1
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Li Q, Dong M, Chen P. Advances in structural-guided modifications of siRNA. Bioorg Med Chem 2024; 110:117825. [PMID: 38954918 DOI: 10.1016/j.bmc.2024.117825] [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: 05/16/2024] [Revised: 06/27/2024] [Accepted: 06/27/2024] [Indexed: 07/04/2024]
Abstract
To date, the US Food and Drug Administration (FDA) has approved six small interfering RNA (siRNA) drugs: patisiran, givosiran, lumasiran, inclisiran, vutrisiran, and nedosiran, serving as compelling evidence of the promising potential of RNA interference (RNAi) therapeutics. The successful implementation of siRNA therapeutics is improved through a combination of various chemical modifications and diverse delivery approaches. The utilization of chemically modified siRNA at specific sites on either the sense strand (SS) or antisense strand (AS) has the potential to enhance resistance to ribozyme degradation, improve stability and specificity, and prolong the efficacy of drugs. Herein, we provide comprehensive analyses concerning the correlation between chemical modifications and structure-guided siRNA design. Various modifications, such as 2'-modifications, 2',4'-dual modifications, non-canonical sugar modifications, and phosphonate mimics, are crucial for the activity of siRNA. We also emphasize the essential strategies for enhancing overhang stability, improving RISC loading efficacy and strand selection, reducing off-target effects, and discussing the future of targeted delivery.
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Affiliation(s)
- Qiang Li
- Department of Medicinal Chemistry, School of Pharmacy, Qingdao University, Qingdao 266021, China; Research and Development Department, NanoPeptide (Qingdao) Biotechnology Ltd., Qingdao, China.
| | - Mingxin Dong
- Department of Medicinal Chemistry, School of Pharmacy, Qingdao University, Qingdao 266021, China.
| | - Pu Chen
- Research and Development Department, NanoPeptide (Qingdao) Biotechnology Ltd., Qingdao, China; Department of Chemical Engineering and Waterloo Institute for Nanotechnology, University of Waterloo, Waterloo, ON, Canada.
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2
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Wilson B, Su Z, Kumar P, Dutta A. XRN2 suppresses aberrant entry of tRNA trailers into argonaute in humans and Arabidopsis. PLoS Genet 2023; 19:e1010755. [PMID: 37146074 PMCID: PMC10191329 DOI: 10.1371/journal.pgen.1010755] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2022] [Revised: 05/17/2023] [Accepted: 04/21/2023] [Indexed: 05/07/2023] Open
Abstract
MicroRNAs (miRNAs) are a well-characterized class of small RNAs (sRNAs) that regulate gene expression post-transcriptionally. miRNAs function within a complex milieu of other sRNAs of similar size and abundance, with the best characterized being tRNA fragments or tRFs. The mechanism by which the RNA-induced silencing complex (RISC) selects for specific sRNAs over others is not entirely understood in human cells. Several highly expressed tRNA trailers (tRF-1s) are strikingly similar to microRNAs in length but are generally excluded from the microRNA effector pathway. This exclusion provides a paradigm for identifying mechanisms of RISC selectivity. Here, we show that 5' to 3' exoribonuclease XRN2 contributes to human RISC selectivity. Although highly abundant, tRF-1s are highly unstable and degraded by XRN2 which blocks tRF-1 accumulation in RISC. We also find that XRN mediated degradation of tRF-1s and subsequent exclusion from RISC is conserved in plants. Our findings reveal a conserved mechanism that prevents aberrant entry of a class of highly produced sRNAs into Ago2.
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Affiliation(s)
- Briana Wilson
- Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, Charlottesville, Virginia, United States of America
| | - Zhangli Su
- Department of Genetics, University of Alabama, Birmingham, Alabama, United States of America
| | - Pankaj Kumar
- Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, Charlottesville, Virginia, United States of America
| | - Anindya Dutta
- Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, Charlottesville, Virginia, United States of America
- Department of Genetics, University of Alabama, Birmingham, Alabama, United States of America
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3
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Li Z, Wang X, Zhou X, Wang J, Guan Z, Yang Z. Optimization in Chemical Modification of Single-Stranded siRNA Encapsulated by Neutral Cytidinyl/Cationic Lipids. Front Chem 2022; 10:843181. [PMID: 35345539 PMCID: PMC8957067 DOI: 10.3389/fchem.2022.843181] [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: 12/25/2021] [Accepted: 02/07/2022] [Indexed: 11/13/2022] Open
Abstract
Single-stranded siRNA (ss-siRNA) refers to the antisense strand of siRNA, which plays the role of gene silencing. Since single-stranded RNA is unstable, the present study employed a homemade neutral cytidinyl/cationic lipid delivery system and chemical modifications to improve its stability. The results showed that with the aid of mixed lipids, ss-siRNA could knock down 40% of target mRNA at 25 nM. With 2ʹ-F/2ʹ-OMe, phosphorothioate and 5ʹ-terminal phosphorylation, the optimized ss-siRNA could knock down 80% of target mRNA at 25 nM. Further knocking down AGO2, the ss-siRNAs could not effectively silence target mRNAs. Analysis of the biodistribution in vivo showed that ss-siRNA was less durable than siRNA, but spread more quickly to tissues. This study provides a safe and efficient ss-siRNA delivery and modification strategy, which lays the foundation for future works.
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4
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Avital A, Muzika NS, Persky Z, Karny A, Bar G, Michaeli Y, Shklover J, Shainsky J, Weissman H, Shoseyov O, Schroeder A. Foliar Delivery of siRNA Particles for Treating Viral Infections in Agricultural Grapevines. ADVANCED FUNCTIONAL MATERIALS 2021; 31:2101003. [PMID: 34744552 PMCID: PMC7611933 DOI: 10.1002/adfm.202101003] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Indexed: 05/05/2023]
Abstract
Grapevine leafroll disease (GLD) is a globally spreading viral infection that causes major economic losses by reducing crop yield, plant longevity and berry quality, with no effective treatment. Grapevine leafroll associated virus-3 (GLRaV-3) is the most severe and prevalent GLD strain. Here, we evaluated the ability of RNA interference (RNAi), a non-GMO gene-silencing pathway, to treat GLRaV-3 in infected Cabernet Sauvignon grapevines. We synthesized lipid-modified polyethylenimine (lmPEI) as a carrier for long double-stranded RNA (dsRNA, 250-bp-long) that targets RNA polymerase and coat protein genes that are conserved in the GLRaV-3 genome. Self-assembled dsRNA-lmPEI particles, 220 nm in diameter, displayed inner ordered domains spaced 7.3±2 nm from one another, correlating to lmPEI wrapping spirally around the dsRNA. The particles effectively protected RNA from degradation by ribonucleases, and Europium-loaded particles applied to grapevine leaves were detected as far as 60-cm from the foliar application point. In three field experiments, a single dose of foliar administration knocked down GLRaV-3 titer, and multiple doses of the treatment kept the viral titer at baseline and triggered recovery of the vine and berries. This study demonstrates RNAi as a promising platform for treating viral diseases in agriculture.
