1
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Hariharan VN, Caiazzi J, Miller R, Ferguson C, Sapp E, Fakih H, Tang Q, Yamada N, Furgal R, Paquette J, Bramato B, McHugh N, Summers A, Lochmann C, Godinho B, Hildebrand S, Echeverria D, Hassler M, Alterman J, DiFiglia M, Aronin N, Khvorova A, Yamada K. Extended Nucleic Acid (exNA): A Novel, Biologically Compatible Backbone that Significantly Enhances Oligonucleotide Efficacy in vivo. RESEARCH SQUARE 2023:rs.3.rs-2987323. [PMID: 37398145 PMCID: PMC10312934 DOI: 10.21203/rs.3.rs-2987323/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/04/2023]
Abstract
Metabolic stabilization of therapeutic oligonucleotides requires both sugar and backbone modifications, where phosphorothioate (PS) is the only backbone chemistry used in the clinic. Here, we describe the discovery, synthesis, and characterization of a novel biologically compatible backbone, extended nucleic acid (exNA). Upon exNA precursor scale up, exNA incorporation is fully compatible with common nucleic acid synthetic protocols. The novel backbone is orthogonal to PS and shows profound stabilization against 3'- and 5'-exonucleases. Using small interfering RNAs (siRNAs) as an example, we show exNA is tolerated at most nucleotide positions and profoundly improves in vivo efficacy. A combined exNA-PS backbone enhances siRNA resistance to serum 3'-exonuclease by ~ 32-fold over PS backbone and > 1000-fold over the natural phosphodiester backbone, thereby enhancing tissue exposure (~ 6-fold), tissues accumulation (4- to 20-fold), and potency both systemically and in brain. The improved potency and durability imparted by exNA opens more tissues and indications to oligonucleotide-driven therapeutic interventions.
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Affiliation(s)
| | | | | | - Chantal Ferguson
- RNA Therapeutics Institute, University of Massachusetts Medical School
| | | | | | - Qi Tang
- University of Massachusetts Chan Medical School
| | | | | | | | | | - Nicholas McHugh
- RNA Therapeutics Institute, University of Massachusetts Medical School
| | | | | | - Bruno Godinho
- RNA Therapeutics Institute, University of Massachusetts Medical School
| | - Samuel Hildebrand
- RNA Therapeutics Institute, University of Massachusetts Medical School
| | - Dimas Echeverria
- RNA Therapeutics Institute, University of Massachusetts Medical School
| | | | | | | | - Neil Aronin
- University of Massachusetts Worcester Campus
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2
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Yamada K, Hariharan VN, Caiazzi J, Miller R, Furguson C, Sapp E, Fakih H, Tan Q, Yamada N, Furgal RC, Paquette J, Bramato B, McHugh N, Summers A, Lochmann C, Godinho BM, Hildebrand S, Echeverria D, Hassler MR, Alterman JF, DiFiglia M, Aronin N, Khvorova A. Extended Nucleic Acid (exNA): A Novel, Biologically Compatible Backbone that Significantly Enhances Oligonucleotide Efficacy in vivo. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.26.542506. [PMID: 37292886 PMCID: PMC10245983 DOI: 10.1101/2023.05.26.542506] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Metabolic stabilization of therapeutic oligonucleotides requires both sugar and backbone modifications, where phosphorothioate (PS) is the only backbone chemistry used in the clinic. Here, we describe the discovery, synthesis, and characterization of a novel biologically compatible backbone, extended nucleic acid (exNA). Upon exNA precursor scale up, exNA incorporation is fully compatible with common nucleic acid synthetic protocols. The novel backbone is orthogonal to PS and shows profound stabilization against 3'- and 5'-exonucleases. Using small interfering RNAs (siRNAs) as an example, we show exNA is tolerated at most nucleotide positions and profoundly improves in vivo efficacy. A combined exNA-PS backbone enhances siRNA resistance to serum 3'-exonuclease by ~32-fold over PS backbone and >1000-fold over the natural phosphodiester backbone, thereby enhancing tissue exposure (~6-fold), tissues accumulation (4- to 20-fold), and potency both systemically and in brain. The improved potency and durability imparted by exNA opens more tissues and indications to oligonucleotide-driven therapeutic interventions.
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Affiliation(s)
- Ken Yamada
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, 368 Plantation Street, Worcester, Massachusetts 01605, United States
| | - Vignesh Narayan Hariharan
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, 368 Plantation Street, Worcester, Massachusetts 01605, United States
| | - Jillian Caiazzi
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, 368 Plantation Street, Worcester, Massachusetts 01605, United States
| | - Rachael Miller
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, 368 Plantation Street, Worcester, Massachusetts 01605, United States
- Department of Medicine, University of Massachusetts Chan Medical School; Charlestown, Massachusetts, United State
| | - Chantal Furguson
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, 368 Plantation Street, Worcester, Massachusetts 01605, United States
- Department of Medicine, University of Massachusetts Chan Medical School; Charlestown, Massachusetts, United State
| | - Ellen Sapp
- Department of Neurology, Harvard Medical School and Mass General Institute for Neurodegenerative Disease, Charlestown, Massachusetts, United State
| | - Hassan Fakih
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, 368 Plantation Street, Worcester, Massachusetts 01605, United States
| | - Qi Tan
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, 368 Plantation Street, Worcester, Massachusetts 01605, United States
| | - Nozomi Yamada
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, 368 Plantation Street, Worcester, Massachusetts 01605, United States
| | - Raymond C. Furgal
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, 368 Plantation Street, Worcester, Massachusetts 01605, United States
| | - Joseph Paquette
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, 368 Plantation Street, Worcester, Massachusetts 01605, United States
- Department of Medicine, University of Massachusetts Chan Medical School; Charlestown, Massachusetts, United State
| | - Brianna Bramato
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, 368 Plantation Street, Worcester, Massachusetts 01605, United States
| | - Nicholas McHugh
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, 368 Plantation Street, Worcester, Massachusetts 01605, United States
| | - Ashley Summers
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, 368 Plantation Street, Worcester, Massachusetts 01605, United States
| | - Clemens Lochmann
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, 368 Plantation Street, Worcester, Massachusetts 01605, United States
| | - Bruno M.D.C. Godinho
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, 368 Plantation Street, Worcester, Massachusetts 01605, United States
| | - Samuel Hildebrand
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, 368 Plantation Street, Worcester, Massachusetts 01605, United States
| | - Dimas Echeverria
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, 368 Plantation Street, Worcester, Massachusetts 01605, United States
| | - Matthew R. Hassler
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, 368 Plantation Street, Worcester, Massachusetts 01605, United States
| | - Julia F. Alterman
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, 368 Plantation Street, Worcester, Massachusetts 01605, United States
| | - Marian DiFiglia
- Department of Neurology, Harvard Medical School and Mass General Institute for Neurodegenerative Disease, Charlestown, Massachusetts, United State
| | - Neil Aronin
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, 368 Plantation Street, Worcester, Massachusetts 01605, United States
- Department of Medicine, University of Massachusetts Chan Medical School; Charlestown, Massachusetts, United State
| | - Anastasia Khvorova
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, 368 Plantation Street, Worcester, Massachusetts 01605, United States
- Program in Molecular Medicine, University of Massachusetts Chan Medical School; Charlestown, Massachusetts, United State
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3
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CNS Delivery of Nucleic Acid Therapeutics: Beyond the Blood-Brain Barrier and Towards Specific Cellular Targeting. Pharm Res 2023; 40:77-105. [PMID: 36380168 DOI: 10.1007/s11095-022-03433-5] [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: 07/01/2022] [Accepted: 11/03/2022] [Indexed: 11/16/2022]
Abstract
Nucleic acid-based therapeutic molecules including small interfering RNA (siRNA), microRNA(miRNA), antisense oligonucleotides (ASOs), messenger RNA (mRNA), and DNA-based gene therapy have tremendous potential for treating diseases in the central nervous system (CNS). However, achieving clinically meaningful delivery to the brain and particularly to target cells and sub-cellular compartments is typically very challenging. Mediating cell-specific delivery in the CNS would be a crucial advance that mitigates off-target effects and toxicities. In this review, we describe these challenges and provide contemporary evidence of advances in cellular and sub-cellular delivery using a variety of delivery mechanisms and alternative routes of administration, including the nose-to-brain approach. Strategies to achieve subcellular localization, endosomal escape, cytosolic bioavailability, and nuclear transfer are also discussed. Ultimately, there are still many challenges to translating these experimental strategies into effective and clinically viable approaches for treating patients.
