1
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Sarli SL, Fakih HH, Kelly K, Devi G, Rembetsy-Brown J, McEachern H, Ferguson C, Echeverria D, Lee J, Sousa J, Sleiman H, Khvorova A, Watts J. Quantifying the activity profile of ASO and siRNA conjugates in glioblastoma xenograft tumors in vivo. Nucleic Acids Res 2024; 52:4799-4817. [PMID: 38613388 PMCID: PMC11109979 DOI: 10.1093/nar/gkae260] [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: 01/07/2024] [Revised: 03/06/2024] [Accepted: 03/27/2024] [Indexed: 04/14/2024] Open
Abstract
Glioblastoma multiforme is a universally lethal brain tumor that largely resists current surgical and drug interventions. Despite important advancements in understanding GBM biology, the invasiveness and heterogeneity of these tumors has made it challenging to develop effective therapies. Therapeutic oligonucleotides-antisense oligonucleotides and small-interfering RNAs-are chemically modified nucleic acids that can silence gene expression in the brain. However, activity of these oligonucleotides in brain tumors remains inadequately characterized. In this study, we developed a quantitative method to differentiate oligonucleotide-induced gene silencing in orthotopic GBM xenografts from gene silencing in normal brain tissue, and used this method to test the differential silencing activity of a chemically diverse panel of oligonucleotides. We show that oligonucleotides chemically optimized for pharmacological activity in normal brain tissue do not show consistent activity in GBM xenografts. We then survey multiple advanced oligonucleotide chemistries for their activity in GBM xenografts. Attaching lipid conjugates to oligonucleotides improves silencing in GBM cells across several different lipid classes. Highly hydrophobic lipid conjugates cholesterol and docosanoic acid enhance silencing but at the cost of higher neurotoxicity. Moderately hydrophobic, unsaturated fatty acid and amphiphilic lipid conjugates still improve activity without compromising safety. These oligonucleotide conjugates show promise for treating glioblastoma.
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Affiliation(s)
- Samantha L Sarli
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Hassan H Fakih
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Karen Kelly
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Gitali Devi
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Julia M Rembetsy-Brown
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Holly R McEachern
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Chantal M Ferguson
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Dimas Echeverria
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Jonathan Lee
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Jacquelyn Sousa
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Hanadi F Sleiman
- Department of Chemistry, McGill University, Montréal, Québec, Canada
| | - Anastasia Khvorova
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA, USA
- Program in Molecular Medicine, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Jonathan K Watts
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA, USA
- Department of Biochemistry and Molecular Biotechnology, University of Massachusetts Chan Medical School, Worcester, MA, USA
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2
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Anwar S, Mir F, Yokota T. Enhancing the Effectiveness of Oligonucleotide Therapeutics Using Cell-Penetrating Peptide Conjugation, Chemical Modification, and Carrier-Based Delivery Strategies. Pharmaceutics 2023; 15:pharmaceutics15041130. [PMID: 37111616 PMCID: PMC10140998 DOI: 10.3390/pharmaceutics15041130] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Revised: 03/28/2023] [Accepted: 03/28/2023] [Indexed: 04/29/2023] Open
Abstract
Oligonucleotide-based therapies are a promising approach for treating a wide range of hard-to-treat diseases, particularly genetic and rare diseases. These therapies involve the use of short synthetic sequences of DNA or RNA that can modulate gene expression or inhibit proteins through various mechanisms. Despite the potential of these therapies, a significant barrier to their widespread use is the difficulty in ensuring their uptake by target cells/tissues. Strategies to overcome this challenge include cell-penetrating peptide conjugation, chemical modification, nanoparticle formulation, and the use of endogenous vesicles, spherical nucleic acids, and smart material-based delivery vehicles. This article provides an overview of these strategies and their potential for the efficient delivery of oligonucleotide drugs, as well as the safety and toxicity considerations, regulatory requirements, and challenges in translating these therapies from the laboratory to the clinic.