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Affiliation(s)
- Aviram Avital
- Laboratory for Targeted Drug Delivery and Personalized Medicine Technologies, Department of Chemical Engineering, Technion – Israel Institute of Technology, Haifa 3200003, Israel
- The Norman Seiden Multidisciplinary Program for Nanoscience and Nanotechnology, Technion – Israel Institute of Technology, Haifa 3200003, Israel
| | - Noy Sadot Muzika
- Robert H. Smith Faculty of Agriculture, Food and Environment, Hebrew University, Rehovot 76100, Israel
| | - Zohar Persky
- Robert H. Smith Faculty of Agriculture, Food and Environment, Hebrew University, Rehovot 76100, Israel
| | - Avishai Karny
- Laboratory for Targeted Drug Delivery and Personalized Medicine Technologies, Department of Chemical Engineering, Technion – Israel Institute of Technology, Haifa 3200003, Israel
| | - Gili Bar
- Laboratory for Targeted Drug Delivery and Personalized Medicine Technologies, Department of Chemical Engineering, Technion – Israel Institute of Technology, Haifa 3200003, Israel
| | - Yuval Michaeli
- Laboratory for Targeted Drug Delivery and Personalized Medicine Technologies, Department of Chemical Engineering, Technion – Israel Institute of Technology, Haifa 3200003, Israel
| | - Jeny Shklover
- Laboratory for Targeted Drug Delivery and Personalized Medicine Technologies, Department of Chemical Engineering, Technion – Israel Institute of Technology, Haifa 3200003, Israel
| | - Janna Shainsky
- Laboratory for Targeted Drug Delivery and Personalized Medicine Technologies, Department of Chemical Engineering, Technion – Israel Institute of Technology, Haifa 3200003, Israel
| | - Haim Weissman
- The Weizmann Institute of Science, Department of Organic Chemistry, Rehovot 76100, Israel
| | - Oded Shoseyov
- Robert H. Smith Faculty of Agriculture, Food and Environment, Hebrew University, Rehovot 76100, Israel
| | - Avi Schroeder
- Laboratory for Targeted Drug Delivery and Personalized Medicine Technologies, Department of Chemical Engineering, Technion – Israel Institute of Technology, Haifa 3200003, Israel
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5
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Lin WY, Zhu R, Zhang Z, Lu X, Wang H, He W, Hu Y, Tang L. RNAi targeting heparin cofactor II promotes hemostasis in hemophilia A. MOLECULAR THERAPY-NUCLEIC ACIDS 2021; 24:658-668. [PMID: 33996250 PMCID: PMC8093307 DOI: 10.1016/j.omtn.2021.03.022] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/22/2020] [Accepted: 03/31/2021] [Indexed: 01/15/2023]
Abstract
Hemophilia A is a hemorrhagic disease due to congenital deficiencies of coagulation factor VIII (FVIII). Studies show that hemophilia patients with anticoagulant deficiency present less severe hemorrhagic phenotypes. We aimed to find a new therapeutic option for hemophilia patients by RNA interference (RNAi) targeting heparin cofactor II (HCII), a critical anticoagulant protein inactivating the thrombin. The optimal small interfering RNA (siRNA) was conjugated to an asialoglycoprotein receptor ligand (N-acetylgalactosamine [GalNAc]-HCII), promoting targeted delivery to the liver. After administration, GalNAc-HCII demonstrated effective, dose-dependent, and persistent HCII inhibition. After 7 days, in normal mice, GalNAc-HCII reduced HCII levels to 25.04% ± 2.56%, 11.65% ± 2.41%, and 6.50% ± 1.73% with 2, 5, and 10 mg/kg GalNAc-HCII, respectively. The hemostatic ability of hemophilia mice in the GalNAc-HCII-treated group significantly improved, with low thrombus formation time in the carotid artery thrombosis models and short bleeding time in the tail-clipping assays. After repeated administration, the prolonged activated partial thromboplastin time (APTT) was reduced. A 30 mg/kg dose did not cause pathological thrombosis. Our study confirmed that GalNAc-HCII therapy is effective for treating hemophilia mice and can be considered a new option for treating hemophilia patients.
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Affiliation(s)
- Wen-Yi Lin
- Institute of Hematology, Union Hospital Affiliated Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Ruiqi Zhu
- Institute of Hematology, Union Hospital Affiliated Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Zhen Zhang
- Institute of Hematology, Union Hospital Affiliated Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Xuan Lu
- Institute of Hematology, Union Hospital Affiliated Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Huafang Wang
- Institute of Hematology, Union Hospital Affiliated Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Wenjuan He
- Institute of Hematology, Union Hospital Affiliated Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Yu Hu
- Institute of Hematology, Union Hospital Affiliated Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Liang Tang
- Institute of Hematology, Union Hospital Affiliated Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
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6
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Ashrafizadeh M, Hushmandi K, Rahmani Moghadam E, Zarrin V, Hosseinzadeh Kashani S, Bokaie S, Najafi M, Tavakol S, Mohammadinejad R, Nabavi N, Hsieh CL, Zarepour A, Zare EN, Zarrabi A, Makvandi P. Progress in Delivery of siRNA-Based Therapeutics Employing Nano-Vehicles for Treatment of Prostate Cancer. Bioengineering (Basel) 2020; 7:E91. [PMID: 32784981 PMCID: PMC7552721 DOI: 10.3390/bioengineering7030091] [Citation(s) in RCA: 51] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2020] [Revised: 07/31/2020] [Accepted: 08/06/2020] [Indexed: 02/06/2023] Open
Abstract
Prostate cancer (PCa) accounts for a high number of deaths in males with no available curative treatments. Patients with PCa are commonly diagnosed in advanced stages due to the lack of symptoms in the early stages. Recently, the research focus was directed toward gene editing in cancer therapy. Small interfering RNA (siRNA) intervention is considered as a powerful tool for gene silencing (knockdown), enabling the suppression of oncogene factors in cancer. This strategy is applied to the treatment of various cancers including PCa. The siRNA can inhibit proliferation and invasion of PCa cells and is able to promote the anti-tumor activity of chemotherapeutic agents. However, the off-target effects of siRNA therapy remarkably reduce its efficacy in PCa therapy. To date, various carriers were designed to improve the delivery of siRNA and, among them, nanoparticles are of importance. Nanoparticles enable the targeted delivery of siRNAs and enhance their potential in the downregulation of target genes of interest. Additionally, nanoparticles can provide a platform for the co-delivery of siRNAs and anti-tumor drugs, resulting in decreased growth and migration of PCa cells. The efficacy, specificity, and delivery of siRNAs are comprehensively discussed in this review to direct further studies toward using siRNAs and their nanoscale-delivery systems in PCa therapy and perhaps other cancer types.
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Affiliation(s)
- Milad Ashrafizadeh
- Department of Basic Science, Faculty of Veterinary Medicine, University of Tabriz, Tabriz 5166616471, Iran;
| | - Kiavash Hushmandi
- Department of Food Hygiene and Quality Control, Division of Epidemiology & Zoonoses, Faculty of Veterinary Medicine, University of Tehran, Tehran 1419963114, Iran; (K.H.); (S.B.)
| | - Ebrahim Rahmani Moghadam
- Department of Anatomical Sciences, School of Medicine, Student Research Committee, Shiraz University of Medical Sciences, Shiraz 7134814336, Iran;
| | - Vahideh Zarrin
- Laboratory for Stem Cell Research, Shiraz University of Medical Sciences, Shiraz 7134814336, Iran;
| | | | - Saied Bokaie
- Department of Food Hygiene and Quality Control, Division of Epidemiology & Zoonoses, Faculty of Veterinary Medicine, University of Tehran, Tehran 1419963114, Iran; (K.H.); (S.B.)