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4
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Whelan R, Hargaden GC, Knox AJS. Modulating the Blood-Brain Barrier: A Comprehensive Review. Pharmaceutics 2021; 13:1980. [PMID: 34834395 PMCID: PMC8618722 DOI: 10.3390/pharmaceutics13111980] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2021] [Revised: 10/22/2021] [Accepted: 10/27/2021] [Indexed: 12/23/2022] Open
Abstract
The highly secure blood-brain barrier (BBB) restricts drug access to the brain, limiting the molecular toolkit for treating central nervous system (CNS) diseases to small, lipophilic drugs. Development of a safe and effective BBB modulator would revolutionise the treatment of CNS diseases and future drug development in the area. Naturally, the field has garnered a great deal of attention, leading to a vast and diverse range of BBB modulators. In this review, we summarise and compare the various classes of BBB modulators developed over the last five decades-their recent advancements, advantages and disadvantages, while providing some insight into their future as BBB modulators.
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Affiliation(s)
- Rory Whelan
- School of Biological and Health Sciences, Technological University Dublin, Central Quad, Grangegorman, D07 XT95 Dublin, Ireland;
- Chemical and Structural Biology, Environmental Sustainability and Health Institute, Technological University Dublin, D07 H6K8 Dublin, Ireland
| | - Grainne C. Hargaden
- School of Chemical and Pharmaceutical Sciences, Technological University Dublin, Central Quad, Grangegorman, D07 XT95 Dublin, Ireland;
| | - Andrew J. S. Knox
- School of Biological and Health Sciences, Technological University Dublin, Central Quad, Grangegorman, D07 XT95 Dublin, Ireland;
- Chemical and Structural Biology, Environmental Sustainability and Health Institute, Technological University Dublin, D07 H6K8 Dublin, Ireland
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5
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Bortolozzi A, Manashirov S, Chen A, Artigas F. Oligonucleotides as therapeutic tools for brain disorders: Focus on major depressive disorder and Parkinson's disease. Pharmacol Ther 2021; 227:107873. [PMID: 33915178 DOI: 10.1016/j.pharmthera.2021.107873] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2020] [Accepted: 04/05/2021] [Indexed: 12/25/2022]
Abstract
Remarkable advances in understanding the role of RNA in health and disease have expanded considerably in the last decade. RNA is becoming an increasingly important target for therapeutic intervention; therefore, it is critical to develop strategies for therapeutic modulation of RNA function. Oligonucleotides, including antisense oligonucleotide (ASO), small interfering RNA (siRNA), microRNA mimic (miRNA), and anti-microRNA (antagomir) are perhaps the most direct therapeutic strategies for addressing RNA. Among other mechanisms, most oligonucleotide designs involve the formation of a hybrid with RNA that promotes its degradation by activation of endogenous enzymes such as RNase-H (e.g., ASO) or the RISC complex (e.g. RNA interference - RNAi for siRNA and miRNA). However, the use of oligonucleotides for the treatment of brain disorders is seriously compromised by two main limitations: i) how to deliver oligonucleotides to the brain compartment, avoiding the action of peripheral RNAses? and once there, ii) how to target specific neuronal populations? We review the main molecular pathways in major depressive disorder (MDD) and Parkinson's disease (PD), and discuss the challenges associated with the development of novel oligonucleotide therapeutics. We pay special attention to the use of conjugated ligand-oligonucleotide approach in which the oligonucleotide sequence is covalently bound to monoamine transporter inhibitors (e.g. sertraline, reboxetine, indatraline). This strategy allows their selective accumulation in the monoamine neurons of mice and monkeys after their intranasal or intracerebroventricular administration, evoking preclinical changes predictive of a clinical therapeutic action after knocking-down disease-related genes. In addition, recent advances in oligonucleotide therapeutic clinical trials are also reviewed.
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Affiliation(s)
- Analia Bortolozzi
- Institut d'Investigacions Biomèdiques de Barcelona (IIBB), Consejo Superior de Investigaciones Científicas (CSIC), 08036 Barcelona, Spain; Institut d'Investigacions August Pi i Sunyer (IDIBAPS), 08036 Barcelona, Spain; Centro de Investigación Biomédica en Red de Salud Mental (CIBERSAM), ISCIII, Madrid, Spain.
| | - Sharon Manashirov
- Centro de Investigación Biomédica en Red de Salud Mental (CIBERSAM), ISCIII, Madrid, Spain; miCure Therapeutics LTD., Tel-Aviv, Israel; Department of Stress Neurobiology and Neurogenetics, Max Planck Institute of Psychiatry, 80804 Munich, Germany
| | - Alon Chen
- Department of Stress Neurobiology and Neurogenetics, Max Planck Institute of Psychiatry, 80804 Munich, Germany; Department of Neurobiology, Weizmann Institute of Science, 76100 Rehovot, Israel
| | - Francesc Artigas
- Institut d'Investigacions Biomèdiques de Barcelona (IIBB), Consejo Superior de Investigaciones Científicas (CSIC), 08036 Barcelona, Spain; Institut d'Investigacions August Pi i Sunyer (IDIBAPS), 08036 Barcelona, Spain; Centro de Investigación Biomédica en Red de Salud Mental (CIBERSAM), ISCIII, Madrid, Spain
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6
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Mendonça MCP, Kont A, Aburto MR, Cryan JF, O'Driscoll CM. Advances in the Design of (Nano)Formulations for Delivery of Antisense Oligonucleotides and Small Interfering RNA: Focus on the Central Nervous System. Mol Pharm 2021; 18:1491-1506. [PMID: 33734715 PMCID: PMC8824433 DOI: 10.1021/acs.molpharmaceut.0c01238] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
![]()
RNA-based therapeutics have emerged
as one of the most powerful
therapeutic options used for the modulation of gene/protein expression
and gene editing with the potential to treat neurodegenerative diseases.
However, the delivery of nucleic acids to the central nervous system
(CNS), in particular by the systemic route, remains a major hurdle.
This review will focus on the strategies for systemic delivery of
therapeutic nucleic acids designed to overcome these barriers. Pathways
and mechanisms of transport across the blood–brain barrier
which could be exploited for delivery are described, focusing in particular
on smaller nucleic acids including antisense oligonucleotides (ASOs)
and small interfering RNA (siRNA). Approaches used to enhance delivery
including chemical modifications, nanocarrier systems, and target
selection (cell-specific delivery) are critically analyzed. Learnings
achieved from a comparison of the successes and failures reported
for CNS delivery of ASOs versus siRNA will help identify opportunities
for a wider range of nucleic acids and accelerate the clinical translation
of these innovative therapies.
