinnati College of Medicine, Cincinnati, OH 45267, USA
| | - Patompon Wongtrakoongate
- Department of Biochemistry, Faculty of Science, Mahidol University, Bangkok 10400, Thailand; Extracellular Vesicle Working Group, University of Cincinnati College of Medicine, Cincinnati, OH 45267, USA
| | - Suradej Hongeng
- Division of Hematology and Oncology, Department of Pediatrics, Faculty of Medicine Ra-mathibodi Hospital, Mahidol University, Bangkok 10400, Thailand; Extracellular Vesicle Working Group, University of Cincinnati College of Medicine, Cincinnati, OH 45267, USA
| | - Dumnoensun Pruksakorn
- Musculoskeletal Science and Translational Research Center, Department of Orthopedics, Faculty of Medicine, Chiang Mai University, Chiang Mai 50200, Thailand; Center of Multidisciplinary Technology for Advanced Medicine (CMUTEAM), Faculty of Medicine, Chiang Mai University, Chiang Mai 50200, Thailand; Extracellular Vesicle Working Group, University of Cincinnati College of Medicine, Cincinnati, OH 45267, USA.
| | - Somchai Chutipongtanate
- Pediatric Translational Research Unit, Department of Pediatrics, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Bangkok 10400, Thailand; Division of Hematology and Oncology, Department of Pediatrics, Faculty of Medicine Ra-mathibodi Hospital, Mahidol University, Bangkok 10400, Thailand; MILCH and Novel Therapeutics Lab, Division of Epidemiology, Department of Environmental and Public Health Sciences, University of Cincinnati College of Medicine, Cincinnati, OH 45267, USA; Extracellular Vesicle Working Group, University of Cincinnati College of Medicine, Cincinnati, OH 45267, USA.
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3
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Androsavich JR. Frameworks for transformational breakthroughs in RNA-based medicines. Nat Rev Drug Discov 2024; 23:421-444. [PMID: 38740953 DOI: 10.1038/s41573-024-00943-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/04/2024] [Indexed: 05/16/2024]
Abstract
RNA has sparked a revolution in modern medicine, with the potential to transform the way we treat diseases. Recent regulatory approvals, hundreds of new clinical trials, the emergence of CRISPR gene editing, and the effectiveness of mRNA vaccines in dramatic response to the COVID-19 pandemic have converged to create tremendous momentum and expectation. However, challenges with this relatively new class of drugs persist and require specialized knowledge and expertise to overcome. This Review explores shared strategies for developing RNA drug platforms, including layering technologies, addressing common biases and identifying gaps in understanding. It discusses the potential of RNA-based therapeutics to transform medicine, as well as the challenges associated with improving applicability, efficacy and safety profiles. Insights gained from RNA modalities such as antisense oligonucleotides (ASOs) and small interfering RNAs are used to identify important next steps for mRNA and gene editing technologies.
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Affiliation(s)
- John R Androsavich
- RNA Accelerator, Pfizer Inc, Cambridge, MA, USA.
- Ginkgo Bioworks, Boston, MA, USA.
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4
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Yoshida T, Hagihara T, Uchida Y, Horiuchi Y, Sasaki K, Yamamoto T, Yamashita T, Goda Y, Saito Y, Yamaguchi T, Obika S, Yamamoto S, Inoue T. Introduction of sugar-modified nucleotides into CpG-containing antisense oligonucleotides inhibits TLR9 activation. Sci Rep 2024; 14:11540. [PMID: 38773176 PMCID: PMC11109122 DOI: 10.1038/s41598-024-61666-3] [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: 03/18/2024] [Accepted: 05/08/2024] [Indexed: 05/23/2024] Open
Abstract
Antisense oligonucleotides (ASOs) are synthetic single-stranded oligonucleotides that bind to RNAs through Watson-Crick base pairings. They are actively being developed as therapeutics for various human diseases. ASOs containing unmethylated deoxycytidylyl-deoxyguanosine dinucleotide (CpG) motifs are known to trigger innate immune responses via interaction with toll-like receptor 9 (TLR9). However, the TLR9-stimulatory properties of ASOs, specifically those with lengths equal to or less than 20 nucleotides, phosphorothioate linkages, and the presence and arrangement of sugar-modified nucleotides-crucial elements for ASO therapeutics under development-have not been thoroughly investigated. In this study, we first established SY-ODN18, an 18-nucleotide phosphorothioate oligodeoxynucleotide with sufficient TLR9-stimulatory activity. We demonstrated that an unmethylated CpG motif near its 5'-end was indispensable for TLR9 activation. Moreover, by utilizing various sugar-modified nucleotides, we systematically generated model ASOs, including gapmer, mixmer, and fully modified designs, in accordance with the structures of ASO therapeutics. Our results illustrated that introducing sugar-modified nucleotides in such designs significantly reduces TLR9-stimulatory activity, even without methylation of CpG motifs. These findings would be useful for drug designs on several types of ASOs.
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Affiliation(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
- Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Tomoko Hagihara
- Fuso Pharmaceutical Industries, Ltd., 2-3-30 Morinomiya, Joto-ku, Osaka, Osaka, 536-8523, Japan
| | - Yasunori Uchida
- Division of Molecular Target and Gene Therapy Products, National Institute of Health Sciences, 3-25-26 Tonomachi, Kawasaki-ku, Kawasaki, Kanagawa, 210-9501, Japan
| | - Yoshiyuki Horiuchi
- Fuso Pharmaceutical Industries, Ltd., 2-3-30 Morinomiya, Joto-ku, Osaka, Osaka, 536-8523, Japan
| | - Kiyomi Sasaki
- Division of Molecular Target and Gene Therapy Products, National Institute of Health Sciences, 3-25-26 Tonomachi, Kawasaki-ku, Kawasaki, Kanagawa, 210-9501, Japan
| | - Takenori Yamamoto
- Division of Molecular Target and Gene Therapy Products, National Institute of Health Sciences, 3-25-26 Tonomachi, Kawasaki-ku, Kawasaki, Kanagawa, 210-9501, Japan
| | - Takuma Yamashita
- Division of Molecular Target and Gene Therapy Products, National Institute of Health Sciences, 3-25-26 Tonomachi, Kawasaki-ku, Kawasaki, Kanagawa, 210-9501, Japan
| | - Yukihiro Goda
- National Institute of Health Sciences, 3-25-26 Tonomachi, Kawasaki-ku, Kawasaki, Kanagawa, 210-9501, Japan
| | - Yoshiro Saito
- National Institute of Health Sciences, 3-25-26 Tonomachi, Kawasaki-ku, Kawasaki, Kanagawa, 210-9501, Japan
| | - Takao Yamaguchi
- 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
| | - Seiji Yamamoto
- Fuso Pharmaceutical Industries, Ltd., 2-3-30 Morinomiya, Joto-ku, Osaka, Osaka, 536-8523, Japan.
| | - 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.
- Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka, 565-0871, Japan.
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5
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Ghosh C, Popella L, Dhamodharan V, Jung J, Dietzsch J, Barquist L, Höbartner C, Vogel J. A comparative analysis of peptide-delivered antisense antibiotics using diverse nucleotide mimics. RNA (NEW YORK, N.Y.) 2024; 30:624-643. [PMID: 38413166 PMCID: PMC11098465 DOI: 10.1261/rna.079969.124] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/30/2024] [Accepted: 02/02/2024] [Indexed: 02/29/2024]
Abstract
Antisense oligomer (ASO)-based antibiotics that target mRNAs of essential bacterial genes have great potential for counteracting antimicrobial resistance and for precision microbiome editing. To date, the development of such antisense antibiotics has primarily focused on using phosphorodiamidate morpholino (PMO) and peptide nucleic acid (PNA) backbones, largely ignoring the growing number of chemical modalities that have spurred the success of ASO-based human therapy. Here, we directly compare the activities of seven chemically distinct 10mer ASOs, all designed to target the essential gene acpP upon delivery with a KFF-peptide carrier into Salmonella. Our systematic analysis of PNA, PMO, phosphorothioate (PTO)-modified DNA, 2'-methylated RNA (RNA-OMe), 2'-methoxyethylated RNA (RNA-MOE), 2'-fluorinated RNA (RNA-F), and 2'-4'-locked RNA (LNA) is based on a variety of in vitro and in vivo methods to evaluate ASO uptake, target pairing and inhibition of bacterial growth. Our data show that only PNA and PMO are efficiently delivered by the KFF peptide into Salmonella to inhibit bacterial growth. Nevertheless, the strong target binding affinity and in vitro translational repression activity of LNA and RNA-MOE make them promising modalities for antisense antibiotics that will require the identification of an effective carrier.
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Affiliation(s)
- Chandradhish Ghosh
- Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz Centre for Infection Research (HZI), D-97080 Würzburg, Germany
| | - Linda Popella
- Institute of Molecular Infection Biology (IMIB), University of Würzburg, D-97080 Würzburg, Germany
- Cluster for Nucleic Acid Therapeutics Munich (CNATM), Munich, Germany
| | - V Dhamodharan
- Institute of Organic Chemistry, Center for Nanosystems Chemistry, University of Würzburg, 97074 Würzburg, Germany
| | - Jakob Jung
- Institute of Molecular Infection Biology (IMIB), University of Würzburg, D-97080 Würzburg, Germany
| | - Julia Dietzsch
- Institute of Organic Chemistry, Center for Nanosystems Chemistry, University of Würzburg, 97074 Würzburg, Germany
| | - Lars Barquist
- Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz Centre for Infection Research (HZI), D-97080 Würzburg, Germany
- Faculty of Medicine, University of Würzburg, 97080, Würzburg, Germany
| | - Claudia Höbartner
- Institute of Organic Chemistry, Center for Nanosystems Chemistry, University of Würzburg, 97074 Würzburg, Germany
| | - Jörg Vogel
- Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz Centre for Infection Research (HZI), D-97080 Würzburg, Germany
- Institute of Molecular Infection Biology (IMIB), University of Würzburg, D-97080 Würzburg, Germany
- Cluster for Nucleic Acid Therapeutics Munich (CNATM), Munich, Germany
- Faculty of Medicine, University of Würzburg, 97080, Würzburg, Germany
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6
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Ellenbroek BD, Kahler JP, Evers SR, Pomplun SJ. Synthetic Peptides: Promising Modalities for the Targeting of Disease-Related Nucleic Acids. Angew Chem Int Ed Engl 2024; 63:e202401704. [PMID: 38456368 DOI: 10.1002/anie.202401704] [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: 01/24/2024] [Revised: 03/06/2024] [Accepted: 03/08/2024] [Indexed: 03/09/2024]
Abstract
DNA and RNA play pivotal roles in life processes by storing and transferring genetic information, modulating gene expression, and contributing to essential cellular machinery such as ribosomes. Dysregulation and mutations in nucleic acid-related processes are implicated in numerous diseases. Despite the critical impact on health of nucleic acid mutations or dysregulation, therapeutic compounds addressing these biomolecules remain limited. Peptides have emerged as a promising class of molecules for biomedical research, offering potential solutions for challenging drug targets. This review focuses on the use of synthetic peptides to target disease-related nucleic acids. We discuss examples of peptides targeting double-stranded DNA, including the clinical candidate Omomyc, and compounds designed for regulatory G-quadruplexes. Further, we provide insights into both library-based screenings and the rational design of peptides to target regulatory human RNA scaffolds and viral RNAs, emphasizing the potential of peptides in addressing nucleic acid-related diseases.
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Affiliation(s)
| | | | - Sophie R Evers
- Leiden University, 2333 CC, Leiden, The Netherlands
- Present address, Department of Chemistry, University of Zurich, Wintherthurerstrasse 190, 8057, Zurich, Switzerland
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7
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Recinos Y, Ustianenko D, Yeh YT, Wang X, Jacko M, Yesantharao LV, Wu Q, Zhang C. CRISPR-dCas13d-based deep screening of proximal and distal splicing-regulatory elements. Nat Commun 2024; 15:3839. [PMID: 38714659 PMCID: PMC11076525 DOI: 10.1038/s41467-024-47140-8] [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: 06/21/2023] [Accepted: 03/16/2024] [Indexed: 05/10/2024] Open
Abstract
Pre-mRNA splicing, a key process in gene expression, can be therapeutically modulated using various drug modalities, including antisense oligonucleotides (ASOs). However, determining promising targets is hampered by the challenge of systematically mapping splicing-regulatory elements (SREs) in their native sequence context. Here, we use the catalytically inactive CRISPR-RfxCas13d RNA-targeting system (dCas13d/gRNA) as a programmable platform to bind SREs and modulate splicing by competing against endogenous splicing factors. SpliceRUSH, a high-throughput screening method, was developed to map SREs in any gene of interest using a lentivirus gRNA library that tiles the genetic region, including distal intronic sequences. When applied to SMN2, a therapeutic target for spinal muscular atrophy, SpliceRUSH robustly identifies not only known SREs but also a previously unknown distal intronic SRE, which can be targeted to alter exon 7 splicing using either dCas13d/gRNA or ASOs. This technology enables a deeper understanding of splicing regulation with applications for RNA-based drug discovery.
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Affiliation(s)
- Yocelyn Recinos
- Department of Systems Biology, Columbia University, New York, NY, 10032, USA
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, 10032, USA
| | - Dmytro Ustianenko
- Department of Systems Biology, Columbia University, New York, NY, 10032, USA
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, 10032, USA
- Flagship Pioneering, Cambridge, MA, 02142, USA
| | - Yow-Tyng Yeh
- Department of Systems Biology, Columbia University, New York, NY, 10032, USA
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, 10032, USA
| | - Xiaojian Wang
- Department of Systems Biology, Columbia University, New York, NY, 10032, USA
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, 10032, USA
| | - Martin Jacko
- Department of Systems Biology, Columbia University, New York, NY, 10032, USA
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, 10032, USA
- Aperture Therapeutics, Inc., San Carlos, CA, 94070, USA
| | - Lekha V Yesantharao
- Department of Systems Biology, Columbia University, New York, NY, 10032, USA
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, 10032, USA
- Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
| | - Qiyang Wu
- Department of Systems Biology, Columbia University, New York, NY, 10032, USA
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, 10032, USA
| | - Chaolin Zhang
- Department of Systems Biology, Columbia University, New York, NY, 10032, USA.
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, 10032, USA.
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8
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Pals MJ, Wijnberg L, Yildiz Ç, Velema WA. Catechol-Siderophore Mimics Convey Nucleic Acid Therapeutics into Bacteria. Angew Chem Int Ed Engl 2024; 63:e202402405. [PMID: 38407513 DOI: 10.1002/anie.202402405] [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: 02/04/2024] [Revised: 02/23/2024] [Accepted: 02/24/2024] [Indexed: 02/27/2024]
Abstract
Antibacterial resistance is a major threat for human health. There is a need for new antibacterials to stay ahead of constantly-evolving resistant bacteria. Nucleic acid therapeutics hold promise as powerful antibiotics, but issues with their delivery hamper their applicability. Here, we exploit the siderophore-mediated iron uptake pathway to efficiently transport antisense oligomers into bacteria. We appended a synthetic siderophore to antisense oligomers targeting the essential acpP gene in Escherichia coli. Siderophore-conjugated PNA and PMO antisense oligomers displayed potent antibacterial properties. Conjugates bearing a minimal siderophore consisting of a mono-catechol group showed equally effective. Targeting the lacZ transcript resulted in dose-dependent decreased β-galactosidase production, demonstrating selective protein downregulation. Applying this concept to Acinetobacter baumannii also showed concentration-dependent growth inhibition. Whole-genome sequencing of resistant mutants and competition experiments with the endogenous siderophore verified selective uptake through the siderophore-mediated iron uptake pathway. Lastly, no toxicity towards mammalian cells was found. Collectively, we demonstrate for the first time that large nucleic acid therapeutics can be efficiently transported into bacteria using synthetic siderophore mimics.