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Affiliation(s)
- Saeed Anwar
- Department of Medical Genetics, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, AB T6G 2H7, Canada
| | - Farin Mir
- Department of Medical Genetics, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, AB T6G 2H7, Canada
| | - Toshifumi Yokota
- Department of Medical Genetics, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, AB T6G 2H7, Canada
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3
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Saher O, Zaghloul EM, Umek T, Hagey DW, Mozafari N, Danielsen MB, Gouda AS, Lundin KE, Jørgensen PT, Wengel J, Smith CIE, Zain R. Chemical Modifications and Design Influence the Potency of Huntingtin Anti-Gene Oligonucleotides. Nucleic Acid Ther 2023; 33:117-131. [PMID: 36735581 PMCID: PMC10066784 DOI: 10.1089/nat.2022.0046] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
Huntington's disease is a neurodegenerative, trinucleotide repeat (TNR) disorder affecting both males and females. It is caused by an abnormal increase in the length of CAG•CTG TNR in exon 1 of the Huntingtin gene (HTT). The resultant, mutant HTT mRNA and protein cause neuronal toxicity, suggesting that reduction of their levels would constitute a promising therapeutic approach. We previously reported a novel strategy in which chemically modified oligonucleotides (ONs) directly target chromosomal DNA. These anti-gene ONs were able to downregulate both HTT mRNA and protein. In this study, various locked nucleic acid (LNA)/DNA mixmer anti-gene ONs were tested to investigate the effects of varying ON length, LNA content, and fatty acid modification on HTT expression. Altering the length did not significantly influence the ON potency, while LNA content was critical for activity. Utilization of palmitoyl-modified LNA monomers enhanced the ON activity relatively to the corresponding nonmodified LNA under serum starvation conditions. Furthermore, the number of palmitoylated LNA monomers and their positioning greatly affected ON potency. In addition, we performed RNA sequencing analysis, which showed that the anti-gene ONs affect the "immune system process, mRNA processing, and neurogenesis." Furthermore, we observed that for repeat containing genes, there is a higher tendency for antisense off-targeting. Taken together, our findings provide an optimized design of anti-gene ONs that could potentially be developed as DNA-targeting therapeutics for this class of TNR-related diseases.
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Affiliation(s)
- Osama Saher
- Department of Laboratory Medicine, Translational Research Center Karolinska (TRACK), Karolinska Institutet, Karolinska University Hospital, SE-14186 Huddinge, Sweden.,Department of Pharmaceutics and Industrial Pharmacy, Faculty of Pharmacy, Cairo University, Cairo, Egypt
| | - Eman M Zaghloul
- Department of Laboratory Medicine, Translational Research Center Karolinska (TRACK), Karolinska Institutet, Karolinska University Hospital, SE-14186 Huddinge, Sweden.,Department of Pharmaceutics, Faculty of Pharmacy, Alexandria University, Alexandria, Egypt
| | - Tea Umek
- Department of Laboratory Medicine, Translational Research Center Karolinska (TRACK), Karolinska Institutet, Karolinska University Hospital, SE-14186 Huddinge, Sweden
| | - Daniel W Hagey
- Department of Laboratory Medicine, Translational Research Center Karolinska (TRACK), Karolinska Institutet, Karolinska University Hospital, SE-14186 Huddinge, Sweden
| | - Negin Mozafari
- Department of Laboratory Medicine, Translational Research Center Karolinska (TRACK), Karolinska Institutet, Karolinska University Hospital, SE-14186 Huddinge, Sweden
| | - Mathias B Danielsen
- Department of Physics, Chemistry and Pharmacy, Biomolecular Nanoscale Engineering Center, University of Southern Denmark, Odense, Denmark
| | - Alaa S Gouda
- Department of Physics, Chemistry and Pharmacy, Biomolecular Nanoscale Engineering Center, University of Southern Denmark, Odense, Denmark.,Department of Chemistry, Faculty of Science, Benha University, Benha, Egypt
| | - Karin E Lundin
- Department of Laboratory Medicine, Translational Research Center Karolinska (TRACK), Karolinska Institutet, Karolinska University Hospital, SE-14186 Huddinge, Sweden
| | - Per T Jørgensen
- Department of Physics, Chemistry and Pharmacy, Biomolecular Nanoscale Engineering Center, University of Southern Denmark, Odense, Denmark
| | - Jesper Wengel
- Department of Physics, Chemistry and Pharmacy, Biomolecular Nanoscale Engineering Center, University of Southern Denmark, Odense, Denmark
| | - C I Edvard Smith
- Department of Laboratory Medicine, Translational Research Center Karolinska (TRACK), Karolinska Institutet, Karolinska University Hospital, SE-14186 Huddinge, Sweden
| | - Rula Zain