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Affiliation(s)
- Monique C P Mendonça
- Pharmacodelivery Group, School of Pharmacy, University College Cork, T12 YT20 Cork, Ireland
| | - Ayse Kont
- Pharmacodelivery Group, School of Pharmacy, University College Cork, T12 YT20 Cork, Ireland
| | - Maria Rodriguez Aburto
- APC Microbiome Ireland, University College Cork, T12 YT20 Cork, Ireland.,Department of Anatomy and Neuroscience, University College Cork, T12 XF62 Cork, Ireland
| | - John F Cryan
- APC Microbiome Ireland, University College Cork, T12 YT20 Cork, Ireland.,Department of Anatomy and Neuroscience, University College Cork, T12 XF62 Cork, Ireland
| | - Caitriona M O'Driscoll
- Pharmacodelivery Group, School of Pharmacy, University College Cork, T12 YT20 Cork, Ireland
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7
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Hu B, Zhong L, Weng Y, Peng L, Huang Y, Zhao Y, Liang XJ. Therapeutic siRNA: state of the art. Signal Transduct Target Ther 2020; 5:101. [PMID: 32561705 PMCID: PMC7305320 DOI: 10.1038/s41392-020-0207-x] [Citation(s) in RCA: 630] [Impact Index Per Article: 157.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2020] [Revised: 04/08/2020] [Accepted: 05/03/2020] [Indexed: 02/07/2023] Open
Abstract
RNA interference (RNAi) is an ancient biological mechanism used to defend against external invasion. It theoretically can silence any disease-related genes in a sequence-specific manner, making small interfering RNA (siRNA) a promising therapeutic modality. After a two-decade journey from its discovery, two approvals of siRNA therapeutics, ONPATTRO® (patisiran) and GIVLAARI™ (givosiran), have been achieved by Alnylam Pharmaceuticals. Reviewing the long-term pharmaceutical history of human beings, siRNA therapy currently has set up an extraordinary milestone, as it has already changed and will continue to change the treatment and management of human diseases. It can be administered quarterly, even twice-yearly, to achieve therapeutic effects, which is not the case for small molecules and antibodies. The drug development process was extremely hard, aiming to surmount complex obstacles, such as how to efficiently and safely deliver siRNAs to desired tissues and cells and how to enhance the performance of siRNAs with respect to their activity, stability, specificity and potential off-target effects. In this review, the evolution of siRNA chemical modifications and their biomedical performance are comprehensively reviewed. All clinically explored and commercialized siRNA delivery platforms, including the GalNAc (N-acetylgalactosamine)-siRNA conjugate, and their fundamental design principles are thoroughly discussed. The latest progress in siRNA therapeutic development is also summarized. This review provides a comprehensive view and roadmap for general readers working in the field.
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Affiliation(s)
- Bo Hu
- School of Life Science, Advanced Research Institute of Multidisciplinary Science, Institute of Engineering Medicine, Key Laboratory of Molecular Medicine and Biotherapy, Beijing Institute of Technology, 100081, Beijing, People's Republic of China
| | - Liping Zhong
- National Center for International Biotargeting Theranostics, Guangxi Key Laboratory of Biotargeting Theranostics, Collaborative Innovation Center for Targeting Tumor Theranostics, Guangxi Medical University, 530021, Guangxi, People's Republic of China
| | - Yuhua Weng
- School of Life Science, Advanced Research Institute of Multidisciplinary Science, Institute of Engineering Medicine, Key Laboratory of Molecular Medicine and Biotherapy, Beijing Institute of Technology, 100081, Beijing, People's Republic of China
| | - Ling Peng
- Aix-Marseille University, CNRS, Centre Interdisciplinaire de Nanoscience de Marseille (CINaM), Equipe Labellisée Ligue Contre le Cancer, 13288, Marseille, France
| | - Yuanyu Huang
- School of Life Science, Advanced Research Institute of Multidisciplinary Science, Institute of Engineering Medicine, Key Laboratory of Molecular Medicine and Biotherapy, Beijing Institute of Technology, 100081, Beijing, People's Republic of China.
| | - Yongxiang Zhao
- National Center for International Biotargeting Theranostics, Guangxi Key Laboratory of Biotargeting Theranostics, Collaborative Innovation Center for Targeting Tumor Theranostics, Guangxi Medical University, 530021, Guangxi, People's Republic of China.
| | - Xing-Jie Liang
- Chinese Academy of Sciences (CAS), Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology of China, 100190, Beijing, People's Republic of China.
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8
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Nakamoto K, Shu Z, Abe H. Disulfide-unit Conjugation Enables Ultrafast Cytosolic Internalization of Antisense DNA and siRNA. J SYN ORG CHEM JPN 2020. [DOI: 10.5059/yukigoseikyokaishi.78.456] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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9
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Abstract
Small interfering RNAs (siRNAs) are a new class of promising therapeutic molecules that can be used for sequence-specific downregulation of disease-causing genes. However, endosomal entrapment of siRNA is a key hurdle for most delivery strategies, limiting the therapeutic effect. Here, we use live-cell microscopy and cytosolic galectin-9 as a sensor of membrane damage, to probe fundamental properties of endosomal escape of cholesterol-conjugated siRNA induced by endosome-disrupting compounds. We demonstrate efficient release of ligand-conjugated siRNA from vesicles damaged by small molecules, enhancing target knockdown up to ∼47-fold in tumor cells. Still, mismatch between siRNA-containing and drug-targeted endolysosomal compartments limits siRNA activity improvement. We also show widespread endosomal damage in macroscopic tumor spheroids after small molecule treatment, substantially improving siRNA delivery and knockdown throughout the spheroid. We believe the strategy to characterize endosomal escape presented here will be widely applicable, facilitating efforts to improve delivery of siRNA and other nucleic acid-based therapeutics.
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10
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Osborn MF, Coles AH, Biscans A, Haraszti RA, Roux L, Davis S, Ly S, Echeverria D, Hassler MR, Godinho BMDC, Nikan M, Khvorova A. Hydrophobicity drives the systemic distribution of lipid-conjugated siRNAs via lipid transport pathways. Nucleic Acids Res 2019; 47:1070-1081. [PMID: 30535404 PMCID: PMC6379714 DOI: 10.1093/nar/gky1232] [Citation(s) in RCA: 79] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2018] [Revised: 11/26/2018] [Accepted: 12/06/2018] [Indexed: 12/22/2022] Open
Abstract
Efficient delivery of therapeutic RNA beyond the liver is the fundamental obstacle preventing its clinical utility. Lipid conjugation increases plasma half-life and enhances tissue accumulation and cellular uptake of small interfering RNAs (siRNAs). However, the mechanism relating lipid hydrophobicity, structure, and siRNA pharmacokinetics is unclear. Here, using a diverse panel of biologically occurring lipids, we show that lipid conjugation directly modulates siRNA hydrophobicity. When administered in vivo, highly hydrophobic lipid-siRNAs preferentially and spontaneously associate with circulating low-density lipoprotein (LDL), while less lipophilic lipid-siRNAs bind to high-density lipoprotein (HDL). Lipid-siRNAs are targeted to lipoprotein receptor-enriched tissues, eliciting significant mRNA silencing in liver (65%), adrenal gland (37%), ovary (35%), and kidney (78%). Interestingly, siRNA internalization may not be completely driven by lipoprotein endocytosis, but the extent of siRNA phosphorothioate modifications may also be a factor. Although biomimetic lipoprotein nanoparticles have been explored for the enhancement of siRNA delivery, our findings suggest that hydrophobic modifications can be leveraged to incorporate therapeutic siRNA into endogenous lipid transport pathways without the requirement for synthetic formulation.
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Affiliation(s)
- Maire F Osborn
- RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, MA, USA.,Department of Molecular Medicine, University of Massachusetts Medical School, Worcester, MA, USA
| | - Andrew H Coles
- RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, MA, USA.,Department of Molecular Medicine, University of Massachusetts Medical School, Worcester, MA, USA
| | - Annabelle Biscans
- RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, MA, USA.,Department of Molecular Medicine, University of Massachusetts Medical School, Worcester, MA, USA
| | - Reka A Haraszti
- RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, MA, USA.,Department of Molecular Medicine, University of Massachusetts Medical School, Worcester, MA, USA
| | - Loic Roux
- RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, MA, USA.,Department of Molecular Medicine, University of Massachusetts Medical School, Worcester, MA, USA
| | - Sarah Davis
- RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, MA, USA.,Department of Molecular Medicine, University of Massachusetts Medical School, Worcester, MA, USA
| | - Socheata Ly
- RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, MA, USA.,Department of Molecular Medicine, University of Massachusetts Medical School, Worcester, MA, USA
| | - Dimas Echeverria
- RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, MA, USA.,Department of Molecular Medicine, University of Massachusetts Medical School, Worcester, MA, USA
| | - Matthew R Hassler
- RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, MA, USA.,Department of Molecular Medicine, University of Massachusetts Medical School, Worcester, MA, USA
| | - Bruno M D C Godinho
- RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, MA, USA.,Department of Molecular Medicine, University of Massachusetts Medical School, Worcester, MA, USA
| | - Mehran Nikan
- RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, MA, USA.,Department of Molecular Medicine, University of Massachusetts Medical School, Worcester, MA, USA
| | - Anastasia Khvorova
- RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, MA, USA.,Department of Molecular Medicine, University of Massachusetts Medical School, Worcester, MA, USA
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11
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A divalent siRNA chemical scaffold for potent and sustained modulation of gene expression throughout the central nervous system. Nat Biotechnol 2019; 37:884-894. [PMID: 31375812 PMCID: PMC6879195 DOI: 10.1038/s41587-019-0205-0] [Citation(s) in RCA: 119] [Impact Index Per Article: 23.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2018] [Accepted: 06/27/2019] [Indexed: 12/20/2022]
Abstract
Sustained silencing of gene expression in deep regions of the brain using small interfering RNAs (siRNAs) has not been achieved. Here we describe an siRNA architecture, divalent-siRNA (Di-siRNA), that supports potent, sustained gene silencing in the central nervous system (CNS) of mice and non-human primates following a single injection into cerebrospinal fluid. Di-siRNAs are composed of two fully chemically modified, phosphorothioate-containing siRNAs connected by a linker. In mice, Di-siRNAs induced potent silencing of huntingtin, the causative gene in Huntington’s disease, reducing mRNA and protein throughout the brain. Silencing persisted for at least six months, with the degree of gene silencing correlating to guide strand tissue accumulation levels. In Cynomolgus macaques, a bolus injection of Di-siRNA showed substantial distribution and robust silencing throughout the brain and spinal cord without detectable toxicity and with minimal off-target effects. This siRNA design may enable RNAi-based gene silencing in the CNS for the treatment of neurological disorders.