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Affiliation(s)
- Mathijs J Pals
- Institute for Molecules and Materials, Radboud University Nijmegen, Heyendaalseweg 135, 6525 AJ, Nijmegen, The Netherlands
| | - Luuk Wijnberg
- Institute for Molecules and Materials, Radboud University Nijmegen, Heyendaalseweg 135, 6525 AJ, Nijmegen, The Netherlands
| | - Çağlar Yildiz
- Institute for Molecules and Materials, Radboud University Nijmegen, Heyendaalseweg 135, 6525 AJ, Nijmegen, The Netherlands
| | - Willem A Velema
- Institute for Molecules and Materials, Radboud University Nijmegen, Heyendaalseweg 135, 6525 AJ, Nijmegen, The Netherlands
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9
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Svenningsen SW, Luige O, Abdulkarim Z, Strömberg R, Williams NH. Zinc N, N-bis(2-picolyl)amine Chelates Show Substitution-Dependent Cleavage of Phosphodiesters in Models as Well as of PNAzyme-RNA Bulges. Molecules 2024; 29:2123. [PMID: 38731616 PMCID: PMC11085541 DOI: 10.3390/molecules29092123] [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: 03/01/2024] [Revised: 04/20/2024] [Accepted: 04/24/2024] [Indexed: 05/13/2024] Open
Abstract
PNAzymes are a group of artificial enzymes which show promising results in selective and efficient cleavage of RNA targets. In the present study, we introduce a series of metal chelating groups based on N,N-bis(2-picolyl) groups (parent, 6-methyl and 6-amino substituted) as the active sites of novel PNAzymes. An improved synthetic route for the 6-amino analogues is described. The catalytic activity of the chelating groups for cleaving phosphodiesters were assessed with the model substrate 2-hydroxypropyl p-nitrophenyl phosphate (HPNPP), confirming that the zinc complexes have the reactivity order of parent < 2-methyl < 2-amino. The three ligands were conjugated to a PNA oligomer to form three PNAzymes which showed the same order of reactivity and some sensitivity to the size of the RNA bulge designed into the catalyst-substrate complex. This work demonstrates that the kinetic activity observed for the model substrate HPNPP could be translated onto the PNAzymes, but that more reactive Zn complexes are required for such PNAzymes to be viable therapeutic agents.
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Affiliation(s)
- Søren W. Svenningsen
- Department of Chemistry, University of Sheffield, Richard Roberts Building, Sheffield S3 7HF, UK; (S.W.S.); (Z.A.)
| | - Olivia Luige
- Department of Biosciences and Nutrition, Karolinska Institutet, Neo, Halsovagen 9, 14157 Huddinge, Sweden;
| | - Zeyed Abdulkarim
- Department of Chemistry, University of Sheffield, Richard Roberts Building, Sheffield S3 7HF, UK; (S.W.S.); (Z.A.)
| | - Roger Strömberg
- Department of Biosciences and Nutrition, Karolinska Institutet, Neo, Halsovagen 9, 14157 Huddinge, Sweden;
- Department of Laboratory Medicine, Karolinska Institutet, ANA Futura, Nobels alle 8 B, 14152 Huddinge, Sweden
| | - Nicholas H. Williams
- Department of Chemistry, University of Sheffield, Richard Roberts Building, Sheffield S3 7HF, UK; (S.W.S.); (Z.A.)
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10
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Segovia D, Tepes PS. p160 nuclear receptor coactivator family members and their role in rare fusion‑driven neoplasms (Review). Oncol Lett 2024; 27:210. [PMID: 38572059 PMCID: PMC10988192 DOI: 10.3892/ol.2024.14343] [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] [Received: 01/05/2024] [Accepted: 02/22/2024] [Indexed: 04/05/2024] Open
Abstract
Gene fusions with translocations involving nuclear receptor coactivators (NCoAs) are relatively common among fusion-driven malignancies. NCoAs are essential mediators of environmental cues and can modulate the transcription of downstream target genes upon binding to activated nuclear receptors. Therefore, fusion proteins containing NCoAs can become strong oncogenic drivers, affecting the cell transcriptional profile. These tumors show a strong dependency on the fusion oncogene; therefore, the direct pharmacological targeting of the fusion protein becomes an attractive strategy for therapy. Currently, different combinations of chemotherapy regimens are used to treat a variety of NCoA-fusion-driven tumors, but given the frequent tumor reoccurrence, more efficient treatment strategies are needed. Specific approaches directed towards inhibition or silencing of the fusion gene need to be developed while minimizing the interference with the original genes. This review highlights the relevant literature describing the normal function and structure of NCoAs and their oncogenic activity in NCoA-gene fusion-driven cancers, and explores potential strategies that could be effective in targeting these fusions.
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Affiliation(s)
- Danilo Segovia
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
- Stony Brook University, Stony Brook, NY 11794, USA
| | - Polona Safaric Tepes
- Robert S. Boas Center for Genomics and Human Genetics, Feinstein Institutes for Medical Research, Northwell Health, Manhasset, NY 11030, USA
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11
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Vandermeulen L, Geric I, Fumagalli L, Kreir M, Lu A, Nonneman A, Premereur J, Wolfs L, Policarpo R, Fattorelli N, De Bondt A, Van Den Wyngaert I, Asselbergh B, Fiers M, De Strooper B, d'Ydewalle C, Mancuso R. Regulation of human microglial gene expression and function via RNAase-H active antisense oligonucleotides in vivo in Alzheimer's disease. Mol Neurodegener 2024; 19:37. [PMID: 38654375 PMCID: PMC11040766 DOI: 10.1186/s13024-024-00725-9] [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: 11/24/2023] [Accepted: 03/17/2024] [Indexed: 04/25/2024] Open
Abstract
BACKGROUND Microglia play important roles in maintaining brain homeostasis and neurodegeneration. The discovery of genetic variants in genes predominately or exclusively expressed in myeloid cells, such as Apolipoprotein E (APOE) and triggering receptor expressed on myeloid cells 2 (TREM2), as the strongest risk factors for Alzheimer's disease (AD) highlights the importance of microglial biology in the brain. The sequence, structure and function of several microglial proteins are poorly conserved across species, which has hampered the development of strategies aiming to modulate the expression of specific microglial genes. One way to target APOE and TREM2 is to modulate their expression using antisense oligonucleotides (ASOs). METHODS In this study, we identified, produced, and tested novel, selective and potent ASOs for human APOE and TREM2. We used a combination of in vitro iPSC-microglia models, as well as microglial xenotransplanted mice to provide proof of activity in human microglial in vivo. RESULTS We proved their efficacy in human iPSC microglia in vitro, as well as their pharmacological activity in vivo in a xenografted microglia model. We demonstrate ASOs targeting human microglia can modify their transcriptional profile and their response to amyloid-β plaques in vivo in a model of AD. CONCLUSIONS This study is the first proof-of-concept that human microglial can be modulated using ASOs in a dose-dependent manner to manipulate microglia phenotypes and response to neurodegeneration in vivo.
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Affiliation(s)
- Lina Vandermeulen
- Neuroscience Discovery, Janssen Research & Development, Janssen Pharmaceutica NV, 2340, Beerse, Belgium
| | - Ivana Geric
- VIB-KU Leuven Center for Brain & Disease Research, Leuven, 3000, Belgium
- Laboratory for the Research of Neurodegenerative Diseases, Department of Neurosciences, Leuven Brain Institute (LBI), KU Leuven, Leuven, 3000, Belgium
| | - Laura Fumagalli
- MIND Lab, VIB Center for Molecular Neurology, VIB, 2610, Antwerp, Belgium
- Department of Biomedical Sciences, University of Antwerp, 2610, Antwerp, Belgium
| | - Mohamed Kreir
- Preclinical Development & Safety, Janssen Research & Development, Janssen Pharmaceutica NV, 2340, Beerse, Belgium
| | - Ashley Lu
- VIB-KU Leuven Center for Brain & Disease Research, Leuven, 3000, Belgium
- Laboratory for the Research of Neurodegenerative Diseases, Department of Neurosciences, Leuven Brain Institute (LBI), KU Leuven, Leuven, 3000, Belgium
| | - Annelies Nonneman
- Neuroscience Discovery, Janssen Research & Development, Janssen Pharmaceutica NV, 2340, Beerse, Belgium
| | - Jessie Premereur
- MIND Lab, VIB Center for Molecular Neurology, VIB, 2610, Antwerp, Belgium
- Department of Biomedical Sciences, University of Antwerp, 2610, Antwerp, Belgium
| | - Leen Wolfs
- VIB-KU Leuven Center for Brain & Disease Research, Leuven, 3000, Belgium
- Laboratory for the Research of Neurodegenerative Diseases, Department of Neurosciences, Leuven Brain Institute (LBI), KU Leuven, Leuven, 3000, Belgium
| | - Rafaela Policarpo
- Neuroscience Discovery, Janssen Research & Development, Janssen Pharmaceutica NV, 2340, Beerse, Belgium
- VIB-KU Leuven Center for Brain & Disease Research, Leuven, 3000, Belgium
- Laboratory for the Research of Neurodegenerative Diseases, Department of Neurosciences, Leuven Brain Institute (LBI), KU Leuven, Leuven, 3000, Belgium
| | - Nicola Fattorelli
- VIB-KU Leuven Center for Brain & Disease Research, Leuven, 3000, Belgium
- Laboratory for the Research of Neurodegenerative Diseases, Department of Neurosciences, Leuven Brain Institute (LBI), KU Leuven, Leuven, 3000, Belgium
| | - An De Bondt
- Discovery Sciences, Janssen Research & Development, Janssen Pharmaceutica NV, 2340, Beerse, Belgium
| | - Ilse Van Den Wyngaert
- Discovery Sciences, Janssen Research & Development, Janssen Pharmaceutica NV, 2340, Beerse, Belgium
| | - Bob Asselbergh
- Neuromics Support Facility, VIB Center for Molecular Neurology, University of Antwerp, 2610, Antwerp, Belgium
- Neuromics Support Facility, Department of Biomedical Sciences, University of Antwerp, 2610, Antwerp, Belgium
| | - Mark Fiers
- VIB-KU Leuven Center for Brain & Disease Research, Leuven, 3000, Belgium
- Laboratory for the Research of Neurodegenerative Diseases, Department of Neurosciences, Leuven Brain Institute (LBI), KU Leuven, Leuven, 3000, Belgium
- UK Dementia Research Institute, University College London, London, W1T 7NF, UK
| | - Bart De Strooper
- VIB-KU Leuven Center for Brain & Disease Research, Leuven, 3000, Belgium
- Laboratory for the Research of Neurodegenerative Diseases, Department of Neurosciences, Leuven Brain Institute (LBI), KU Leuven, Leuven, 3000, Belgium
- UK Dementia Research Institute, University College London, London, W1T 7NF, UK
| | - Constantin d'Ydewalle
- Neuroscience Discovery, Janssen Research & Development, Janssen Pharmaceutica NV, 2340, Beerse, Belgium.
| | - Renzo Mancuso
- VIB-KU Leuven Center for Brain & Disease Research, Leuven, 3000, Belgium.
- Laboratory for the Research of Neurodegenerative Diseases, Department of Neurosciences, Leuven Brain Institute (LBI), KU Leuven, Leuven, 3000, Belgium.
- MIND Lab, VIB Center for Molecular Neurology, VIB, 2610, Antwerp, Belgium.
- Department of Biomedical Sciences, University of Antwerp, 2610, Antwerp, Belgium.
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12
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Murphy A, Hill R, Berna M. Bioanalytical Approaches to Support the Development of Antibody-Oligonucleotide Conjugate (AOC) Therapeutic Proteins. Xenobiotica 2024:1-23. [PMID: 38607350 DOI: 10.1080/00498254.2024.2339983] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2024] [Accepted: 04/03/2024] [Indexed: 04/13/2024]
Abstract
RNA interference (RNAi) is a biological process that evolved to protect eukaryotic organisms from foreign genes delivered by viruses. This process has been adapted as a powerful tool to treat numerous diseases through the delivery of small-interfering RNAs (siRNAs) to target cells to alter aberrant gene expression.Antibody-oligonucleotide conjugates (AOCs) are monoclonal antibodies with complexed siRNA or antisense oligonucleotides (ASOs) that have emerged to address some of the challenges faced by naked or chemically conjugated siRNA, which include rapid clearance from systemic circulation and lack of selective delivery of siRNA to target cells.It is essential to characterize the ADME properties of an AOC during development to optimize distribution to target tissues, to minimize the impact of biotransformation on exposure, and to characterize the PK/PD relationship to guide translation. However, owing to the complexity of AOC structure, this presents significant bioanalytical challenges, and multiple bioanalytical measurements are required to investigate the pharmacokinetics and biotransformation of the antibody, linker, and siRNA payload.In this paper, we describe an analytical workflow that details in vivo characterization of AOCs through measurement of their distinct molecular components to provide the basis for greater understanding of their ADME properties. Although the approaches herein can be applied to in vitro characterization of AOCs, this paper will focus on in vivo applications. This workflow relies on high-resolution mass spectrometry as the principal means of detection and leverages chromatographic, affinity-based, and enzymatic sample preparation steps.
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Affiliation(s)
- Anthony Murphy
- Investigative ADME/Toxicology and Bioanalytical Research, Eli Lilly and Company, Indianapolis, IN, USA
| | - Ryan Hill
- Investigative ADME/Toxicology and Bioanalytical Research, Eli Lilly and Company, Indianapolis, IN, USA
| | - Michael Berna
- Investigative ADME/Toxicology and Bioanalytical Research, Eli Lilly and Company, Indianapolis, IN, USA
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13
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Saini S, Goel K, Ghosh S, Das A, Saraogi I. Effects of PNA Sequence and Target Site Selection on Function of a 4.5S Non-Coding RNA. Chembiochem 2024:e202400029. [PMID: 38595046 DOI: 10.1002/cbic.202400029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2024] [Revised: 04/09/2024] [Accepted: 04/09/2024] [Indexed: 04/11/2024]
Abstract
Peptide nucleic acid (PNA) based antisense strategy is a promising therapeutic approach to specifically inhibit target gene expression. However, unlike protein coding genes, identification of an ideal PNA binding site for non-coding RNA is not straightforward. Here, we compare the inhibitory activities of PNA molecules that bind a non-coding 4.5S RNA called SRP RNA, a key component of the bacterial signal recognition particle (SRP). A 9-mer PNA (PNA9) complementary to the tetraloop region of the RNA was more potent in inhibiting its interaction with the SRP protein, compared to an 8-mer PNA (PNA8) targeting a stem-loop. PNA9, which contained a homo-pyrimidine sequence could form a triplex with the complementary stretch of RNA in vitro as confirmed using a fluorescent derivative of PNA9 (F-PNA13). The RNA-PNA complex formation resulted in inhibition of SRP function with PNA9 and F-PNA13, but not PNA8 highlighting the importance of target site selection. Surprisingly, F-PNA13 which was more potent in inhibiting SRP function in vitro, showed weaker antibacterial activity compared to PNA9 likely due to poor cell penetration of the longer PNA. Our results underscore the importance of suitable target site selection and optimum PNA length to develop better antisense molecules against non-coding RNA.