- Department of Laboratory Medicine, Translational Research Center Karolinska (TRACK), Karolinska Institutet, Karolinska University Hospital, SE-14186 Huddinge, Sweden.,Centre for Rare Diseases, Department of Clinical Genetics, Karolinska University Hospital, SE-17176 Stockholm, Sweden
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4
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Mitani F, Hayasaka R, Hirayama A, Oneyama C. SNAP23-Mediated Perturbation of Cholesterol-Enriched Membrane Microdomain Promotes Extracellular Vesicle Production in Src-Activated Cancer Cells. Biol Pharm Bull 2022; 45:1572-1580. [PMID: 36184518 DOI: 10.1248/bpb.b22-00560] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Extracellular vesicles (EVs) originating from intraluminal vesicles (ILVs) formed within multivesicular bodies (MVBs), often referred to as small EV (sEV) or exosomes, are aberrantly produced by cancer cells and regulate the tumor microenvironment. The tyrosine kinase c-Src is upregulated in a wide variety of human cancers and is involved in promoting sEV secretion, suggesting its role in malignant progression. In this study, we found that activated Src liberated synaptosomal-associated protein 23 (SNAP23), a SNARE molecule, from lipid rafts to non-rafts on cellular membrane. We also demonstrated that SNAP23 localized in non-rafts induced cholesterol downregulation and ILV formation, resulting in the upregulation of sEV production in c-Src-transformed cells. Furthermore, the contribution of the SNAP23-cholesterol axis on sEV upregulation was confirmed in pancreatic cancer cells. High SNAP23 expression is associated with poor prognosis in patients with pancreatic cancer. These findings suggest a unique mechanism for the upregulation of sEV production via SNAP23-mediated cholesterol downregulation in Src-activated cancer cells.
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Affiliation(s)
- Fumie Mitani
- Division of Cancer Cell Regulation, Aichi Cancer Center Research Institute.,Department of Oncology, Graduate School of Pharmaceutical Sciences, Nagoya City University
| | - Ryosuke Hayasaka
- Institute for Advanced Biosciences, Keio University.,Systems Biology Program, Graduate School of Media and Governance, Keio University
| | - Akiyoshi Hirayama
- Institute for Advanced Biosciences, Keio University.,Systems Biology Program, Graduate School of Media and Governance, Keio University.,Institute of Nano-Life-Systems, Institutes of Innovation for Future Society, Nagoya University
| | - Chitose Oneyama
- Division of Cancer Cell Regulation, Aichi Cancer Center Research Institute.,Department of Oncology, Graduate School of Pharmaceutical Sciences, Nagoya City University.,Department of Target and Drug Discovery, Graduate School of Medicine, Nagoya University
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5
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A novel aptamer-based small RNA delivery platform and its application to cancer therapy. Genes Dis 2022. [DOI: 10.1016/j.gendis.2022.05.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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6
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Van de Vyver T, De Smedt SC, Raemdonck K. Modulating intracellular pathways to improve non-viral delivery of RNA therapeutics. Adv Drug Deliv Rev 2022; 181:114041. [PMID: 34763002 DOI: 10.1016/j.addr.2021.114041] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2021] [Revised: 10/12/2021] [Accepted: 11/02/2021] [Indexed: 12/12/2022]
Abstract
RNA therapeutics (e.g. siRNA, oligonucleotides, mRNA, etc.) show great potential for the treatment of a myriad of diseases. However, to reach their site of action in the cytosol or nucleus of target cells, multiple intra- and extracellular barriers have to be surmounted. Several non-viral delivery systems, such as nanoparticles and conjugates, have been successfully developed to meet this requirement. Unfortunately, despite these clear advances, state-of-the-art delivery agents still suffer from relatively low intracellular delivery efficiencies. Notably, our current understanding of the intracellular delivery process is largely oversimplified. Gaining mechanistic insight into how RNA formulations are processed by cells will fuel rational design of the next generation of delivery carriers. In addition, identifying which intracellular pathways contribute to productive RNA delivery could provide opportunities to boost the delivery performance of existing nanoformulations. In this review, we discuss both established as well as emerging techniques that can be used to assess the impact of different intracellular barriers on RNA transfection performance. Next, we highlight how several modulators, including small molecules but also genetic perturbation technologies, can boost RNA delivery by intervening at differing stages of the intracellular delivery process, such as cellular uptake, intracellular trafficking, endosomal escape, autophagy and exocytosis.