| | - Masoud Najafi
- Radiology and Nuclear Medicine Department, School of Paramedical Sciences, Kermanshah University of Medical Sciences, Kermanshah 6715847141, Iran;
| | - Shima Tavakol
- Cellular and Molecular Research Center, Iran University of Medical Sciences, Tehran 1449614525, Iran;
| | - Reza Mohammadinejad
- Pharmaceutics Research Center, Institute of Neuropharmacology, Kerman University of Medical Sciences, Kermaan 55425147, Iran;
| | - Noushin Nabavi
- Research Services, University of Victoria, Victoria, BC V8W 2Y2, Canada;
| | - Chia-Ling Hsieh
- Ph.D. Program for Translational Medicine, College of Medical Science and Technology, Taipei Medical University, Taipei City 110, Taiwan;
| | - Atefeh Zarepour
- Department of Biotechnology, Faculty of Biological Science and Technology, University of Isfahan, Isfahan 8174673441, Iran;
| | | | - Ali Zarrabi
- Sabanci University Nanotechnology Research and Application Center (SUNUM), Tuzla, Istanbul 34956, Turkey
- Center of Excellence for Functional Surfaces and Interfaces (EFSUN), Faculty of Engineering and Natural Sciences, Sabanci University, Tuzla, Istanbul 34956, Turkey
| | - Pooyan Makvandi
- Istituto Italiano di Tecnologia, Centre for Micro-BioRobotics, viale Rinaldo Piaggio 34, 56025 Pontedera, Pisa, Italy
- Chemistry Department, Faculty of Science, Shahid Chamran University of Ahvaz, Ahvaz 61537-53843, Iran
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7
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Glackin CA. Nanoparticle Delivery of TWIST Small Interfering RNA and Anticancer Drugs: A Therapeutic Approach for Combating Cancer. Enzymes 2018; 44:83-101. [PMID: 30360816 DOI: 10.1016/bs.enz.2018.08.004] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Breast and ovarian cancer are the leading cause of cancer-related deaths in women in the United States with over 232,000 new Breast Cancer (BC) diagnoses expected in 2018 and almost 40,000 deaths and an estimated 239,000 new ovarian cancer (OC) cases and 152,000 deaths worldwide annually. OC is the most lethal gynecologic malignancy. This high mortality rate is due to tumor recurrence and metastasis, primarily caused by chemoresistant cancer stem-like cells (CSCs). Triple Negative Breast Cancer (TNBC) patients also become resistant to chemotherapy due to recurrence of CSCs. Currently, no ovarian or breast cancer therapies target CSC specifically. TWIST is overexpressed in the majority of chemoresistant cancers resulting in a low survival rate. Our long-term goal is to develop novel treatments for women with ovarian and breast cancer, specifically treatments that sensitize chemoresistant tumors. Despite successful initial surgery and chemotherapy, over 70% of advanced EOC will recur, and only 15-30% of recurrent disease will respond to chemotherapy (Cortez et al., 2017; Berezhnaya, 2010; Jackson et al., 2015). Moreover, drug resistance causes treatment failure in over 90% of patients with metastatic disease (Solmaz et al., 2015). Thus, recurrent metastatic disease is a major clinical challenge without effective therapy. One of the major challenges in the treatment of breast cancer is the presence of a subpopulation of cancer cells that are chemoresistant (CRC) and metastatic. Given that metastasis is the driving force behind mortality for breast and ovarian cancer patients, it is essential to identify the characteristics of these aberrant cancer cells that allow them to spread to distant sites in the body and develop into metastatic tumors. Understanding the metastatic mechanisms driving cancer cell dispersal will open the door to developing novel therapies that prevent metastasis and improve long-term outcomes for patients. In this chapter we assess the feasibility of targeting the Twist and EMT signaling pathways in breast and ovarian cancer. Additional discussions of the pathways that mediate epithelial-mesenchymal transition (EMT), a process that can give rise to chemoresistance. We review potential treatment strategies for targeting EMT and drug resistance as well as the problems that may arise with these targeted delivery therapeutic approaches. Finally, we examine recent advances in the field, including cancer stem cell targeted nanoparticle delivery and small interference RNA (siRNA) technology, and discuss the impact that these approaches may have on translating much needed therapeutic approaches into the clinic, for the benefit of patients battling this devastating disease.
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Affiliation(s)
- Carlotta A Glackin
- Developmental and Stem Cell Biology, City of Hope Medical Center, Duarte, CA, United States.
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8
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Nikam RR, Gore KR. Journey of siRNA: Clinical Developments and Targeted Delivery. Nucleic Acid Ther 2018; 28:209-224. [PMID: 29584585 DOI: 10.1089/nat.2017.0715] [Citation(s) in RCA: 121] [Impact Index Per Article: 20.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Since the evolutionary discovery of RNA interference and its utilization for gene knockdown in mammalian cell, a remarkable progress has been achieved in small interfering RNA (siRNA) therapeutics. siRNA is a promising tool, utilized as therapeutic agent against various diseases. Despite its significant potential benefits, safe, efficient, and target oriented delivery of siRNA is one of the major challenges in siRNA therapeutics. This review covers major achievements in clinical trials and targeted delivery of siRNAs using various targeting ligand-receptor pair. Local and systemically administered siRNA drug candidates at various phases in clinical trials are described in this review. This review also provides a deep insight in development of targeted delivery of siRNA. Various targeting ligand-siRNA pair with complexation and conjugation approaches are discussed in this review. This will help to achieve further optimization and development in targeted delivery of siRNAs to achieve higher gene silencing efficiency with lowest siRNA dose availability.
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Affiliation(s)
| | - Kiran R Gore
- Department of Chemistry, University of Mumbai , Mumbai, India
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9
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Janas MM, Schlegel MK, Harbison CE, Yilmaz VO, Jiang Y, Parmar R, Zlatev I, Castoreno A, Xu H, Shulga-Morskaya S, Rajeev KG, Manoharan M, Keirstead ND, Maier MA, Jadhav V. Selection of GalNAc-conjugated siRNAs with limited off-target-driven rat hepatotoxicity. Nat Commun 2018; 9:723. [PMID: 29459660 PMCID: PMC5818625 DOI: 10.1038/s41467-018-02989-4] [Citation(s) in RCA: 166] [Impact Index Per Article: 27.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2017] [Accepted: 01/11/2018] [Indexed: 11/30/2022] Open
Abstract
Small interfering RNAs (siRNAs) conjugated to a trivalent N-acetylgalactosamine (GalNAc) ligand are being evaluated in investigational clinical studies for a variety of indications. The typical development candidate selection process includes evaluation of the most active compounds for toxicity in rats at pharmacologically exaggerated doses. The subset of GalNAc-siRNAs that show rat hepatotoxicity is not advanced to clinical development. Potential mechanisms of hepatotoxicity can be associated with the intracellular accumulation of oligonucleotides and their metabolites, RNA interference (RNAi)-mediated hybridization-based off-target effects, and/or perturbation of endogenous RNAi pathways. Here we show that rodent hepatotoxicity observed at supratherapeutic exposures can be largely attributed to RNAi-mediated off-target effects, but not chemical modifications or the perturbation of RNAi pathways. Furthermore, these off-target effects can be mitigated by modulating seed-pairing using a thermally destabilizing chemical modification, which significantly improves the safety profile of a GalNAc-siRNA in rat and may minimize the occurrence of hepatotoxic siRNAs across species.
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Affiliation(s)
- Maja M Janas
- Alnylam Pharmaceuticals, 300 Third Street, Cambridge, MA, 02142, USA
| | - Mark K Schlegel
- Alnylam Pharmaceuticals, 300 Third Street, Cambridge, MA, 02142, USA
| | - Carole E Harbison
- Alnylam Pharmaceuticals, 300 Third Street, Cambridge, MA, 02142, USA
| | - Vedat O Yilmaz
- Alnylam Pharmaceuticals, 300 Third Street, Cambridge, MA, 02142, USA
| | - Yongfeng Jiang
- Alnylam Pharmaceuticals, 300 Third Street, Cambridge, MA, 02142, USA
| | - Rubina Parmar
- Alnylam Pharmaceuticals, 300 Third Street, Cambridge, MA, 02142, USA
| | - Ivan Zlatev
- Alnylam Pharmaceuticals, 300 Third Street, Cambridge, MA, 02142, USA
| | - Adam Castoreno
- Alnylam Pharmaceuticals, 300 Third Street, Cambridge, MA, 02142, USA
| | - Huilei Xu
- Alnylam Pharmaceuticals, 300 Third Street, Cambridge, MA, 02142, USA
| | | | | | - Muthiah Manoharan
- Alnylam Pharmaceuticals, 300 Third Street, Cambridge, MA, 02142, USA
| | | | - Martin A Maier
- Alnylam Pharmaceuticals, 300 Third Street, Cambridge, MA, 02142, USA
| | - Vasant Jadhav
- Alnylam Pharmaceuticals, 300 Third Street, Cambridge, MA, 02142, USA.