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Affiliation(s)
- Snehlata Saini
- Department of Biological Sciences, Indian Institute of Science Education and Research Bhopal Bhauri, Bhopal Bypass Road, Bhopal, 462066, Madhya Pradesh, India
| | - Khushboo Goel
- Department of Chemistry, Indian Institute of Science Education and Research Bhopal Bhauri, Bhopal Bypass Road, Bhopal, 462066, Madhya Pradesh, India
| | - Sudipta Ghosh
- Department of Chemistry, Indian Institute of Science Education and Research Bhopal Bhauri, Bhopal Bypass Road, Bhopal, 462066, Madhya Pradesh, India
| | - Anirban Das
- Department of Chemistry, Indian Institute of Science Education and Research Bhopal Bhauri, Bhopal Bypass Road, Bhopal, 462066, Madhya Pradesh, India
| | - Ishu Saraogi
- Department of Biological Sciences, Indian Institute of Science Education and Research Bhopal Bhauri, Bhopal Bypass Road, Bhopal, 462066, Madhya Pradesh, India
- Department of Chemistry, Indian Institute of Science Education and Research Bhopal Bhauri, Bhopal Bypass Road, Bhopal, 462066, Madhya Pradesh, India
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14
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Ma S, Howden SA, Keane SC. Use of steric blocking antisense oligonucleotides for the targeted inhibition of junction containing precursor microRNAs. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.08.588531. [PMID: 38645194 PMCID: PMC11030329 DOI: 10.1101/2024.04.08.588531] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/23/2024]
Abstract
Antisense oligonucleotides (ASOs) are widely used as therapeutics for neurodegenerative diseases, cancers, and virus infections. One class of ASOs functions to enhance protein expression by sequestering the mature microRNA (miRNA) in a double-stranded structure within the RNA-induced silencing complex (RISC). An alternative approach for the targeted control of gene expression is to use ASOs that bind to the pre-elements of miRNAs (pre-miRNAs) and modulate their enzymatic processing. Here, we demonstrate that ASOs can be used to disrupt a specific structural feature, "junction," within pre-miR-31 that is important in directing efficient processing by the Dicer/TRBP complex. Furthermore, we extend and validate this strategy to pre-miR-144, which has a similar junction-dependent structure-function relationship. We found that a significant number of human pre-miRNAs are predicted to contain junctions, and validated our ASO approach on several members of this group. Importantly, we also verified the application of junction-targeting ASOs for the specific inhibition of pre-miRNA processing in cell . Our study reemphasizes the important roles of RNA structure in regulating Dicer/TRBP processing of pre-miRNAs and provides the framework to develop structure-informed ASOs that serve to inhibit miRNA production.
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15
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Bäckström E, Bonetti A, Johnsson P, Öhlin S, Dahlén A, Andersson P, Andersson S, Gennemark P. Tissue pharmacokinetics of antisense oligonucleotides. MOLECULAR THERAPY. NUCLEIC ACIDS 2024; 35:102133. [PMID: 38419941 PMCID: PMC10899043 DOI: 10.1016/j.omtn.2024.102133] [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: 05/11/2023] [Accepted: 01/30/2024] [Indexed: 03/02/2024]
Abstract
Pharmacokinetics (PK) of antisense oligonucleotides (ASOs) is characterized by rapid distribution from plasma to tissue and slow terminal plasma elimination driven by re-distribution from tissue. Quantitative understanding of tissue PK and RNA knockdown for various ASO chemistries, conjugations, and administration routes is critical for successful drug discovery. Here, we report concentration-time and RNA knockdown profiles for a gapmer ASO with locked nucleic acid ribose chemistry in mouse liver, kidney, heart, and lung after subcutaneous and intratracheal administration. Additionally, the same ASO with liver targeting conjugation (galactosamine-N-acetyl) is evaluated for subcutaneous administration. Data indicate that exposure and knockdown differ between tissues and strongly depend on administration route and conjugation. In a second study, we show that tissue PK is similar between the three different ribose chemistries locked nucleic acid, constrained ethyl and 2'-O-methoxyethyl, both after subcutaneous and intratracheal administration. Further, we show that the half-life in mouse liver may vary with ASO sequence. Finally, we report less than dose-proportional increase in liver concentration in the dose range of 3-30 μmol/kg. Overall, our studies contribute pivotal data to support design and interpretation of ASO in vivo studies, thereby increasing the probability of delivering novel ASO therapies to patients.
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Affiliation(s)
- Erica Bäckström
- Drug Metabolism and Pharmacokinetics, Research and Early Development, Respiratory & Immunology (R&I), BioPharmaceuticals R&D, AstraZeneca, 431 83 Gothenburg, Sweden
| | - Alessandro Bonetti
- Oligonucleotide Discovery, Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, 431 83 Gothenburg, Sweden
| | - Per Johnsson
- Oligonucleotide Discovery, Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, 431 83 Gothenburg, Sweden
| | - Stefan Öhlin
- Business, Planning Operations, Clinical Pharmacology and Safety Sciences, BioPharmaceuticals R&D, AstraZeneca, 431 83 Gothenburg, Sweden
| | - Anders Dahlén
- Oligonucleotide Discovery, Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, 431 83 Gothenburg, Sweden
| | - Patrik Andersson
- Safety Innovation, Safety Sciences, Clinical Pharmacology and Safety Sciences, BioPharmaceuticals R&D, AstraZeneca, 431 83 Gothenburg, Sweden
| | - Shalini Andersson
- Oligonucleotide Discovery, Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, 431 83 Gothenburg, Sweden
| | - Peter Gennemark
- Drug Metabolism and Pharmacokinetics, Research and Early Development, Cardiovascular, Renal and Metabolism (CVRM), BioPharmaceuticals R&D, AstraZeneca, 431 83 Gothenburg, Sweden
- Department of Biomedical Engineering, Linköping University, 581 85 Linköping, Sweden
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16
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Sergeeva O, Akhmetova E, Dukova S, Beloglazkina E, Uspenskaya A, Machulkin A, Stetsenko D, Zatsepin T. Structure-activity relationship study of mesyl and busyl phosphoramidate antisense oligonucleotides for unaided and PSMA-mediated uptake into prostate cancer cells. Front Chem 2024; 12:1342178. [PMID: 38501046 PMCID: PMC10944894 DOI: 10.3389/fchem.2024.1342178] [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: 11/21/2023] [Accepted: 02/13/2024] [Indexed: 03/20/2024] Open
Abstract
Phosphorothioate (PS) group is a key component of a majority of FDA approved oligonucleotide drugs that increase stability to nucleases whilst maintaining interactions with many proteins, including RNase H in the case of antisense oligonucleotides (ASOs). At the same time, uniform PS modification increases nonspecific protein binding that can trigger toxicity and pro-inflammatory effects, so discovery and characterization of alternative phosphate mimics for RNA therapeutics is an actual task. Here we evaluated the effects of the introduction of several N-alkane sulfonyl phosphoramidate groups such as mesyl (methanesulfonyl) or busyl (1-butanesulfonyl) phosphoramidates into gapmer ASOs on the efficiency and pattern of RNase H cleavage, cellular uptake in vitro, and intracellular localization. Using Malat1 lncRNA as a target, we have identified patterns of mesyl or busyl modifications in the ASOs for optimal knockdown in vitro. Combination of the PSMA ligand-mediated delivery with optimized mesyl and busyl ASOs resulted in the efficient target depletion in the prostate cancer cells. Our study demonstrated that other N-alkanesulfonyl phosphoramidate groups apart from a known mesyl phosphoramidate can serve as an essential component of mixed backbone gapmer ASOs to reduce drawbacks of uniformly PS-modified gapmers, and deserve further investigation in RNA therapeutics.
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Affiliation(s)
- O. Sergeeva
- Skolkovo Institute of Science and Technology, Moscow, Russia
| | - E. Akhmetova
- Skolkovo Institute of Science and Technology, Moscow, Russia
| | - S. Dukova
- Skolkovo Institute of Science and Technology, Moscow, Russia
| | - E. Beloglazkina
- Department of Chemistry, Lomonosov Moscow State University, Moscow, Russia
| | - A. Uspenskaya
- Department of Chemistry, Lomonosov Moscow State University, Moscow, Russia
| | - A. Machulkin
- Department of Chemistry, Lomonosov Moscow State University, Moscow, Russia
- Department for Biochemistry, People’s Friendship University of Russia Named after Patrice Lumumba (RUDN University), Moscow, Russia
| | - D. Stetsenko
- Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - T. Zatsepin
- Department of Chemistry, Lomonosov Moscow State University, Moscow, Russia
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17
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Damacena de Angelis C, Meddeb M, Chen N, Fisher SA. An antisense oligonucleotide efficiently suppresses splicing of an alternative exon in vascular smooth muscle in vivo. Am J Physiol Heart Circ Physiol 2024; 326:H860-H869. [PMID: 38276948 DOI: 10.1152/ajpheart.00745.2023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/28/2023] [Revised: 12/21/2023] [Accepted: 01/18/2024] [Indexed: 01/27/2024]
Abstract
Targeting alternative exons for therapeutic gain has been achieved in a few instances and potentially could be applied more broadly. The myosin phosphatase (MP) enzyme is a critical hub upon which signals converge to regulate vessel tone. Alternative exon 24 of myosin phosphatase regulatory subunit (Mypt1 E24) is an ideal target as toggling between the two isoforms sets smooth muscle sensitivity to vasodilators such as nitric oxide (NO). This study aimed to develop a gene-based therapy to suppress splicing of Mypt1 E24 thereby switching MP enzyme to the NO-responsive isoform. CRISPR/Cas9 constructs were effective at editing of Mypt1 E24 in vitro; however, targeting of vascular smooth muscle in vivo with AAV9 was inefficient. In contrast, an octo-guanidine conjugated antisense oligonucleotide targeting the 5' splice site of Mypt1 E24 was highly efficient in vivo. It reduced the percent splicing inclusion of Mypt1 E24 from 80% to 10% in mesenteric arteries. The maximal and half-maximal effects occurred at 12.5 and 6.25 mg/kg, respectively. The effect persisted for at least 1 mo without toxicity. This highly effective splice-blocking antisense oligonucleotide could be developed as a novel therapy to reverse vascular dysfunction common to diseases such as hypertension and heart failure.NEW & NOTEWORTHY Alternative exon usage is a major driver of phenotypic diversity in all cell types including smooth muscle. However, the functional significance of most of the hundreds of thousands of alternative exons has not been defined, nor in most cases even tested. If their importance to vascular function were known these alternative exons could represent novel therapeutic targets. Here, we present injection of Vivo-morpholino splice-blocking antisense oligonucleotides as a simple, efficient, and cost-effective method for suppression of alternative exon usage in vascular smooth muscle in vivo.
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Affiliation(s)
| | - Mariam Meddeb
- Division of Cardiology, Department of Medicine, Baltimore, Maryland, United States
| | - Nelson Chen
- University of Maryland-Baltimore Scholars Program, Baltimore, Maryland, United States
| | - Steven A Fisher
- Division of Cardiology, Department of Medicine, Baltimore, Maryland, United States
- Department of Physiology, University of Maryland School of Medicine, Baltimore, Maryland, United States
- Baltimore Veterans Affairs Medical Center, Baltimore, Maryland, United States
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18
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Chen S, Heendeniya SN, Le BT, Rahimizadeh K, Rabiee N, Zahra QUA, Veedu RN. Splice-Modulating Antisense Oligonucleotides as Therapeutics for Inherited Metabolic Diseases. BioDrugs 2024; 38:177-203. [PMID: 38252341 PMCID: PMC10912209 DOI: 10.1007/s40259-024-00644-7] [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] [Accepted: 01/03/2024] [Indexed: 01/23/2024]
Abstract
The last decade (2013-2023) has seen unprecedented successes in the clinical translation of therapeutic antisense oligonucleotides (ASOs). Eight such molecules have been granted marketing approval by the United States Food and Drug Administration (US FDA) during the decade, after the first ASO drug, fomivirsen, was approved much earlier, in 1998. Splice-modulating ASOs have also been developed for the therapy of inborn errors of metabolism (IEMs), due to their ability to redirect aberrant splicing caused by mutations, thus recovering the expression of normal transcripts, and correcting the deficiency of functional proteins. The feasibility of treating IEM patients with splice-switching ASOs has been supported by FDA permission (2018) of the first "N-of-1" study of milasen, an investigational ASO drug for Batten disease. Although for IEM, owing to the rarity of individual disease and/or pathogenic mutation, only a low number of patients may be treated by ASOs that specifically suppress the aberrant splicing pattern of mutant precursor mRNA (pre-mRNA), splice-switching ASOs represent superior individualized molecular therapeutics for IEM. In this work, we first summarize the ASO technology with respect to its mechanisms of action, chemical modifications of nucleotides, and rational design of modified oligonucleotides; following that, we precisely provide a review of the current understanding of developing splice-modulating ASO-based therapeutics for IEM. In the concluding section, we suggest potential ways to improve and/or optimize the development of ASOs targeting IEM.
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Affiliation(s)
- Suxiang Chen
- Centre for Molecular Medicine and Innovative Therapeutics, Health Futures Institute, Murdoch University, Murdoch, WA, 6150, Australia
- Precision Nucleic Acid Therapeutics, Perron Institute for Neurological and Translational Science, Nedlands, WA, 6009, Australia
| | - Saumya Nishanga Heendeniya
- Centre for Molecular Medicine and Innovative Therapeutics, Health Futures Institute, Murdoch University, Murdoch, WA, 6150, Australia
- Precision Nucleic Acid Therapeutics, Perron Institute for Neurological and Translational Science, Nedlands, WA, 6009, Australia
| | - Bao T Le
- Centre for Molecular Medicine and Innovative Therapeutics, Health Futures Institute, Murdoch University, Murdoch, WA, 6150, Australia
- Precision Nucleic Acid Therapeutics, Perron Institute for Neurological and Translational Science, Nedlands, WA, 6009, Australia
- ProGenis Pharmaceuticals Pty Ltd, Bentley, WA, 6102, Australia
| | - Kamal Rahimizadeh
- Centre for Molecular Medicine and Innovative Therapeutics, Health Futures Institute, Murdoch University, Murdoch, WA, 6150, Australia
- Precision Nucleic Acid Therapeutics, Perron Institute for Neurological and Translational Science, Nedlands, WA, 6009, Australia
| | - Navid Rabiee
- Centre for Molecular Medicine and Innovative Therapeutics, Health Futures Institute, Murdoch University, Murdoch, WA, 6150, Australia
- Precision Nucleic Acid Therapeutics, Perron Institute for Neurological and Translational Science, Nedlands, WA, 6009, Australia
| | - Qurat Ul Ain Zahra
- Centre for Molecular Medicine and Innovative Therapeutics, Health Futures Institute, Murdoch University, Murdoch, WA, 6150, Australia
- Precision Nucleic Acid Therapeutics, Perron Institute for Neurological and Translational Science, Nedlands, WA, 6009, Australia
| | - Rakesh N Veedu
- Centre for Molecular Medicine and Innovative Therapeutics, Health Futures Institute, Murdoch University, Murdoch, WA, 6150, Australia.
