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Tekintaş Y, Temel A. Antisense oligonucleotides: a promising therapeutic option against infectious diseases. NUCLEOSIDES, NUCLEOTIDES & NUCLEIC ACIDS 2023; 43:1-39. [PMID: 37395450 DOI: 10.1080/15257770.2023.2228841] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/07/2022] [Accepted: 06/19/2023] [Indexed: 07/04/2023]
Abstract
Infectious diseases have been one of the biggest health problems of humanity for centuries. Nucleic acid-based therapeutics have received attention in recent years with their effectiveness in the treatment of various infectious diseases and vaccine development studies. This review aims to provide a comprehensive understanding of the basic properties underlying the mechanism of antisense oligonucleotides (ASOs), their applications, and their challenges. The efficient delivery of ASOs is the greatest challenge for their therapeutic success, but this problem is overcome with new-generation antisense molecules developed with chemical modifications. The types, carrier molecules, and gene regions targeted by sequences have been summarized in detail. Research and development of antisense therapy is still in its infancy; however, gene silencing therapies appear to have the potential for faster and longer-lasting activity than conventional treatment strategies. On the other hand, realizing the potential of antisense therapy will require a large initial economic investment to ascertain the pharmacological properties and learn how to optimize them. The ability of ASOs to be rapidly designed and synthesized to target different microbes can reduce drug discovery time from 6 years to 1 year. Since ASOs are not particularly affected by resistance mechanisms, they come to the fore in the fight against antimicrobial resistance. The design-based flexibility of ASOs has enabled it to be used for different types of microorganisms/genes and successful in vitro and in vivo results have been revealed. The current review summarized a comprehensive understanding of ASO therapy in combating bacterial and viral infections.
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Affiliation(s)
- Yamaç Tekintaş
- Department of Pharmaceutical Microbiology, Faculty of Pharmacy, Izmir Katip Celebi University, Izmir, Türkiye
| | - Aybala Temel
- Department of Pharmaceutical Microbiology, Faculty of Pharmacy, Izmir Katip Celebi University, Izmir, Türkiye
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2
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Friedman L, Avitzur OB, Galai EO, Ferrari N, Choen A, Dahan S, Mordechai T, Hart G. The safety and toxicity profile of SPL84, an inhaled antisense oligonucleotide for treatment of cystic fibrosis patients with the 3849 +10kb C->T mutation, supports a Phase 1/2 clinical study. Expert Opin Drug Metab Toxicol 2023; 19:709-720. [PMID: 37799089 DOI: 10.1080/17425255.2023.2266361] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2023] [Accepted: 09/15/2023] [Indexed: 10/07/2023]
Abstract
INTRODUCTION SPL84 is an inhaled antisense oligonucleotide (ASO) in development for the treatment of cystic fibrosis (CF) patients carrying the 3849 + 10kb C->T (3849) mutation. To support the initiation of the first clinical study, a full battery of safety and toxicology studies were performed. RESEARCH DESIGN AND METHODS SPL84 was administered by inhalation to mice and monkeys to determine the no observed adverse effect level (NOAEL) and establish sufficient safety margins for the starting clinical dose. RESULTS There were no preclinical safety findings with SPL84; no related clinical signs, nor any effect on body weight, food consumption, or clinical pathology. The microscopic changes in the lungs were regarded as non-adverse and reflected a normal clearance process for inhaled compounds. Systemic exposure in both species was low. The NOAEL for mice and monkeys was the highest administered dose in both species, resulting in safety margins ~ 40X the proposed starting clinical dose. CONCLUSION These successful results supported the initiation of a phase 1/2 clinical study of SPL84 (ongoing), assessing the safety, tolerability, and pharmacokinetics of a single ascending dose in healthy subjects to be followed by assessment of safety, tolerability, pharmacokinetics, and preliminary efficacy of multiple ascending doses in CF patients carrying the 3849 mutation.
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Affiliation(s)
- Lital Friedman
- SpliSense, BiohouseLabs, Haddasah Ein Kerem, Jerusalem, Israel
| | | | | | | | - Asa Choen
- SpliSense, BiohouseLabs, Haddasah Ein Kerem, Jerusalem, Israel
| | - Sara Dahan
- SpliSense, BiohouseLabs, Haddasah Ein Kerem, Jerusalem, Israel
| | - Tamar Mordechai
- SpliSense, BiohouseLabs, Haddasah Ein Kerem, Jerusalem, Israel
| | - Gili Hart
- SpliSense, BiohouseLabs, Haddasah Ein Kerem, Jerusalem, Israel
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3
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Huang S, Hao XY, Li YJ, Wu JY, Xiang DX, Luo S. Nonviral delivery systems for antisense oligonucleotide therapeutics. Biomater Res 2022; 26:49. [PMID: 36180936 PMCID: PMC9523189 DOI: 10.1186/s40824-022-00292-4] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2022] [Accepted: 08/30/2022] [Indexed: 11/10/2022] Open
Abstract
Antisense oligonucleotides (ASOs) are an important tool for the treatment of many genetic disorders. However, similar to other gene drugs, vectors are often required to protect them from degradation and clearance, and to accomplish their transport in vivo. Compared with viral vectors, artificial nonviral nanoparticles have a variety of design, synthesis, and formulation possibilities that can be selected to accomplish protection and delivery for specific applications, and they have served critical therapeutic purposes in animal model research and clinical applications, allowing safe and efficient gene delivery processes into the target cells. We believe that as new ASO drugs develop, the exploration for corresponding nonviral vectors is inevitable. Intensive development of nonviral vectors with improved delivery strategies based on specific targets can continue to expand the value of ASO therapeutic approaches. Here, we provide an overview of current nonviral delivery strategies, including ASOs modifications, action mechanisms, and multi-carrier methods, which aim to address the irreplaceable role of nonviral vectors in the progressive development of ASOs delivery.
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Affiliation(s)
- Si Huang
- Department of Pharmacy, the Second Xiangya Hospital, Central South University, Changsha, 410011, People's Republic of China.,Hunan Provincial Engineering Research Centre of Translational Medicine and Innovative Drug, Changsha, 410011, People's Republic of China.,Institute of Clinical Pharmacy, Central South University, Changsha, China
| | - Xin-Yan Hao
- Department of Pharmacy, the Second Xiangya Hospital, Central South University, Changsha, 410011, People's Republic of China.,Hunan Provincial Engineering Research Centre of Translational Medicine and Innovative Drug, Changsha, 410011, People's Republic of China.,Institute of Clinical Pharmacy, Central South University, Changsha, China
| | - Yong-Jiang Li
- Department of Pharmacy, the Second Xiangya Hospital, Central South University, Changsha, 410011, People's Republic of China.,Hunan Provincial Engineering Research Centre of Translational Medicine and Innovative Drug, Changsha, 410011, People's Republic of China.,Institute of Clinical Pharmacy, Central South University, Changsha, China
| | - Jun-Yong Wu
- Department of Pharmacy, the Second Xiangya Hospital, Central South University, Changsha, 410011, People's Republic of China.,Hunan Provincial Engineering Research Centre of Translational Medicine and Innovative Drug, Changsha, 410011, People's Republic of China.,Institute of Clinical Pharmacy, Central South University, Changsha, China
| | - Da-Xiong Xiang
- Department of Pharmacy, the Second Xiangya Hospital, Central South University, Changsha, 410011, People's Republic of China.,Hunan Provincial Engineering Research Centre of Translational Medicine and Innovative Drug, Changsha, 410011, People's Republic of China.,Institute of Clinical Pharmacy, Central South University, Changsha, China
| | - Shilin Luo
- Department of Pharmacy, the Second Xiangya Hospital, Central South University, Changsha, 410011, People's Republic of China. .,Hunan Provincial Engineering Research Centre of Translational Medicine and Innovative Drug, Changsha, 410011, People's Republic of China. .,Institute of Clinical Pharmacy, Central South University, Changsha, China.
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4
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Rouse WB, O'Leary CA, Booher NJ, Moss WN. Expansion of the RNAStructuromeDB to include secondary structural data spanning the human protein-coding transcriptome. Sci Rep 2022; 12:14515. [PMID: 36008510 PMCID: PMC9403969 DOI: 10.1038/s41598-022-18699-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2022] [Accepted: 08/17/2022] [Indexed: 11/22/2022] Open
Abstract
RNA plays vital functional roles in almost every component of biology, and these functional roles are often influenced by its folding into secondary and tertiary structures. An important role of RNA secondary structure is in maintaining proper gene regulation; therefore, making accurate predictions of the structures involved in these processes is important. In this study, we have expanded on our previous work that led to the creation of the RNAStructuromeDB. Unlike this previous study that analyzed the human genome at low resolution, we have now scanned the protein-coding human transcriptome at high (single nt) resolution. This provides more robust structure predictions for over 100,000 isoforms of known protein-coding genes. Notably, we also utilize the motif identification tool, ScanFold, to model structures with high propensity for ordered/evolved stability. All data have been uploaded to the RNAStructuromeDB, allowing for easy searching of transcripts, visualization of data tracks (via the Integrative Genomics Viewer or IGV), and download of ScanFold data—including unique highly-ordered motifs. Herein, we provide an example analysis of MAT2A to demonstrate the utility of ScanFold at finding known and novel secondary structures, highlighting regions of potential functionality, and guiding generation of functional hypotheses through use of the data.