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Affiliation(s)
- Thijs Van de Vyver
- Ghent Research Group on Nanomedicines, Laboratory of General Biochemistry and Physical Pharmacy, Faculty of Pharmaceutical Sciences, Ghent University, Ottergemsesteenweg 460, 9000 Ghent, Belgium.
| | - Stefaan C De Smedt
- Ghent Research Group on Nanomedicines, Laboratory of General Biochemistry and Physical Pharmacy, Faculty of Pharmaceutical Sciences, Ghent University, Ottergemsesteenweg 460, 9000 Ghent, Belgium.
| | - Koen Raemdonck
- Ghent Research Group on Nanomedicines, Laboratory of General Biochemistry and Physical Pharmacy, Faculty of Pharmaceutical Sciences, Ghent University, Ottergemsesteenweg 460, 9000 Ghent, Belgium.
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7
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Bost JP, Barriga H, Holme MN, Gallud A, Maugeri M, Gupta D, Lehto T, Valadi H, Esbjörner EK, Stevens MM, El-Andaloussi S. Delivery of Oligonucleotide Therapeutics: Chemical Modifications, Lipid Nanoparticles, and Extracellular Vesicles. ACS NANO 2021; 15:13993-14021. [PMID: 34505766 PMCID: PMC8482762 DOI: 10.1021/acsnano.1c05099] [Citation(s) in RCA: 61] [Impact Index Per Article: 20.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Indexed: 05/04/2023]
Abstract
Oligonucleotides (ONs) comprise a rapidly growing class of therapeutics. In recent years, the list of FDA-approved ON therapies has rapidly expanded. ONs are small (15-30 bp) nucleotide-based therapeutics which are capable of targeting DNA and RNA as well as other biomolecules. ONs can be subdivided into several classes based on their chemical modifications and on the mechanisms of their target interactions. Historically, the largest hindrance to the widespread usage of ON therapeutics has been their inability to effectively internalize into cells and escape from endosomes to reach their molecular targets in the cytosol or nucleus. While cell uptake has been improved, "endosomal escape" remains a significant problem. There are a range of approaches to overcome this, and in this review, we focus on three: altering the chemical structure of the ONs, formulating synthetic, lipid-based nanoparticles to encapsulate the ONs, or biologically loading the ONs into extracellular vesicles. This review provides a background to the design and mode of action of existing FDA-approved ONs. It presents the most common ON classifications and chemical modifications from a fundamental scientific perspective and provides a roadmap of the cellular uptake pathways by which ONs are trafficked. Finally, this review delves into each of the above-mentioned approaches to ON delivery, highlighting the scientific principles behind each and covering recent advances.
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Affiliation(s)
- Jeremy P. Bost
- Department
of Laboratory Medicine, Karolinska Institutet, Huddinge 14152, Sweden
| | - Hanna Barriga
- Department
of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm 17177, Sweden
| | - Margaret N. Holme
- Department
of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm 17177, Sweden
| | - Audrey Gallud
- Department
of Biology and Biological Engineering, Chalmers
University of Technology, Gothenburg 41296, Sweden
- Advanced
Drug Delivery, Pharmaceutical Sciences, R&D, AstraZeneca, Gothenburg 43150, Sweden
| | - Marco Maugeri
- Department
of Rheumatology and Inflammation Research, Institute of Medicine,
Sahlgrenska Academy, University of Gothenburg, Gothenburg 41390, Sweden
| | - Dhanu Gupta
- Department
of Laboratory Medicine, Karolinska Institutet, Huddinge 14152, Sweden
| | - Taavi Lehto
- Department
of Laboratory Medicine, Karolinska Institutet, Huddinge 14152, Sweden
- Institute
of Technology, University of Tartu, Nooruse 1, Tartu 50411, Estonia
| | - Hadi Valadi
- Department
of Rheumatology and Inflammation Research, Institute of Medicine,
Sahlgrenska Academy, University of Gothenburg, Gothenburg 41390, Sweden