- Precision Nucleic Acid Therapeutics, Perron Institute for Neurological and Translational Science, Nedlands, WA, 6009, Australia.
- ProGenis Pharmaceuticals Pty Ltd, Bentley, WA, 6102, Australia.
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19
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Coan M, Haefliger S, Ounzain S, Johnson R. Targeting and engineering long non-coding RNAs for cancer therapy. Nat Rev Genet 2024:10.1038/s41576-024-00693-2. [PMID: 38424237 DOI: 10.1038/s41576-024-00693-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/17/2024] [Indexed: 03/02/2024]
Abstract
RNA therapeutics (RNATx) aim to treat diseases, including cancer, by targeting or employing RNA molecules for therapeutic purposes. Amongst the most promising targets are long non-coding RNAs (lncRNAs), which regulate oncogenic molecular networks in a cell type-restricted manner. lncRNAs are distinct from protein-coding genes in important ways that increase their therapeutic potential yet also present hurdles to conventional clinical development. Advances in genome editing, oligonucleotide chemistry, multi-omics and RNA engineering are paving the way for efficient and cost-effective lncRNA-focused drug discovery pipelines. In this Review, we present the emerging field of lncRNA therapeutics for oncology, with emphasis on the unique strengths and challenges of lncRNAs within the broader RNATx framework. We outline the necessary steps for lncRNA therapeutics to deliver effective, durable, tolerable and personalized treatments for cancer.
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Affiliation(s)
- Michela Coan
- School of Biology and Environmental Science, University College Dublin, Dublin, Ireland
- Conway Institute of Biomedical and Biomolecular Research, University College Dublin, Dublin, Ireland
- School of Medicine, University College Dublin, Dublin, Ireland
| | - Simon Haefliger
- Department of Medical Oncology, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland
- Department for BioMedical Research, University of Bern, Bern, Switzerland
| | | | - Rory Johnson
- School of Biology and Environmental Science, University College Dublin, Dublin, Ireland.
- Conway Institute of Biomedical and Biomolecular Research, University College Dublin, Dublin, Ireland.
- Department of Medical Oncology, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland.
- Department for BioMedical Research, University of Bern, Bern, Switzerland.
- FutureNeuro, SFI Research Centre for Chronic and Rare Neurological Diseases, Dublin, Ireland.
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20
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Kovecses O, Mercier FE, McKeague M. Nucleic acid therapeutics as differentiation agents for myeloid leukemias. Leukemia 2024:10.1038/s41375-024-02191-0. [PMID: 38424137 DOI: 10.1038/s41375-024-02191-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2023] [Revised: 02/15/2024] [Accepted: 02/19/2024] [Indexed: 03/02/2024]
Abstract
Differentiation therapy has proven to be a success story for patients with acute promyelocytic leukemia. However, the remaining subtypes of acute myeloid leukemia (AML) are treated with cytotoxic chemotherapies that have limited efficacy and a high likelihood of resistance. As differentiation arrest is a hallmark of AML, there is increased interest in developing differentiation-inducing agents to enhance disease-free survival. Here, we provide a comprehensive review of current reports and future avenues of nucleic acid therapeutics for AML, focusing on the use of targeted nucleic acid drugs to promote differentiation. Specifically, we compare and discuss the precision of small interfering RNA, small activating RNA, antisense oligonucleotides, and aptamers to modulate gene expression patterns that drive leukemic cell differentiation. We delve into preclinical and clinical studies that demonstrate the efficacy of nucleic acid-based differentiation therapies to induce leukemic cell maturation and reduce disease burden. By directly influencing the expression of key genes involved in myeloid maturation, nucleic acid therapeutics hold the potential to induce the differentiation of leukemic cells towards a more mature and less aggressive phenotype. Furthermore, we discuss the most critical challenges associated with developing nucleic acid therapeutics for myeloid malignancies. By introducing the progress in the field and identifying future opportunities, we aim to highlight the power of nucleic acid therapeutics in reshaping the landscape of myeloid leukemia treatment.
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Affiliation(s)
- Olivia Kovecses
- Department of Pharmacology and Therapeutics, McGill University, Montreal, H3G 1Y6, QC, Canada
| | - François E Mercier
- Division of Hematology and Experimental Medicine, Department of Medicine, McGill University, Montreal, H3T 1E2, QC, Canada
| | - Maureen McKeague
- Department of Pharmacology and Therapeutics, McGill University, Montreal, H3G 1Y6, QC, Canada.
- Department of Chemistry, McGill University, Montreal, H3A 0B8, QC, Canada.
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21
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Katkevics M, MacKay JA, Rozners E. Triplex-forming peptide nucleic acids as emerging ligands to modulate structure and function of complex RNAs. Chem Commun (Camb) 2024; 60:1999-2008. [PMID: 38259187 PMCID: PMC10922694 DOI: 10.1039/d3cc05409h] [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] [Indexed: 01/24/2024]
Abstract
Over the last three decades, our view of RNA has changed from a simple intermediate supporting protein synthesis to a major regulator of biological processes. In the expanding area of RNA research, peptide nucleic acid (PNA) is emerging as a promising ligand for triple-helical recognition of complex RNAs. As discussed in this feature article, the key advantages of PNAs are high sequence specificity and affinity for RNA (>10 fold higher than for DNA) that are difficult to achieve with small molecule ligands. Emerging studies demonstrate that triple-helical binding of PNAs can modulate biological function and control dynamic conformational equilibria of complex folded RNAs. These results suggest that PNA has a unique potential as a research tool and therapeutic compound targeting RNA. The remaining problems hampering advances in these directions are limitations of sequences that can be recognized by Hoogsteen triplexes (typically purine rich tracts), poor cellular uptake and bioavailability of PNA, and potential off-target effects in biological systems. Recent exciting studies are discussed that illustrate how synthetic nucleic acid chemistry provides innovative solutions for these problems.
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Affiliation(s)
- Martins Katkevics
- Latvian Institute of Organic Synthesis, Aizkraukles 21, Riga, LV-1006, Latvia
| | - James A MacKay
- Department of Chemistry and Biochemistry, Elizabethtown College, Elizabethtown, PA 17022, USA
| | - Eriks Rozners
- Department of Chemistry, Binghamton University, Binghamton, NY 13902, USA.
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22
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Jones CH, Androsavich JR, So N, Jenkins MP, MacCormack D, Prigodich A, Welch V, True JM, Dolsten M. Breaking the mold with RNA-a "RNAissance" of life science. NPJ Genom Med 2024; 9:2. [PMID: 38195675 PMCID: PMC10776758 DOI: 10.1038/s41525-023-00387-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2023] [Accepted: 12/07/2023] [Indexed: 01/11/2024] Open
Abstract
In the past decade, RNA therapeutics have gone from being a promising concept to one of the most exciting frontiers in healthcare and pharmaceuticals. The field is now entering what many call a renaissance or "RNAissance" which is being fueled by advances in genetic engineering and delivery systems to take on more ambitious development efforts. However, this renaissance is occurring at an unprecedented pace, which will require a different way of thinking if the field is to live up to its full potential. Recognizing this need, this article will provide a forward-looking perspective on the field of RNA medical products and the potential long-term innovations and policy shifts enabled by this revolutionary and game-changing technological platform.
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Affiliation(s)
| | | | - Nina So
- Pfizer, 66 Hudson Boulevard, New York, NY, 10018, USA
| | | | | | | | - Verna Welch
- Pfizer, 66 Hudson Boulevard, New York, NY, 10018, USA
| | - Jane M True
- Pfizer, 66 Hudson Boulevard, New York, NY, 10018, USA.
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23
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Asano D, Takakusa H, Nakai D. Oral Absorption of Middle-to-Large Molecules and Its Improvement, with a Focus on New Modality Drugs. Pharmaceutics 2023; 16:47. [PMID: 38258058 PMCID: PMC10820198 DOI: 10.3390/pharmaceutics16010047] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Revised: 12/11/2023] [Accepted: 12/26/2023] [Indexed: 01/24/2024] Open
Abstract
To meet unmet medical needs, middle-to-large molecules, including peptides and oligonucleotides, have emerged as new therapeutic modalities. Owing to their middle-to-large molecular sizes, middle-to-large molecules are not suitable for oral absorption, but there are high expectations around orally bioavailable macromolecular drugs, since oral administration is the most convenient dosing route. Therefore, extensive efforts have been made to create bioavailable middle-to-large molecules or develop absorption enhancement technology, from which some successes have recently been reported. For example, Rybelsus® tablets and Mycapssa® capsules, both of which contain absorption enhancers, were approved as oral medications for type 2 diabetes and acromegaly, respectively. The oral administration of Rybelsus and Mycapssa exposes their pharmacologically active peptides with molecular weights greater than 1000, namely, semaglutide and octreotide, respectively, into systemic circulation. Although these two medications represent major achievements in the development of orally absorbable peptide formulations, the oral bioavailability of peptides after taking Rybelsus and Mycapssa is still only around 1%. In this article, we review the approaches and recent advances of orally bioavailable middle-to-large molecules and discuss challenges for improving their oral absorption.
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Affiliation(s)
- Daigo Asano
- Drug Metabolism and Pharmacokinetics Research Laboratories, Daiichi Sankyo Co., Ltd., 1-2-58, Hiromachi, Shinagawa-ku, Tokyo 140-8710, Japan; (H.T.); (D.N.)
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24
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Le BT, Chen S, Veedu RN. Evaluation of Chemically Modified Nucleic Acid Analogues for Splice Switching Application. ACS OMEGA 2023; 8:48650-48661. [PMID: 38162739 PMCID: PMC10753547 DOI: 10.1021/acsomega.3c07618] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/02/2023] [Revised: 10/30/2023] [Accepted: 11/21/2023] [Indexed: 01/03/2024]
Abstract
In recent years, several splice switching antisense oligonucleotide (ASO)-based therapeutics have gained significant interest, and several candidates received approval for clinical use for treating rare diseases, in particular, Duchenne muscular dystrophy and spinal muscular atrophy. These ASOs are fully modified; in other words, they are composed of chemically modified nucleic acid analogues instead of natural RNA oligomers. This has significantly improved drug-like properties of these ASOs in terms of efficacy, stability, pharmacokinetics, and safety. Although chemical modifications of oligonucleotides have been discussed previously for numerous applications including nucleic acid aptamers, small interfering RNA, DNAzyme, and ASO, to the best of our knowledge, none of them have solely focused on the analogues that have been utilized for splice switching applications. To this end, we present here a comprehensive review of different modified nucleic acid analogues that have been explored for developing splice switching ASOs. In addition to the antisense chemistry, we also endeavor to provide a brief historical overview of the approved spice switching ASO drugs, including a list of drugs that have entered human clinical trials. We hope this work will inspire further investigations into expanding the potential of novel nucleic acid analogues for constructing splice switching ASOs.
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Affiliation(s)
- Bao T. Le
- Centre
for Molecular Medicine and Innovative Therapeutics, Health Futures
Institute, Murdoch University, Murdoch, Western Australia 6150, Australia
- Precision
Nucleic Acid Therapeutics, Perron Institute
for Neurological and Translational Science, Nedlands, Western Australia 6009, Australia
- ProGenis
Pharmaceuticals Pty Ltd., Bentley, Western Australia 6102, Australia
| | - Suxiang Chen
- Centre
for Molecular Medicine and Innovative Therapeutics, Health Futures
Institute, Murdoch University, Murdoch, Western Australia 6150, Australia
- Precision
Nucleic Acid Therapeutics, Perron Institute
for Neurological and Translational Science, Nedlands, Western Australia 6009, Australia
| | - Rakesh N. Veedu
- Centre
for Molecular Medicine and Innovative Therapeutics, Health Futures
Institute, Murdoch University, Murdoch, Western Australia 6150, Australia
- Precision
Nucleic Acid Therapeutics, Perron Institute
for Neurological and Translational Science, Nedlands, Western Australia 6009, Australia
- ProGenis
Pharmaceuticals Pty Ltd., Bentley, Western Australia 6102, Australia
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25
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Vemula P, Schoch KM, Miller TM. Evaluating the efficacy of purchased antisense oligonucleotides to reduce mouse and human tau in vivo. Front Mol Neurosci 2023; 16:1320182. [PMID: 38192302 PMCID: PMC10773814 DOI: 10.3389/fnmol.2023.1320182] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2023] [Accepted: 11/23/2023] [Indexed: 01/10/2024] Open
Abstract
Many preclinical and clinical studies support the use of antisense oligonucleotides (ASOs) as effective therapeutic strategies. However, acquiring ASOs for research purposes may be limited by partnerships with the pharmaceutical companies. Our lab previously developed an effective ASO strategy to lower human tau and reverse pathology in aged tauopathy model mice. Testing the efficacy of purchased tau lowering ASOs would provide support for these reagents as broad research tools. Purchased mouse and human tau lowering ASOs were infused or injected intracerebroventricularly into wildtype and tau transgenic mice. Following treatment, brain tissue evaluated for ASO distribution and levels of tau mRNA, protein, and phosphorylated tau. We show that purchased ASOs enter cell types of the brain and effectively decrease mouse or human tau mRNA and protein levels. Human tau lowering ASO treatment in PS19 mice decreased phosphorylated tau and gliosis relative to saline-treated PS19 mice, consistent with our previous study using a non-commercial tau lowering ASO. The results of this study demonstrate the efficacy of purchased tau targeting ASOs in vivo to support their broad use by researchers.
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Affiliation(s)
- Pranav Vemula
- Department of Neurology, Hope Center for Neurological Disorders, Washington University in St. Louis School of Medicine, St. Louis, MO, United States
| | - Kathleen M Schoch
- Department of Neurology, Hope Center for Neurological Disorders, Washington University in St. Louis School of Medicine, St. Louis, MO, United States
| | - Timothy M Miller
- Department of Neurology, Hope Center for Neurological Disorders, Washington University in St. Louis School of Medicine, St. Louis, MO, United States
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26
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Huang SH, Chen SC, Wu TY, Chen CY, Yu CH. Programmable modulation of ribosomal frameshifting by mRNA targeting CRISPR-Cas12a system. iScience 2023; 26:108492. [PMID: 38125012 PMCID: PMC10730746 DOI: 10.1016/j.isci.2023.108492] [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] [Received: 05/12/2023] [Revised: 09/13/2023] [Accepted: 11/16/2023] [Indexed: 12/23/2023] Open
Abstract
Minus 1 programmed ribosomal frameshifting (-1 PRF) is a conserved translational regulation event essential for critical biological processes, including the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) replication. Efficient trans-modulation of the structured RNA element crucial to -1 PRF will endow the therapeutic application. Here, we demonstrate that CRISPR RNA can stimulate efficient -1 PRF. Assembled CRISPR-Cas12a, but not CRISPR-Cas9, complex further enhances -1 PRF efficiency through its higher capacity to stall translating ribosomes. We additionally perform CRISPR-Cas12a targeting to impair the SARS-CoV-2 frameshifting pseudoknot structure via a focused screening. We demonstrate that targeting CRISPR-Cas12a results in more than 70% suppression of -1 PRF in vitro and about 50% suppression in mammalian cells. Our results show the expanded function of the CRISPR-Cas12 system in modulating -1 PRF efficiency through stalling ribosomes and deforming frameshifting stimulatory signals, which could serve as a new strategy for future coronavirus pandemics.