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12
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Chemical modulation of siRNA lipophilicity for efficient delivery. J Control Release 2019; 307:98-107. [DOI: 10.1016/j.jconrel.2019.06.022] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2019] [Revised: 06/17/2019] [Accepted: 06/19/2019] [Indexed: 11/19/2022]
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13
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Current Aspects of siRNA Bioconjugate for In Vitro and In Vivo Delivery. Molecules 2019; 24:molecules24122211. [PMID: 31200490 PMCID: PMC6631009 DOI: 10.3390/molecules24122211] [Citation(s) in RCA: 53] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2019] [Revised: 06/03/2019] [Accepted: 06/08/2019] [Indexed: 02/07/2023] Open
Abstract
Studies on siRNA delivery have seen intense growth in the past decades since siRNA has emerged as a new class of gene therapeutics for the treatment of various diseases. siRNA bioconjugate, as one of the major delivery strategies, offers the potential to enhance and broaden pharmacological properties of siRNA, while minimizing the heterogeneity and stability-correlated toxicology. This review summarizes the recent developments of siRNA bioconjugate, including the conjugation with antibody, peptide, aptamer, small chemical, lipidoid, cell-penetrating peptide polymer, and nanoparticle. These siRNA bioconjugate, either administrated alone or formulated with other agents, could significantly improve pharmacokinetic behavior, enhance the biological half-life, and increase the targetability while maintaining sufficient gene silencing activity, with a concomitant improvement of the therapeutic outcomes and diminishment of adverse effects. This review emphasizes the delivery application of these siRNA bioconjugates, especially the conjugation strategy that control the integrity, stability and release of siRNA bioconjugates. The limitations conferred by these conjugation strategies have also been covered.
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14
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Biscans A, Coles A, Echeverria D, Khvorova A. The valency of fatty acid conjugates impacts siRNA pharmacokinetics, distribution, and efficacy in vivo. J Control Release 2019; 302:116-125. [PMID: 30940496 PMCID: PMC6546539 DOI: 10.1016/j.jconrel.2019.03.028] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2018] [Revised: 03/02/2019] [Accepted: 03/29/2019] [Indexed: 12/17/2022]
Abstract
Lipid-conjugated small-interfering RNAs (siRNAs) exhibit accumulation and gene silencing in extrahepatic tissues, providing an opportunity to expand therapeutic siRNA utility beyond the liver. Chemically engineering lipids may further improve siRNA delivery and efficacy, but the relationship between lipid structure/configuration and siRNA pharmacodynamics is unclear. Here, we synthesized a panel of mono-, di-, and tri-meric fatty acid-conjugated siRNAs to systematically evaluate the impact of fatty acid structure and valency on siRNA clearance, distribution, and efficacy. Fatty acid valency significantly altered the physicochemical properties of conjugated siRNAs, including hydrophobicity and micelle formation, which affected distribution. Trivalent lipid-conjugated siRNAs were predominantly retained at the site of injection with minimal systemic exposure, whereas monovalent lipid-conjugated siRNAs were quickly released into the circulation and accumulated primarily in kidney. Divalent lipid-conjugated siRNAs showed intermediate behavior, and preferentially accumulated in liver with functional distribution to lung, heart, and fat. The chemical structure of the conjugate, rather than overall physicochemical properties (i.e. hydrophobicity), predicted the degree of extrahepatic tissue accumulation necessary for productive gene silencing. Our findings will inform chemical engineering strategies for enhancing the extrahepatic delivery of lipophilic siRNAs.
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Affiliation(s)
- Annabelle Biscans
- RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, MA 01604, USA; Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01604, USA
| | - Andrew Coles
- RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, MA 01604, USA; Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01604, USA
| | - Dimas Echeverria
- RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, MA 01604, USA; Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01604, USA
| | - Anastasia Khvorova
- RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, MA 01604, USA; Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01604, USA.
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15
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Chernikov IV, Vlassov VV, Chernolovskaya EL. Current Development of siRNA Bioconjugates: From Research to the Clinic. Front Pharmacol 2019; 10:444. [PMID: 31105570 PMCID: PMC6498891 DOI: 10.3389/fphar.2019.00444] [Citation(s) in RCA: 121] [Impact Index Per Article: 24.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2019] [Accepted: 04/08/2019] [Indexed: 12/12/2022] Open
Abstract
Small interfering RNAs (siRNAs) acting via RNA interference mechanisms are able to recognize a homologous mRNA sequence in the cell and induce its degradation. The main problems in the development of siRNA-based drugs for therapeutic use are the low efficiency of siRNA delivery to target cells and the degradation of siRNAs by nucleases in biological fluids. Various approaches have been proposed to solve the problem of siRNA delivery in vivo (e.g., viruses, cationic lipids, polymers, nanoparticles), but all have limitations for therapeutic use. One of the most promising approaches to solve the problem of siRNA delivery to target cells is bioconjugation; i.e., the covalent connection of siRNAs with biogenic molecules (lipophilic molecules, antibodies, aptamers, ligands, peptides, or polymers). Bioconjugates are "ideal nanoparticles" since they do not need a positive charge to form complexes, are less toxic, and are less effectively recognized by components of the immune system because of their small size. This review is focused on strategies and principles for constructing siRNA bioconjugates for in vivo use.
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Affiliation(s)
- Ivan V Chernikov
- Laboratory of Nucleic Acids Biochemistry, Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - Valentin V Vlassov
- Laboratory of Nucleic Acids Biochemistry, Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - Elena L Chernolovskaya
- Laboratory of Nucleic Acids Biochemistry, Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
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16
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Biscans A, Coles A, Haraszti R, Echeverria D, Hassler M, Osborn M, Khvorova A. Diverse lipid conjugates for functional extra-hepatic siRNA delivery in vivo. Nucleic Acids Res 2019; 47:1082-1096. [PMID: 30544191 PMCID: PMC6379722 DOI: 10.1093/nar/gky1239] [Citation(s) in RCA: 113] [Impact Index Per Article: 22.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2018] [Revised: 11/13/2018] [Accepted: 11/29/2018] [Indexed: 12/24/2022] Open
Abstract
Small interfering RNA (siRNA)-based therapies are proving to be efficient for treating liver-associated disorders. However, extra-hepatic delivery remains challenging, limiting therapeutic siRNA utility. We synthesized a panel of fifteen lipid-conjugated siRNAs and systematically evaluated the impact of conjugate on siRNA tissue distribution and efficacy. Generally, conjugate hydrophobicity defines the degree of clearance and the liver-to-kidney distribution profile. In addition to primary clearance tissues, several conjugates achieve significant siRNA accumulation in muscle, lung, heart, adrenal glands and fat. Oligonucleotide distribution to extra-hepatic tissues with some conjugates was significantly higher than with cholesterol, a well studied conjugate, suggesting that altering conjugate structure can enhance extra-hepatic delivery. These conjugated siRNAs enable functional gene silencing in lung, muscle, fat, heart and adrenal gland. Required levels for productive silencing vary (5-200 μg/g) per tissue, suggesting that the chemical nature of conjugates impacts tissue-dependent cellular/intracellular trafficking mechanisms. The collection of conjugated siRNA described here enables functional gene modulation in vivo in several extra-hepatic tissues opening these tissues for gene expression modulation. A systemic evaluation of a panel of conjugated siRNA, as reported here, has not previously been investigated and shows that chemical engineering of lipid siRNAs is essential to advance the RNA therapeutic field.