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Affiliation(s)
- Warren B Rouse
- Roy J. Carver Department of Biophysics, Biochemistry and Molecular Biology, Iowa State University, Ames, IA, 50011, USA
| | - Collin A O'Leary
- Roy J. Carver Department of Biophysics, Biochemistry and Molecular Biology, Iowa State University, Ames, IA, 50011, USA
| | - Nicholas J Booher
- Infrastructure and Research IT Services, Iowa State University, Ames, IA, 50011, USA
| | - Walter N Moss
- Roy J. Carver Department of Biophysics, Biochemistry and Molecular Biology, Iowa State University, Ames, IA, 50011, USA.
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5
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RNA modifications can affect RNase H1-mediated PS-ASO activity. MOLECULAR THERAPY - NUCLEIC ACIDS 2022; 28:814-828. [PMID: 35664704 PMCID: PMC9136273 DOI: 10.1016/j.omtn.2022.05.024] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/21/2021] [Accepted: 05/07/2022] [Indexed: 11/21/2022]
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6
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Kim YJ, Nomakuchi T, Papaleonidopoulou F, Yang L, Zhang Q, Krainer AR. Gene-specific nonsense-mediated mRNA decay targeting for cystic fibrosis therapy. Nat Commun 2022; 13:2978. [PMID: 35624092 PMCID: PMC9142507 DOI: 10.1038/s41467-022-30668-y] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2021] [Accepted: 05/06/2022] [Indexed: 12/20/2022] Open
Abstract
Low CFTR mRNA expression due to nonsense-mediated mRNA decay (NMD) is a major hurdle in developing a therapy for cystic fibrosis (CF) caused by the W1282X mutation in the CFTR gene. CFTR-W1282X truncated protein retains partial function, so increasing its levels by inhibiting NMD of its mRNA will likely be beneficial. Because NMD regulates the normal expression of many genes, gene-specific stabilization of CFTR-W1282X mRNA expression is more desirable than general NMD inhibition. Synthetic antisense oligonucleotides (ASOs) designed to prevent binding of exon junction complexes (EJC) downstream of premature termination codons (PTCs) attenuate NMD in a gene-specific manner. We describe cocktails of three ASOs that specifically increase the expression of CFTR-W1282X mRNA and CFTR protein upon delivery into human bronchial epithelial cells. This treatment increases the CFTR-mediated chloride current. These results set the stage for clinical development of an allele-specific therapy for CF caused by the W1282X mutation. The W1282X nonsense mutation in the CFTR gene causes cystic fibrosis by reducing its mRNA and functional protein levels. Here the authors developed antisense-oligonucleotide cocktails that restore CFTR protein function by gene-specific stabilization of CFTR mRNA.
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Affiliation(s)
- Young Jin Kim
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, 11724, USA.,Graduate Program in Genetics, Stony Brook University, Stony Brook, NY, 11794, USA.,Medical Scientist Training Program, Stony Brook University School of Medicine, Stony Brook, NY, 11794, USA
| | - Tomoki Nomakuchi
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, 11724, USA.,Medical Scientist Training Program, Stony Brook University School of Medicine, Stony Brook, NY, 11794, USA.,Division of Human Genetics, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA
| | - Foteini Papaleonidopoulou
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, 11724, USA.,Francis Crick Institute, London, 1140062, UK
| | - Lucia Yang
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, 11724, USA.,Graduate Program in Genetics, Stony Brook University, Stony Brook, NY, 11794, USA.,Medical Scientist Training Program, Stony Brook University School of Medicine, Stony Brook, NY, 11794, USA
| | - Qian Zhang
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, 11724, USA.,Graduate Program in Molecular and Cell Biology, Stony Brook University, Stony Brook, NY, 11794, USA
| | - Adrian R Krainer
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, 11724, USA.
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7
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Tang PCT, Zhang YY, Li JSF, Chan MKK, Chen J, Tang Y, Zhou Y, Zhang D, Leung KT, To KF, Tang SCW, Lan HY, Tang PMK. LncRNA-Dependent Mechanisms of Transforming Growth Factor-β: From Tissue Fibrosis to Cancer Progression. Noncoding RNA 2022; 8:ncrna8030036. [PMID: 35736633 PMCID: PMC9227532 DOI: 10.3390/ncrna8030036] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2022] [Revised: 05/19/2022] [Accepted: 05/21/2022] [Indexed: 11/16/2022] Open
Abstract
Transforming growth factor-β (TGF-β) is a crucial pathogenic mediator of inflammatory diseases. In tissue fibrosis, TGF-β regulates the pathogenic activity of infiltrated immunocytes and promotes extracellular matrix production via de novo myofibroblast generation and kidney cell activation. In cancer, TGF-β promotes cancer invasion and metastasis by enhancing the stemness and epithelial mesenchymal transition of cancer cells. However, TGF-β is highly pleiotropic in both tissue fibrosis and cancers, and thus, direct targeting of TGF-β may also block its protective anti-inflammatory and tumor-suppressive effects, resulting in undesirable outcomes. Increasing evidence suggests the involvement of long non-coding RNAs (lncRNAs) in TGF-β-driven tissue fibrosis and cancer progression with a high cell-type and disease specificity, serving as an ideal target for therapeutic development. In this review, the mechanism and translational potential of TGF-β-associated lncRNAs in tissue fibrosis and cancer will be discussed.
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Affiliation(s)
- Philip Chiu-Tsun Tang
- Department of Anatomical and Cellular Pathology, State Key Laboratory of Translational Oncology, The Chinese University of Hong Kong, Hong Kong 999077, China; (P.C.-T.T.); (J.S.-F.L.); (M.K.-K.C.); (K.-F.T.)
| | - Ying-Ying Zhang
- Department of Nephrology, Tongji University School of Medicine, Shanghai 200065, China;
| | - Jane Siu-Fan Li
- Department of Anatomical and Cellular Pathology, State Key Laboratory of Translational Oncology, The Chinese University of Hong Kong, Hong Kong 999077, China; (P.C.-T.T.); (J.S.-F.L.); (M.K.-K.C.); (K.-F.T.)
| | - Max Kam-Kwan Chan
- Department of Anatomical and Cellular Pathology, State Key Laboratory of Translational Oncology, The Chinese University of Hong Kong, Hong Kong 999077, China; (P.C.-T.T.); (J.S.-F.L.); (M.K.-K.C.); (K.-F.T.)
| | - Jiaoyi Chen
- Division of Nephrology, Department of Medicine, The University of Hong Kong, Hong Kong 999077, China; (J.C.); (S.C.-W.T.)
| | - Ying Tang
- Department of Nephrology, The Third Affiliated Hospital of Southern Medical University, Guangzhou 510080, China;
| | - Yiming Zhou
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Guangdong-Hong Kong Joint Laboratory for RNA Medicine, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou 510120, China;
| | - Dongmei Zhang
- College of Pharmacy, Jinan University, Guangzhou 510632, China;
| | - Kam-Tong Leung
- Department of Paediatrics, The Chinese University of Hong Kong, Hong Kong 999077, China;
| | - Ka-Fai To
- Department of Anatomical and Cellular Pathology, State Key Laboratory of Translational Oncology, The Chinese University of Hong Kong, Hong Kong 999077, China; (P.C.-T.T.); (J.S.-F.L.); (M.K.-K.C.); (K.-F.T.)
| | - Sydney Chi-Wai Tang
- Division of Nephrology, Department of Medicine, The University of Hong Kong, Hong Kong 999077, China; (J.C.); (S.C.-W.T.)
| | - Hui-Yao Lan
- Department of Medicine and Therapeutics, Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Hong Kong 999077, China;
| | - Patrick Ming-Kuen Tang
- Department of Anatomical and Cellular Pathology, State Key Laboratory of Translational Oncology, The Chinese University of Hong Kong, Hong Kong 999077, China; (P.C.-T.T.); (J.S.-F.L.); (M.K.-K.C.); (K.-F.T.)
- Correspondence:
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8
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Zhang K, Zheludev IN, Hagey RJ, Haslecker R, Hou YJ, Kretsch R, Pintilie GD, Rangan R, Kladwang W, Li S, Wu MTP, Pham EA, Bernardin-Souibgui C, Baric RS, Sheahan TP, D'Souza V, Glenn JS, Chiu W, Das R. Cryo-EM and antisense targeting of the 28-kDa frameshift stimulation element from the SARS-CoV-2 RNA genome. Nat Struct Mol Biol 2021; 28:747-754. [PMID: 34426697 PMCID: PMC8848339 DOI: 10.1038/s41594-021-00653-y] [Citation(s) in RCA: 81] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Accepted: 07/29/2021] [Indexed: 02/07/2023]
Abstract
Drug discovery campaigns against COVID-19 are beginning to target the SARS-CoV-2 RNA genome. The highly conserved frameshift stimulation element (FSE), required for balanced expression of viral proteins, is a particularly attractive SARS-CoV-2 RNA target. Here we present a 6.9 Å resolution cryo-EM structure of the FSE (88 nucleotides, ~28 kDa), validated through an RNA nanostructure tagging method. The tertiary structure presents a topologically complex fold in which the 5' end is threaded through a ring formed inside a three-stem pseudoknot. Guided by this structure, we develop antisense oligonucleotides that impair FSE function in frameshifting assays and knock down SARS-CoV-2 virus replication in A549-ACE2 cells at 100 nM concentration.
