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Kang YG, Kim J, Lee K, Choe JY, Dua P, Lee DK. Retinoic Acid-Inducible Gene I-Mediated Innate Immune Stimulation by Chemically Synthesized Long Double-Stranded RNAs Is Structure and Sequence Dependent. Nucleic Acid Ther 2022; 32:321-332. [PMID: 35263174 DOI: 10.1089/nat.2021.0104] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Double-stranded RNAs (dsRNAs) longer than 30 bp have not been considered desirable RNA interference (RNAi) triggering structures in mammalian cells as they nonspecifically activate innate immune response. However, in earlier studies, not only dsRNA length but also 5'-triphosphate moiety produced by in vitro transcription might have affected the stimulation of innate immune system. Herein, using chemically synthesized long dsRNAs without 5'-triphosphate, we elucidated direct relationship between length of dsRNAs and innate immune stimulation. First, we found that blunt-ended, chemically synthesized 38/40-60 bp-long dsRNAs induced retinoic acid-inducible gene I (RIG-I)-mediated innate immune response, which was suppressed by the introduction of the 2-nt 3' overhang structure. Surprisingly, we discovered that RIG-I activation by these long dsRNAs is also sequence dependent, and the sequence composition at dsRNA termini is important for RIG-I activation. In addition, we identified that long dsRNAs over 38 bp could elicit single- or dual-target gene silencing in a Dicer-independent manner. Taken together, our findings may serve as guidelines to develop an immunostimulatory RNAi trigger to exploit host's innate immune system, as well as a specific dual-gene targeting RNAi therapeutics platform without nonspecific innate immune stimulation by RIG-I.
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Affiliation(s)
- Young Gyu Kang
- Department of Chemistry, Sungkyunkwan University, Suwon, Korea.,OliX Pharmaceuticals, Inc., Suwon, Korea
| | - Jaejin Kim
- Department of Chemistry, Sungkyunkwan University, Suwon, Korea
| | - Kyeongmin Lee
- Department of Chemistry, Sungkyunkwan University, Suwon, Korea
| | - Jeong Yong Choe
- Department of Chemistry, Sungkyunkwan University, Suwon, Korea.,OliX Pharmaceuticals, Inc., Suwon, Korea
| | - Pooja Dua
- OliX Pharmaceuticals, Inc., Suwon, Korea
| | - Dong Ki Lee
- Department of Chemistry, Sungkyunkwan University, Suwon, Korea.,OliX Pharmaceuticals, Inc., Suwon, Korea
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2
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Kang YG, Choe JY, Lee S, Hwang J, Lim H, Lee J, Lee DK. Tripodal RNA with 3' Overhangs Prevents RIG-I-Mediated Innate Immune Response. Nucleic Acid Ther 2019; 29:291-299. [PMID: 31314672 DOI: 10.1089/nat.2019.0778] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
RNA interference (RNAi) offers great promise in life science research and therapeutic development, as it easily achieves a potent target gene knockdown with high specificity. Since the conventional small interfering RNA (siRNA) structure, known as 19 bp double-stranded RNA (dsRNA) with 2-nucleotide (nt) 3' overhang, has been introduced to successfully elicit the RNAi in mammalian cells, a variety of structural variants of RNAi trigger have been developed. Our group previously reported branched, tripodal interfering RNA (tiRNA) structures as a multigene targeting RNA structure inducing RNAi. However, the immune stimulatory effect of branched tiRNA structure has not been thoroughly evaluated. In this study, we show that tiRNA with blunt ends triggers innate immune response in T98G cell and mouse macrophage cells, which is dependent upon the retinoic acid-inducible gene I (RIG-I), a well-known cytoplasmic dsRNA sensor. Interestingly, immune response triggered by tiRNA can be suppressed by the introduction of 2-nt 3' overhang structure. Our finding expands the structural diversity of RIG-I ligands and provides a guide to develop a safe multitargeting RNA structure for therapeutic application.