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Affiliation(s)
- Shih-Hong Huang
- Department of Biochemistry and Molecular Biology, College of Medicine, National Cheng Kung University, Tainan, Taiwan
- Institute of Basic Medical Sciences, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Shih-Cheng Chen
- Department of Biochemistry and Molecular Biology, College of Medicine, National Cheng Kung University, Tainan, Taiwan
- National Institute of Cancer Research, National Health Research Institutes, Tainan, Taiwan
| | | | - Cheng-Yao Chen
- YD BioLabs, Inc., Hsinchu, Taiwan
- School of Medical Laboratory Science and Biotechnology, Taipei Medical University, Taipei, Taiwan
| | - Chien-Hung Yu
- Department of Biochemistry and Molecular Biology, College of Medicine, National Cheng Kung University, Tainan, Taiwan
- Institute of Basic Medical Sciences, College of Medicine, National Cheng Kung University, Tainan, Taiwan
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27
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Gruber C, Gursinsky T, Gago-Zachert S, Pantaleo V, Behrens SE. Effective Antiviral Application of Antisense in Plants by Exploiting Accessible Sites in the Target RNA. Int J Mol Sci 2023; 24:17153. [PMID: 38138982 PMCID: PMC10743417 DOI: 10.3390/ijms242417153] [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: 10/18/2023] [Revised: 12/01/2023] [Accepted: 12/03/2023] [Indexed: 12/24/2023] Open
Abstract
Antisense oligodeoxynucleotides (ASOs) have long been used to selectively inhibit or modulate gene expression at the RNA level, and some ASOs are approved for clinical use. However, the practicability of antisense technologies remains limited by the difficulty of reliably predicting the sites accessible to ASOs in complex folded RNAs. Recently, we applied a plant-based method that reproduces RNA-induced RNA silencing in vitro to reliably identify sites in target RNAs that are accessible to small interfering RNA (siRNA)-guided Argonaute endonucleases. Here, we show that this method is also suitable for identifying ASOs that are effective in DNA-induced RNA silencing by RNases H. We show that ASOs identified in this way that target a viral genome are comparably effective in protecting plants from infection as siRNAs with the corresponding sequence. The antiviral activity of the ASOs could be further enhanced by chemical modification. This led to two important conclusions: siRNAs and ASOs that can effectively knock down complex RNA molecules can be identified using the same approach, and ASOs optimized in this way could find application in crop protection. The technology developed here could be useful not only for effective RNA silencing in plants but also in other organisms.
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Affiliation(s)
- Cornelia Gruber
- Institute of Biochemistry and Biotechnology, Section Microbial Biotechnology, Martin Luther University Halle-Wittenberg, D-06120 Halle (Saale), Germany; (C.G.); (T.G.); (S.G.-Z.)
| | - Torsten Gursinsky
- Institute of Biochemistry and Biotechnology, Section Microbial Biotechnology, Martin Luther University Halle-Wittenberg, D-06120 Halle (Saale), Germany; (C.G.); (T.G.); (S.G.-Z.)
| | - Selma Gago-Zachert
- Institute of Biochemistry and Biotechnology, Section Microbial Biotechnology, Martin Luther University Halle-Wittenberg, D-06120 Halle (Saale), Germany; (C.G.); (T.G.); (S.G.-Z.)
| | - Vitantonio Pantaleo
- Institute for Sustainable Plant Protection, Department of Biology, Agricultural and Food Sciences National Research Council, Bari Unit, I-70126 Bari, Italy;
| | - Sven-Erik Behrens
- Institute of Biochemistry and Biotechnology, Section Microbial Biotechnology, Martin Luther University Halle-Wittenberg, D-06120 Halle (Saale), Germany; (C.G.); (T.G.); (S.G.-Z.)
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28
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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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29
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Kowalski K. Synthesis and chemical transformations of glycol nucleic acid (GNA) nucleosides. Bioorg Chem 2023; 141:106921. [PMID: 37871392 DOI: 10.1016/j.bioorg.2023.106921] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2023] [Revised: 10/09/2023] [Accepted: 10/16/2023] [Indexed: 10/25/2023]
Abstract
Xeno nucleic acids (XNA) are an increasingly important class of hypermodified nucleic acids with great potential in bioorganic chemistry and synthetic biology. Glycol nucleic acid (GNA) is constructed from a three-carbon 1,2-propanediol (propylene glycol) backbone attached to a nucleobase entity, representing the simplest known XNA. This review is intended to present GNA nucleosides from a synthetic chemistry perspective-a perspective that serves as a starting point for biological studies. Therefore this account focuses on synthetic methods for GNA nucleoside synthesis, as well as their postsynthetic chemical transformations. The properties and biological activity of GNA constituents are also highlighted. A literature survey shows four major approaches toward GNA nucleoside scaffold synthesis. These approaches pertain to glycidol ring-opening, Mitsunobu, SN2, and dihydroxylation reactions. The general arsenal of reactions used in GNA chemistry is versatile and encompasses the Sonogashira reaction, Michael addition, silyl-Hilbert-Johnson reaction, halogenation, alkylation, cyclization, Rh-catalyzed N-allylation, Sharpless catalytic dihydroxylation, and Yb(OTf)3-catalyzed etherification. Additionally, various phosphorylation reactions have enabled the synthesis of diverse types of GNA nucleotides, dinucleoside phosphates, phosphordiamidites, and oligos. Furthermore, recent advances in GNA chemistry have resulted in the synthesis of previously unknown redox-active (ferrocenyl) and luminescent (pyrenyl and phenanthrenyl) GNA nucleosides, which are also covered in this review.
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Affiliation(s)
- Konrad Kowalski
- University of Lodz, Faculty of Chemistry, Department of Organic Chemistry, Tamka 12, PL-91403 Lodz, Poland.
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30
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Man HSJ, Moosa VA, Singh A, Wu L, Granton JT, Juvet SC, Hoang CD, de Perrot M. Unlocking the potential of RNA-based therapeutics in the lung: current status and future directions. Front Genet 2023; 14:1281538. [PMID: 38075698 PMCID: PMC10703483 DOI: 10.3389/fgene.2023.1281538] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2023] [Accepted: 11/06/2023] [Indexed: 02/12/2024] Open
Abstract
Awareness of RNA-based therapies has increased after the widespread adoption of mRNA vaccines against SARS-CoV-2 during the COVID-19 pandemic. These mRNA vaccines had a significant impact on reducing lung disease and mortality. They highlighted the potential for rapid development of RNA-based therapies and advances in nanoparticle delivery systems. Along with the rapid advancement in RNA biology, including the description of noncoding RNAs as major products of the genome, this success presents an opportunity to highlight the potential of RNA as a therapeutic modality. Here, we review the expanding compendium of RNA-based therapies, their mechanisms of action and examples of application in the lung. The airways provide a convenient conduit for drug delivery to the lungs with decreased systemic exposure. This review will also describe other delivery methods, including local delivery to the pleura and delivery vehicles that can target the lung after systemic administration, each providing access options that are advantageous for a specific application. We present clinical trials of RNA-based therapy in lung disease and potential areas for future directions. This review aims to provide an overview that will bring together researchers and clinicians to advance this burgeoning field.
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Affiliation(s)
- H. S. Jeffrey Man
- Temerty Faculty of Medicine, Institute of Medical Science, Toronto, ON, Canada
- Department of Immunology, University of Toronto, Toronto, ON, Canada
- Latner Thoracic Research Laboratories, Toronto General Hospital Research Institute, Toronto, ON, Canada
- Division of Respirology and Critical Care Medicine, Department of Medicine, University Health Network, Toronto, ON, Canada
| | - Vaneeza A. Moosa
- Latner Thoracic Research Laboratories, Toronto General Hospital Research Institute, Toronto, ON, Canada
- Division of Thoracic Surgery, Toronto General Hospital, Toronto, ON, Canada
| | - Anand Singh
- Thoracic Surgery Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD, United States
| | - Licun Wu
- Latner Thoracic Research Laboratories, Toronto General Hospital Research Institute, Toronto, ON, Canada
- Division of Thoracic Surgery, Toronto General Hospital, Toronto, ON, Canada
| | - John T. Granton
- Division of Respirology and Critical Care Medicine, Department of Medicine, University Health Network, Toronto, ON, Canada
| | - Stephen C. Juvet
- Temerty Faculty of Medicine, Institute of Medical Science, Toronto, ON, Canada
- Department of Immunology, University of Toronto, Toronto, ON, Canada
- Latner Thoracic Research Laboratories, Toronto General Hospital Research Institute, Toronto, ON, Canada
- Division of Respirology and Critical Care Medicine, Department of Medicine, University Health Network, Toronto, ON, Canada
| | - Chuong D. Hoang
- Thoracic Surgery Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD, United States
| | - Marc de Perrot
- Department of Immunology, University of Toronto, Toronto, ON, Canada
- Latner Thoracic Research Laboratories, Toronto General Hospital Research Institute, Toronto, ON, Canada
- Division of Thoracic Surgery, Toronto General Hospital, Toronto, ON, Canada
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31
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Cale JM, Ham KA, Li D, McIntosh CS, Watts GF, Wilton SD, Aung-Htut MT. Induced alternative splicing an opportunity to study PCSK9 protein isoforms at physiologically relevant concentrations. Sci Rep 2023; 13:19725. [PMID: 37957262 PMCID: PMC10643364 DOI: 10.1038/s41598-023-47005-y] [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: 06/05/2023] [Accepted: 11/07/2023] [Indexed: 11/15/2023] Open
Abstract
Splice modulating antisense oligomers (AOs) are increasingly used to modulate RNA processing. While most are investigated for their use as therapeutics, AOs can also be used for basic research. This study examined their use to investigate internally and terminally truncated proprotein convertase subtilisin/kexin type 9 (PCSK9) protein isoforms. Previous studies have used plasmid or viral-vector-mediated protein overexpression to study different PCSK9 protein isoforms, creating an artificial environment within the cell. Here we designed and tested AOs to remove specific exons that encode for PCSK9 protein domains and produced protein isoforms at more physiologically relevant levels. We evaluated the isoforms' expression, secretion, and subsequent impact on the low-density lipoprotein (LDL) receptor and its activity in Huh-7 cells. We found that modifying the Cis-His-rich domain by targeting exons 10 or 11 negatively affected LDL receptor activity and hence did not enhance LDL uptake although the levels of LDL receptor were increased. On the other hand, removing the hinge region encoded by exon 8, or a portion of the prodomain encoded by exon 2, have the potential as therapeutics for hypercholesterolemia. Our findings expand the understanding of PCSK9 isoforms and their impact on the LDL receptor and its activity at physiologically relevant concentrations.
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Affiliation(s)
- Jessica M Cale
- Centre for Molecular Medicine and Innovative Therapeutics, Health Futures Institute, Murdoch University, 90 South Street, Murdoch, WA, 6150, Australia
| | - Kristin A Ham
- Centre for Molecular Medicine and Innovative Therapeutics, Health Futures Institute, Murdoch University, 90 South Street, Murdoch, WA, 6150, Australia
- Perron Institute for Neurological and Translational Science, Perth, WA, 6009, Australia
| | - Dunhui Li
- Centre for Molecular Medicine and Innovative Therapeutics, Health Futures Institute, Murdoch University, 90 South Street, Murdoch, WA, 6150, Australia
- Perron Institute for Neurological and Translational Science, Perth, WA, 6009, Australia
| | - Craig S McIntosh
- Centre for Molecular Medicine and Innovative Therapeutics, Health Futures Institute, Murdoch University, 90 South Street, Murdoch, WA, 6150, Australia
- Perron Institute for Neurological and Translational Science, Perth, WA, 6009, Australia
| | - Gerald F Watts
- School of Medicine, Faculty of Health and Medical Sciences, University of Western Australia, Perth, WA, 6009, Australia
- Cardiometabolic Clinic, Departments of Cardiology and Internal Medicine, Royal Perth Hospital, Perth, WA, 6000, Australia
| | - Steve D Wilton
- Centre for Molecular Medicine and Innovative Therapeutics, Health Futures Institute, Murdoch University, 90 South Street, Murdoch, WA, 6150, Australia
- Perron Institute for Neurological and Translational Science, Perth, WA, 6009, Australia
| | - May T Aung-Htut
- Centre for Molecular Medicine and Innovative Therapeutics, Health Futures Institute, Murdoch University, 90 South Street, Murdoch, WA, 6150, Australia.
- Perron Institute for Neurological and Translational Science, Perth, WA, 6009, Australia.
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32
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Sparmann A, Vogel J. RNA-based medicine: from molecular mechanisms to therapy. EMBO J 2023; 42:e114760. [PMID: 37728251 PMCID: PMC10620767 DOI: 10.15252/embj.2023114760] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2023] [Revised: 08/24/2023] [Accepted: 08/29/2023] [Indexed: 09/21/2023] Open
Abstract
RNA-based therapeutics have the potential to revolutionize the treatment and prevention of human diseases. While early research faced setbacks, it established the basis for breakthroughs in RNA-based drug design that culminated in the extraordinarily fast development of mRNA vaccines to combat the COVID-19 pandemic. We have now reached a pivotal moment where RNA medicines are poised to make a broad impact in the clinic. In this review, we present an overview of different RNA-based strategies to generate novel therapeutics, including antisense and RNAi-based mechanisms, mRNA-based approaches, and CRISPR-Cas-mediated genome editing. Using three rare genetic diseases as examples, we highlight the opportunities, but also the challenges to wide-ranging applications of this class of drugs.