| | - Elin K. Esbjörner
- Department
of Biology and Biological Engineering, Chalmers
University of Technology, Gothenburg 41296, Sweden
| | - Molly M. Stevens
- Department
of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm 17177, Sweden
- Department
of Materials, Department of Bioengineering, Institute of Biomedical
Engineering, Imperial College London, London SW7 2BU, United Kingdom
| | - Samir El-Andaloussi
- Department
of Laboratory Medicine, Karolinska Institutet, Huddinge 14152, Sweden
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8
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Dastpeyman M, Sharifi R, Amin A, Karas JA, Cuic B, Pan Y, Nicolazzo JA, Turner BJ, Shabanpoor F. Endosomal escape cell-penetrating peptides significantly enhance pharmacological effectiveness and CNS activity of systemically administered antisense oligonucleotides. Int J Pharm 2021; 599:120398. [PMID: 33640427 DOI: 10.1016/j.ijpharm.2021.120398] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Revised: 02/11/2021] [Accepted: 02/14/2021] [Indexed: 12/19/2022]
Abstract
Antisense oligonucleotides (ASOs) are an emerging class of gene-specific therapeutics for diseases associated with the central nervous system (CNS). However, ASO delivery across the blood-brain barrier (BBB) to their CNS target cells remains a major challenge. Since ASOs are mainly taken up into the brain capillary endothelial cells interface through endosomal routes, entrapment in the endosomal compartment is a major obstacle for efficient CNS delivery of ASOs. Therefore, we evaluated the effectiveness of a panel of cell-penetrating peptides (CPPs) bearing several endosomal escape domains for the intracellular delivery, endosomal release and antisense activity of FDA-approved Spinraza (Nusinersen), an ASO used to treat spinal muscular atrophy (SMA). We identified a CPP, HA2-ApoE(131-150), which, when conjugated to Nusinersen, showed efficient endosomal escape capability and significantly increased the level of full-length functional mRNA of the survival motor neuron 2 (SMN2) gene in SMA patient-derived fibroblasts. Treatment of SMN2 transgenic adult mice with this CPP-PMO conjugate resulted in a significant increase in the level of full-length SMN2 in the brain and spinal cord. This work provides proof-of-principle that integration of endosomal escape domains with CPPs enables higher cytosolic delivery of ASOs, and more importantly enhances the efficiency of BBB-permeability and CNS activity of systemically administered ASOs.
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Affiliation(s)
- Mohadeseh Dastpeyman
- The Florey Institute of Neuroscience and Mental Health, University of Melbourne, Parkville 3010, VIC, Australia
| | - Ramin Sharifi
- The Florey Institute of Neuroscience and Mental Health, University of Melbourne, Parkville 3010, VIC, Australia
| | - Azin Amin
- The Florey Institute of Neuroscience and Mental Health, University of Melbourne, Parkville 3010, VIC, Australia
| | - John A Karas
- School of Chemistry, The University of Melbourne, VIC 3010, Australia; The Bio21 Institute, University of Melbourne, 30 Flemington Rd., VIC 3010, Australia
| | - Brittany Cuic
- The Florey Institute of Neuroscience and Mental Health, University of Melbourne, Parkville 3010, VIC, Australia
| | - Yijun Pan
- Drug Delivery, Disposition and Dynamics, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville 3052, VIC, Australia
| | - Joseph A Nicolazzo
- Drug Delivery, Disposition and Dynamics, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville 3052, VIC, Australia
| | - Bradley J Turner
- The Florey Institute of Neuroscience and Mental Health, University of Melbourne, Parkville 3010, VIC, Australia; The Perron Institute for Neurological and Translational Science, Queen Elizabeth Medical Centre, Nedlands, Western Australia 6150, Australia
| | - Fazel Shabanpoor
- The Florey Institute of Neuroscience and Mental Health, University of Melbourne, Parkville 3010, VIC, Australia.