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10
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Basu P, Suresh Kumar G. Small molecule-RNA recognition: Binding of the benzophenanthridine alkaloids sanguinarine and chelerythrine to single stranded polyribonucleotides. JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY B-BIOLOGY 2017; 174:173-181. [PMID: 28779690 DOI: 10.1016/j.jphotobiol.2017.07.022] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Received: 05/30/2017] [Revised: 07/18/2017] [Accepted: 07/21/2017] [Indexed: 01/18/2023]
Abstract
Single stranded RNAs are biologically potent as they participate in various key cellular processes. The binding efficacy of two potent anticancer alkaloids, sanguinarine (here after SANG) and chelerythrine (here after CHEL), with single-stranded ribonucleic acids poly(rI), poly(rG), and poly(rC) were studied using spectroscopic and thermodynamic tools. Results reveal that both SANG and CHEL binds well with single stranded RNAs with affinity in the order poly(rI)>poly(rG)>poly(rC). CHEL showed slightly higher affinity compared to SANG with all the single stranded RNAs. Both SANG and CHEL showed association affinity of the lower 106 order with poly(rI), higher 105 order binding with poly(rG) and lower 105 order with poly(rC). The binding mode was partial intercalation due to the staking interaction between the bases and the alkaloids. The complexation of both the SANG and CHEL to the RNAs were mainly enthalpy driven and also favoured by entropy changes. Perturbation was observed in the RNA conformation due to binding of the alkaloids. In this present study we have deciphered the fundamental structural and calorimetric aspects of the interaction of the natural benzophenanthridine alkaloids with single stranded RNAs and these results may help to develop new generation alkaloid based therapeutics targeting single stranded RNAs.
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Affiliation(s)
- Pritha Basu
- Organic and Medicinal Chemistry Division, CSIR-Indian Institute of Chemical Biology, Kolkata 700 032, India
| | - Gopinatha Suresh Kumar
- Organic and Medicinal Chemistry Division, CSIR-Indian Institute of Chemical Biology, Kolkata 700 032, India.
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11
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Abstract
Over the last decades, it has become evident that highly complex networks of regulators govern post-transcriptional regulation of gene expression. A novel class of Argonaute (Ago)-associated RNA molecules, the agotrons, was recently shown to function in a Drosha- and Dicer-independent manner, hence bypassing the maturation steps required for canonical microRNA (miRNA) biogenesis. Agotrons are found in most mammals and associate with Ago as ∼100 nucleotide (nt) long RNA species. Here, we speculate on the functional and biological relevance of agotrons: (i) agotrons could serve as non-promiscuous miRNA-like regulators with reduced off-targeting or (ii) agotrons could encompass other putative functions, such as protecting Ago proteins from taking up aberrant short RNAs or by rescuing and stabilizing otherwise unloaded Ago-proteins from degradation. Collectively, agotrons have emerged as a novel class of interesting non-coding RNA molecules, but their full functional potential and biological impact still remain to be disclosed.
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Affiliation(s)
- Lotte V W Stagsted
- Department of Molecular Biology and Genetics (MBG), and Interdisciplinary Nanoscience Center (iNANO), Aarhus University, Aarhus, Denmark
| | - Iben Daugaard
- Department of Molecular Biology and Genetics (MBG), and Interdisciplinary Nanoscience Center (iNANO), Aarhus University, Aarhus, Denmark
| | - Thomas B Hansen
- Department of Molecular Biology and Genetics (MBG), and Interdisciplinary Nanoscience Center (iNANO), Aarhus University, Aarhus, Denmark
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12
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Giraud L, Viricel W, Leblond J, Giasson S. Single stranded siRNA complexation through non-electrostatic interactions. Biomaterials 2017; 113:230-242. [DOI: 10.1016/j.biomaterials.2016.10.035] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2016] [Revised: 10/19/2016] [Accepted: 10/23/2016] [Indexed: 11/24/2022]
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13
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Chang W, Pei Y, Guidry EN, Zewge D, Parish CA, Sherer EC, DiMuzio J, Zhang H, South VJ, Strapps WR, Sepp-Lorenzino L, Colletti SL, Stanton MG. Systematic chemical modifications of single stranded siRNAs significantly improved CTNNB1 mRNA silencing. Bioorg Med Chem Lett 2016; 26:4513-4517. [DOI: 10.1016/j.bmcl.2016.07.064] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2016] [Revised: 07/25/2016] [Accepted: 07/27/2016] [Indexed: 11/25/2022]
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14
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Ohno SI, Itano K, Harada Y, Asada K, Oikawa K, Kashiwazako M, Okuyama H, Kumagai K, Takanashi M, Sudo K, Ikeda N, Kuroda M. Development of Novel Small Hairpin RNAs That do not Require Processing by Dicer or AGO2. Mol Ther 2016; 24:1278-89. [PMID: 27109632 PMCID: PMC5088761 DOI: 10.1038/mt.2016.81] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2015] [Accepted: 04/04/2016] [Indexed: 01/08/2023] Open
Abstract
The innate cytokine response to nucleic acid is the most challenging problem confronting the practical use of nucleic acid medicine. The degree of stimulation of the innate cytokine response strongly depends on the length of the nucleic acid. In this study, we developed a 30-nucleotide single-strand RNA, termed "guide hairpin RNA (ghRNA, ghR)", that has a physiological function similar to that of miRNA and siRNA. The ghR caused no innate cytokine response either in vitro or in vivo. In addition, its structure does not contain a passenger strand seed sequence, reducing the unwanted gene repression relative to existing short RNA reagents. Systemic and local injection of ghR-form miR-34a (ghR-34a) suppressed tumor growth in a mouse model of RAS-induced lung cancer. Furthermore, Dicer and AGO2 are not required for ghR-34a function. This novel RNA interference (RNAi) technology may provide a novel, safe, and effective nucleic acid drug platform that will increase the clinical usefulness of nucleic acid therapy.
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Affiliation(s)
- Shin-ichiro Ohno
- Department of Molecular Pathology,
Tokyo Medical University, Tokyo, Japan
| | - Karen Itano
- Department of Molecular Pathology,
Tokyo Medical University, Tokyo, Japan
| | - Yuichirou Harada
- Department of Molecular Pathology,
Tokyo Medical University, Tokyo, Japan
| | - Koutaro Asada
- Department of Molecular Pathology,
Tokyo Medical University, Tokyo, Japan
| | - Keiki Oikawa
- Department of Molecular Pathology,
Tokyo Medical University, Tokyo, Japan
| | - Mikie Kashiwazako
- Department of Molecular Pathology,
Tokyo Medical University, Tokyo, Japan
| | - Hikaru Okuyama
- Department of Molecular Pathology,
Tokyo Medical University, Tokyo, Japan
| | - Katsuyoshi Kumagai
- Department of Animal Research Center,
Tokyo Medical University, Tokyo, Japan
| | | | - Katsuko Sudo
- Department of Animal Research Center,
Tokyo Medical University, Tokyo, Japan
| | - Norihiko Ikeda
- Department of Respiratory Surgery,
Tokyo Medical University, Tokyo, Japan
| | - Masahiko Kuroda
- Department of Molecular Pathology,
Tokyo Medical University, Tokyo, Japan
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15
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Liu HY, Yu X, Liu H, Wu D, She JX. Co-targeting EGFR and survivin with a bivalent aptamer-dual siRNA chimera effectively suppresses prostate cancer. Sci Rep 2016; 6:30346. [PMID: 27456457 PMCID: PMC4960556 DOI: 10.1038/srep30346] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2016] [Accepted: 07/04/2016] [Indexed: 12/25/2022] Open
Abstract
Current targeted therapies using small kinase inhibitors and antibodies have limited efficacy in treating prostate cancer (PCa), a leading cause of cancer death in American men. We have developed a novel strategy by engineering an RNA-based aptamer-siRNA chimera, in which a bivalent aptamer specifically binds prostate-specific membrane antigen (PSMA) via an antibody-like structure to promote siRNA internalization in PCa cells, and two siRNAs specific to EGFR and survivin are fused between two aptamers. The chimera is able to inhibit EGFR and survivin simultaneously and induce apoptosis effectively in vitro and in vivo. In the C4-2 PCa xenograft model, the treatment with the chimera significantly suppresses tumor growth and angiogenesis. The inhibition of angiogenesis is mediated by an EGFR-HIF1α-VEGF-dependent mechanism. Our results support that the bivalent aptamer-driven delivery of two siRNAs could be a new combination therapeutic strategy to effectively inhibit multiple and conventionally "undruggable" targets.