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Affiliation(s)
- Kaiming Zhang
- Departments of Bioengineering, James H. Clark Center, Stanford University, Stanford, CA, USA
- MOE Key Laboratory for Membraneless Organelles and Cellular Dynamics, Hefei National Laboratory for Physical Sciences at the Microscale and School of Life Sciences, University of Science and Technology of China, Hefei, China
| | - Ivan N Zheludev
- Department of Biochemistry Stanford University, Stanford, CA, USA
| | - Rachel J Hagey
- Departments of Medicine (Division of Gastroenterology and Hepatology) and Microbiology & Immunology, Stanford School of Medicine, Stanford, CA, USA
| | - Raphael Haslecker
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA, USA
| | - Yixuan J Hou
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | | | - Grigore D Pintilie
- Departments of Bioengineering, James H. Clark Center, Stanford University, Stanford, CA, USA
| | - Ramya Rangan
- Biophysics Program, Stanford University, Stanford, CA, USA
| | - Wipapat Kladwang
- Department of Biochemistry Stanford University, Stanford, CA, USA
| | - Shanshan Li
- Departments of Bioengineering, James H. Clark Center, Stanford University, Stanford, CA, USA
- MOE Key Laboratory for Membraneless Organelles and Cellular Dynamics, Hefei National Laboratory for Physical Sciences at the Microscale and School of Life Sciences, University of Science and Technology of China, Hefei, China
| | - Marie Teng-Pei Wu
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA, USA
| | - Edward A Pham
- Departments of Medicine (Division of Gastroenterology and Hepatology) and Microbiology & Immunology, Stanford School of Medicine, Stanford, CA, USA
| | - Claire Bernardin-Souibgui
- Departments of Medicine (Division of Gastroenterology and Hepatology) and Microbiology & Immunology, Stanford School of Medicine, Stanford, CA, USA
| | - Ralph S Baric
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Timothy P Sheahan
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Victoria D'Souza
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA, USA
| | - Jeffrey S Glenn
- Departments of Medicine (Division of Gastroenterology and Hepatology) and Microbiology & Immunology, Stanford School of Medicine, Stanford, CA, USA.
- Palo Alto Veterans Administration, Palo Alto, CA, USA.
| | - Wah Chiu
- Departments of Bioengineering, James H. Clark Center, Stanford University, Stanford, CA, USA.
- Biophysics Program, Stanford University, Stanford, CA, USA.
- CryoEM and Bioimaging Division, Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Stanford University, Menlo Park, CA, USA.
| | - Rhiju Das
- Department of Biochemistry Stanford University, Stanford, CA, USA.
- Biophysics Program, Stanford University, Stanford, CA, USA.
- Department of Physics, Stanford University, Stanford, CA, USA.
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Antisense technology: an overview and prospectus. Nat Rev Drug Discov 2021; 20:427-453. [PMID: 33762737 DOI: 10.1038/s41573-021-00162-z] [Citation(s) in RCA: 302] [Impact Index Per Article: 100.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/08/2021] [Indexed: 12/13/2022]
Abstract
Antisense technology is now beginning to deliver on its promise to treat diseases by targeting RNA. Nine single-stranded antisense oligonucleotide (ASO) drugs representing four chemical classes, two mechanisms of action and four routes of administration have been approved for commercial use, including the first RNA-targeted drug to be a major commercial success, nusinersen. Although all the approved drugs are for use in patients with rare diseases, many of the ASOs in late- and middle-stage clinical development are intended to treat patients with very common diseases. ASOs in development are showing substantial improvements in potency and performance based on advances in medicinal chemistry, understanding of molecular mechanisms and targeted delivery. Moreover, the ASOs in development include additional mechanisms of action and routes of administration such as aerosol and oral formulations. Here, we describe the key technological advances that have enabled this progress and discuss recent clinical trials that illustrate the impact of these advances on the performance of ASOs in a wide range of therapeutic applications. We also consider strategic issues such as target selection and provide perspectives on the future of the field.
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10
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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: 146] [Impact Index Per Article: 48.7] [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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11
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12
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Liang XH, Nichols JG, De Hoyos CL, Crooke ST. Some ASOs that bind in the coding region of mRNAs and induce RNase H1 cleavage can cause increases in the pre-mRNAs that may blunt total activity. Nucleic Acids Res 2020; 48:9840-9858. [PMID: 32870273 PMCID: PMC7515700 DOI: 10.1093/nar/gkaa715] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2020] [Revised: 08/13/2020] [Accepted: 08/19/2020] [Indexed: 01/06/2023] Open
Abstract
Antisense oligonucleotide (ASO) drugs that trigger RNase H1 cleavage of target RNAs have been developed to treat various diseases. Basic pharmacological principles suggest that the development of tolerance is a common response to pharmacological interventions. In this manuscript, for the first time we report a molecular mechanism of tolerance that occurs with some ASOs. Two observations stimulated our interest: some RNA targets are difficult to reduce with RNase H1 activating ASOs and some ASOs display a shorter duration of activity than the prolonged target reduction typically observed. We found that certain ASOs targeting the coding region of some mRNAs that initially reduce target mRNAs can surprisingly increase the levels of the corresponding pre-mRNAs. The increase in pre-mRNA is delayed and due to enhanced transcription and likely also slower processing. This process requires that the ASOs bind in the coding region and reduce the target mRNA by RNase H1 while the mRNA resides in the ribosomes. The pre-mRNA increase is dependent on UPF3A and independent of the NMD pathway or the XRN1-CNOT pathway. The response is consistent in multiple cell lines and independent of the methods used to introduce ASOs into cells.
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Affiliation(s)
- Xue-hai Liang
- Core Antisense Research, Ionis Pharmaceuticals, 2855 Gazelle Court, Carlsbad, CA 92010, USA
| | - Joshua G Nichols
- Core Antisense Research, Ionis Pharmaceuticals, 2855 Gazelle Court, Carlsbad, CA 92010, USA
| | - Cheryl L De Hoyos
- Core Antisense Research, Ionis Pharmaceuticals, 2855 Gazelle Court, Carlsbad, CA 92010, USA
| | - Stanley T Crooke
- Core Antisense Research, Ionis Pharmaceuticals, 2855 Gazelle Court, Carlsbad, CA 92010, USA
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13
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Antisense drug discovery and development technology considered in a pharmacological context. Biochem Pharmacol 2020; 189:114196. [PMID: 32800852 DOI: 10.1016/j.bcp.2020.114196] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2020] [Revised: 08/07/2020] [Accepted: 08/10/2020] [Indexed: 02/06/2023]
Abstract
When coined, the term "antisense" included oligonucleotides of any structure, with any chemical modification and designed to work through any post-RNA hybridization mechanism. However, in practice the term "antisense" has been used to describe single stranded oligonucleotides (ss ASOs) designed to hybridize to RNAswhile the term "siRNA" has come to mean double stranded oligonucleotides designed to activate Ago2. However, the two approaches share many common features. The medicinal chemistry developed for ASOs greatly facilitated the development of siRNA technology and remains the chemical basis for both approaches. Many of challenges faced and solutions achieved share many common features. In fact, because ss ASOs can be designed to activate Ago2, the two approaches intersect at this remarkably important protein. There are also meaningful differences. The pharmacokinetic properties are quite different and thus potential routes of delivery differ. ASOs may be designedto use a variety of post-RNA binding mechanismswhile siRNAs depend solely on the robust activity of Ago2. However, siRNAs and ASOs are both used for therapeutic purposes and both must be and can be understood in a pharmacological context. Thus, the goals of this review are to put ASOs in pharmacological context and compare their behavior as pharmacological agents to the those of siRNAs.
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14
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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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15
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Vickers TA, Migawa MT, Seth PP, Crooke ST. Interaction of ASOs with PC4 Is Highly Influenced by the Cellular Environment and ASO Chemistry. J Am Chem Soc 2020; 142:9661-9674. [PMID: 32374993 DOI: 10.1021/jacs.0c01808] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
The activity of PS-ASOs is strongly influenced by association with both inter- and intracellular proteins. The sequence, chemical nature, and structure of the ASO can have profound influences on the interaction of PS-ASOs with specific proteins. A more thorough understanding of how these pharmacological agents interact with various proteins and how chemical modifications, sequence, and structure influence interactions with proteins is needed to inform future ASO design efforts. To better understand the chemistry of PS-ASO interactions, we have focused on human positive cofactor 4 (PC4). Although several studies have investigated the in vitro binding properties of PC4 with endogenous nucleic acids, little is known about the chemistry of interaction of PS-ASOs with this protein. Here we examine in detail the impact of ASO backbone chemistry, 2'-modifications, and buffer environment on the binding affinity of PC4. In addition, using site-directed mutagenesis, we identify those amino acids that are specifically required for ASO binding interactions, and by substitution of abasic nucleotides we identify the positions on the ASO that most strongly influence affinity for PC4. Finally, to confirm that the interactions observed in vitro are biologically relevant, we use a recently developed complementation reporter system to evaluate the kinetics and subcellular localization of the interaction of ASO and PC4 in live cells.