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9
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He C, Migawa MT, Chen K, Weston TA, Tanowitz M, Song W, Guagliardo P, Iyer KS, Bennett CF, Fong LG, Seth PP, Young SG, Jiang H. High-resolution visualization and quantification of nucleic acid-based therapeutics in cells and tissues using Nanoscale secondary ion mass spectrometry (NanoSIMS). Nucleic Acids Res 2021; 49:1-14. [PMID: 33275144 PMCID: PMC7797060 DOI: 10.1093/nar/gkaa1112] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Revised: 10/27/2020] [Accepted: 11/04/2020] [Indexed: 01/19/2023] Open
Abstract
Nucleic acid therapeutics (NATs) have proven useful in promoting the degradation of specific transcripts, modifying gene expression, and regulating mRNA splicing. In each situation, efficient delivery of nucleic acids to cells, tissues and intracellular compartments is crucial—both for optimizing efficacy and reducing side effects. Despite successes in NATs, our understanding of their cellular uptake and distribution in tissues is limited. Current methods have yielded insights into distribution of NATs within cells and tissues, but the sensitivity and resolution of these approaches are limited. Here, we show that nanoscale secondary ion mass spectrometry (NanoSIMS) imaging can be used to define the distribution of 5-bromo-2′-deoxythymidine (5-BrdT) modified antisense oligonucleotides (ASO) in cells and tissues with high sensitivity and spatial resolution. This approach makes it possible to define ASO uptake and distribution in different subcellular compartments and to quantify the impact of targeting ligands designed to promote ASO uptake by cells. Our studies showed that phosphorothioate ASOs are associated with filopodia and the inner nuclear membrane in cultured cells, and also revealed substantial cellular and subcellular heterogeneity of ASO uptake in mouse tissues. NanoSIMS imaging represents a significant advance in visualizing uptake and distribution of NATs; this approach will be useful in optimizing efficacy and delivery of NATs for treating human disease.
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Affiliation(s)
- Cuiwen He
- Department of Medicine, University of California, Los Angeles, CA 90095, USA
| | | | - Kai Chen
- School of Molecular Sciences, University of Western Australia, Perth 6009, Australia
| | - Thomas A Weston
- Department of Medicine, University of California, Los Angeles, CA 90095, USA
| | | | - Wenxin Song
- Department of Medicine, University of California, Los Angeles, CA 90095, USA
| | - Paul Guagliardo
- Centre for Microscopy, Characterisation and Analysis, University of Western Australia, Perth 6009, Australia
| | - K Swaminathan Iyer
- School of Molecular Sciences, University of Western Australia, Perth 6009, Australia
| | | | - Loren G Fong
- Department of Medicine, University of California, Los Angeles, CA 90095, USA
| | - Punit P Seth
- Ionis Pharmaceuticals, Inc., Carlsbad, CA 92010, USA
| | - Stephen G Young
- Department of Medicine, University of California, Los Angeles, CA 90095, USA.,Department of Human Genetics, University of California, Los Angeles, CA 90095, USA
| | - Haibo Jiang
- School of Molecular Sciences, University of Western Australia, Perth 6009, Australia.,Department of Chemistry, The University of Hong Kong, Hong Kong, China
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10
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Eilers W, Cleasby M, Foster K. Development of antisense-mediated myostatin knockdown for the treatment of insulin resistance. Sci Rep 2021; 11:1604. [PMID: 33452345 PMCID: PMC7810755 DOI: 10.1038/s41598-021-81222-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2020] [Accepted: 12/23/2020] [Indexed: 12/27/2022] Open
Abstract
Myostatin is a negative regulator of muscle mass and its inhibition represents a promising strategy for the treatment of muscle disorders and type 2 diabetes. However, there is currently no clinically effective myostatin inhibitor, and therefore novel methods are required. We evaluated the use of antisense phosphorodiamidate morpholino oligomers (PMO) to reduce myostatin expression in skeletal muscle and measured their effects on muscle mass and glucose uptake. C57/Bl6 mice received intramuscular or intravenous injections of anti-myostatin PMOs. Repeated intramuscular administration lead to a reduction in myostatin transcript levels (~ 20–40%), and an increase in muscle mass in chow and high-fat diet (HFD)-fed mice, but insulin-stimulated glucose uptake was reduced in PMO-treated muscles of HFD-fed mice. Five weekly intravenous administrations of 100 nmol PMO did not reduce myostatin expression, and therefore had no significant physiological effects. Unexpectedly, exon skipping levels were higher after intramuscular administration of PMO in HFD- than chow-fed mice. These results suggest that a modest PMO-induced reduction in myostatin transcript levels is sufficient to induce an increase in muscle mass, but that a greater degree of inhibition may be required to improve muscle glucose uptake.