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Affiliation(s)
- Annabelle Biscans
- RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, MA 01604, USA
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01604, USA
| | - Andrew Coles
- RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, MA 01604, USA
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01604, USA
| | - Reka Haraszti
- RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, MA 01604, USA
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01604, USA
| | - Dimas Echeverria
- RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, MA 01604, USA
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01604, USA
| | - Matthew Hassler
- RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, MA 01604, USA
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01604, USA
| | - Maire Osborn
- RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, MA 01604, USA
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01604, USA
| | - Anastasia Khvorova
- RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, MA 01604, USA
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01604, USA
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17
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Kubo T, Nishimura Y, Hatori Y, Akagi R, Mihara K, Yanagihara K, Seyama T. Antitumor effect of palmitic acid‐conjugated Dsi
RNA
for colon cancer in a mouse subcutaneous tumor model. Chem Biol Drug Des 2019; 93:570-581. [DOI: 10.1111/cbdd.13454] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2018] [Accepted: 12/07/2018] [Indexed: 12/11/2022]
Affiliation(s)
- Takanori Kubo
- Department of Life ScienceFaculty of PharmacyYasuda Women's University Hiroshima Japan
| | - Yoshio Nishimura
- Department of Life ScienceFaculty of PharmacyYasuda Women's University Hiroshima Japan
| | - Yuta Hatori
- Department of Life ScienceFaculty of PharmacyYasuda Women's University Hiroshima Japan
| | - Reiko Akagi
- Department of Life ScienceFaculty of PharmacyYasuda Women's University Hiroshima Japan
| | - Keichiro Mihara
- Department of Hematology and OncologyResearch Institute for Radiation Biology and MedicineHiroshima University Hiroshima Japan
| | - Kazuyoshi Yanagihara
- Exploratory Oncology Research & Clinical Trial CenterNational Cancer Center Kashiwa Chiba Japan
| | - Toshio Seyama
- Department of Life ScienceFaculty of PharmacyYasuda Women's University Hiroshima Japan
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18
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Gene Silencing in the Right Place at the Right Time. Mol Ther 2018; 26:2539-2541. [PMID: 30366821 DOI: 10.1016/j.ymthe.2018.10.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
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19
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Godinho BMDC, Henninger N, Bouley J, Alterman JF, Haraszti RA, Gilbert JW, Sapp E, Coles AH, Biscans A, Nikan M, Echeverria D, DiFiglia M, Aronin N, Khvorova A. Transvascular Delivery of Hydrophobically Modified siRNAs: Gene Silencing in the Rat Brain upon Disruption of the Blood-Brain Barrier. Mol Ther 2018; 26:2580-2591. [PMID: 30143435 PMCID: PMC6225091 DOI: 10.1016/j.ymthe.2018.08.005] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2018] [Revised: 08/01/2018] [Accepted: 08/03/2018] [Indexed: 12/19/2022] Open
Abstract
Effective transvascular delivery of therapeutic oligonucleotides to the brain presents a major hurdle to the development of gene silencing technologies for treatment of genetically defined neurological disorders. Distribution to the brain after systemic administrations is hampered by the low permeability of the blood-brain barrier (BBB) and the rapid clearance kinetics of these drugs from the blood. Here we show that transient osmotic disruption of the BBB enables transvascular delivery of hydrophobically modified small interfering RNA (hsiRNA) to the rat brain. Intracarotid administration of 25% mannitol and hsiRNA conjugated to phosphocholine-docosahexanoic acid (PC-DHA) resulted in broad ipsilateral distribution of PC-DHA-hsiRNAs in the brain. PC-DHA conjugation enables hsiRNA retention in the parenchyma proximal to the brain vasculature and enabled active internalization by neurons and astrocytes. Moreover, transvascular delivery of PC-DHA-hsiRNAs effected Htt mRNA silencing in the striatum (55%), hippocampus (51%), somatosensory cortex (52%), motor cortex (37%), and thalamus (33%) 1 week after administration. Aside from mild gliosis induced by osmotic disruption of the BBB, transvascular delivery of PC-DHA-hsiRNAs was not associated with neurotoxicity. Together, these findings provide proof-of-concept that temporary disruption of the BBB is an effective strategy for the delivery of therapeutic oligonucleotides to the brain.
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Affiliation(s)
- Bruno M D C Godinho
- RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, MA 01605, USA; Department of Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01605, USA.
| | - Nils Henninger
- Department of Neurology, University of Massachusetts Medical School, Worcester, MA 01605, USA; Department of Psychiatry, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - James Bouley
- Department of Neurology, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Julia F Alterman
- RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, MA 01605, USA; Department of Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Reka A Haraszti
- RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, MA 01605, USA; Department of Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - James W Gilbert
- RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, MA 01605, USA; Department of Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Ellen Sapp
- Department of Neurology, Mass General Institute for Neurodegenerative Disease, Charlestown, MA 02129, USA
| | - Andrew H Coles
- RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, MA 01605, USA; Department of Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Annabelle Biscans
- RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, MA 01605, USA; Department of Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Mehran Nikan
- RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, MA 01605, USA; Department of Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Dimas Echeverria
- RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, MA 01605, USA; Department of Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Marian DiFiglia
- Department of Neurology, Mass General Institute for Neurodegenerative Disease, Charlestown, MA 02129, USA
| | - Neil Aronin
- RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, MA 01605, USA; Department of Medicine, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Anastasia Khvorova
- RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, MA 01605, USA; Department of Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01605, USA.
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20
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Nakamoto K, Akao Y, Furuichi Y, Ueno Y. Enhanced Intercellular Delivery of cRGD-siRNA Conjugates by an Additional Oligospermine Modification. ACS OMEGA 2018; 3:8226-8232. [PMID: 30087937 PMCID: PMC6072241 DOI: 10.1021/acsomega.8b00850] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/29/2018] [Accepted: 06/07/2018] [Indexed: 05/07/2023]
Abstract
Small interfering RNA (siRNA), consisting a 21-mer duplex molecule, is often modified by conjugation with specific ligands to enhance its capacity for tissue-specific delivery. However, these attempts are hampered by the low permeability of negatively charged RNA molecules to enter the cell membrane. In this study, we designed and synthesized siRNA conjugates modified with cationic oligospermine and cyclic RGD (cRGD) to overcome the low-membrane permeability of siRNA. The siRNA conjugate, which contains 15 spermines and a cRGD peptide, showed sufficient gene-silencing activity at 250 nM final concentration without a transfection reagent. Under these conditions, the cationic oligospermine and cRGD-siRNA conjugate did not show any cytotoxicity.
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Affiliation(s)
- Kosuke Nakamoto
- United
Graduate School of Agricultural Science, United Graduate School of Drug
Discovery and Medical Information Sciences, and Faculty of Applied Biological Sciences, Gifu University, 1-1 Yanagido, Gifu 501-1193, Japan
| | - Yukihiro Akao
- United
Graduate School of Agricultural Science, United Graduate School of Drug
Discovery and Medical Information Sciences, and Faculty of Applied Biological Sciences, Gifu University, 1-1 Yanagido, Gifu 501-1193, Japan
| | - Yasuhiro Furuichi
- GeneCare
Research Institute Co., Ltd., 19-2 Kajiwara, Kamakura 247-0063, Japan
| | - Yoshihito Ueno
- United
Graduate School of Agricultural Science, United Graduate School of Drug
Discovery and Medical Information Sciences, and Faculty of Applied Biological Sciences, Gifu University, 1-1 Yanagido, Gifu 501-1193, Japan
- Center
of Highly Advanced Integration of Nano and Life Sciences, Gifu University (G-CHAIN), 1-1 Yanagido, Gifu 501-1193, Japan
- E-mail: . Phone: +81-58-293-2919. Fax: +81-58-293-2919 (Y.U.)