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Affiliation(s)
- Hong Yan Liu
- Center for Biotechnology and Genomic Medicine, Medical College of Georgia, Augusta University, Augusta, GA, 30912, USA,
| | - Xiaolin Yu
- Center for Biotechnology and Genomic Medicine, Medical College of Georgia, Augusta University, Augusta, GA, 30912, USA
| | - Haitao Liu
- Center for Biotechnology and Genomic Medicine, Medical College of Georgia, Augusta University, Augusta, GA, 30912, USA
| | - Daqing Wu
- Georgia Cancer Center at Augusta University, and Department of Biochemistry and Molecular Biology, Medical College of Georgia, Augusta University, Augusta, GA, 30912, USA.,
| | - Jin-Xiong She
- Center for Biotechnology and Genomic Medicine, Medical College of Georgia, Augusta University, Augusta, GA, 30912, USA
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16
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Zlatev I, Foster DJ, Liu J, Charisse K, Brigham B, Parmar RG, Jadhav V, Maier MA, Rajeev KG, Egli M, Manoharan M. 5'-C-Malonyl RNA: Small Interfering RNAs Modified with 5'-Monophosphate Bioisostere Demonstrate Gene Silencing Activity. ACS Chem Biol 2016; 11:953-60. [PMID: 26675211 DOI: 10.1021/acschembio.5b00654] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
5'-Phosphorylation is a critical step in the cascade of events that leads to loading of small interfering RNAs (siRNAs) into the RNA-induced silencing complex (RISC) to elicit gene silencing. 5'-Phosphorylation of exogenous siRNAs is generally accomplished by a cytosolic Clp1 kinase, and in most cases, the presence of a 5'-monophosphate on synthetic siRNAs is not a prerequisite for activity. Chemically introduced, metabolically stable 5'-phosphate mimics can lead to higher metabolic stability, increased RISC loading, and higher gene silencing activities of chemically modified siRNAs. In this study, we report the synthesis of 5'-C-malonyl RNA, a 5'-monophosphate bioisostere. A 5'-C-malonyl-modified nucleotide was incorporated at the 5'-terminus of chemically modified RNA oligonucleotides using solid-phase synthesis. In vitro silencing activity, in vitro metabolic stability, and in vitro RISC loading of 5'-C-malonyl siRNA was compared to corresponding 5'-phosphorylated and 5'-nonphosphorylated siRNAs. The 5'-C-malonyl siRNAs showed sustained or improved in vitro gene silencing and high levels of Ago2 loading and conferred dramatically improved metabolic stability to the antisense strand of the siRNA duplexes. In silico modeling studies indicate a favorable fit of the 5'-C-malonyl group within the 5'-phosphate binding pocket of human Ago2MID domain.
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Affiliation(s)
- Ivan Zlatev
- Alnylam Pharmaceuticals, 300
Third Street, Cambridge, Massachusetts 02142, United States
| | - Donald J. Foster
- Alnylam Pharmaceuticals, 300
Third Street, Cambridge, Massachusetts 02142, United States
| | - Jingxuan Liu
- Alnylam Pharmaceuticals, 300
Third Street, Cambridge, Massachusetts 02142, United States
| | - Klaus Charisse
- Alnylam Pharmaceuticals, 300
Third Street, Cambridge, Massachusetts 02142, United States
| | - Benjamin Brigham
- Alnylam Pharmaceuticals, 300
Third Street, Cambridge, Massachusetts 02142, United States
| | - Rubina G. Parmar
- Alnylam Pharmaceuticals, 300
Third Street, Cambridge, Massachusetts 02142, United States
| | - Vasant Jadhav
- Alnylam Pharmaceuticals, 300
Third Street, Cambridge, Massachusetts 02142, United States
| | - Martin A. Maier
- Alnylam Pharmaceuticals, 300
Third Street, Cambridge, Massachusetts 02142, United States
| | | | - Martin Egli
- Department
of Biochemistry, Vanderbilt University, Nashville, Tennessee 37232, United States
| | - Muthiah Manoharan
- Alnylam Pharmaceuticals, 300
Third Street, Cambridge, Massachusetts 02142, United States
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17
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siRNAmod: A database of experimentally validated chemically modified siRNAs. Sci Rep 2016; 6:20031. [PMID: 26818131 PMCID: PMC4730238 DOI: 10.1038/srep20031] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2015] [Accepted: 12/21/2015] [Indexed: 11/21/2022] Open
Abstract
Small interfering RNA (siRNA) technology has vast potential for functional genomics and development of therapeutics. However, it faces many obstacles predominantly instability of siRNAs due to nuclease digestion and subsequently biologically short half-life. Chemical modifications in siRNAs provide means to overcome these shortcomings and improve their stability and potency. Despite enormous utility bioinformatics resource of these chemically modified siRNAs (cm-siRNAs) is lacking. Therefore, we have developed siRNAmod, a specialized databank for chemically modified siRNAs. Currently, our repository contains a total of 4894 chemically modified-siRNA sequences, comprising 128 unique chemical modifications on different positions with various permutations and combinations. It incorporates important information on siRNA sequence, chemical modification, their number and respective position, structure, simplified molecular input line entry system canonical (SMILES), efficacy of modified siRNA, target gene, cell line, experimental methods, reference etc. It is developed and hosted using Linux Apache MySQL PHP (LAMP) software bundle. Standard user-friendly browse, search facility and analysis tools are also integrated. It would assist in understanding the effect of chemical modifications and further development of stable and efficacious siRNAs for research as well as therapeutics. siRNAmod is freely available at: http://crdd.osdd.net/servers/sirnamod.
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18
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Modulation of the RNA Interference Activity Using Central Mismatched siRNAs and Acyclic Threoninol Nucleic Acids (aTNA) Units. Molecules 2015; 20:7602-19. [PMID: 25919280 PMCID: PMC6272285 DOI: 10.3390/molecules20057602] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2015] [Revised: 04/21/2015] [Accepted: 04/22/2015] [Indexed: 02/06/2023] Open
Abstract
The understanding of the mechanisms behind nucleotide recognition by Argonaute 2, core protein of the RNA-induced silencing complex, is a key aspect in the optimization of small interfering RNAs (siRNAs) activity. To date, great efforts have been focused on the modification of certain regions of siRNA, such as the 3'/5'-termini and the seed region. Only a few reports have described the roles of central positions flanking the cleavage site during the silence process. In this study, we investigate the potential correlations between the thermodynamic and silencing properties of siRNA molecules carrying, at internal positions, an acyclic L-threoninol nucleic acid (aTNA) modification. Depending on position, the silencing is weakened or impaired. Furthermore, we evaluate the contribution of mismatches facing either a natural nucleotide or an aTNA modification to the siRNA potency. The position 11 of the antisense strand is more permissive to mismatches and aTNA modification, in respect to the position 10. Additionally, comparing the ON-/OFF-target silencing of central mismatched siRNAs with 5'-terminal modified siRNA, we concluded: (i) central perturbation of duplex pairing features weights more on potency rather than silencing asymmetry; (ii) complete bias for the ON-target silencing can be achieved with single L-threoninol modification near the 5'-end of the sense strand.