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Affiliation(s)
- Anke Sparmann
- Helmholtz Institute for RNA‐based Infection Research (HIRI), Helmholtz Centre for Infection Research (HZI)WürzburgGermany
| | - Jörg Vogel
- Helmholtz Institute for RNA‐based Infection Research (HIRI), Helmholtz Centre for Infection Research (HZI)WürzburgGermany
- Institute of Molecular Infection Biology (IMIB)University of WürzburgWürzburgGermany
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33
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Martínez-Montero S, Rajwanshi VK, Pandey RK, De Costa NTS, Hong J, Beigelman L, Gryaznov SM, Pourshahian S. New Oligonucleotide 2'-O-Alkyl N3'→P5' (Thio)-Phosphoramidates as Potent Antisense Agents: Physicochemical Properties and Biological Activity. Nucleic Acid Ther 2023; 33:319-328. [PMID: 37638793 DOI: 10.1089/nat.2023.0014] [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] [Indexed: 08/29/2023] Open
Abstract
We describe here the design, synthesis, physicochemical properties, and hepatitis B antiviral activity of new 2'-O-alkyl ribonucleotide N3'→P5' phosphoramidate (2'-O-alkyl-NPO) and (thio)-phosphoramidite (2'-O-alkyl-NPS) oligonucleotide analogs. Oligonucleotides with different 2'-O-alkyl modifications such as 2'-O-methyl, -O-ethyl, -O-allyl, and -O-methoxyethyl combined with 3'-amino sugar-phosphate backbone were synthesized and evaluated. These molecules form stable duplexes with complementary DNA and RNA strands. They show an increase in duplex melting temperatures of up to 2.5°C and 4°C per linkage, respectively, compared to unmodified DNA. The results agree with predominantly C3'-endo sugar pucker conformation. Moreover, 2'-O-alkyl phosphoramidites demonstrate higher hydrolytic stability at pH 5.5 than 2'-deoxy NPOs. In addition, the relative lipophilicity of the 2'-O-alkyl-NPO and NPS oligonucleotides is higher than that of their 3'-O- counterparts. The 2'-O-alkyl-NPS oligonucleotides were evaluated as antisense (ASO) compounds in vitro and in vivo using Hepatitis B virus as a model system. Subcutaneous delivery of GalNAc conjugated 2'-O-MOE-NPS gapmers demonstrated higher activity than the 3'-O-containing 2'-O-MOE counterpart. The properties of 2'-O-alkyl-NPS constructs make them attractive candidates as ASO suitable for further evaluation and development.
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Affiliation(s)
- Saúl Martínez-Montero
- Janssen Pharmaceutical Companies of Johnson and Johnson, South San Francisco, California, USA
| | - Vivek K Rajwanshi
- Janssen Pharmaceutical Companies of Johnson and Johnson, South San Francisco, California, USA
| | - Rajendra K Pandey
- Janssen Pharmaceutical Companies of Johnson and Johnson, South San Francisco, California, USA
| | - N Tilani S De Costa
- Janssen Pharmaceutical Companies of Johnson and Johnson, South San Francisco, California, USA
| | - Jin Hong
- Janssen Pharmaceutical Companies of Johnson and Johnson, South San Francisco, California, USA
| | - Leonid Beigelman
- Janssen Pharmaceutical Companies of Johnson and Johnson, South San Francisco, California, USA
| | - Sergei M Gryaznov
- Janssen Pharmaceutical Companies of Johnson and Johnson, South San Francisco, California, USA
| | - Soheil Pourshahian
- Janssen Pharmaceutical Companies of Johnson and Johnson, South San Francisco, California, USA
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34
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Bangari DS, Lanigan LG, Cramer SD, Grieves JL, Meisner R, Rogers AB, Galbreath EJ, Bolon B. Toxicologic Neuropathology of Novel Biotherapeutics. Toxicol Pathol 2023; 51:414-431. [PMID: 38380881 DOI: 10.1177/01926233241230542] [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] [Indexed: 02/22/2024]
Abstract
Biotherapeutic modalities such as cell therapies, gene therapies, nucleic acids, and proteins are increasingly investigated as disease-modifying treatments for severe and life-threatening neurodegenerative disorders. Such diverse bio-derived test articles are fraught with unique and often unpredictable biological consequences, while guidance regarding nonclinical experimental design, neuropathology evaluation, and interpretation is often limited. This paper summarizes key messages offered during a half-day continuing education course on toxicologic neuropathology of neuro-targeted biotherapeutics. Topics included fundamental neurobiology concepts, pharmacology, frequent toxicological findings, and their interpretation including adversity decisions. Covered biotherapeutic classes included cell therapies, gene editing and gene therapy vectors, nucleic acids, and proteins. If agents are administered directly into the central nervous system, initial screening using hematoxylin and eosin (H&E)-stained sections of currently recommended neural organs (brain [7 levels], spinal cord [3 levels], and sciatic nerve) may need to expand to include other components (e.g., more brain levels, ganglia, and/or additional nerves) and/or special neurohistological procedures to characterize possible neural effects (e.g., cell type-specific markers for reactive glial cells). Scientists who evaluate the safety of novel biologics will find this paper to be a practical reference for preclinical safety testing and risk assessment.
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Affiliation(s)
| | | | | | | | - René Meisner
- Denali Therapeutics, South San Francisco, California, USA
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35
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Podlaski F, Cornwell S, Wong K, McKittrick B, Kim JH, Jung D, Jeon Y, Jung KB, Tolias P, Windsor WT. Peptide Nucleic Acids Containing Cationic/Amino-Alkyl Modified Bases Promote Enhanced Hybridization Kinetics and Thermodynamics with Single-Strand DNA. ACS OMEGA 2023; 8:33426-33436. [PMID: 37744819 PMCID: PMC10515352 DOI: 10.1021/acsomega.3c03184] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/08/2023] [Accepted: 08/18/2023] [Indexed: 09/26/2023]
Abstract
Peptide nucleic acids (PNAs) are antisense molecules with excellent polynucleotide hybridization properties; they are resistant to nuclease degradation but often have poor cell permeability leading to moderate cellular activity and limited clinical results. The addition of cationic substitutions (positive charges) to PNA molecules greatly increases cell permeability. In this report, we describe the synthesis and polynucleotide hybridization properties of a novel cationic/amino-alkyl nucleotide base-modified PNA (OPNA). This study was designed to quantitate the effect the cationic/amino-alkyl nucleotide base modification had on the kinetic and thermodynamic properties of OPNA-DNA hybridization using surface plasmon resonance and UV thermal melt studies. Kinetic studies reveal a favorable 10-30 fold increase in affinity for a single cationic modification on the base of an adenine, cytosine, or guanidine OPNA sequence compared to the nonmodified PNA strand. The increase in affinity is correlated directly with a favorable decrease in the dissociation rate constant and increase in the association rate constant. Introducing additional amino-alkyl base modifications further favors a decrease in the dissociation rate (3-10-fold per amino-alkyl). The thermodynamics driving the OPNA hybridization is promoted by an additional favorable -80 kJ/mol enthalpy of binding for a single amino-alkyl modification compared to the PNA strand. This increase in enthalpy is consistent with an ion-ion interaction with the DNA strand. These kinetic and thermodynamic hybridization studies reveal for the first time that this type of cationic/amino-alkyl base-modified PNA has favorable hybridization properties suitable for development as an antisense oligomer.
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Affiliation(s)
- Frank Podlaski
- Department
of Chemistry and Chemical Biology, Stevens
Institute of Technology, 1 Castle Point Terrace, Hoboken, New Jersey 07030, United States
| | - Stephen Cornwell
- Department
of Chemistry and Chemical Biology, Stevens
Institute of Technology, 1 Castle Point Terrace, Hoboken, New Jersey 07030, United States
| | - Kenny Wong
- Department
of Chemistry and Chemical Biology, Stevens
Institute of Technology, 1 Castle Point Terrace, Hoboken, New Jersey 07030, United States
| | - Brian McKittrick
- Department
of Global Sciences & Strategy, OliPass
Corporation, Yongin, Gyeonggi 17015, Republic of Korea
| | - Jae-Hun Kim
- Department
of Monomer Research, OliPass Corporation, Suwon, Gyeonggi 16229, Republic
of Korea
| | - Daram Jung
- Department
of Oligo Sciences, OliPass Corporation, Yongin, Gyeonggi 17015, Republic
of Korea
| | - Yeasel Jeon
- Department
of Oligo Sciences, OliPass Corporation, Yongin, Gyeonggi 17015, Republic
of Korea
| | - Kwang-Bok Jung
- Department
of Monomer Manufacture, OliPass Corporation, Suwon, Gyeonggi 16229, Republic
of Korea
| | - Peter Tolias
- Department
of Biology, School of Natural and Behavioral Sciences, Brooklyn College, CUNY, Brooklyn, New York 11210, United States
| | - William T. Windsor
- Department
of Chemistry and Chemical Biology, Stevens
Institute of Technology, 1 Castle Point Terrace, Hoboken, New Jersey 07030, United States
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36
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Pollak AJ, Zhao L, Crooke ST. Characterization of cooperative PS-oligo activation of human TLR9. MOLECULAR THERAPY. NUCLEIC ACIDS 2023; 33:832-844. [PMID: 37675184 PMCID: PMC10477407 DOI: 10.1016/j.omtn.2023.08.011] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/23/2023] [Accepted: 08/11/2023] [Indexed: 09/08/2023]
Abstract
Single-stranded phosphorothioate oligonucleotides (PS-oligos) can activate TLR9, leading to an innate immune response. This can occur with PS-oligos containing unmethylated CpG sites, the canonical motif, or PS-oligos that do not contain those motifs (non-CpG). Structural evidence shows that TLR9 contains two PS-oligo binding sites, and recent data suggest that synergistic cooperative activation of TLR9 can be achieved by adding two separate PS-oligos to cells, each engaging with a separate site on TLR9 to enhance TLR9 activation as a pair. Here, we demonstrate and characterize this cooperativity phenomenon using PS-oligos in human cell lines, and we introduce several novel PS-oligo pairs (CpG and non-CpG pairs) that show cooperative activation. Indeed, we find that cooperative PS-oligos likely bind at different sites on TLR9. Interestingly, we find that PS-oligos that generate little TLR9 activation on their own can prime TLR9 to be activated by other PS-oligos. Finally, we determine that previous models of TLR9 activation cannot be used to fully explain data from systems using human TLR9 and PS-oligos. Overall, we reveal new details of TLR9 activation, but we also find that more work needs to be done to determine where certain PS-oligos are binding to TLR9.
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Affiliation(s)
| | - Luyi Zhao
- Ionis Pharmaceuticals, Inc., Carlsbad, CA 92010, USA
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37
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Mangla P, Vicentini Q, Biscans A. Therapeutic Oligonucleotides: An Outlook on Chemical Strategies to Improve Endosomal Trafficking. Cells 2023; 12:2253. [PMID: 37759475 PMCID: PMC10527716 DOI: 10.3390/cells12182253] [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: 06/21/2023] [Revised: 08/30/2023] [Accepted: 09/07/2023] [Indexed: 09/29/2023] Open
Abstract
The potential of oligonucleotide therapeutics is undeniable as more than 15 drugs have been approved to treat various diseases in the liver, central nervous system (CNS), and muscles. However, achieving effective delivery of oligonucleotide therapeutics to specific tissues still remains a major challenge, limiting their widespread use. Chemical modifications play a crucial role to overcome biological barriers to enable efficient oligonucleotide delivery to the tissues/cells of interest. They provide oligonucleotide metabolic stability and confer favourable pharmacokinetic/pharmacodynamic properties. This review focuses on the various chemical approaches implicated in mitigating the delivery problem of oligonucleotides and their limitations. It highlights the importance of linkers in designing oligonucleotide conjugates and discusses their potential role in escaping the endosomal barrier, a bottleneck in the development of oligonucleotide therapeutics.
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Affiliation(s)
- Priyanka Mangla
- Oligonucleotide Discovery, Discovery Sciences Research and Development, AstraZeneca, 431 38 Gothenburg, Sweden; (P.M.); (Q.V.)
| | - Quentin Vicentini
- Oligonucleotide Discovery, Discovery Sciences Research and Development, AstraZeneca, 431 38 Gothenburg, Sweden; (P.M.); (Q.V.)
- Department of Laboratory Medicine, Clinical Research Centre, Karolinska Institute, 141 57 Stockholm, Sweden
| | - Annabelle Biscans
- Oligonucleotide Discovery, Discovery Sciences Research and Development, AstraZeneca, 431 38 Gothenburg, Sweden; (P.M.); (Q.V.)
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38
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Recinos Y, Ustianenko D, Yeh YT, Wang X, Jacko M, Yesantharao LV, Wu Q, Zhang C. Deep screening of proximal and distal splicing-regulatory elements in a native sequence context. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.21.554109. [PMID: 37662340 PMCID: PMC10473672 DOI: 10.1101/2023.08.21.554109] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/05/2023]
Abstract
Pre-mRNA splicing, a key process in gene expression, can be therapeutically modulated using various drug modalities, including antisense oligonucleotides (ASOs). However, determining promising targets is impeded by the challenge of systematically mapping splicing-regulatory elements (SREs) in their native sequence context. Here, we use the catalytically dead CRISPR-RfxCas13d RNA-targeting system (dCas13d/gRNA) as a programmable platform to bind SREs and modulate splicing by competing against endogenous splicing factors. SpliceRUSH, a high-throughput screening method, was developed to map SREs in any gene of interest using a lentivirus gRNA library that tiles the genetic region, including distal intronic sequences. When applied to SMN2, a therapeutic target for spinal muscular atrophy, SpliceRUSH robustly identified not only known SREs, but also a novel distal intronic splicing enhancer, which can be targeted to alter exon 7 splicing using either dCas13d/gRNA or ASOs. This technology enables a deeper understanding of splicing regulation with applications for RNA-based drug discovery.
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Affiliation(s)
- Yocelyn Recinos
- Department of Systems Biology, Department of Biochemistry and Molecular Biophysics, Center for Motor Neuron Biology and Disease, Columbia University, New York, NY 10032, USA
| | - Dmytro Ustianenko
- Department of Systems Biology, Department of Biochemistry and Molecular Biophysics, Center for Motor Neuron Biology and Disease, Columbia University, New York, NY 10032, USA
- Present address: Flagship Pioneering, Cambridge, MA 02142, USA
| | - Yow-Tyng Yeh
- Department of Systems Biology, Department of Biochemistry and Molecular Biophysics, Center for Motor Neuron Biology and Disease, Columbia University, New York, NY 10032, USA
| | - Xiaojian Wang
- Department of Systems Biology, Department of Biochemistry and Molecular Biophysics, Center for Motor Neuron Biology and Disease, Columbia University, New York, NY 10032, USA
| | - Martin Jacko
- Department of Systems Biology, Department of Biochemistry and Molecular Biophysics, Center for Motor Neuron Biology and Disease, Columbia University, New York, NY 10032, USA
- Present address: Aperture Therapeutics, Inc., San Carlos, CA 94070, USA
| | - Lekha V. Yesantharao
- Department of Systems Biology, Department of Biochemistry and Molecular Biophysics, Center for Motor Neuron Biology and Disease, Columbia University, New York, NY 10032, USA
- Present address: Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Qiyang Wu
- Department of Systems Biology, Department of Biochemistry and Molecular Biophysics, Center for Motor Neuron Biology and Disease, Columbia University, New York, NY 10032, USA
| | - Chaolin Zhang
- Department of Systems Biology, Department of Biochemistry and Molecular Biophysics, Center for Motor Neuron Biology and Disease, Columbia University, New York, NY 10032, USA
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39
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Takahashi Y, Kakuta K, Namioka Y, Igarashi A, Sakamoto T, Iwata Hara R, Sato K, Wada T. Synthesis of P-Modified DNA from Boranophosphate DNA as a Precursor via Acyl Phosphite Intermediates. J Org Chem 2023; 88:10617-10631. [PMID: 37462534 PMCID: PMC10407935 DOI: 10.1021/acs.joc.3c00659] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2023] [Indexed: 08/05/2023]
Abstract
In this study, we successfully synthesized several kinds of P-modified nucleic acids from boranophosphate DNAs via an acyl phosphite intermediate in solution and on a solid support. In the solution-phase synthesis, phosphorothioate diester, phosphotriester, and phosphoramidate diester were synthesized in a one-pot reaction from boranophosphodiester via the conversion of an acyl phosphite as a key intermediate. In addition, doubly P-modified nucleic acid derivatives which were difficult to synthesize by the phosphoramidite and H-phosphonate methods were also obtained by the conversion reaction. In the solid-phase synthesis, a boranophosphate derivative was synthesized on a solid support using the H-boranophosphonate method. Then, an acyl phosphite intermediate was formed by treatment with pivaloyl chloride in pyridine, followed by appropriate transformations to obtain the P-modified derivatives such as phosphotriester and phosphorothioate diester. Notably, it was suggested that the conversion reaction of a boranophosphate to a phosphorothioate diester proceeded with retention of the stereochemistry of the phosphorous center. In addition, a phosphorothioate/phosphate chimeric dodecamer was successfully synthesized from a boranophosphate/phosphate chimeric dodecamer using the same strategy. Therefore, boranophosphate derivatives are versatile precursors for the synthesis of P-modified DNA, including chimeric derivatives.