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21
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Haraszti RA, Miller R, Didiot MC, Biscans A, Alterman JF, Hassler MR, Roux L, Echeverria D, Sapp E, DiFiglia M, Aronin N, Khvorova A. Optimized Cholesterol-siRNA Chemistry Improves Productive Loading onto Extracellular Vesicles. Mol Ther 2018; 26:1973-1982. [PMID: 29937418 DOI: 10.1016/j.ymthe.2018.05.024] [Citation(s) in RCA: 57] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2018] [Revised: 05/27/2018] [Accepted: 05/30/2018] [Indexed: 01/01/2023] Open
Abstract
Extracellular vesicles are promising delivery vesicles for therapeutic RNAs. Small interfering RNA (siRNA) conjugation to cholesterol enables efficient and reproducible loading of extracellular vesicles with the therapeutic cargo. siRNAs are typically chemically modified to fit an application. However, siRNA chemical modification pattern has not been specifically optimized for extracellular vesicle-mediated delivery. Here we used cholesterol-conjugated, hydrophobically modified asymmetric siRNAs (hsiRNAs) to evaluate the effect of backbone, 5'-phosphate, and linker chemical modifications on productive hsiRNA loading onto extracellular vesicles. hsiRNAs with a combination of 5'-(E)-vinylphosphonate and alternating 2'-fluoro and 2'-O-methyl backbone modifications outperformed previously used partially modified siRNAs in extracellular vesicle-mediated Huntingtin silencing in neurons. Between two commercially available linkers (triethyl glycol [TEG] and 2-aminobutyl-1-3-propanediol [C7]) widely used to attach cholesterol to siRNAs, TEG is preferred compared to C7 for productive exosomal loading. Destabilization of the linker completely abolished silencing activity of loaded extracellular vesicles. The loading of cholesterol-conjugated siRNAs was saturated at ∼3,000 siRNA copies per extracellular vesicle. Overloading impaired the silencing activity of extracellular vesicles. The data reported here provide an optimization scheme for the successful use of hydrophobic modification as a strategy for productive loading of RNA cargo onto extracellular vesicles.
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Affiliation(s)
- Reka Agnes Haraszti
- RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, MA, USA; Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA, USA
| | - Rachael Miller
- RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, MA, USA; Department of Medicine, University of Massachusetts Medical School, Worcester, MA, USA
| | - Marie-Cecile Didiot
- RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, MA, USA; Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA, USA
| | - Annabelle Biscans
- RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, MA, USA; Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA, USA
| | - Julia F Alterman
- RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, MA, USA; Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA, USA
| | - Matthew R Hassler
- RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, MA, USA; Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA, USA
| | - Loic Roux
- RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, MA, USA; Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA, USA
| | - Dimas Echeverria
- RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, MA, USA; Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA, USA
| | - Ellen Sapp
- Mass General Institute for Neurodegenerative Disease, Boston, MA, USA
| | - Marian DiFiglia
- Mass General Institute for Neurodegenerative Disease, Boston, MA, USA
| | - Neil Aronin
- RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, MA, USA; Department of Medicine, University of Massachusetts Medical School, Worcester, MA, USA.
| | - Anastasia Khvorova
- RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, MA, USA; Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA, USA.
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22
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Osborn MF, Khvorova A. Improving siRNA Delivery In Vivo Through Lipid Conjugation. Nucleic Acid Ther 2018; 28:128-136. [PMID: 29746209 DOI: 10.1089/nat.2018.0725] [Citation(s) in RCA: 77] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
RNA interference (RNAi)-based therapeutics are approaching clinical approval for genetically defined diseases. Current clinical success is a result of significant innovations in the development of chemical architectures that support sustained, multi-month efficacy in vivo following a single administration. Conjugate-mediated delivery has established itself as the most promising platform for safe and targeted small interfering RNA (siRNA) delivery. Lipophilic conjugates represent a major class of modifications that improve siRNA pharmacokinetics and enable efficacy in a broad range of tissues. Here, we review current literature and define key features and limitations of this approach for in vivo modulation of gene expression.
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Affiliation(s)
- Maire F Osborn
- 1 RNA Therapeutics Institute, University of Massachusetts Medical School , Worcester, Massachusetts
| | - Anastasia Khvorova
- 1 RNA Therapeutics Institute, University of Massachusetts Medical School , Worcester, Massachusetts.,2 Department of Molecular Medicine, University of Massachusetts Medical School , Worcester, Massachusetts
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23
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Osborn MF, Coles AH, Golebiowski D, Echeverria D, Moazami MP, Watts JK, Sena-Esteves M, Khvorova A. Efficient Gene Silencing in Brain Tumors with Hydrophobically Modified siRNAs. Mol Cancer Ther 2018; 17:1251-1258. [PMID: 29654062 DOI: 10.1158/1535-7163.mct-17-1144] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2017] [Revised: 02/01/2018] [Accepted: 04/03/2018] [Indexed: 02/06/2023]
Abstract
Glioblastoma (GBM) is the most common and lethal form of primary brain tumor with dismal median and 2-year survivals of 14.5 months and 18%, respectively. The paucity of new therapeutic agents stems from the complex biology of a highly adaptable tumor that uses multiple survival and proliferation mechanisms to circumvent current treatment approaches. Here, we investigated the potency of a new generation of siRNAs to silence gene expression in orthotopic brain tumors generated by transplantation of human glioma stem-like cells in athymic nude mice. We demonstrate that cholesterol-conjugated, nuclease-resistant siRNAs (Chol-hsiRNAs) decrease mRNA and silence luciferase expression by 90% in vitro in GBM neurospheres. Furthermore, Chol-hsiRNAs distribute broadly in brain tumors after a single intratumoral injection, achieving sustained and potent (>45% mRNA and >90% protein) tumor-specific gene silencing. This readily available platform is sequence-independent and can be adapted to target one or more candidate GBM driver genes, providing a straightforward means of modulating GBM biology in vivoMol Cancer Ther; 17(6); 1251-8. ©2018 AACR.
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Affiliation(s)
- Maire F Osborn
- RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, Massachusetts.,Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, Massachusetts
| | - Andrew H Coles
- RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, Massachusetts.,Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, Massachusetts
| | - Diane Golebiowski
- Department of Neurology, University of Massachusetts Medical School, Worcester, Massachusetts.,Horae Gene Therapy Center, University of Massachusetts Medical School, Worcester, Massachusetts
| | - Dimas Echeverria
- RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, Massachusetts.,Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, Massachusetts
| | - Michael P Moazami
- RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, Massachusetts.,Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts
| | - Jonathan K Watts
- RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, Massachusetts.,Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts
| | - Miguel Sena-Esteves
- Department of Neurology, University of Massachusetts Medical School, Worcester, Massachusetts. .,Horae Gene Therapy Center, University of Massachusetts Medical School, Worcester, Massachusetts
| | - Anastasia Khvorova
- RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, Massachusetts. .,Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, Massachusetts
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24
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Biscans A, Haraszti RA, Echeverria D, Miller R, Didiot MC, Nikan M, Roux L, Aronin N, Khvorova A. Hydrophobicity of Lipid-Conjugated siRNAs Predicts Productive Loading to Small Extracellular Vesicles. Mol Ther 2018; 26:1520-1528. [PMID: 29699940 DOI: 10.1016/j.ymthe.2018.03.019] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2018] [Revised: 03/28/2018] [Accepted: 03/28/2018] [Indexed: 12/28/2022] Open
Abstract
Small extracellular vesicles (sEVs) show promise as natural nano-devices for delivery of therapeutic RNA, but efficient loading of therapeutic RNA remains a challenge. We have recently shown that the attachment of cholesterol to small interfering RNAs (siRNAs) enables efficient and productive loading into sEVs. Here, we systematically explore the ability of lipid conjugates-fatty acids, sterols, and vitamins-to load siRNAs into sEVs and support gene silencing in primary neurons. Hydrophobicity of the conjugated siRNAs defined loading efficiency and the silencing activity of siRNA-sEVs complexes. Vitamin-E-conjugated siRNA supported the best loading into sEVs and productive RNA delivery to neurons.