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Affiliation(s)
- Young Gyu Kang
- Department of Chemistry, Sungkyunkwan University, Suwon, Korea
| | - Jeong Yong Choe
- Department of Chemistry, Sungkyunkwan University, Suwon, Korea.,OliX Pharmaceuticals, Inc., Suwon, Korea
| | - Sehyun Lee
- Department of Chemistry, Sungkyunkwan University, Suwon, Korea
| | - Joonwoo Hwang
- Department of Chemistry, Sungkyunkwan University, Suwon, Korea
| | - Hyeji Lim
- Department of Chemistry, Sungkyunkwan University, Suwon, Korea
| | - Jinhaeng Lee
- Department of Chemistry, Sungkyunkwan University, Suwon, Korea
| | - Dong-Ki Lee
- Department of Chemistry, Sungkyunkwan University, Suwon, Korea.,OliX Pharmaceuticals, Inc., Suwon, Korea
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3
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Kim Y, Kang YG, Choe JY, Lee D, Shin C, Hong SW, Lee DK. RNA Interference-Mediated Gene Silencing by Branched Tripodal RNAs Does Not Require Dicer Processing. Nucleic Acid Ther 2018; 28:44-49. [PMID: 29195056 DOI: 10.1089/nat.2017.0681] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Specific gene silencing through RNA interference (RNAi) holds great promise as the next-generation therapeutic development platform. Previously, we have shown that branched, tripodal interfering RNA (tiRNA) structures could simultaneously trigger RNAi-mediated gene silencing of three target genes with 38 nt-long guide strands associated with Argonaute 2. Herein, we show that the branched RNA structure can trigger effective gene silencing in Dicer knockout cell line, demonstrating that the Dicer-mediated processing is not required for tiRNA activity. The finding of this study confirms the flexibility of the structure of RNAi triggers as well as the length of the guide strand in RNAi-mediated gene silencing.
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Affiliation(s)
- Yanghee Kim
- 1 Global Research Laboratory for RNAi Medicine, Department of Chemistry, Sungkyunkwan University , Suwon, Republic of Korea
| | - Young Gyu Kang
- 1 Global Research Laboratory for RNAi Medicine, Department of Chemistry, Sungkyunkwan University , Suwon, Republic of Korea
| | - Jeong Yong Choe
- 1 Global Research Laboratory for RNAi Medicine, Department of Chemistry, Sungkyunkwan University , Suwon, Republic of Korea
| | - Dooyoung Lee
- 2 Department of Agricultural Biotechnology, Seoul National University , Seoul, Republic of Korea
| | - Chanseok Shin
- 2 Department of Agricultural Biotechnology, Seoul National University , Seoul, Republic of Korea
| | - Sun Woo Hong
- 3 OliX Pharmaceuticals, Inc. , Suwon, Republic of Korea
| | - Dong-Ki Lee
- 1 Global Research Laboratory for RNAi Medicine, Department of Chemistry, Sungkyunkwan University , Suwon, Republic of Korea
- 3 OliX Pharmaceuticals, Inc. , Suwon, Republic of Korea
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4
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Swamy MN, Wu H, Shankar P. Recent advances in RNAi-based strategies for therapy and prevention of HIV-1/AIDS. Adv Drug Deliv Rev 2016; 103:174-186. [PMID: 27013255 PMCID: PMC4935623 DOI: 10.1016/j.addr.2016.03.005] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2015] [Revised: 03/10/2016] [Accepted: 03/11/2016] [Indexed: 12/15/2022]
Abstract
RNA interference (RNAi) provides a powerful tool to silence specific gene expression and has been widely used to suppress host factors such as CCR5 and/or viral genes involved in HIV-1 replication. Newer nuclease-based gene-editing technologies, such as zinc finger nucleases (ZFN), transcription activator-like effector nucleases (TALEN) and the clustered regularly interspaced short palindromic repeats (CRISPR)/Cas9 system, also provide powerful tools to ablate specific genes. Because of differences in co-receptor usage and the high mutability of the HIV-1 genome, a combination of host factors and viral genes needs to be suppressed for effective prevention and treatment of HIV-1 infection. Whereas the continued presence of small interfering/short hairpin RNA (si/shRNA) mediators is needed for RNAi to be effective, the continued expression of nucleases in the gene-editing systems is undesirable. Thus, RNAi provides the only practical way for expression of multiple silencers in infected and uninfected cells, which is needed for effective prevention/treatment of infection. There have been several advances in the RNAi field in terms of si/shRNA design, targeted delivery to HIV-1 susceptible cells, and testing for efficacy in preclinical humanized mouse models. Here, we comprehensively review the latest advances in RNAi technology towards prevention and treatment of HIV-1.