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Affiliation(s)
- Timothy A Vickers
- Department of Core Antisense Research, IONIS Pharmaceuticals, Inc., 2855 Gazelle Court, Carlsbad, California 92010, United States
| | - Michael T Migawa
- Department of Medicinal ChemistryIONIS Pharmaceuticals, Inc.2855 Gazelle CourtCarlsbadCalifornia92010United States
| | - Punit P Seth
- Department of Medicinal ChemistryIONIS Pharmaceuticals, Inc.2855 Gazelle CourtCarlsbadCalifornia92010United States
| | - Stanley T Crooke
- Department of Core Antisense Research, IONIS Pharmaceuticals, Inc., 2855 Gazelle Court, Carlsbad, California 92010, United States
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16
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Liu X, Haniff HS, Childs-Disney JL, Shuster A, Aikawa H, Adibekian A, Disney MD. Targeted Degradation of the Oncogenic MicroRNA 17-92 Cluster by Structure-Targeting Ligands. J Am Chem Soc 2020; 142:6970-6982. [PMID: 32233464 DOI: 10.1021/jacs.9b13159] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Many RNAs are processed into biologically active transcripts, the aberrant expression of which can contribute to disease phenotypes. For example, the primary microRNA-17-92 (pri-miR-17-92) cluster contains six microRNAs (miRNAs) that collectively act in several disease settings. Herein, we used sequence-based design of structure-specific ligands to target a common structure in the Dicer processing sites of three miRNAs in the cluster, miR-17, miR-18a, and miR-20a, thereby inhibiting their biogenesis. The compound was optimized to afford a dimeric molecule that binds the Dicer processing site and an adjacent bulge, affording a 100-fold increase in potency. The dimer's mode of action was then extended from simple binding to direct cleavage by conjugation to bleomycin A5 in a manner that imparts RNA-selective cleavage or to indirect cleavage by recruiting an endogenous nuclease, or a ribonuclease targeting chimera (RIBOTAC). Interestingly, the dimer-bleomycin conjugate cleaves the entire pri-miR-17-92 cluster and hence functionally inhibits all six miRNAs emanating from it. The compound selectively reduced levels of the cluster in three disease models: polycystic kidney disease, prostate cancer, and breast cancer, rescuing disease-associated phenotypes in the latter two. Further, the bleomycin conjugate exerted selective effects on the miRNome and proteome in prostate cancer cells. In contrast, the RIBOTAC only depleted levels of pre- and mature miR-17, -18a, and 20a, with no effect on the primary transcript, in accordance with the cocellular localization of RNase L, the pre-miRNA targets, and the compound. These studies demonstrate a strategy to tune RNA structure-targeting compounds to the cellular localization of the target.
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Affiliation(s)
- Xiaohui Liu
- Department of Chemistry, The Scripps Research Institute, 130 Scripps Way, Jupiter, Florida 33458, United States
| | - Hafeez S Haniff
- Department of Chemistry, The Scripps Research Institute, 130 Scripps Way, Jupiter, Florida 33458, United States
| | - Jessica L Childs-Disney
- Department of Chemistry, The Scripps Research Institute, 130 Scripps Way, Jupiter, Florida 33458, United States
| | - Anton Shuster
- Department of Chemistry, The Scripps Research Institute, 130 Scripps Way, Jupiter, Florida 33458, United States
| | - Haruo Aikawa
- Department of Chemistry, The Scripps Research Institute, 130 Scripps Way, Jupiter, Florida 33458, United States
| | - Alexander Adibekian
- Department of Chemistry, The Scripps Research Institute, 130 Scripps Way, Jupiter, Florida 33458, United States
| | - Matthew D Disney
- Department of Chemistry, The Scripps Research Institute, 130 Scripps Way, Jupiter, Florida 33458, United States
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17
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Scharner J, Ma WK, Zhang Q, Lin KT, Rigo F, Bennett CF, Krainer AR. Hybridization-mediated off-target effects of splice-switching antisense oligonucleotides. Nucleic Acids Res 2020; 48:802-816. [PMID: 31802121 PMCID: PMC6954394 DOI: 10.1093/nar/gkz1132] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2019] [Revised: 10/03/2019] [Accepted: 12/03/2019] [Indexed: 12/12/2022] Open
Abstract
Splice-switching antisense oligonucleotides (ASOs), which bind specific RNA-target sequences and modulate pre-mRNA splicing by sterically blocking the binding of splicing factors to the pre-mRNA, are a promising therapeutic modality to treat a range of genetic diseases. ASOs are typically 15–25 nt long and considered to be highly specific towards their intended target sequence, typically elements that control exon definition and/or splice-site recognition. However, whether or not splice-modulating ASOs also induce hybridization-dependent mis-splicing of unintended targets has not been systematically studied. Here, we tested the in vitro effects of splice-modulating ASOs on 108 potential off-targets predicted on the basis of sequence complementarity, and identified 17 mis-splicing events for one of the ASOs tested. Based on analysis of data from two overlapping ASO sequences, we conclude that off-target effects are difficult to predict, and the choice of ASO chemistry influences the extent of off-target activity. The off-target events caused by the uniformly modified ASOs tested in this study were significantly reduced with mixed-chemistry ASOs of the same sequence. Furthermore, using shorter ASOs, combining two ASOs, and delivering ASOs by free uptake also reduced off-target activity. Finally, ASOs with strategically placed mismatches can be used to reduce unwanted off-target splicing events.
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Affiliation(s)
| | - Wai Kit Ma
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
| | - Qian Zhang
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
| | - Kuan-Ting Lin
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
| | - Frank Rigo
- Ionis Pharmaceuticals, Carlsbad, CA, USA
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18
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Yang L, Ma F, Liu F, Chen J, Zhao X, Xu Q. Efficient Delivery of Antisense Oligonucleotides Using Bioreducible Lipid Nanoparticles In Vitro and In Vivo. MOLECULAR THERAPY-NUCLEIC ACIDS 2020; 19:1357-1367. [PMID: 32160706 PMCID: PMC7036716 DOI: 10.1016/j.omtn.2020.01.018] [Citation(s) in RCA: 53] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/05/2019] [Revised: 11/30/2019] [Accepted: 01/14/2020] [Indexed: 12/11/2022]
Abstract
The efficient delivery of antisense oligonucleotides (ASOs) to the targeted cells and organs remains a challenge, in particular, in vivo. Here, we investigated the ability of a library of biodegradable lipid nanoparticles (LNPs) in delivering ASO to both cultured human cells and animal models. We first identified three top-performing lipids through in vitro screening using GFP-expressing HEK293 cells. Next, we explored these three candidates for delivering ASO to target proprotein convertase subtilisin/kexin type 9 (PCSK9) mRNA in mice. We found that lipid 306-O12B-3 showed efficiency with the median effective dose (ED50) as low as 0.034 mg·kg-1, which is a notable improvement over the efficiency reported in the literature. No liver or kidney toxicity was observed with a dose up to 5 mg·kg-1 of this ASO/LNP formulation. The biodegradable LNPs are efficient and safe in the delivery of ASO and pave the way for clinical translation.
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Affiliation(s)
- Liu Yang
- Department of Biomedical Engineering, Tufts University, Medford, MA 02155, USA
| | - Feihe Ma
- Department of Biomedical Engineering, Tufts University, Medford, MA 02155, USA
| | - Fang Liu
- Department of Biomedical Engineering, Tufts University, Medford, MA 02155, USA
| | - Jinjin Chen
- Department of Biomedical Engineering, Tufts University, Medford, MA 02155, USA
| | - Xuewei Zhao
- Department of Biomedical Engineering, Tufts University, Medford, MA 02155, USA
| | - Qiaobing Xu
- Department of Biomedical Engineering, Tufts University, Medford, MA 02155, USA.
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19
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Directed RNase H Cleavage of Nascent Transcripts Causes Transcription Termination. Mol Cell 2020; 77:1032-1043.e4. [PMID: 31924447 DOI: 10.1016/j.molcel.2019.12.029] [Citation(s) in RCA: 62] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2019] [Revised: 11/20/2019] [Accepted: 12/25/2019] [Indexed: 11/22/2022]
Abstract
An attractive approach to reduce gene expression is via the use of antisense oligonucleotides (ASOs) that harness the RNase H1 mechanism. Here we show that RNase H ASOs targeted to introns or exons robustly reduce the level of spliced RNA associated with chromatin. Surprisingly, intron-targeted ASOs reduce the level of pre-mRNA associated with chromatin to a greater extent than exon-targeted ASOs. This indicates that exon-targeted ASOs achieve full activity after the pre-mRNA has undergone splicing, but before the mRNA is released from chromatin. Even though RNase H ASOs can reduce the level of RNA associated with chromatin, the effect of ASO-directed RNA degradation on transcription has never been documented. Here we show that intron-targeted ASOs and, to a lesser extent, exon-targeted ASOs cause RNA polymerase II (Pol II) transcription termination in cultured cells and mice. Furthermore, ASO-directed transcription termination is mediated by the nuclear exonuclease XRN2.
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20
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Hagedorn PH, Pontoppidan M, Bisgaard TS, Berrera M, Dieckmann A, Ebeling M, Møller MR, Hudlebusch H, Jensen ML, Hansen HF, Koch T, Lindow M. Identifying and avoiding off-target effects of RNase H-dependent antisense oligonucleotides in mice. Nucleic Acids Res 2019; 46:5366-5380. [PMID: 29790953 PMCID: PMC6009603 DOI: 10.1093/nar/gky397] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2017] [Accepted: 04/30/2018] [Indexed: 12/12/2022] Open
Abstract
Antisense oligonucleotides that are dependent on RNase H for cleavage and subsequent degradation of complementary RNA are being developed as therapeutics. Besides the intended RNA target, such oligonucleotides may also cause degradation of unintended RNA off-targets by binding to partially complementary target sites. Here, we characterized the global effects on the mouse liver transcriptome of four oligonucleotides designed as gapmers, two targeting Apob and two targeting Pcsk9, all in different regions on their respective intended targets. This study design allowed separation of intended- and off-target effects on the transcriptome for each gapmer. Next, we used sequence analysis to identify possible partially complementary binding sites among the potential off-targets, and validated these by measurements of melting temperature and RNase H-cleavage rates. Generally, our observations were as expected in that fewer mismatches or bulges in the gapmer/transcript duplexes resulted in a higher chance of those duplexes being effective substrates for RNase H. Follow-up experiments in mice and cells show, that off-target effects can be mitigated by ensuring that gapmers have minimal sequence complementarity to any RNA besides the intended target, and that they do not have exaggerated binding affinity to the intended target.