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19
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Valenzuela RAP, Suter SR, Ball-Jones AA, Ibarra-Soza JM, Zheng Y, Beal PA. Base modification strategies to modulate immune stimulation by an siRNA. Chembiochem 2014; 16:262-7. [PMID: 25487859 DOI: 10.1002/cbic.201402551] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2014] [Indexed: 12/24/2022]
Abstract
Immune stimulation triggered by siRNAs is one of the major challenges in the development of safe RNAi-based therapeutics. Within an immunostimulatory siRNA sequence, this hurdle is commonly addressed by using ribose modifications (e.g., 2'-OMe or 2'-F), which results in decreased cytokine production. However, as immune stimulation by siRNAs is a sequence-dependent phenomenon, recognition of the nucleobases by the trigger receptor(s) is also likely. Here, we use the recently published crystal structures of Toll-like receptor 8 (TLR8) bound to small-molecule agonists to generate computational models for ribonucleotide binding by this immune receptor. Our modeling suggested that modification of either the Watson-Crick or Hoogsteen face of adenosine would disrupt nucleotide/TLR8 interactions. We employed chemical synthesis to alter either the Watson-Crick or Hoogsteen face of adenosine and evaluated the effect of these modifications in an siRNA guide strand by measuring the immunostimulatory and RNA interference properties. For the siRNA guide strand tested, we found that modifying the Watson-Crick face is generally more effective at blocking TNFα production in human peripheral blood mononuclear cells (PBMCs) than modification at the Hoogsteen edge. We also observed that modifications near the 5'-end were more effective at blocking cytokine production than those placed at the 3'-end. This work advances our understanding of how chemical modifications can be used to optimize siRNA performance.
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20
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RNA/aTNA chimeras: RNAi effects and nucleases resistance of single and double stranded RNAs. Molecules 2014; 19:17872-96. [PMID: 25375332 PMCID: PMC6271724 DOI: 10.3390/molecules191117872] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2014] [Revised: 10/14/2014] [Accepted: 10/15/2014] [Indexed: 12/13/2022] Open
Abstract
The RNA interference pathway (RNAi) is a specific and powerful biological process, triggered by small non-coding RNA molecules and involved in gene expression regulation. In this work, we explored the possibility of increasing the biological stability of these RNA molecules by replacing their natural ribose ring with an acyclic L-threoninol backbone. In particular, this modification has been incorporated at certain positions of the oligonucleotide strands and its effects on the biological properties of the siRNA have been evaluated. In vitro cellular RNAi assays have demonstrated that the L-threoninol backbone is well tolerated by the RNAi machinery in both double and single-stranded fashion, with activities significantly higher than those evinced by the unmodified RNAs and comparable to the well-known phosphorothioate modification. Additionally, this modification conferred extremely strong resistance to serum and 3'/5'-exonucleases. In view of these results, we applied this modification to the knockdown of a therapeutically relevant human gene such as apolipoprotein B (ApoB). Further studies on the activation of the innate immune system showed that L-threoninol-modified RNAs are slightly less stimulatory than unmodified RNAs.
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21
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Chak LL, Okamura K. Argonaute-dependent small RNAs derived from single-stranded, non-structured precursors. Front Genet 2014; 5:172. [PMID: 24959173 PMCID: PMC4050365 DOI: 10.3389/fgene.2014.00172] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2014] [Accepted: 05/22/2014] [Indexed: 12/31/2022] Open
Abstract
A general feature of Argonaute-dependent small RNAs is their base-paired precursor structures, and precursor duplex structures are often required for confident annotation of miRNA genes. However, this rule has been broken by discoveries of functional small RNA species whose precursors lack a predictable double-stranded (ds-) RNA structure, arguing that duplex structures are not prerequisite for small RNA loading to Argonautes. The biological significance of single-stranded (ss-) RNA loading has been recognized particularly in systems where active small RNA amplification mechanisms are involved, because even a small amount of RNA molecules can trigger the production of abundant RNA species leading to profound biological effects. However, even in the absence of small RNA amplification mechanisms, recent studies have demonstrated that potent gene silencing can be achieved using chemically modified synthetic ssRNAs that are resistant to RNases in mice. Therefore, such ssRNA-mediated gene regulation may have broader roles than previously recognized, and the findings have opened the door for further research to optimize the design of ss-siRNAs toward future pharmaceutical and biomedical applications of gene silencing technologies. In this review, we will summarize studies about endogenous ssRNA species that are bound by Argonaute proteins and how ssRNA precursors are recognized by various small RNA pathways.
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Affiliation(s)
- Li-Ling Chak
- Temasek Life Sciences Laboratory, 1 Research Link, National University of Singapore Singapore, Singapore
| | - Katsutomo Okamura
- Temasek Life Sciences Laboratory, 1 Research Link, National University of Singapore Singapore, Singapore ; School of Biological Sciences, Nanyang Technological University Singapore, Singapore
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22
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Allison SJ, Milner J. RNA Interference by Single- and Double-stranded siRNA With a DNA Extension Containing a 3' Nuclease-resistant Mini-hairpin Structure. MOLECULAR THERAPY-NUCLEIC ACIDS 2014; 2:e141. [PMID: 24399205 PMCID: PMC3894584 DOI: 10.1038/mtna.2013.68] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/22/2013] [Accepted: 11/06/2013] [Indexed: 11/30/2022]
Abstract
Selective gene silencing by RNA interference (RNAi) involves double-stranded small interfering RNA (ds siRNA) composed of single-stranded (ss) guide and passenger RNAs. siRNA is recognized and processed by Ago2 and C3PO, endonucleases of the RNA-induced silencing complex (RISC). RISC cleaves passenger RNA, exposing the guide RNA for base-pairing with its homologous mRNA target. Remarkably, the 3′ end of passenger RNA can accommodate a DNA extension of 19-nucleotides without loss of RNAi function. This construct is termed passenger-3′-DNA/ds siRNA and includes a 3′-nuclease-resistant mini-hairpin structure. To test this novel modification further, we have now compared the following constructs: (I) guide-3′-DNA/ds siRNA, (II) passenger-3′-DNA/ds siRNA, (III) guide-3′-DNA/ss siRNA, and (IV) passenger-3′-DNA/ss siRNA. The RNAi target was SIRT1, a cancer-specific survival factor. Constructs I–III each induced selective knock-down of SIRT1 mRNA and protein in both noncancer and cancer cells, accompanied by apoptotic cell death in the cancer cells. Construct IV, which lacks the SIRT1 guide strand, had no effect. Importantly, the 3′-DNA mini-hairpin conferred nuclease resistance to constructs I and II. Resistance required the double-stranded RNA structure since single-stranded guide-3′-DNA/ss siRNA (construct III) was susceptible to serum nucleases with associated loss of RNAi activity. The potential applications of 3′-DNA/siRNA constructs are discussed.
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Affiliation(s)
- Simon J Allison
- 1] Department of Biology, University of York, York, UK [2] Current address: Institute of Cancer Therapeutics, University of Bradford, Bradford, UK
| | - Jo Milner
- Department of Biology, University of York, York, UK
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23
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Yang L, Li X, Jiang S, Qiu L, Zhou F, Liu W, Jiang S. Characterization of Argonaute2 gene from black tiger shrimp (Penaeus monodon) and its responses to immune challenges. FISH & SHELLFISH IMMUNOLOGY 2014; 36:261-9. [PMID: 24262300 DOI: 10.1016/j.fsi.2013.11.010] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/25/2013] [Revised: 11/04/2013] [Accepted: 11/11/2013] [Indexed: 05/06/2023]
Abstract
Argonaute2 binds to a short guide RNA (microRNA or short interfering RNA) and guides RNAs direct RISC to complementary mRNAs that are targets for RISC-mediated gene silencing. Here we identified and characterized Argonaute2 from black tiger shrimp Penaeus monodon (designated as PmAgo2). The full-length cDNA of PmAgo2 contained a 5' untranslated region (UTR) of 106 bp, an open reading frame (ORF) of 2616 bp and a 3' UTR of 123 bp. The predicted PmAgo2 protein is 99.4 KDa with the theoretical isoelectric point of 9.54. PmAgo2 shared the highest similarity of amino acid with Marsupenaeus japonicus Argonaute2 and Litopenaeus vannamei Argonaute2, at 69.0% and 68.5%, respectively. Phylogenic analysis showed PmAgo2 clustered with shrimp Argonaute2, and closed to the group of insects. Real-time quantitative PCR showed that PmAgo2 was widely expressed in almost all examined tissues except eyestalk, with high expression in lymph and haemocyte. mRNA expression also revealed that PmAgo2 was significantly up-regulated by Staphylococcus aureus and White Spot Syndrome Virus (WSSV) in hepatopancreas. Furthermore, our study also confirmed that dsRNA and ssRNA homologous poly (I:C) and R848 activated the expression of PmAgo2. The result indicated that PmAgo2 responded to both bacterial infection and viral infection, especially, it may induce an ssRNA-mediated RNAi with other core members of siRNA pathway in black tiger shrimp.