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Affiliation(s)
- Annabelle Biscans
- RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, MA 01605, USA; Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Reka A Haraszti
- RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, MA 01605, USA; Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Dimas Echeverria
- RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, MA 01605, USA; Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Rachael Miller
- RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, MA 01605, USA; Department of Medicine, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Marie-Cecile Didiot
- RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, MA 01605, USA; Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | | | - Loic Roux
- RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, MA 01605, USA; Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Neil Aronin
- RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, MA 01605, USA; Department of Medicine, University of Massachusetts Medical School, Worcester, MA 01605, USA.
| | - Anastasia Khvorova
- RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, MA 01605, USA; Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01605, USA.
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25
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Hassler MR, Turanov AA, Alterman JF, Haraszti RA, Coles AH, Osborn MF, Echeverria D, Nikan M, Salomon WE, Roux L, Godinho BMDC, Davis SM, Morrissey DV, Zamore PD, Karumanchi SA, Moore MJ, Aronin N, Khvorova A. Comparison of partially and fully chemically-modified siRNA in conjugate-mediated delivery in vivo. Nucleic Acids Res 2018; 46:2185-2196. [PMID: 29432571 PMCID: PMC5861422 DOI: 10.1093/nar/gky037] [Citation(s) in RCA: 103] [Impact Index Per Article: 17.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2017] [Revised: 01/09/2018] [Accepted: 01/19/2018] [Indexed: 12/13/2022] Open
Abstract
Small interfering RNA (siRNA)-based drugs require chemical modifications or formulation to promote stability, minimize innate immunity, and enable delivery to target tissues. Partially modified siRNAs (up to 70% of the nucleotides) provide significant stabilization in vitro and are commercially available; thus are commonly used to evaluate efficacy of bio-conjugates for in vivo delivery. In contrast, most clinically-advanced non-formulated compounds, using conjugation as a delivery strategy, are fully chemically modified (100% of nucleotides). Here, we compare partially and fully chemically modified siRNAs in conjugate mediated delivery. We show that fully modified siRNAs are retained at 100x greater levels in various tissues, independently of the nature of the conjugate or siRNA sequence, and support productive mRNA silencing. Thus, fully chemically stabilized siRNAs may provide a better platform to identify novel moieties (peptides, aptamers, small molecules) for targeted RNAi delivery.
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Affiliation(s)
- Matthew R Hassler
- RNA Therapeutics Institute, University of Massachusetts Medical School, USA
| | - Anton A Turanov
- RNA Therapeutics Institute, University of Massachusetts Medical School, USA
| | - Julia F Alterman
- RNA Therapeutics Institute, University of Massachusetts Medical School, USA
| | - Reka A Haraszti
- RNA Therapeutics Institute, University of Massachusetts Medical School, USA
| | - Andrew H Coles
- RNA Therapeutics Institute, University of Massachusetts Medical School, USA
| | - Maire F Osborn
- RNA Therapeutics Institute, University of Massachusetts Medical School, USA
| | - Dimas Echeverria
- RNA Therapeutics Institute, University of Massachusetts Medical School, USA
| | - Mehran Nikan
- RNA Therapeutics Institute, University of Massachusetts Medical School, USA
| | - William E Salomon
- RNA Therapeutics Institute, University of Massachusetts Medical School, USA
| | - Loïc Roux
- RNA Therapeutics Institute, University of Massachusetts Medical School, USA
| | | | - Sarah M Davis
- RNA Therapeutics Institute, University of Massachusetts Medical School, USA
| | | | - Phillip D Zamore
- RNA Therapeutics Institute, University of Massachusetts Medical School, USA
| | | | - Melissa J Moore
- RNA Therapeutics Institute, University of Massachusetts Medical School, USA
| | - Neil Aronin
- RNA Therapeutics Institute, University of Massachusetts Medical School, USA
- Department of Medicine, University of Massachusetts Medical School, USA
| | - Anastasia Khvorova
- RNA Therapeutics Institute, University of Massachusetts Medical School, USA
- Department of Molecular Medicine, University of Massachusetts Medical School, USA
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26
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Grijalvo S, Alagia A, Jorge AF, Eritja R. Covalent Strategies for Targeting Messenger and Non-Coding RNAs: An Updated Review on siRNA, miRNA and antimiR Conjugates. Genes (Basel) 2018; 9:E74. [PMID: 29415514 PMCID: PMC5852570 DOI: 10.3390/genes9020074] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2018] [Revised: 01/26/2018] [Accepted: 01/26/2018] [Indexed: 12/11/2022] Open
Abstract
Oligonucleotide-based therapy has become an alternative to classical approaches in the search of novel therapeutics involving gene-related diseases. Several mechanisms have been described in which demonstrate the pivotal role of oligonucleotide for modulating gene expression. Antisense oligonucleotides (ASOs) and more recently siRNAs and miRNAs have made important contributions either in reducing aberrant protein levels by sequence-specific targeting messenger RNAs (mRNAs) or restoring the anomalous levels of non-coding RNAs (ncRNAs) that are involved in a good number of diseases including cancer. In addition to formulation approaches which have contributed to accelerate the presence of ASOs, siRNAs and miRNAs in clinical trials; the covalent linkage between non-viral vectors and nucleic acids has also added value and opened new perspectives to the development of promising nucleic acid-based therapeutics. This review article is mainly focused on the strategies carried out for covalently modifying siRNA and miRNA molecules. Examples involving cell-penetrating peptides (CPPs), carbohydrates, polymers, lipids and aptamers are discussed for the synthesis of siRNA conjugates whereas in the case of miRNA-based drugs, this review article makes special emphasis in using antagomiRs, locked nucleic acids (LNAs), peptide nucleic acids (PNAs) as well as nanoparticles. The biomedical applications of siRNA and miRNA conjugates are also discussed.
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Affiliation(s)
- Santiago Grijalvo
- Institute of Advanced Chemistry of Catalonia (IQAC, CSIC), Jordi Girona 18-26, 08034 Barcelona, Spain.
- Networking Centre in Bioengineering, Biomaterials and Nanomedicine (CIBER-BBN), Jordi Girona 18-26, 08034 Barcelona, Spain.
| | - Adele Alagia
- Networking Centre in Bioengineering, Biomaterials and Nanomedicine (CIBER-BBN), Jordi Girona 18-26, 08034 Barcelona, Spain.
| | - Andreia F Jorge
- Coimbra Chemistry Centre, (CQC), Department of Chemistry, University of Coimbra, Rua Larga, 3004-535 Coimbra, Portugal.
| | - Ramon Eritja
- Institute of Advanced Chemistry of Catalonia (IQAC, CSIC), Jordi Girona 18-26, 08034 Barcelona, Spain.
- Networking Centre in Bioengineering, Biomaterials and Nanomedicine (CIBER-BBN), Jordi Girona 18-26, 08034 Barcelona, Spain.
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27
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Godinho BMDC, Gilbert JW, Haraszti RA, Coles AH, Biscans A, Roux L, Nikan M, Echeverria D, Hassler M, Khvorova A. Pharmacokinetic Profiling of Conjugated Therapeutic Oligonucleotides: A High-Throughput Method Based Upon Serial Blood Microsampling Coupled to Peptide Nucleic Acid Hybridization Assay. Nucleic Acid Ther 2017; 27:323-334. [PMID: 29022758 DOI: 10.1089/nat.2017.0690] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Therapeutic oligonucleotides, such as small interfering RNAs (siRNAs), hold great promise for the treatment of incurable genetically defined disorders by targeting cognate toxic gene products for degradation. To achieve meaningful tissue distribution and efficacy in vivo, siRNAs must be conjugated or formulated. Clear understanding of the pharmacokinetic (PK)/pharmacodynamic behavior of these compounds is necessary to optimize and characterize the performance of therapeutic oligonucleotides in vivo. In this study, we describe a simple and reproducible methodology for the evaluation of in vivo blood/plasma PK profiles and tissue distribution of oligonucleotides. The method is based on serial blood microsampling from the saphenous vein, coupled to peptide nucleic acid hybridization assay for quantification of guide strands. Performed with minimal number of animals, this method allowed unequivocal detection and sensitive quantification without the need for amplification, or further modification of the oligonucleotides. Using this methodology, we compared plasma clearances and tissue distribution profiles of two different hydrophobically modified siRNAs (hsiRNAs). Notably, cholesterol-hsiRNA presented slow plasma clearances and mainly accumulated in the liver, whereas, phosphocholine-docosahexaenoic acid-hsiRNA was rapidly cleared from the plasma and preferably accumulated in the kidney. These data suggest that the PK/biodistribution profiles of modified hsiRNAs are determined by the chemical nature of the conjugate. Importantly, the method described in this study constitutes a simple platform to conduct pilot assessments of the basic clearance and tissue distribution profiles, which can be broadly applied for evaluation of new chemical variants of siRNAs and micro-RNAs.