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Affiliation(s)
- Yuhei Takahashi
- Department
of Medicinal and Life Sciences, Faculty of Pharmaceutical Sciences, Tokyo University of Science, 2641 Yamazaki, Noda, Chiba 278-8510, Japan
| | - Kiyoshi Kakuta
- Department
of Medicinal and Life Sciences, Faculty of Pharmaceutical Sciences, Tokyo University of Science, 2641 Yamazaki, Noda, Chiba 278-8510, Japan
| | - Yukichi Namioka
- Department
of Medicinal and Life Sciences, Faculty of Pharmaceutical Sciences, Tokyo University of Science, 2641 Yamazaki, Noda, Chiba 278-8510, Japan
| | - Ayumi Igarashi
- Department
of Medical Genome Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Chiba 277-8562, Japan
| | - Taiichi Sakamoto
- Department
of Life Science, Chiba Institute of Technology, Graduate School of Advanced Engineering, Chiba 275-0016, Japan
| | - Rintaro Iwata Hara
- Department
of Medicinal and Life Sciences, Faculty of Pharmaceutical Sciences, Tokyo University of Science, 2641 Yamazaki, Noda, Chiba 278-8510, Japan
- Department
of Neurology and Neurological Science, Graduate School of Medicinal
and Dental Sciences, Tokyo Medical and Dental
University, Tokyo 113-8519, Japan
| | - Kazuki Sato
- Department
of Medicinal and Life Sciences, Faculty of Pharmaceutical Sciences, Tokyo University of Science, 2641 Yamazaki, Noda, Chiba 278-8510, Japan
| | - Takeshi Wada
- Department
of Medicinal and Life Sciences, Faculty of Pharmaceutical Sciences, Tokyo University of Science, 2641 Yamazaki, Noda, Chiba 278-8510, Japan
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40
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Kaviani S, Fakih HH, Asohan J, Katolik A, Damha MJ, Sleiman HF. Sequence-Controlled Spherical Nucleic Acids: Gene Silencing, Encapsulation, and Cellular Uptake. Nucleic Acid Ther 2023; 33:265-276. [PMID: 37196168 DOI: 10.1089/nat.2022.0062] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/19/2023] Open
Abstract
Antisense oligonucleotides (ASOs) can predictably alter RNA processing and control protein expression; however, challenges in the delivery of these therapeutics to specific tissues, poor cellular uptake, and endosomal escape have impeded progress in translating these agents into the clinic. Spherical nucleic acids (SNAs) are nanoparticles with a DNA external shell and a hydrophobic core that arise from the self-assembly of ASO strands conjugated to hydrophobic polymers. SNAs have recently shown significant promise as vehicles for improving the efficacy of ASO cellular uptake and gene silencing. However, to date, no studies have investigated the effect of the hydrophobic polymer sequence on the biological properties of SNAs. In this study, we created a library of ASO conjugates by covalently attaching polymers with linear or branched [dodecanediol phosphate] units and systematically varying polymer sequence and composition. We show that these parameters can significantly impact encapsulation efficiency, gene silencing activity, SNA stability, and cellular uptake, thus outlining optimized polymer architectures for gene silencing.
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Affiliation(s)
- Sepideh Kaviani
- Department of Chemistry, McGill University, Montreal, Canada
| | - Hassan H Fakih
- Department of Chemistry, McGill University, Montreal, Canada
| | - Jathavan Asohan
- Department of Chemistry, McGill University, Montreal, Canada
| | - Adam Katolik
- Department of Chemistry, McGill University, Montreal, Canada
| | - Masad J Damha
- Department of Chemistry, McGill University, Montreal, Canada
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41
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Malecova B, Burke RS, Cochran M, Hood MD, Johns R, Kovach PR, Doppalapudi VR, Erdogan G, Arias JD, Darimont B, Miller CD, Huang H, Geall A, Younis H, Levin AA. Targeted tissue delivery of RNA therapeutics using antibody-oligonucleotide conjugates (AOCs). Nucleic Acids Res 2023; 51:5901-5910. [PMID: 37224533 PMCID: PMC10325888 DOI: 10.1093/nar/gkad415] [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: 09/19/2022] [Revised: 04/05/2023] [Accepted: 05/11/2023] [Indexed: 05/26/2023] Open
Abstract
Although targeting TfR1 to deliver oligonucleotides to skeletal muscle has been demonstrated in rodents, effectiveness and pharmacokinetic/pharmacodynamic (PKPD) properties remained unknown in higher species. We developed antibody-oligonucleotide conjugates (AOCs) towards mice or monkeys utilizing anti-TfR1 monoclonal antibodies (αTfR1) conjugated to various classes of oligonucleotides (siRNA, ASOs and PMOs). αTfR1 AOCs delivered oligonucleotides to muscle tissue in both species. In mice, αTfR1 AOCs achieved a > 15-fold higher concentration to muscle tissue than unconjugated siRNA. A single dose of an αTfR1 conjugated to an siRNA against Ssb mRNA produced > 75% Ssb mRNA reduction in mice and monkeys, and mRNA silencing was greatest in skeletal and cardiac (striated) muscle with minimal to no activity in other major organs. In mice the EC50 for Ssb mRNA reduction in skeletal muscle was >75-fold less than in systemic tissues. Oligonucleotides conjugated to control antibodies or cholesterol produced no mRNA reduction or were 10-fold less potent, respectively. Tissue PKPD of AOCs demonstrated mRNA silencing activity primarily driven by receptor-mediated delivery in striated muscle for siRNA oligonucleotides. In mice, we show that AOC-mediated delivery is operable across various oligonucleotide modalities. AOC PKPD properties translated to higher species, providing promise for a new class of oligonucleotide therapeutics.
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Affiliation(s)
- Barbora Malecova
- Avidity Biosciences, Inc., 10578 Science Center Drive Suite 125, San Diego, CA 92121, USA
| | - Rob S Burke
- Seawolf Therapeutics, One Sansome Street Suite 3630, San Francisco, CA 94104, USA
| | - Michael Cochran
- Avidity Biosciences, Inc., 10578 Science Center Drive Suite 125, San Diego, CA 92121, USA
| | - Michael D Hood
- Avidity Biosciences, Inc., 10578 Science Center Drive Suite 125, San Diego, CA 92121, USA
| | - Rachel Johns
- Avidity Biosciences, Inc., 10578 Science Center Drive Suite 125, San Diego, CA 92121, USA
| | - Philip R Kovach
- Avidity Biosciences, Inc., 10578 Science Center Drive Suite 125, San Diego, CA 92121, USA
| | - Venkata R Doppalapudi
- Avidity Biosciences, Inc., 10578 Science Center Drive Suite 125, San Diego, CA 92121, USA
| | - Gulin Erdogan
- Avidity Biosciences, Inc., 10578 Science Center Drive Suite 125, San Diego, CA 92121, USA
| | - J Danny Arias
- Avidity Biosciences, Inc., 10578 Science Center Drive Suite 125, San Diego, CA 92121, USA
| | | | - Christopher D Miller
- California Northstate University College of Medicine, 9700 W Taron Dr, Elk Grove, CA 95757, USA
| | - Hanhua Huang
- Avidity Biosciences, Inc., 10578 Science Center Drive Suite 125, San Diego, CA 92121, USA
| | - Andrew Geall
- Replicate Biosciences, 10210 Campus Point Dr, Suite 150, San Diego, CA 92121, USA
| | - Husam S Younis
- Avidity Biosciences, Inc., 10578 Science Center Drive Suite 125, San Diego, CA 92121, USA
| | - Arthur A Levin
- Avidity Biosciences, Inc., 10578 Science Center Drive Suite 125, San Diego, CA 92121, USA
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42
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Yadav K, Sahu KK, Sucheta, Gnanakani SPE, Sure P, Vijayalakshmi R, Sundar VD, Sharma V, Antil R, Jha M, Minz S, Bagchi A, Pradhan M. Biomedical applications of nanomaterials in the advancement of nucleic acid therapy: Mechanistic challenges, delivery strategies, and therapeutic applications. Int J Biol Macromol 2023; 241:124582. [PMID: 37116843 DOI: 10.1016/j.ijbiomac.2023.124582] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2023] [Revised: 04/19/2023] [Accepted: 04/20/2023] [Indexed: 04/30/2023]
Abstract
In the past few decades, substantial advancement has been made in nucleic acid (NA)-based therapies. Promising treatments include mRNA, siRNA, miRNA, and anti-sense DNA for treating various clinical disorders by modifying the expression of DNA or RNA. However, their effectiveness is limited due to their concentrated negative charge, instability, large size, and host barriers, which make widespread application difficult. The effective delivery of these medicines requires safe vectors that are efficient & selective while having non-pathogenic qualities; thus, nanomaterials have become an attractive option with promising possibilities despite some potential setbacks. Nanomaterials possess ideal characteristics, allowing them to be tuned into functional bio-entity capable of targeted delivery. In this review, current breakthroughs in the non-viral strategy of delivering NAs are discussed with the goal of overcoming challenges that would otherwise be experienced by therapeutics. It offers insight into a wide variety of existing NA-based therapeutic modalities and techniques. In addition to this, it provides a rationale for the use of non-viral vectors and a variety of nanomaterials to accomplish efficient gene therapy. Further, it discusses the potential for biomedical application of nanomaterials-based gene therapy in various conditions, such as cancer therapy, tissue engineering, neurological disorders, and infections.
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Affiliation(s)
- Krishna Yadav
- Raipur Institute of Pharmaceutical Education and Research, Sarona, Raipur, Chhattisgarh 492010, India
| | - Kantrol Kumar Sahu
- Institute of Pharmaceutical Research, GLA University, Mathura, Uttar Pradesh 281406, India
| | - Sucheta
- School of Medical and Allied Sciences, K. R. Mangalam University, Gurugram, Haryana 122103, India
| | | | - Pavani Sure
- Department of Pharmaceutics, Vignan Institute of Pharmaceutical Sciences, Hyderabad, Telangana, India
| | - R Vijayalakshmi
- Department of Pharmaceutical Analysis, GIET School of Pharmacy, Chaitanya Knowledge City, Rajahmundry, AP 533296, India
| | - V D Sundar
- Department of Pharmaceutical Technology, GIET School of Pharmacy, Chaitanya Knowledge City, Rajahmundry, AP 533296, India
| | - Versha Sharma
- Department of Biotechnology, School of Biological Sciences, Dr. Harisingh Gour Central University, Sagar, M.P. 470003, India
| | - Ruchita Antil
- Addenbrookes Hospital, Cambridge University Hospitals NHS Foundation Trust, England, United Kingdom of Great Britain and Northern Ireland
| | - Megha Jha
- Department of Biotechnology, School of Biological Sciences, Dr. Harisingh Gour Central University, Sagar, M.P. 470003, India
| | - Sunita Minz
- Department of Pharmacy, Indira Gandhi National Tribal University, Amarkantak, M.P., 484887, India
| | - Anindya Bagchi
- Tumor Initiation & Maintenance Program, Sanford Burnham Prebys Medical Discovery Institute, 10901 North Torrey Pines Road La Jolla, CA 92037, USA
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43
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Larouche M, Brisson D, Morissette MC, Gaudet D. Post-prandial analysis of fluctuations in the platelet count and platelet function in patients with the familial chylomicronemia syndrome. Orphanet J Rare Dis 2023; 18:167. [PMID: 37370069 DOI: 10.1186/s13023-023-02743-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2023] [Accepted: 05/18/2023] [Indexed: 06/29/2023] Open
Abstract
BACKGROUND The familial chylomicronemia syndrome (FCS) is an ultra rare disease caused by lipoprotein lipase (LPL) deficiency associated with potentially lethal acute pancreatitis risk. Thrombocytopenia (platelet count < 150,000 × 109/L) has been reported in patients with FCS, treated or not with volanesorsen, a second generation APOC3 anti-sense oligonucleotide. Chylomicrons are the lipoproteins delivering fat after a meal and FCS thus has a post-prandial origin. Platelet count and function have not been studied post-prandially in FCS. OBJECTIVE To evaluate post-prandial fluctuations in the platelet count (PLC) and functional defects of hemostasis in FCS. METHODS PLC, functional defects in hemostasis and hematologic variables were measured up-to 5 h after a meal in 6 homozygotes for FCS causing gene variants (HoLPL), 6 heterozygotes for LPL loss-of-function variants (HeLPL) and 7 normolipidemic controls. RESULTS Hourly post-prandial PLC was significantly lower in HoLPL than in controls (P < 0.009). Compared to the other groups, the PLC tended to decrease rapidly (in the first hour) post-meal in HoLPL (P = 0.03) and remained lower than baseline 5-h post-meal (P = 0.02) whereas it tended to slightly increase in normolipidemic controls (P = 0.02). Platelet function was not affected by the prandial status. In HoLPL, post-prandial fluctuations in the PLC positively correlated with the lymphocyte count (P = 0.005) and negatively with neutrophil/lymphocyte ratio (NLR). CONCLUSION The PLC decreases post-prandially in FCS (HoLPL), is not associated with changes in functional defects of hemostasis and correlates with the NLR, a marker of acute pancreatitis severity.
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Affiliation(s)
- Miriam Larouche
- Department of Medicine, Université de Montréal, ECOGENE-21, 930 Jacques Cartier Est, Chicoutimi, G7H 7K9, Canada
| | - Diane Brisson
- Department of Medicine, Université de Montréal, ECOGENE-21, 930 Jacques Cartier Est, Chicoutimi, G7H 7K9, Canada
| | - Marie-Claude Morissette
- Department of Medicine, Université de Montréal, ECOGENE-21, 930 Jacques Cartier Est, Chicoutimi, G7H 7K9, Canada
| | - Daniel Gaudet
- Department of Medicine, Université de Montréal, ECOGENE-21, 930 Jacques Cartier Est, Chicoutimi, G7H 7K9, Canada.