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Affiliation(s)
- Peter H Hagedorn
- Therapeutic Modalities, Roche Pharma Research and Early Development, Roche Innovation Center Copenhagen, DK-2970 Hørsholm, Denmark
| | - Malene Pontoppidan
- Therapeutic Modalities, Roche Pharma Research and Early Development, Roche Innovation Center Copenhagen, DK-2970 Hørsholm, Denmark.,Department of Biotechnology and Biomedicine, Technical University of Denmark, DK-2800 Kgs. Lyngby, Denmark
| | - Tina S Bisgaard
- Therapeutic Modalities, Roche Pharma Research and Early Development, Roche Innovation Center Copenhagen, DK-2970 Hørsholm, Denmark
| | - Marco Berrera
- Pharmaceutical Sciences, Roche Pharma Research and Early Development, Roche Innovation Center Basel, 4070 Basel, Switzerland
| | - Andreas Dieckmann
- Pharmaceutical Sciences, Roche Pharma Research and Early Development, Roche Innovation Center Basel, 4070 Basel, Switzerland
| | - Martin Ebeling
- Pharmaceutical Sciences, Roche Pharma Research and Early Development, Roche Innovation Center Basel, 4070 Basel, Switzerland
| | - Marianne R Møller
- Therapeutic Modalities, Roche Pharma Research and Early Development, Roche Innovation Center Copenhagen, DK-2970 Hørsholm, Denmark
| | - Heidi Hudlebusch
- Therapeutic Modalities, Roche Pharma Research and Early Development, Roche Innovation Center Copenhagen, DK-2970 Hørsholm, Denmark
| | - Marianne L Jensen
- Therapeutic Modalities, Roche Pharma Research and Early Development, Roche Innovation Center Copenhagen, DK-2970 Hørsholm, Denmark
| | - Henrik F Hansen
- Therapeutic Modalities, Roche Pharma Research and Early Development, Roche Innovation Center Copenhagen, DK-2970 Hørsholm, Denmark
| | - Troels Koch
- Therapeutic Modalities, Roche Pharma Research and Early Development, Roche Innovation Center Copenhagen, DK-2970 Hørsholm, Denmark
| | - Morten Lindow
- Therapeutic Modalities, Roche Pharma Research and Early Development, Roche Innovation Center Copenhagen, DK-2970 Hørsholm, Denmark
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21
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Shen W, De Hoyos CL, Sun H, Vickers TA, Liang XH, Crooke ST. Acute hepatotoxicity of 2' fluoro-modified 5-10-5 gapmer phosphorothioate oligonucleotides in mice correlates with intracellular protein binding and the loss of DBHS proteins. Nucleic Acids Res 2019; 46:2204-2217. [PMID: 29390093 PMCID: PMC5861398 DOI: 10.1093/nar/gky060] [Citation(s) in RCA: 59] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2017] [Accepted: 01/23/2018] [Indexed: 01/06/2023] Open
Abstract
We reported previously that a 2′ fluoro-modified (2′ F) phosphorothioate (PS) antisense oligonucleotides (ASOs) with 5–10–5 gapmer configuration interacted with proteins from Drosophila behavior/human splicing (DBHS) family with higher affinity than PS-ASOs modified with 2′-O-(2-methoxyethyl) (2′ MOE) or 2′,4′-constrained 2′-O-ethyl (cEt) did. Rapid degradation of these proteins and cytotoxicity were observed in cells treated with 2′ F PS-ASO. Here, we report that 2′ F gapmer PS-ASOs of different sequences caused reduction in levels of DBHS proteins and hepatotoxicity in mice. 2′ F PS-ASOs induced activation of the P53 pathway and downregulation of metabolic pathways. Altered levels of RNA and protein markers for hepatotoxicity, liver necrosis, and apoptosis were observed as early as 24 to 48 hours after a single administration of the 2′ F PS-ASO. The observed effects were not likely due to the hybridization-dependent RNase H1 cleavage of on- or potential off-target RNAs, or due to potential toxicity of 2′ F nucleoside metabolites. Instead, we found that 2′ F PS-ASO associated with more intra-cellular proteins including proteins from DBHS family. Our results suggest that protein-binding correlates positively with the 2′ F modification-dependent loss of DBHS proteins and the toxicity of gapmer 2′ F PS-ASO in vivo.
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Affiliation(s)
- Wen Shen
- Department of Core Antisense Research, Ionis Pharmaceuticals, Inc. 2855 Gazelle Court, Carlsbad, CA 92010, USA
| | - Cheryl L De Hoyos
- Department of Core Antisense Research, Ionis Pharmaceuticals, Inc. 2855 Gazelle Court, Carlsbad, CA 92010, USA
| | - Hong Sun
- Department of Core Antisense Research, Ionis Pharmaceuticals, Inc. 2855 Gazelle Court, Carlsbad, CA 92010, USA
| | - Timothy A Vickers
- Department of Core Antisense Research, Ionis Pharmaceuticals, Inc. 2855 Gazelle Court, Carlsbad, CA 92010, USA
| | - Xue-Hai Liang
- Department of Core Antisense Research, Ionis Pharmaceuticals, Inc. 2855 Gazelle Court, Carlsbad, CA 92010, USA
| | - Stanley T Crooke
- Department of Core Antisense Research, Ionis Pharmaceuticals, Inc. 2855 Gazelle Court, Carlsbad, CA 92010, USA
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22
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Liang XH, Nichols JG, Sun H, Crooke ST. Translation can affect the antisense activity of RNase H1-dependent oligonucleotides targeting mRNAs. Nucleic Acids Res 2019; 46:293-313. [PMID: 29165591 PMCID: PMC5758896 DOI: 10.1093/nar/gkx1174] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2017] [Accepted: 11/10/2017] [Indexed: 12/21/2022] Open
Abstract
RNase H1-dependent antisense oligonucleotides (ASOs) can degrade complementary RNAs in both the nucleus and the cytoplasm. Since cytoplasmic mRNAs are actively engaged in translation, ASO activity may thus be affected by translating ribosomes that scan the mRNAs. Here we show that mRNAs associated with ribosomes can be cleaved using ASOs and that translation can alter ASO activity. Translation inhibition tends to increase ASO activity when targeting the coding regions of efficiently translated mRNAs, but not nuclear non-coding RNAs or less efficiently translated mRNAs. Increasing the level of RNase H1 protein eliminated the enhancing effects of translation inhibition on ASO activity, suggesting that RNase H1 recruitment to ASO/mRNA heteroduplexes is a rate limiting step and that translating ribosomes can inhibit RNase H1 recruitment. Consistently, ASO activity was not increased by translation inhibition when targeting the 3′ UTRs, independent of the translation efficiency of the mRNAs. Contrarily, the activity of 3′ UTR-targeting ASOs tended to be reduced upon translation inhibition, likely due to decreased accessibility. These results indicate that ASO activity can be affected by the translation process, and the findings also provide important information toward helping better ASO drug design.
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Affiliation(s)
- Xue-Hai Liang
- Department of Core Antisense Research, Ionis Pharmaceutics, Inc., 2855 Gazelle Court, Carlsbad, CA 92010, USA
| | - Joshua G Nichols
- Department of Core Antisense Research, Ionis Pharmaceutics, Inc., 2855 Gazelle Court, Carlsbad, CA 92010, USA
| | - Hong Sun
- Department of Core Antisense Research, Ionis Pharmaceutics, Inc., 2855 Gazelle Court, Carlsbad, CA 92010, USA
| | - Stanley T Crooke
- Department of Core Antisense Research, Ionis Pharmaceutics, Inc., 2855 Gazelle Court, Carlsbad, CA 92010, USA
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23
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Liang XH, Sun H, Nichols JG, Allen N, Wang S, Vickers TA, Shen W, Hsu CW, Crooke ST. COPII vesicles can affect the activity of antisense oligonucleotides by facilitating the release of oligonucleotides from endocytic pathways. Nucleic Acids Res 2018; 46:10225-10245. [PMID: 30239896 PMCID: PMC6212795 DOI: 10.1093/nar/gky841] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2018] [Revised: 08/23/2018] [Accepted: 09/10/2018] [Indexed: 12/12/2022] Open
Abstract
RNase H1-dependent, phosphorothioate-modified antisense oligonucleotides (PS-ASOs) can enter cells through endocytic pathways and need to be released from the membrane-enclosed organelles, a limiting step for antisense activity. Accumulating evidence has suggested that productive PS-ASO release mainly occurs from late endosomes (LEs). However, how PS-ASOs escape from LEs is not well understood. Here, we report that upon PS-ASO incubation, COPII vesicles, normally involved in ER-Golgi transport, can re-locate to PS-ASO-containing LEs. Reduction of COPII coat proteins significantly decreased PS-ASO activity, without affecting the levels of PS-ASO uptake and early-to-late endosome transport, but caused slower PS-ASO release from LEs. COPII co-localization with PS-ASOs at LEs does not require de novo assembly of COPII at ER. Interestingly, reduction of STX5 and P115, proteins involved in tethering and fusion of COPII vesicles with Golgi membranes, impaired COPII re-localization to LEs and decreased PS-ASO activity. STX5 can re-locate to LEs upon PS-ASO incubation, can bind PS-ASOs, and the binding appears to be required for this pathway. Our study reveals a novel release pathway in which PS-ASO incubation causes LE re-localization of STX5, which mediates the recruitment of COPII vesicles to LEs to facilitate endosomal PS-ASO release, and identifies another key PS-ASO binding protein.