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Affiliation(s)
- Lishi Yang
- Key Laboratory of South China Sea Fishery Resources Exploitation & Utilization, Ministry of Agriculture, The South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510300, PR China.
| | - Xiaolan Li
- Key Laboratory of South China Sea Fishery Resources Exploitation & Utilization, Ministry of Agriculture, The South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510300, PR China; College of Animal Science, South China Agriculture University, Guangzhou 510642, PR China
| | - Song Jiang
- Key Laboratory of South China Sea Fishery Resources Exploitation & Utilization, Ministry of Agriculture, The South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510300, PR China
| | - Lihua Qiu
- Key Laboratory of South China Sea Fishery Resources Exploitation & Utilization, Ministry of Agriculture, The South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510300, PR China
| | - Falin Zhou
- Key Laboratory of South China Sea Fishery Resources Exploitation & Utilization, Ministry of Agriculture, The South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510300, PR China
| | - Wenjing Liu
- Key Laboratory of South China Sea Fishery Resources Exploitation & Utilization, Ministry of Agriculture, The South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510300, PR China
| | - Shigui Jiang
- Key Laboratory of South China Sea Fishery Resources Exploitation & Utilization, Ministry of Agriculture, The South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510300, PR China.
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24
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Angart P, Vocelle D, Chan C, Walton SP. Design of siRNA Therapeutics from the Molecular Scale. Pharmaceuticals (Basel) 2013; 6:440-68. [PMID: 23976875 PMCID: PMC3749788 DOI: 10.3390/ph6040440] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
While protein-based therapeutics is well-established in the market, development of nucleic acid therapeutics has lagged. Short interfering RNAs (siRNAs) represent an exciting new direction for the pharmaceutical industry. These small, chemically synthesized RNAs can knock down the expression of target genes through the use of a native eukaryotic pathway called RNA interference (RNAi). Though siRNAs are routinely used in research studies of eukaryotic biological processes, transitioning the technology to the clinic has proven challenging. Early efforts to design an siRNA therapeutic have demonstrated the difficulties in generating a highly-active siRNA with good specificity and a delivery vehicle that can protect the siRNA as it is transported to a specific tissue. In this review article, we discuss design considerations for siRNA therapeutics, identifying criteria for choosing therapeutic targets, producing highly-active siRNA sequences, and designing an optimized delivery vehicle. Taken together, these design considerations provide logical guidelines for generating novel siRNA therapeutics.
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Affiliation(s)
- Phillip Angart
- Department of Chemical Engineering and Materials Science, Michigan State University, 428 S. Shaw Lane, Room 2527, East Lansing, MI 48824, USA; (P.A.); (D.V.); (C.C.)
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25
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Liu J, Yu D, Aiba Y, Pendergraff H, Swayze EE, Lima WF, Hu J, Prakash TP, Corey DR. ss-siRNAs allele selectively inhibit ataxin-3 expression: multiple mechanisms for an alternative gene silencing strategy. Nucleic Acids Res 2013; 41:9570-83. [PMID: 23935115 PMCID: PMC3814390 DOI: 10.1093/nar/gkt693] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
Single-stranded silencing RNAs (ss-siRNAs) provide an alternative approach to gene silencing. ss-siRNAs combine the simplicity and favorable biodistribution of antisense oligonucleotides with robust silencing through RNA interference (RNAi). Previous studies reported potent and allele-selective inhibition of human huntingtin expression by ss-siRNAs that target the expanded CAG repeats within the mutant allele. Mutant ataxin-3, the genetic cause of Machado-Joseph Disease, also contains an expanded CAG repeat. We demonstrate here that ss-siRNAs are allele-selective inhibitors of ataxin-3 expression and then redesign ss-siRNAs to optimize their selectivity. We find that both RNAi-related and non-RNAi-related mechanisms affect gene expression by either blocking translation or affecting alternative splicing. These results have four broad implications: (i) ss-siRNAs will not always behave similarly to analogous RNA duplexes; (ii) the sequences surrounding CAG repeats affect allele-selectivity of anti-CAG oligonucleotides; (iii) ss-siRNAs can function through multiple mechanisms and; and (iv) it is possible to use chemical modification to optimize ss-siRNA properties and improve their potential for drug discovery.
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Affiliation(s)
- Jing Liu
- Departments of Pharmacology and Biochemistry, UT Southwestern Medical Center at Dallas, Dallas, TX 75390, USA and Department of Medicinal Chemistry and Core Antisense Research, ISIS Pharmaceuticals, Carlsbad, CA 92010, USA
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26
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Gao Y, Yang J, Cancilla MT, Meng F, McLuckey SA. Top-down interrogation of chemically modified oligonucleotides by negative electron transfer and collision induced dissociation. Anal Chem 2013; 85:4713-20. [PMID: 23534847 DOI: 10.1021/ac400448t] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Two sets of synthetic 21-23mer oligonucleotides with various types of 2'-position modifications have been studied with tandem mass spectrometry using ion trap collision-induced dissociation (IT-CID) and negative electron transfer (NET)-CID. A systematic study has been conducted to define the limitations of IT-CID in sequencing such 2'-chemically modified oligonucleotides. We found that IT-CID is sufficient in characterizing oligonucleotide sequences that do not contain DNA residues, where high sequence coverage can be achieved by performing IT-CID on multiple charge states. However, oligonucleotides containing DNA residues gave limited backbone fragmentation with IT-CID, largely due to dominant fragmentation at the DNA residue sites. To overcome this limitation, we employed the negative electron transfer to strip an electron from the multiply charged oligonucleotide anion. Then, the radical anion species formed in this reaction can fragment via an alternative radical-directed dissociation mechanism. Unlike IT-CID, NET-CID mainly generates a noncomplementary d/w ion series. Furthermore, we found that NET-CID did not show preferential dissociations at the DNA residue sites and thus generated higher sequence coverage for the studied oligonucleotide. Information from NET-CID of different charge states is not fully redundant such that the examination of multiple charge states can lead to more extensive sequence confirmation. This work demonstrates that the NET-CID is a valuable tool to provide high sequence coverage for chemically modified oligonucleotides, and such detailed characterization can serve as an important assay to control the quality of therapeutic oligonucleotides that are produced under the good manufacture practice (GMP) regulations.
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Affiliation(s)
- Yang Gao
- Department of Chemistry, Purdue University, West Lafayette, IN 47907-2084, United States
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27
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Matsui M, Prakash TP, Corey DR. Transcriptional silencing by single-stranded RNAs targeting a noncoding RNA that overlaps a gene promoter. ACS Chem Biol 2013; 8:122-6. [PMID: 23082936 DOI: 10.1021/cb300490j] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
RNAi using single-strand RNA would provide new options for therapeutic development and for investigating critical questions of mechanism. Using chemically modified single-strands, we test the hypothesis that single-stranded RNAs can engage the RNAi pathway and silence gene transcription. We find that a chemically modified single-stranded silencing RNA (ss-siRNA) designed to be complementary to a long noncoding RNA (lncRNA) requires argonaute protein, functions through the RNAi pathway, and inhibits gene transcription. These data expand the use of single-stranded RNA to cell nuclei.