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Affiliation(s)
- Bruno M D C Godinho
- 1 RNA Therapeutics Institute, University of Massachusetts Medical School , Worcester, Massachusetts.,2 Department of Molecular Medicine, University of Massachusetts Medical School , Worcester, Massachusetts
| | - James W Gilbert
- 1 RNA Therapeutics Institute, University of Massachusetts Medical School , Worcester, Massachusetts.,2 Department of Molecular Medicine, University of Massachusetts Medical School , Worcester, Massachusetts
| | - Reka A Haraszti
- 1 RNA Therapeutics Institute, University of Massachusetts Medical School , Worcester, Massachusetts.,2 Department of Molecular Medicine, University of Massachusetts Medical School , Worcester, Massachusetts
| | - Andrew H Coles
- 1 RNA Therapeutics Institute, University of Massachusetts Medical School , Worcester, Massachusetts.,2 Department of Molecular Medicine, University of Massachusetts Medical School , Worcester, Massachusetts
| | - Annabelle Biscans
- 1 RNA Therapeutics Institute, University of Massachusetts Medical School , Worcester, Massachusetts.,2 Department of Molecular Medicine, University of Massachusetts Medical School , Worcester, Massachusetts
| | - Loic Roux
- 1 RNA Therapeutics Institute, University of Massachusetts Medical School , Worcester, Massachusetts.,2 Department of Molecular Medicine, University of Massachusetts Medical School , Worcester, Massachusetts
| | - Mehran Nikan
- 1 RNA Therapeutics Institute, University of Massachusetts Medical School , Worcester, Massachusetts.,2 Department of Molecular Medicine, University of Massachusetts Medical School , Worcester, Massachusetts
| | - Dimas Echeverria
- 1 RNA Therapeutics Institute, University of Massachusetts Medical School , Worcester, Massachusetts.,2 Department of Molecular Medicine, University of Massachusetts Medical School , Worcester, Massachusetts
| | - Matthew Hassler
- 1 RNA Therapeutics Institute, University of Massachusetts Medical School , Worcester, Massachusetts.,2 Department of Molecular Medicine, University of Massachusetts Medical School , Worcester, Massachusetts
| | - Anastasia Khvorova
- 1 RNA Therapeutics Institute, University of Massachusetts Medical School , Worcester, Massachusetts.,2 Department of Molecular Medicine, University of Massachusetts Medical School , Worcester, Massachusetts
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28
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Pendergraff HM, Krishnamurthy PM, Debacker AJ, Moazami MP, Sharma VK, Niitsoo L, Yu Y, Tan YN, Haitchi HM, Watts JK. Locked Nucleic Acid Gapmers and Conjugates Potently Silence ADAM33, an Asthma-Associated Metalloprotease with Nuclear-Localized mRNA. MOLECULAR THERAPY. NUCLEIC ACIDS 2017; 8:158-168. [PMID: 28918018 PMCID: PMC5498289 DOI: 10.1016/j.omtn.2017.06.012] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/05/2017] [Revised: 06/15/2017] [Accepted: 06/16/2017] [Indexed: 12/22/2022]
Abstract
Two mechanisms dominate the clinical pipeline for oligonucleotide-based gene silencing, namely, the antisense approach that recruits RNase H to cleave target RNA and the RNAi approach that recruits the RISC complex to cleave target RNA. Multiple chemical designs can be used to elicit each pathway. We compare the silencing of the asthma susceptibility gene ADAM33 in MRC-5 lung fibroblasts using four classes of gene silencing agents, two that use each mechanism: traditional duplex small interfering RNAs (siRNAs), single-stranded small interfering RNAs (ss-siRNAs), locked nucleic acid (LNA) gapmer antisense oligonucleotides (ASOs), and novel hexadecyloxypropyl conjugates of the ASOs. Of these designs, the gapmer ASOs emerged as lead compounds for silencing ADAM33 expression: several gapmer ASOs showed subnanomolar potency when transfected with cationic lipid and low micromolar potency with no toxicity when delivered gymnotically. The preferential susceptibility of ADAM33 mRNA to silencing by RNase H may be related to the high degree of nuclear retention observed for this mRNA. Dynamic light scattering data showed that the hexadecyloxypropyl ASO conjugates self-assemble into clusters. These conjugates showed reduced potency relative to unconjugated ASOs unless the lipophilic tail was conjugated to the ASO using a biocleavable linkage. Finally, based on the lead ASOs from (human) MRC-5 cells, we developed a series of homologous ASOs targeting mouse Adam33 with excellent activity. Our work confirms that ASO-based gene silencing of ADAM33 is a useful tool for asthma research and therapy.
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Affiliation(s)
- Hannah M Pendergraff
- Department of Chemistry, University of Southampton, Southampton SO17 1BJ, UK; Institute for Life Sciences, University of Southampton, Southampton SO17 1BJ, UK
| | - Pranathi Meda Krishnamurthy
- RNA Therapeutics Institute, UMass Medical School, Worcester, MA 01605, USA; Department of Biochemistry and Molecular Pharmacology, UMass Medical School, Worcester, MA 01605, USA
| | - Alexandre J Debacker
- Department of Chemistry, University of Southampton, Southampton SO17 1BJ, UK; Institute for Life Sciences, University of Southampton, Southampton SO17 1BJ, UK; RNA Therapeutics Institute, UMass Medical School, Worcester, MA 01605, USA; Department of Biochemistry and Molecular Pharmacology, UMass Medical School, Worcester, MA 01605, USA
| | - Michael P Moazami
- Department of Chemistry, University of Southampton, Southampton SO17 1BJ, UK; Institute for Life Sciences, University of Southampton, Southampton SO17 1BJ, UK; RNA Therapeutics Institute, UMass Medical School, Worcester, MA 01605, USA; Department of Biochemistry and Molecular Pharmacology, UMass Medical School, Worcester, MA 01605, USA
| | - Vivek K Sharma
- Department of Chemistry, University of Southampton, Southampton SO17 1BJ, UK; Institute for Life Sciences, University of Southampton, Southampton SO17 1BJ, UK; RNA Therapeutics Institute, UMass Medical School, Worcester, MA 01605, USA; Department of Biochemistry and Molecular Pharmacology, UMass Medical School, Worcester, MA 01605, USA
| | - Liisa Niitsoo
- Department of Chemistry, University of Southampton, Southampton SO17 1BJ, UK; Institute for Life Sciences, University of Southampton, Southampton SO17 1BJ, UK
| | - Yong Yu
- Institute of Materials Research and Engineering, A*STAR, Singapore 138634, Singapore
| | - Yen Nee Tan
- Institute of Materials Research and Engineering, A*STAR, Singapore 138634, Singapore
| | - Hans Michael Haitchi
- Institute for Life Sciences, University of Southampton, Southampton SO17 1BJ, UK; Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton SO16 6YD, UK; NIHR Southampton Respiratory Biomedical Research Unit at University Hospital Southampton NHS Foundation Trust, Southampton, Southampton SO16 6YD, UK.
| | - Jonathan K Watts
- Department of Chemistry, University of Southampton, Southampton SO17 1BJ, UK; Institute for Life Sciences, University of Southampton, Southampton SO17 1BJ, UK; RNA Therapeutics Institute, UMass Medical School, Worcester, MA 01605, USA; Department of Biochemistry and Molecular Pharmacology, UMass Medical School, Worcester, MA 01605, USA.
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