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Affiliation(s)
- Wouter Eilers
- School of Biological Sciences, University of Reading, Reading, UK.
| | - Mark Cleasby
- Royal Veterinary College, University of London, London, UK
| | - Keith Foster
- School of Biological Sciences, University of Reading, Reading, UK
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11
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Crooke ST, Liang XH, Baker BF, Crooke RM. Antisense technology: A review. J Biol Chem 2021; 296:100416. [PMID: 33600796 PMCID: PMC8005817 DOI: 10.1016/j.jbc.2021.100416] [Citation(s) in RCA: 136] [Impact Index Per Article: 45.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2020] [Revised: 02/09/2021] [Accepted: 02/10/2021] [Indexed: 12/15/2022] Open
Abstract
Antisense technology is beginning to deliver on the broad promise of the technology. Ten RNA-targeted drugs including eight single-strand antisense drugs (ASOs) and two double-strand ASOs (siRNAs) have now been approved for commercial use, and the ASOs in phase 2/3 trials are innovative, delivered by multiple routes of administration and focused on both rare and common diseases. In fact, two ASOs are used in cardiovascular outcome studies and several others in very large trials. Interest in the technology continues to grow, and the field has been subject to a significant number of reviews. In this review, we focus on the molecular events that result in the effects observed and use recent clinical results involving several different ASOs to exemplify specific molecular mechanisms and specific issues. We conclude with the prospective on the technology.
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Affiliation(s)
- Stanley T Crooke
- Core Antisense Research, Ionis Pharmaceuticals, Inc, Carlsbad, California, USA.
| | - Xue-Hai Liang
- Core Antisense Research, Ionis Pharmaceuticals, Inc, Carlsbad, California, USA
| | - Brenda F Baker
- Development Communication, Ionis Pharmaceuticals, Inc, Carlsbad, California, USA
| | - Rosanne M Crooke
- Antisense Drug Discovery, Ionis Pharmaceuticals, Inc, Carlsbad, California, USA
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12
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Hawner M, Ducho C. Cellular Targeting of Oligonucleotides by Conjugation with Small Molecules. Molecules 2020; 25:molecules25245963. [PMID: 33339365 PMCID: PMC7766908 DOI: 10.3390/molecules25245963] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2020] [Revised: 12/11/2020] [Accepted: 12/11/2020] [Indexed: 12/20/2022] Open
Abstract
Drug candidates derived from oligonucleotides (ON) are receiving increased attention that is supported by the clinical approval of several ON drugs. Such therapeutic ON are designed to alter the expression levels of specific disease-related proteins, e.g., by displaying antigene, antisense, and RNA interference mechanisms. However, the high polarity of the polyanionic ON and their relatively rapid nuclease-mediated cleavage represent two major pharmacokinetic hurdles for their application in vivo. This has led to a range of non-natural modifications of ON structures that are routinely applied in the design of therapeutic ON. The polyanionic architecture of ON often hampers their penetration of target cells or tissues, and ON usually show no inherent specificity for certain cell types. These limitations can be overcome by conjugation of ON with molecular entities mediating cellular 'targeting', i.e., enhanced accumulation at and/or penetration of a specific cell type. In this context, the use of small molecules as targeting units appears particularly attractive and promising. This review provides an overview of advances in the emerging field of cellular targeting of ON via their conjugation with small-molecule targeting structures.
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Crooke ST, Seth PP, Vickers TA, Liang XH. The Interaction of Phosphorothioate-Containing RNA Targeted Drugs with Proteins Is a Critical Determinant of the Therapeutic Effects of These Agents. J Am Chem Soc 2020; 142:14754-14771. [PMID: 32786803 DOI: 10.1021/jacs.0c04928] [Citation(s) in RCA: 67] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Recent progress in understanding phosphorothioate antisense oligonucleotide (PS-ASO) interactions with proteins has revealed that proteins play deterministic roles in the absorption, distribution, cellular uptake, subcellular distribution, molecular mechanisms of action, and toxicity of PS-ASOs. Similarly, such interactions can alter the fates of many intracellular proteins. These and other advances have opened new avenues for the medicinal chemistry of PS-ASOs and research on all elements of the molecular pharmacology of these molecules. These advances have recently been reviewed. In this Perspective article, we summarize some of those learnings, the general principles that have emerged, and a few of the exciting new questions that can now be addressed.