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Zhu A, Chiba S, Shimizu Y, Kunitake K, Okuno Y, Aoki Y, Yokota T. Ensemble-Learning and Feature Selection Techniques for Enhanced Antisense Oligonucleotide Efficacy Prediction in Exon Skipping. Pharmaceutics 2023; 15:1808. [PMID: 37513994 PMCID: PMC10384346 DOI: 10.3390/pharmaceutics15071808] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2023] [Revised: 06/13/2023] [Accepted: 06/15/2023] [Indexed: 07/30/2023] Open
Abstract
Antisense oligonucleotide (ASO)-mediated exon skipping has become a valuable tool for investigating gene function and developing gene therapy. Machine-learning-based computational methods, such as eSkip-Finder, have been developed to predict the efficacy of ASOs via exon skipping. However, these methods are computationally demanding, and the accuracy of predictions remains suboptimal. In this study, we propose a new approach to reduce the computational burden and improve the prediction performance by using feature selection within machine-learning algorithms and ensemble-learning techniques. We evaluated our approach using a dataset of experimentally validated exon-skipping events, dividing it into training and testing sets. Our results demonstrate that using a three-way-voting approach with random forest, gradient boosting, and XGBoost can significantly reduce the computation time to under ten seconds while improving prediction performance, as measured by R2 for both 2'-O-methyl nucleotides (2OMe) and phosphorodiamidate morpholino oligomers (PMOs). Additionally, the feature importance ranking derived from our approach is in good agreement with previously published results. Our findings suggest that our approach has the potential to enhance the accuracy and efficiency of predicting ASO efficacy via exon skipping. It could also facilitate the development of novel therapeutic strategies. This study could contribute to the ongoing efforts to improve ASO design and optimize gene therapy approaches.
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Affiliation(s)
- Alex Zhu
- Phillips Academy, Andover, MA 01810, USA
- Department of Medical Generics, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, AB T6G 2H7, Canada
| | - Shuntaro Chiba
- HPC- and AI-Driven Drug Development Platform Division, RIKEN Center for Computational Science, Yokohama 230-0045, Japan
| | - Yuki Shimizu
- Department of Biomedical Data Intelligence, Graduate School of Medicine, Kyoto University, Kyoto 606-8507, Japan
| | - Katsuhiko Kunitake
- Department of Molecular Therapy, National Institute of Neuroscience, National Center of Neurology and Psychiatry (NCNP), Kodaira, Tokyo 187-8551, Japan
| | - Yasushi Okuno
- HPC- and AI-Driven Drug Development Platform Division, RIKEN Center for Computational Science, Yokohama 230-0045, Japan
- Department of Biomedical Data Intelligence, Graduate School of Medicine, Kyoto University, Kyoto 606-8507, Japan
| | - Yoshitsugu Aoki
- Department of Molecular Therapy, National Institute of Neuroscience, National Center of Neurology and Psychiatry (NCNP), Kodaira, Tokyo 187-8551, Japan
| | - Toshifumi Yokota
- Department of Medical Generics, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, AB T6G 2H7, Canada
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45
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Matsuyama K, Kurihara C, Crawley FP, Kerpel-Fronius S. Utilization of genetic information for medicines development and equitable benefit sharing. Front Genet 2023; 14:1085864. [PMID: 37388927 PMCID: PMC10300349 DOI: 10.3389/fgene.2023.1085864] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Accepted: 05/03/2023] [Indexed: 07/01/2023] Open
Abstract
Advances in genomic research have significantly enhanced modern drug development. However, equitable benefit sharing of the results of scientific advancement has not always been achieved. This paper shows how molecular biology has modified medicines development while also leaving open significant challenges for benefit sharing. Presented here is a conceptual modeling describing the processes in genetic-related medicines development and how these are related to specific ethical considerations. The focus is on three important areas: 1) population genetics and the need for discrimination prevention; 2) pharmacogenomics and the need for inclusive governance; and 3) global health to be achieved in open science frameworks. Benefit sharing is taken as the ethical value that underlies all these aspects. The implementation of benefit sharing requires a value shift in which the outcomes of health science are not viewed simply as trade commodities but also as a "global public good". This approach should lead to genetic science to contribute to promoting the fundamental human right to health to all members of the global community.
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46
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Pan Y, Guan J, Gao Y, Zhu Y, Li H, Guo H, He Q, Guan Z, Yang Z. Modified ASO conjugates encapsulated with cytidinyl/cationic lipids exhibit more potent and longer-lasting anti-HCC effects. MOLECULAR THERAPY. NUCLEIC ACIDS 2023; 32:807-821. [PMID: 37251692 PMCID: PMC10220282 DOI: 10.1016/j.omtn.2023.04.028] [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: 12/12/2022] [Accepted: 04/28/2023] [Indexed: 05/31/2023]
Abstract
Antisense oligonucleotides (ASOs) are a class of therapeutics targeting mRNAs or genes that have attracted much attention. However, effective delivery and optimal accumulation in target tissues in vivo are still challenging issues. CT102 is an ASO that targets IGF1R mRNA and induces cell apoptosis. Herein, a detailed exploration of the tissue distribution of ASOs delivered by liposomes was carried out. A formulation that resulted in increased hepatic accumulation was identified based on multiple intermolecular interactions between DCP (cytidinyl/cationic lipid DNCA/CLD and DSPE-PEG) and oligonucleotides, including hydrogen bonding, π-π stacking, and electrostatic interactions. The structurally optimized CT102s present a novel strategy for the treatment of hepatocellular carcinoma. The gapmer CT102MOE5 and conjugate Glu-CT102MOE5 showed superior antiproliferation and IGF1R mRNA suppression effects at 100 nM in vitro and achieved greater efficacy at a lower dose and administration frequency in vivo. Combined transcriptome and proteome analyses revealed that additional associated targets and functional regulations might simultaneously exist in ASO therapy. These results showed that a combination of lipid encapsulation and structural optimization in the delivery of oligonucleotide drugs has favorable prospects for clinical application.
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Affiliation(s)
- Yufei Pan
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing 100191, China
| | - Jing Guan
- Key Laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), College of Life Sciences/Institute of Agro-bioengineering, Guizhou University, Guiyang 550025, China
| | - Yujing Gao
- School of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, China
| | - Yuejie Zhu
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing 100191, China
| | - Huantong Li
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing 100191, China
| | - Hua Guo
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing 100191, China
| | - Qianyi He
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing 100191, China
| | - Zhu Guan
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing 100191, China
| | - Zhenjun Yang
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing 100191, China
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47
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Ryan C, Rahman MM, Kumar V, Rozners E. Triplex-Forming Peptide Nucleic Acid Controls Dynamic Conformations of RNA Bulges. J Am Chem Soc 2023; 145:10497-10504. [PMID: 37155726 PMCID: PMC10198159 DOI: 10.1021/jacs.2c12488] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Indexed: 05/10/2023]
Abstract
RNA folding is driven by the formation of double-helical segments interspaced by loops of unpaired nucleotides. Among the latter, bulges formed by one or several unpaired nucleotides are one of the most common structural motifs that play an important role in stabilizing RNA-RNA, RNA-protein, and RNA-small molecule interactions. Single-nucleotide bulges can fold in alternative structures where the unpaired nucleobase is either looped-out (flexible) in a solvent or stacked-in (intercalated) between the base pairs. In the present study, we discovered that triplex-forming peptide nucleic acids (PNAs) had unusually high affinity for single-purine-nucleotide bulges in double-helical RNA. Depending on the PNA's sequence, the triplex formation shifted the equilibrium between looped-out and stacked-in conformations. The ability to control the dynamic equilibria of RNA's structure will be an important tool for studying structure-function relationships in RNA biology and may have potential in novel therapeutic approaches targeting disease-related RNAs.
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Affiliation(s)
- Christopher
A. Ryan
- Department of Chemistry, The State
University of New York, Binghamton University, Binghamton, New York 13902, United States
| | - Md Motiar Rahman
- Department of Chemistry, The State
University of New York, Binghamton University, Binghamton, New York 13902, United States
| | - Vipin Kumar
- Department of Chemistry, The State
University of New York, Binghamton University, Binghamton, New York 13902, United States
| | - Eriks Rozners
- Department of Chemistry, The State
University of New York, Binghamton University, Binghamton, New York 13902, United States
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48
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Dawicki-McKenna JM, Felix AJ, Waxman EA, Cheng C, Amado DA, Ranum PT, Bogush A, Dungan LV, Maguire JA, Gagne AL, Heller EA, French DL, Davidson BL, Prosser BL. Mapping PTBP2 binding in human brain identifies SYNGAP1 as a target for therapeutic splice switching. Nat Commun 2023; 14:2628. [PMID: 37149717 PMCID: PMC10164156 DOI: 10.1038/s41467-023-38273-3] [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: 07/12/2022] [Accepted: 04/22/2023] [Indexed: 05/08/2023] Open
Abstract
Alternative splicing of neuronal genes is controlled partly by the coordinated action of polypyrimidine tract binding proteins (PTBPs). While PTBP1 is ubiquitously expressed, PTBP2 is predominantly neuronal. Here, we define the PTBP2 footprint in the human transcriptome using brain tissue and human induced pluripotent stem cell-derived neurons (iPSC-neurons). We map PTBP2 binding sites, characterize PTBP2-dependent alternative splicing events, and identify novel PTBP2 targets including SYNGAP1, a synaptic gene whose loss-of-function leads to a complex neurodevelopmental disorder. We find that PTBP2 binding to SYNGAP1 mRNA promotes alternative splicing and nonsense-mediated decay, and that antisense oligonucleotides (ASOs) that disrupt PTBP binding redirect splicing and increase SYNGAP1 mRNA and protein expression. In SYNGAP1 haploinsufficient iPSC-neurons generated from two patients, we show that PTBP2-targeting ASOs partially restore SYNGAP1 expression. Our data comprehensively map PTBP2-dependent alternative splicing in human neurons and cerebral cortex, guiding development of novel therapeutic tools to benefit neurodevelopmental disorders.
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Affiliation(s)
- Jennine M Dawicki-McKenna
- Department of Physiology, Pennsylvania Muscle Institute, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, 19104, USA
- Center for Epilepsy and Neurodevelopmental Disorders (ENDD), University of Pennsylvania Perelman School of Medicine and Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA
| | - Alex J Felix
- Department of Physiology, Pennsylvania Muscle Institute, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, 19104, USA
- Center for Epilepsy and Neurodevelopmental Disorders (ENDD), University of Pennsylvania Perelman School of Medicine and Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA
| | - Elisa A Waxman
- Center for Epilepsy and Neurodevelopmental Disorders (ENDD), University of Pennsylvania Perelman School of Medicine and Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA
- Center for Cellular and Molecular Therapeutics, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA
| | - Congsheng Cheng
- Center for Cellular and Molecular Therapeutics, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA
| | - Defne A Amado
- Center for Cellular and Molecular Therapeutics, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA
- Department of Neurology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, 19104, USA
| | - Paul T Ranum
- Center for Cellular and Molecular Therapeutics, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA
| | - Alexey Bogush
- Department of Physiology, Pennsylvania Muscle Institute, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, 19104, USA
- Center for Epilepsy and Neurodevelopmental Disorders (ENDD), University of Pennsylvania Perelman School of Medicine and Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA
| | - Lea V Dungan
- Center for Epilepsy and Neurodevelopmental Disorders (ENDD), University of Pennsylvania Perelman School of Medicine and Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA
- Center for Cellular and Molecular Therapeutics, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA
| | - Jean Ann Maguire
- Center for Cellular and Molecular Therapeutics, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA
| | - Alyssa L Gagne
- Center for Cellular and Molecular Therapeutics, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA
| | - Elizabeth A Heller
- Center for Epilepsy and Neurodevelopmental Disorders (ENDD), University of Pennsylvania Perelman School of Medicine and Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA
- Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, 19104, USA
| | - Deborah L French
- Center for Epilepsy and Neurodevelopmental Disorders (ENDD), University of Pennsylvania Perelman School of Medicine and Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA
- Center for Cellular and Molecular Therapeutics, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA
- Department of Pathology and Laboratory Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, 19104, USA
| | - Beverly L Davidson
- Center for Epilepsy and Neurodevelopmental Disorders (ENDD), University of Pennsylvania Perelman School of Medicine and Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA.
- Center for Cellular and Molecular Therapeutics, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA.
- Department of Pathology and Laboratory Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, 19104, USA.
| | - Benjamin L Prosser
- Department of Physiology, Pennsylvania Muscle Institute, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, 19104, USA.
- Center for Epilepsy and Neurodevelopmental Disorders (ENDD), University of Pennsylvania Perelman School of Medicine and Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA.
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Oshchepkova A, Zenkova M, Vlassov V. Extracellular Vesicles for Therapeutic Nucleic Acid Delivery: Loading Strategies and Challenges. Int J Mol Sci 2023; 24:ijms24087287. [PMID: 37108446 PMCID: PMC10139028 DOI: 10.3390/ijms24087287] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2023] [Revised: 04/07/2023] [Accepted: 04/11/2023] [Indexed: 04/29/2023] Open
Abstract
Extracellular vesicles (EVs) are membrane vesicles released into the extracellular milieu by cells of various origins. They contain different biological cargoes, protecting them from degradation by environmental factors. There is an opinion that EVs have a number of advantages over synthetic carriers, creating new opportunities for drug delivery. In this review, we discuss the ability of EVs to function as carriers for therapeutic nucleic acids (tNAs), challenges associated with the use of such carriers in vivo, and various strategies for tNA loading into EVs.
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Affiliation(s)
- Anastasiya Oshchepkova
- Institute of Chemical Biology and Fundamental Medicine SB RAS, 630090 Novosibirsk, Russia
| | - Marina Zenkova
- Institute of Chemical Biology and Fundamental Medicine SB RAS, 630090 Novosibirsk, Russia
| | - Valentin Vlassov
- Institute of Chemical Biology and Fundamental Medicine SB RAS, 630090 Novosibirsk, Russia
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50
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Thibonnier M, Ghosh S. Strategy for Pre-Clinical Development of Active Targeting MicroRNA Oligonucleotide Therapeutics for Unmet Medical Needs. Int J Mol Sci 2023; 24:ijms24087126. [PMID: 37108289 PMCID: PMC10138879 DOI: 10.3390/ijms24087126] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2023] [Revised: 03/27/2023] [Accepted: 03/29/2023] [Indexed: 04/29/2023] Open
Abstract
We present here an innovative modular and outsourced model of drug research and development for microRNA oligonucleotide therapeutics (miRNA ONTs). This model is being implemented by a biotechnology company, namely AptamiR Therapeutics, in collaboration with Centers of Excellence in Academic Institutions. Our aim is to develop safe, effective and convenient active targeting miRNA ONT agents for the metabolic pandemic of obesity and metabolic-associated fatty liver disease (MAFLD), as well as deadly ovarian cancer.
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Affiliation(s)
| | - Sujoy Ghosh
- Duke-NUS Medical School, Singapore and Pennington Biomedical Research Center, Baton Rouge, LA 70808, USA
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