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Affiliation(s)
- Masayuki Matsui
- Departments of Pharmacology
and Biochemistry, UT Southwestern Medical Center, 6001 Forest Park Road, Dallas, Texas 75390-9041, United States
| | - Thazha P. Prakash
- Isis Pharmaceuticals, 2855 Gazelle Court, Carlsbad, California 92010, United States
| | - David R. Corey
- Departments of Pharmacology
and Biochemistry, UT Southwestern Medical Center, 6001 Forest Park Road, Dallas, Texas 75390-9041, United States
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28
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Deleavey GF, Damha MJ. Designing chemically modified oligonucleotides for targeted gene silencing. ACTA ACUST UNITED AC 2012; 19:937-54. [PMID: 22921062 DOI: 10.1016/j.chembiol.2012.07.011] [Citation(s) in RCA: 430] [Impact Index Per Article: 35.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2012] [Revised: 06/28/2012] [Accepted: 07/02/2012] [Indexed: 02/07/2023]
Abstract
Oligonucleotides (ONs), and their chemically modified mimics, are now routinely used in the laboratory as a means to control the expression of fundamentally interesting or therapeutically relevant genes. ONs are also under active investigation in the clinic, with many expressing cautious optimism that at least some ON-based therapies will succeed in the coming years. In this review, we will discuss several classes of ONs used for controlling gene expression, with an emphasis on antisense ONs (AONs), small interfering RNAs (siRNAs), and microRNA-targeting ONs (anti-miRNAs). This review provides a current and detailed account of ON chemical modification strategies for the optimization of biological activity and therapeutic application, while clarifying the biological pathways, chemical properties, benefits, and limitations of oligonucleotide analogs used in nucleic acids research.
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Affiliation(s)
- Glen F Deleavey
- Department of Chemistry, McGill University, 801 Sherbrooke Street West, Montréal, QC H3A 0B8, Canada.
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Single-stranded siRNAs activate RNAi in animals. Cell 2012; 150:883-94. [PMID: 22939618 DOI: 10.1016/j.cell.2012.08.014] [Citation(s) in RCA: 194] [Impact Index Per Article: 16.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2012] [Revised: 05/31/2012] [Accepted: 08/08/2012] [Indexed: 02/01/2023]
Abstract
The therapeutic utility of siRNAs is limited by the requirement for complex formulations to deliver them to tissues. If potent single-stranded RNAs could be identified, they would provide a simpler path to pharmacological agents. Here, we describe single-stranded siRNAs (ss-siRNAs) that silence gene expression in animals absent lipid formulation. Effective ss-siRNAs were identified by iterative design by determining structure-activity relationships correlating chemically modified single strands and Argonaute 2 (AGO2) activities, potency in cells, nuclease stability, and pharmacokinetics. We find that the passenger strand is not necessary for potent gene silencing. The guide-strand activity requires AGO2, demonstrating action through the RNAi pathway. ss-siRNA action requires a 5' phosphate to achieve activity in vivo, and we developed a metabolically stable 5'-(E)-vinylphosphonate (5'-VP) with conformation and sterioelectronic properties similar to the natural phosphate. Identification of potent ss-siRNAs offers an additional option for RNAi therapeutics and an alternate perspective on RNAi mechanism.
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Chorn G, Klein-McDowell M, Zhao L, Saunders MA, Flanagan WM, Willingham AT, Lim LP. Single-stranded microRNA mimics. RNA (NEW YORK, N.Y.) 2012; 18:1796-1804. [PMID: 22912485 PMCID: PMC3446704 DOI: 10.1261/rna.031278.111] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/09/2011] [Accepted: 06/22/2012] [Indexed: 06/01/2023]
Abstract
miRNAs are ∼22-nt RNAs that bind to the Argonaute family of proteins and have important regulatory roles in plants and animals. Here, we show that miRNAs exhibit targeting activity in cells when delivered as single strands that are 5'-phosphorylated and that contain 2'-fluoro ribose modifications. Length preferences, chemical modification sensitivity, and genome-wide seed-based targeting all suggest that this activity is Ago-based. Activity could be enhanced by annealing of segmented passenger strands containing non-nucleic acid spacers. Furthermore, screening of randomly generated sequences identified pyrimidine rich 3' cassette sequences that increased single strand activity. These results provide an initial step in the development of single-stranded miRNA mimics for therapeutic use.
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Affiliation(s)
- Guillaume Chorn
- Sirna Therapeutics, a wholly owned subsidiary of Merck & Co., San Francisco, California 94158, USA
| | - Molly Klein-McDowell
- Sirna Therapeutics, a wholly owned subsidiary of Merck & Co., San Francisco, California 94158, USA
| | - Lihong Zhao
- Sirna Therapeutics, a wholly owned subsidiary of Merck & Co., San Francisco, California 94158, USA
| | - Matthew A. Saunders
- Sirna Therapeutics, a wholly owned subsidiary of Merck & Co., San Francisco, California 94158, USA
| | - W. Michael Flanagan
- Sirna Therapeutics, a wholly owned subsidiary of Merck & Co., San Francisco, California 94158, USA
| | - Aarron T. Willingham
- Sirna Therapeutics, a wholly owned subsidiary of Merck & Co., San Francisco, California 94158, USA
| | - Lee P. Lim
- Sirna Therapeutics, a wholly owned subsidiary of Merck & Co., San Francisco, California 94158, USA
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Yu D, Pendergraff H, Liu J, Kordasiewicz HB, Cleveland DW, Swayze EE, Lima WF, Crooke ST, Prakash TP, Corey DR. Single-stranded RNAs use RNAi to potently and allele-selectively inhibit mutant huntingtin expression. Cell 2012; 150:895-908. [PMID: 22939619 PMCID: PMC3444165 DOI: 10.1016/j.cell.2012.08.002] [Citation(s) in RCA: 218] [Impact Index Per Article: 18.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2012] [Revised: 05/31/2012] [Accepted: 08/01/2012] [Indexed: 01/23/2023]
Abstract
Mutant huntingtin (HTT) protein causes Huntington disease (HD), an incurable neurological disorder. Silencing mutant HTT using nucleic acids would eliminate the root cause of HD. Developing nucleic acid drugs is challenging, and an ideal clinical approach to gene silencing would combine the simplicity of single-stranded antisense oligonucleotides with the efficiency of RNAi. Here, we describe RNAi by single-stranded siRNAs (ss-siRNAs). ss-siRNAs are potent (>100-fold more than unmodified RNA) and allele-selective (>30-fold) inhibitors of mutant HTT expression in cells derived from HD patients. Strategic placement of mismatched bases mimics micro-RNA recognition and optimizes discrimination between mutant and wild-type alleles. ss-siRNAs require Argonaute protein and function through the RNAi pathway. Intraventricular infusion of ss-siRNA produced selective silencing of the mutant HTT allele throughout the brain in a mouse HD model. These data demonstrate that chemically modified ss-siRNAs function through the RNAi pathway and provide allele-selective compounds for clinical development.
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Affiliation(s)
- Dongbo Yu
- Departments of Pharmacology and Biochemistry, UT Southwestern Medical Center, 6001 Forest Park Road, Dallas, Texas, USA, 75390-9041
| | - Hannah Pendergraff
- Departments of Pharmacology and Biochemistry, UT Southwestern Medical Center, 6001 Forest Park Road, Dallas, Texas, USA, 75390-9041
| | - Jing Liu
- Departments of Pharmacology and Biochemistry, UT Southwestern Medical Center, 6001 Forest Park Road, Dallas, Texas, USA, 75390-9041
| | - Holly B. Kordasiewicz
- Department of Cellular and Molecular Medicine, Univ. of California, San Diego 9500 Gilman Drive, La Jolla, CA 92093-0670
- Isis Pharmaceuticals, 2855 Gazelle Court, Carlsbad, California, USA, 92010
| | - Don W. Cleveland
- Department of Cellular and Molecular Medicine, Univ. of California, San Diego 9500 Gilman Drive, La Jolla, CA 92093-0670
| | - Eric E. Swayze
- Isis Pharmaceuticals, 2855 Gazelle Court, Carlsbad, California, USA, 92010
| | - Walt F. Lima
- Isis Pharmaceuticals, 2855 Gazelle Court, Carlsbad, California, USA, 92010
| | - Stanley T. Crooke
- Isis Pharmaceuticals, 2855 Gazelle Court, Carlsbad, California, USA, 92010
| | - Thazha P. Prakash
- Isis Pharmaceuticals, 2855 Gazelle Court, Carlsbad, California, USA, 92010
| | - David R. Corey
- Departments of Pharmacology and Biochemistry, UT Southwestern Medical Center, 6001 Forest Park Road, Dallas, Texas, USA, 75390-9041
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