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Affiliation(s)
- Stanley T Crooke
- Ionis Pharmaceuticals, Inc., Carlsbad, California 92010-6670, United States
| | - Punit P Seth
- Ionis Pharmaceuticals, Inc., Carlsbad, California 92010-6670, United States
| | - Timothy A Vickers
- Ionis Pharmaceuticals, Inc., Carlsbad, California 92010-6670, United States
| | - Xue-Hai Liang
- Ionis Pharmaceuticals, Inc., Carlsbad, California 92010-6670, United States
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Abstract
PURPOSE OF REVIEW To summarize all available data on targeting angiotensinogen with RNA-based therapeutics as a new tool to combat cardiovascular diseases. RECENT FINDINGS Liver-targeted, stable antisense oligonucleotides and small interfering RNA targeting angiotensinogen are now available, and may allow treatment with at most a few injections per year, thereby improving adherence. Promising results have been obtained in hypertensive animal models, as well as in rodent models of atherosclerosis, polycystic kidney disease and pulmonary fibrosis. The next step will be to evaluate the optimal degree of suppression, synergy with existing renin-angiotensin-aldosterone system blockers, and to determine harmful effects of suppressing angiotensinogen in the context of common comorbidities, such as heart failure and chronic kidney disease. SUMMARY Targeting angiotensinogen with RNA-based therapeutics is a promising new tool to treat hypertension and diseases beyond. Their long-lasting effects are particularly exciting, and if translated to a clinical application of at most a few administrations per year, may help to eliminate nonadherence.
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Crooke ST, Vickers TA, Liang XH. Phosphorothioate modified oligonucleotide-protein interactions. Nucleic Acids Res 2020; 48:5235-5253. [PMID: 32356888 PMCID: PMC7261153 DOI: 10.1093/nar/gkaa299] [Citation(s) in RCA: 146] [Impact Index Per Article: 36.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2020] [Revised: 04/08/2020] [Accepted: 04/17/2020] [Indexed: 12/18/2022] Open
Abstract
Antisense oligonucleotides (ASOs) interact with target RNAs via hybridization to modulate gene expression through different mechanisms. ASO therapeutics are chemically modified and include phosphorothioate (PS) backbone modifications and different ribose and base modifications to improve pharmacological properties. Modified PS ASOs display better binding affinity to the target RNAs and increased binding to proteins. Moreover, PS ASO protein interactions can affect many aspects of their performance, including distribution and tissue delivery, cellular uptake, intracellular trafficking, potency and toxicity. In this review, we summarize recent progress in understanding PS ASO protein interactions, highlighting the proteins with which PS ASOs interact, the influence of PS ASO protein interactions on ASO performance, and the structure activity relationships of PS ASO modification and protein interactions. A detailed understanding of these interactions can aid in the design of safer and more potent ASO drugs, as illustrated by recent findings that altering ASO chemical modifications dramatically improves therapeutic index.
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Wang S, Allen N, Prakash TP, Liang XH, Crooke ST. Lipid Conjugates Enhance Endosomal Release of Antisense Oligonucleotides Into Cells. Nucleic Acid Ther 2019; 29:245-255. [PMID: 31158063 DOI: 10.1089/nat.2019.0794] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Antisense oligonucleotides modified with phosphorothioate linkages (PS-ASOs) can enter cells via endocytic pathways and must escape from membraned organelles to reach target RNAs. We recently found that membrane destabilization induced by different lipid species contributes to PS-ASO release from late endosomes (LEs). In this study, we characterized intracellular uptake, trafficking, and activities of PS-ASOs conjugated with different lipid species. We found that palmitic acid-, tocopherol-, and cholesterol-conjugated PS-ASOs have increased protein binding and enhanced intracellular uptake compared to unconjugated PS-ASOs. Similar to the parental PS-ASO, the lipid-conjugated PS-ASOs traffic from early to LEs without incorporation into lipid droplets. Unlike parental PS-ASOs, the lipid-conjugated PS-ASOs tend to remain associated with plasma or endosomal membranes, and this appears to influence their release from endosomes. The lipid-conjugated PS-ASOs were released more rapidly than parental PS-ASO. These results suggest that lipid conjugation enhances the interactions of PS-ASOs with proteins or membranes, in turn facilitating intracellular trafficking and endosomal release.
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Affiliation(s)
- Shiyu Wang
- Department of Core Antisense Research, Ionis Pharmaceuticals, Inc., Carlsbad, California
| | - Nickolas Allen
- Department of Core Antisense Research, Ionis Pharmaceuticals, Inc., Carlsbad, California
| | - Thazha P Prakash
- Department of Medicinal Chemistry, Ionis Pharmaceuticals, Inc., Carlsbad, California
| | - Xue-Hai Liang
- Department of Core Antisense Research, Ionis Pharmaceuticals, Inc., Carlsbad, California
| | - Stanley T Crooke
- Department of Core Antisense Research, Ionis Pharmaceuticals, Inc., Carlsbad, California
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