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Affiliation(s)
- Xue-hai Liang
- Core Antisense Research, Ionis Pharmaceuticals, Inc. 2855 Gazelle Court, Carlsbad, CA 92010, USA
| | - Hong Sun
- Core Antisense Research, Ionis Pharmaceuticals, Inc. 2855 Gazelle Court, Carlsbad, CA 92010, USA
| | - Joshua G Nichols
- Core Antisense Research, Ionis Pharmaceuticals, Inc. 2855 Gazelle Court, Carlsbad, CA 92010, USA
| | - Nickolas Allen
- Core Antisense Research, Ionis Pharmaceuticals, Inc. 2855 Gazelle Court, Carlsbad, CA 92010, USA
| | - Shiyu Wang
- Core Antisense Research, Ionis Pharmaceuticals, Inc. 2855 Gazelle Court, Carlsbad, CA 92010, USA
| | - Timothy A Vickers
- Core Antisense Research, Ionis Pharmaceuticals, Inc. 2855 Gazelle Court, Carlsbad, CA 92010, USA
| | - Wen Shen
- Core Antisense Research, Ionis Pharmaceuticals, Inc. 2855 Gazelle Court, Carlsbad, CA 92010, USA
| | - Chih-Wei Hsu
- Core Antisense Research, Ionis Pharmaceuticals, Inc. 2855 Gazelle Court, Carlsbad, CA 92010, USA
| | - Stanley T Crooke
- Core Antisense Research, Ionis Pharmaceuticals, Inc. 2855 Gazelle Court, Carlsbad, CA 92010, USA
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24
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Abstract
RNA-targeted therapies represent a platform for drug discovery involving chemically modified oligonucleotides, a wide range of cellular RNAs, and a novel target-binding motif, Watson-Crick base pairing. Numerous hurdles considered by many to be impassable have been overcome. Today, four RNA-targeted therapies are approved for commercial use for indications as diverse as Spinal Muscular Atrophy (SMA) and reduction of low-density lipoprotein cholesterol (LDL-C) and by routes of administration including subcutaneous, intravitreal, and intrathecal delivery. The technology is efficient and supports approaching "undruggable" targets. Three additional agents are progressing through registration, and more are in clinical development, representing several chemical and structural classes. Moreover, progress in understanding the molecular mechanisms by which these drugs work has led to steadily better clinical performance and a wide range of mechanisms that may be exploited for therapeutic purposes. Here we summarize the progress, future challenges, and opportunities for this drug discovery platform.
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Affiliation(s)
- Stanley T Crooke
- Ionis Pharmaceuticals, Inc., 2855 Gazelle Court, Carlsbad, CA 92010, USA.
| | - Joseph L Witztum
- University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
| | - C Frank Bennett
- Ionis Pharmaceuticals, Inc., 2855 Gazelle Court, Carlsbad, CA 92010, USA
| | - Brenda F Baker
- Ionis Pharmaceuticals, Inc., 2855 Gazelle Court, Carlsbad, CA 92010, USA
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25
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Hegarty JP, Stewart DB. Advances in therapeutic bacterial antisense biotechnology. Appl Microbiol Biotechnol 2017; 102:1055-1065. [PMID: 29209794 DOI: 10.1007/s00253-017-8671-0] [Citation(s) in RCA: 60] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2017] [Revised: 11/16/2017] [Accepted: 11/17/2017] [Indexed: 12/15/2022]
Abstract
Antisense therapeutics are a biotechnological form of antibiotic therapy using chemical analogues of short single-stranded nucleic acid sequences modified to form stable oligomers. These molecules are termed antisense oligonucleotides (ASOs) because their sequence is complementary, via Watson-Crick specific base pairing, to their target messenger RNA (mRNA). ASOs modify gene expression in this sequence-dependent manner by binding to its complementary mRNA and inhibiting its translation into protein through steric blockage and/or through RNase degradation of the ASO/RNA duplex. The widespread use of conventional antibiotics has led to the increasing emergence of multiple drug-resistant pathogenic bacteria. There is an urgent need to develop alternative therapeutic strategies to reduce the morbidity and mortality associated with bacterial infections, and until recently, the use of ASOs as therapeutic agents has been essentially limited to eukaryotic cells, with ASOs as antibacterials having been largely unexplored primarily due to the poor uptake efficiency of antisense molecules by bacteria. There are conceptual advantages to bacterial antisense antibiotic therapies, including a sequence-dependent approach that allows for a rational design to multiple specific molecular targets. This review summarizes the current knowledge of antisense bacterial biotechnology and highlights the recent progress and the current obstacles in their development for therapeutic applications.
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Affiliation(s)
- John P Hegarty
- College of Medicine, Department of Surgery, The Pennsylvania State University, 500 University Drive, H137, P.O. Box 850, Hershey, PA, 17033-0850, USA
| | - David B Stewart
- College of Medicine, Department of Surgery, The Pennsylvania State University, 500 University Drive, H137, P.O. Box 850, Hershey, PA, 17033-0850, USA.
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26
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Hagedorn PH, Hansen BR, Koch T, Lindow M. Managing the sequence-specificity of antisense oligonucleotides in drug discovery. Nucleic Acids Res 2017; 45:2262-2282. [PMID: 28426096 PMCID: PMC5389529 DOI: 10.1093/nar/gkx056] [Citation(s) in RCA: 65] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2016] [Accepted: 01/21/2017] [Indexed: 01/06/2023] Open
Abstract
All drugs perturb the expression of many genes in the cells that are exposed to them. These gene expression changes can be divided into effects resulting from engaging the intended target and effects resulting from engaging unintended targets. For antisense oligonucleotides, developments in bioinformatics algorithms, and the quality of sequence databases, allow oligonucleotide sequences to be analyzed computationally, in terms of the predictability of their interactions with intended and unintended RNA targets. Applying these tools enables selection of sequence-specific oligonucleotides where no- or only few unintended RNA targets are expected. To evaluate oligonucleotide sequence-specificity experimentally, we recommend a transcriptomics protocol where two or more oligonucleotides targeting the same RNA molecule, but with entirely different sequences, are evaluated together. This helps to clarify which changes in cellular RNA levels result from downstream processes of engaging the intended target, and which are likely to be related to engaging unintended targets. As required for all classes of drugs, the toxic potential of oligonucleotides must be evaluated in cell- and animal models before clinical testing. Since potential adverse effects related to unintended targeting are sequence-dependent and therefore species-specific, in vitro toxicology assays in human cells are especially relevant in oligonucleotide drug discovery.
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Affiliation(s)
- Peter H Hagedorn
- Roche Pharmaceutical Discovery and Early Development, Therapeutic Modalities, Roche Innovation Center Copenhagen, Hørsholm 2970, Denmark.,Center for Computational and Applied Transcriptomics, Department of Biology, University of Copenhagen, Copenhagen 2200, Denmark
| | - Bo R Hansen
- Roche Pharmaceutical Discovery and Early Development, Therapeutic Modalities, Roche Innovation Center Copenhagen, Hørsholm 2970, Denmark
| | - Troels Koch
- Roche Pharmaceutical Discovery and Early Development, Therapeutic Modalities, Roche Innovation Center Copenhagen, Hørsholm 2970, Denmark
| | - Morten Lindow
- Roche Pharmaceutical Discovery and Early Development, Therapeutic Modalities, Roche Innovation Center Copenhagen, Hørsholm 2970, Denmark.,Center for Computational and Applied Transcriptomics, Department of Biology, University of Copenhagen, Copenhagen 2200, Denmark.,The Bioinformatics Centre, Department of Biology, University of Copenhagen, Copenhagen 2200, Denmark
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27
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Liang XH, Sun H, Nichols JG, Crooke ST. RNase H1-Dependent Antisense Oligonucleotides Are Robustly Active in Directing RNA Cleavage in Both the Cytoplasm and the Nucleus. Mol Ther 2017; 25:2075-2092. [PMID: 28663102 PMCID: PMC5589097 DOI: 10.1016/j.ymthe.2017.06.002] [Citation(s) in RCA: 155] [Impact Index Per Article: 22.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2017] [Revised: 06/01/2017] [Accepted: 06/02/2017] [Indexed: 12/14/2022] Open
Abstract
RNase H1-dependent antisense oligonucleotides (ASOs) are active in reducing levels of both cytoplasmic mRNAs and nuclear retained RNAs. Although ASO activity in the nucleus has been well demonstrated, the cytoplasmic activity of ASOs is less clear. Using kinetic and subcellular fractionation studies, we evaluated ASO activity in the cytoplasm. Upon transfection, ASOs targeting exonic regions rapidly reduced cytoplasmically enriched mRNAs, whereas an intron-targeting ASO that only degrades the nuclear pre-mRNA reduced mRNA levels at a slower rate, similar to normal mRNA decay. Importantly, some exon-targeting ASOs can rapidly and vigorously reduce mRNA levels without decreasing pre-mRNA levels, suggesting that pre-existing cytoplasmic mRNAs can be cleaved by RNase H1-ASO treatment. In addition, we expressed a cytoplasm-localized mutant 7SL RNA that contains a partial U16 small nucleolar RNA (snoRNA) sequence. Treatment with an ASO simultaneously reduced both the nuclear U16 snoRNA and the cytoplasmic 7SL mutant RNA as early as 30 min after transfection in an RNase H1-dependent manner. Both the 5′ and 3′ cleavage products of the 7SL mutant RNA were accumulated in the cytoplasm. Together, these results demonstrate that RNase H1-dependent ASOs are robustly active in both the cytoplasm and nucleus.
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Affiliation(s)
- Xue-Hai Liang
- Department of Core Antisense Research, Ionis Pharmaceutics, Inc., Carlsbad, CA 92010, USA.
| | - Hong Sun
- Department of Core Antisense Research, Ionis Pharmaceutics, Inc., Carlsbad, CA 92010, USA
| | - Joshua G Nichols
- Department of Core Antisense Research, Ionis Pharmaceutics, Inc., Carlsbad, CA 92010, USA
| | - Stanley T Crooke
- Department of Core Antisense Research, Ionis Pharmaceutics, Inc., Carlsbad, CA 92010, USA
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Crooke ST. Molecular Mechanisms of Antisense Oligonucleotides. Nucleic Acid Ther 2017; 27:70-77. [PMID: 28080221 PMCID: PMC5372764 DOI: 10.1089/nat.2016.0656] [Citation(s) in RCA: 221] [Impact Index Per Article: 31.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2016] [Accepted: 12/14/2016] [Indexed: 12/12/2022] Open
Abstract
In 1987, when I became interested in the notion of antisense technology, I returned to my roots in RNA biochemistry and began work to understand how oligonucleotides behave in biological systems. Since 1989, my research has focused primarily on this topic, although I have been involved in most areas of research in antisense technology. I believe that the art of excellent science is to frame large important questions that are perhaps not immediately answerable with existing knowledge and methods, and then conceive a long-term (multiyear) research strategy that begins by answering the most pressing answerable questions on the path to the long-term goals. Then, a step-by-step research pathway that will address the strategic questions posed must be implemented, adjusting the plan as new things are learned. This is the approach we have taken at Ionis. Obviously, to create antisense technology, we have had to address a wide array of strategic questions, for example, the medicinal chemistry of oligonucleotides, manufacturing and analytical methods, pharmacokinetics and toxicology, as well as questions about the molecular pharmacology of antisense oligonucleotides (ASOs). Each of these endeavors has consumed nearly three decades of scientific effort, is still very much a work-in-progress, and has resulted in hundreds of publications. As a recipient of the Lifetime Achievement Award 2016 granted by the Oligonucleotide Therapeutic Society, in this note, my goal is to summarize the contributions of my group to the efforts to understand the molecular mechanisms of ASOs.
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Affiliation(s)
- Stanley T Crooke
- Department of Core Antisense Research, Ionis Pharmaceuticals, Inc. , Carlsbad, California
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29
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Hegarty JP, Krzeminski J, Sharma AK, Guzman-Villanueva D, Weissig V, Stewart DB. Bolaamphiphile-based nanocomplex delivery of phosphorothioate gapmer antisense oligonucleotides as a treatment for Clostridium difficile. Int J Nanomedicine 2016; 11:3607-19. [PMID: 27536102 PMCID: PMC4975145 DOI: 10.2147/ijn.s109600] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Despite being a conceptually appealing alternative to conventional antibiotics, a major challenge toward the successful implementation of antisense treatments for bacterial infections is the development of efficient oligonucleotide delivery systems. Cationic vesicles (bolasomes) composed of dequalinium chloride ("DQAsomes") have been used to deliver plasmid DNA across the cardiolipin-rich inner membrane of mitochondria. As cardiolipin is also a component of many bacterial membranes, we investigated the application of cationic bolasomes to bacteria as an oligonucleotide delivery system. Antisense sequences designed in silico to target the expression of essential genes of the bacterial pathogen, Clostridium difficile, were synthesized as 2'-O-methyl phosphorothioate gapmer antisense oligonucleotides (ASO). These antisense gapmers were quantitatively assessed for their ability to block mRNA translation using luciferase reporter and C. difficile protein expression plasmid constructs in a coupled transcription-translation system. Cationic bolaamphiphile compounds (dequalinium derivatives) of varying alkyl chain length were synthesized and bolasomes were prepared via probe sonication of an aqueous suspension. Bolasomes were characterized by particle size distribution, zeta potential, and binding capacities for anionic oligonucleotide. Bolasomes and antisense gapmers were combined to form antisense nanocomplexes. Anaerobic C. difficile log phase cultures were treated with serial doses of gapmer nanocomplexes or equivalent amounts of empty bolasomes for 24 hours. Antisense gapmers for four gene targets achieved nanomolar minimum inhibitory concentrations for C. difficile, with the lowest values observed for oligonucleotides targeting polymerase genes rpoB and dnaE. No inhibition of bacterial growth was observed from treatments at matched dosages of scrambled gapmer nanocomplexes or plain, oligonucleotide-free bolasomes compared to untreated control cultures. We describe the novel application of cationic bolasomes to deliver ASOs into bacteria. We also report the first successful in vitro antisense treatment to inhibit the growth of C. difficile.
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Affiliation(s)
- John P Hegarty
- Deparment of Surgery, Pennsylvania State University College of Medicine Hershey, PA, USA
| | - Jacek Krzeminski
- Department of Pharmacology, Penn State Hershey Cancer Institute, Hershey, PA, USA
| | - Arun K Sharma
- Department of Pharmacology, Penn State Hershey Cancer Institute, Hershey, PA, USA
| | - Diana Guzman-Villanueva
- Department of Pharmaceutical Sciences, College of Pharmacy, Nanomedicine Center of Excellence in Translational Research, Midwestern University, Glendale, AZ, USA
| | - Volkmar Weissig
- Department of Pharmaceutical Sciences, College of Pharmacy, Nanomedicine Center of Excellence in Translational Research, Midwestern University, Glendale, AZ, USA
| | - David B Stewart
- Deparment of Surgery, Pennsylvania State University College of Medicine Hershey, PA, USA
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30
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Integrated Safety Assessment of 2'-O-Methoxyethyl Chimeric Antisense Oligonucleotides in NonHuman Primates and Healthy Human Volunteers. Mol Ther 2016; 24:1771-1782. [PMID: 27357629 PMCID: PMC5112040 DOI: 10.1038/mt.2016.136] [Citation(s) in RCA: 79] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2016] [Accepted: 06/21/2016] [Indexed: 02/07/2023] Open
Abstract
The common chemical and biological properties of antisense oligonucleotides provide the opportunity to identify and characterize chemical class effects across species. The chemical class that has proven to be the most versatile and best characterized is the 2′-O-methoxyethyl chimeric antisense oligonucleotides. In this report we present an integrated safety assessment of data obtained from controlled dose-ranging studies in nonhuman primates (macaques) and healthy human volunteers for 12 unique 2′-O-methoxyethyl chimeric antisense oligonucleotides. Safety was assessed by the incidence of safety signals in standardized laboratory tests for kidney and liver function, hematology, and complement activation; as well as by the mean test results as a function of dose level over time. At high doses a number of toxicities were observed in nonhuman primates. However, no class safety effects were identified in healthy human volunteers from this integrated data analysis. Effects on complement in nonhuman primates were not observed in humans. Nonhuman primates predicted safe doses in humans, but over predicted risk of complement activation and effects on platelets. Although limited to a single chemical class, comparisons from this analysis are considered valid and accurate based on the carefully controlled setting for the specified study populations and within the total exposures studied.
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31
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Zhou T, Kim Y, MacLeod AR. Targeting Long Noncoding RNA with Antisense Oligonucleotide Technology as Cancer Therapeutics. Methods Mol Biol 2016; 1402:199-213. [PMID: 26721493 DOI: 10.1007/978-1-4939-3378-5_16] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Recent annotation of the human transcriptome revealed that only 2 % of the genome encodes proteins while the majority of human genome is transcribed into noncoding RNAs. Although we are just beginning to understand the diverse roles long noncoding RNAs (lncRNAs) play in molecular and cellular processes, they have potentially important roles in human development and pathophysiology. However, targeting of RNA by traditional structure-based design of small molecule inhibitors has been difficult, due to a lack of understanding of the dynamic tertiary structures most RNA molecules adopt. Antisense oligonucleotides (ASOs) are capable of targeting specific genes or transcripts directly through Watson-Crick base pairing and thus can be designed based on sequence information alone. These agents have made possible specific targeting of "non-druggable targets" including RNA molecules. Here we describe how ASOs can be applied in preclinical studies to reduce levels of lncRNAs of interest.
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Affiliation(s)
- Tianyuan Zhou
- Antisense Drug Discovery, Oncology, Isis Pharmaceuticals, Inc, 2855 Gazelle Court, Carlsbad, CA, 92010, USA.
| | - Youngsoo Kim
- Antisense Drug Discovery, Oncology, Isis Pharmaceuticals, Inc, 2855 Gazelle Court, Carlsbad, CA, 92010, USA
| | - A Robert MacLeod
- Antisense Drug Discovery, Oncology, Isis Pharmaceuticals, Inc, 2855 Gazelle Court, Carlsbad, CA, 92010, USA
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32
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Magner D, Biala E, Lisowiec-Wachnicka J, Kierzek E, Kierzek R. A Tandem Oligonucleotide Approach for SNP-Selective RNA Degradation Using Modified Antisense Oligonucleotides. PLoS One 2015; 10:e0142139. [PMID: 26544037 PMCID: PMC4704561 DOI: 10.1371/journal.pone.0142139] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2015] [Accepted: 10/19/2015] [Indexed: 12/19/2022] Open
Abstract
Antisense oligonucleotides have been studied for many years as a tool for gene silencing. One of the most difficult cases of selective RNA silencing involves the alleles of single nucleotide polymorphisms, in which the allele sequence is differentiated by a single nucleotide. A new approach to improve the performance of allele selectivity for antisense oligonucleotides is proposed. It is based on the simultaneous application of two oligonucleotides. One is complementary to the mutated form of the targeted RNA and is able to activate RNase H to cleave the RNA. The other oligonucleotide, which is complementary to the wild type allele of the targeted RNA, is able to inhibit RNase H cleavage. Five types of SNPs, C/G, G/C, G/A, A/G, and C/U, were analyzed within the sequence context of genes associated with neurodegenerative disorders such as Alzheimer’s disease, Parkinson’s disease, ALS (Amyotrophic Lateral Sclerosis), and Machado-Joseph disease. For most analyzed cases, the application of the tandem approach increased allele-selective RNA degradation 1.5–15 fold relative to the use of a single antisense oligonucleotide. The presented study proves that differentiation between single substitution is highly dependent on the nature of the SNP and surrounding nucleotides. These variables are crucial for determining the proper length of the inhibitor antisense oligonucleotide. In the tandem approach, the comparison of thermodynamic stability of the favorable duplexes WT RNA-inhibitor and Mut RNA-gapmer with the other possible duplexes allows for the evaluation of chances for the allele-selective degradation of RNA. A larger difference in thermodynamic stability between favorable duplexes and those that could possibly form, usually results in the better allele selectivity of RNA degradation.
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Affiliation(s)
- Dorota Magner
- Institute of Bioorganic Chemistry Polish Academy of Sciences, 61-704 Poznan, Noskowskiego, 12/14, Poland
| | - Ewa Biala
- Institute of Bioorganic Chemistry Polish Academy of Sciences, 61-704 Poznan, Noskowskiego, 12/14, Poland
| | - Jolanta Lisowiec-Wachnicka
- Institute of Bioorganic Chemistry Polish Academy of Sciences, 61-704 Poznan, Noskowskiego, 12/14, Poland
| | - Elzbieta Kierzek
- Institute of Bioorganic Chemistry Polish Academy of Sciences, 61-704 Poznan, Noskowskiego, 12/14, Poland
| | - Ryszard Kierzek
- Institute of Bioorganic Chemistry Polish Academy of Sciences, 61-704 Poznan, Noskowskiego, 12/14, Poland
- * E-mail:
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33
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Vickers TA, Crooke ST. The rates of the major steps in the molecular mechanism of RNase H1-dependent antisense oligonucleotide induced degradation of RNA. Nucleic Acids Res 2015; 43:8955-63. [PMID: 26384424 PMCID: PMC4605327 DOI: 10.1093/nar/gkv920] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2015] [Accepted: 09/04/2015] [Indexed: 11/25/2022] Open
Abstract
Antisense oligonucleotides (ASOs) are most commonly designed to reduce targeted RNA via RNase H1-dependent degradation, however kinetic parameters for ASO-mediated targeting and subsequent cleavage and degradation of RNA in living cells are poorly understood. In this manuscript we use an inducible minigene system to determine the time course of ASO activity in the cell. Estimates of the time required for the ASO to enter and traverse the cell, scan the target mRNA, bind the cognate site, recruit RNase H1 and initiate cleavage, are presented in the context of transcription and mRNA processing rates. Data are also presented which indicate that rates for RNase H1-dependent ASO-mediated degradation of the targeted RNAs are different for nuclear-retained versus RNAs exported to the cytoplasm and that the level of RNase H1 in the cell and cellular compartments is limiting to the rate of ASO activity. In both cellular compartments RNase H1 ASOs essentially double the endogenous rates of clearance of the target RNA. Overexpression of Escherichia coli RNase H1 or the presence of multiple cognate sites each further increase the rate of target RNA degradation.
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Affiliation(s)
- Timothy A Vickers
- Department of Core Antisense Research, ISIS Pharmaceuticals, Inc. 2855 Gazelle Court, Carlsbad, CA 92010, USA
| | - Stanley T Crooke
- Department of Core Antisense Research, ISIS Pharmaceuticals, Inc. 2855 Gazelle Court, Carlsbad, CA 92010, USA
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Liang XH, Sun H, Shen W, Crooke ST. Identification and characterization of intracellular proteins that bind oligonucleotides with phosphorothioate linkages. Nucleic Acids Res 2015; 43:2927-45. [PMID: 25712094 PMCID: PMC4357732 DOI: 10.1093/nar/gkv143] [Citation(s) in RCA: 139] [Impact Index Per Article: 15.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Although the RNase H-dependent mechanism of inhibition of gene expression by chemically modified antisense oligonucleotides (ASOs) has been well characterized, little is known about the interactions between ASOs and intracellular proteins that may alter cellular localization and/or potency of ASOs. Here, we report the identification of 56 intracellular ASO-binding proteins using multi-step affinity selection approaches. Many of the tested proteins had no significant effect on ASO activity; however, some proteins, including La/SSB, NPM1, ANXA2, VARS and PC4, appeared to enhance ASO activities, likely through mechanisms related to subcellular distribution. VARS and ANXA2 co-localized with ASOs in endocytic organelles, and reduction in the level of VARS altered lysosome/ASO localization patterns, implying that these proteins may facilitate ASO release from the endocytic pathway. Depletion of La and NPM1 reduced nuclear ASO levels, suggesting potential roles in ASO nuclear accumulation. On the other hand, Ku70 and Ku80 proteins inhibited ASO activity, most likely by competition with RNase H1 for ASO/RNA duplex binding. Our results demonstrate that phosphorothioate-modified ASOs bind a set of cellular proteins that affect ASO activity via different mechanisms.
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Affiliation(s)
- Xue-hai Liang
- Department of Core Antisense Research, ISIS Pharmaceuticals, Carlsbad, CA 92010, USA
| | - Hong Sun
- Department of Core Antisense Research, ISIS Pharmaceuticals, Carlsbad, CA 92010, USA
| | - Wen Shen
- Department of Core Antisense Research, ISIS Pharmaceuticals, Carlsbad, CA 92010, USA
| | - Stanley T Crooke
- Department of Core Antisense Research, ISIS Pharmaceuticals, Carlsbad, CA 92010, USA
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35
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Vickers TA, Freier SM, Bui HH, Watt A, Crooke ST. Targeting of repeated sequences unique to a gene results in significant increases in antisense oligonucleotide potency. PLoS One 2014; 9:e110615. [PMID: 25334092 PMCID: PMC4198294 DOI: 10.1371/journal.pone.0110615] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2014] [Accepted: 09/15/2014] [Indexed: 11/19/2022] Open
Abstract
A new strategy for identifying potent RNase H-dependent antisense oligonucleotides (ASOs) is presented. Our analysis of the human transcriptome revealed that a significant proportion of genes contain unique repeated sequences of 16 or more nucleotides in length. Activities of ASOs targeting these repeated sites in several representative genes were compared to those of ASOs targeting unique single sites in the same transcript. Antisense activity at repeated sites was also evaluated in a highly controlled minigene system. Targeting both native and minigene repeat sites resulted in significant increases in potency as compared to targeting of non-repeated sites. The increased potency at these sites is a result of increased frequency of ASO/RNA interactions which, in turn, increases the probability of a productive interaction between the ASO/RNA heteroduplex and human RNase H1 in the cell. These results suggest a new, highly efficient strategy for rapid identification of highly potent ASOs.
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Affiliation(s)
- Timothy A. Vickers
- Department of Core Antisense Research, ISIS Pharmaceuticals, Inc., Carlsbad, California, United States of America
| | - Susan M. Freier
- Department of Core Antisense Research, ISIS Pharmaceuticals, Inc., Carlsbad, California, United States of America
| | - Huynh-Hoa Bui
- Department of Core Antisense Research, ISIS Pharmaceuticals, Inc., Carlsbad, California, United States of America
| | - Andrew Watt
- Department of Core Antisense Research, ISIS Pharmaceuticals, Inc., Carlsbad, California, United States of America
| | - Stanley T. Crooke
- Department of Core Antisense Research, ISIS Pharmaceuticals, Inc., Carlsbad, California, United States of America
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36
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Antisense oligonucleotides capable of promoting specific target mRNA reduction via competing RNase H1-dependent and independent mechanisms. PLoS One 2014; 9:e108625. [PMID: 25299183 PMCID: PMC4191969 DOI: 10.1371/journal.pone.0108625] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2014] [Accepted: 09/03/2014] [Indexed: 11/19/2022] Open
Abstract
Antisense oligonucleotides (ASOs) are most commonly designed to reduce targeted RNA via RNase H1-dependent degradation. In this paper we demonstrate that cellular proteins can compete for sites targeted by RNase H1-dependent ASOs. We further show that some ASOs designed to mediate RNase H1 cleavage can, in certain instances, promote target reduction both by RNase H1-mediated cleavage and by steric inhibition of binding of splicing factors at a site required for efficient processing of the pre-mRNA. In the latter case, RNase H cleavage was prevented by binding of a second protein, HSPA8, to the ASO/pre-mRNA heteroduplex. In addition, using a precisely controlled minigene system, we directly demonstrated that activity of ASOs targeting sites in introns is strongly influenced by splicing efficiency.
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