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Affiliation(s)
- Manjunath N Swamy
- Center of Emphasis in Infectious Disease, Department of Biomedical Sciences, Paul L. Foster School of Medicine, Texas Tech University Health Sciences Center, El Paso, TX 79905, USA.
| | - Haoquan Wu
- Center of Emphasis in Infectious Disease, Department of Biomedical Sciences, Paul L. Foster School of Medicine, Texas Tech University Health Sciences Center, El Paso, TX 79905, USA
| | - Premlata Shankar
- Center of Emphasis in Infectious Disease, Department of Biomedical Sciences, Paul L. Foster School of Medicine, Texas Tech University Health Sciences Center, El Paso, TX 79905, USA.
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5
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Alagia A, Eritja R. siRNA and RNAi optimization. WILEY INTERDISCIPLINARY REVIEWS-RNA 2016; 7:316-29. [PMID: 26840434 DOI: 10.1002/wrna.1337] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/28/2015] [Revised: 12/17/2015] [Accepted: 12/18/2015] [Indexed: 12/12/2022]
Abstract
The discovery and examination of the posttranscriptional gene regulatory mechanism known as RNA interference (RNAi) contributed to the identification of small interfering RNA (siRNA) and the comprehension of its enormous potential for clinical purposes. Theoretically, the ability of specific target gene downregulation makes the RNAi pathway an appealing solution for several diseases. Despite numerous hurdles resulting from the inherent properties of siRNA molecule and proper delivery to the target tissue, more than 50 RNA-based drugs are currently under clinical testing. In this work, we analyze the recent literature in the optimization of siRNA molecules. In detail, we focused on describing the most recent advances of siRNA field aimed at optimize siRNA pharmacokinetic properties. Special attention has been given in describing the impact of RNA modifications in the potential off-target effects (OTEs) such as saturation of the RNAi machinery, passenger strand-mediated silencing, immunostimulation, and miRNA-like OTEs as well as to recent developments on the delivery issue. The novel delivery systems and modified siRNA provide significant steps toward the development of reliable siRNA molecules for therapeutic use. WIREs RNA 2016, 7:316-329. doi: 10.1002/wrna.1337 For further resources related to this article, please visit the WIREs website.
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Affiliation(s)
- Adele Alagia
- Chemical and Biomolecular Nanotechnology, CIBER-BBN, Institute for Advanced Chemistry of Catalonia, IQAC-CSIC, Barcelona, Spain
| | - Ramon Eritja
- Chemical and Biomolecular Nanotechnology, CIBER-BBN, Institute for Advanced Chemistry of Catalonia, IQAC-CSIC, Barcelona, Spain
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6
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Loczenski Rose V, Shubber S, Sajeesh S, Spain SG, Puri S, Allen S, Lee DK, Winkler GS, Mantovani G. Phosphonium Polymethacrylates for Short Interfering RNA Delivery: Effect of Polymer and RNA Structural Parameters on Polyplex Assembly and Gene Knockdown. Biomacromolecules 2015; 16:3480-90. [DOI: 10.1021/acs.biomac.5b00898] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Affiliation(s)
- Vanessa Loczenski Rose
- School
of Pharmacy, University of Nottingham, Boots Science Building, University
Park, Nottingham NG7 2RD, U.K
| | - Saif Shubber
- School
of Pharmacy, University of Nottingham, Boots Science Building, University
Park, Nottingham NG7 2RD, U.K
| | - S. Sajeesh
- Global
Research Laboratory for RNAi Medicine, Department of Chemistry, Sungkyunkwan University, Suwon 440-746, Republic of Korea
| | - Sebastian G. Spain
- Department
of Chemistry, University of Sheffield, Dainton Building, Sheffield S3 7HF, U.K
| | - Sanyogitta Puri
- Pharmaceutical
Development, Astrazeneca UK Ltd., Alderley Park, Macclesfield SK10 2NA, U.K
| | - Stephanie Allen
- School
of Pharmacy, University of Nottingham, Boots Science Building, University
Park, Nottingham NG7 2RD, U.K
| | - Dong-Ki Lee
- Global
Research Laboratory for RNAi Medicine, Department of Chemistry, Sungkyunkwan University, Suwon 440-746, Republic of Korea
| | - G. Sebastiaan Winkler
- School
of Pharmacy, University of Nottingham, Boots Science Building, University
Park, Nottingham NG7 2RD, U.K
| | - Giuseppe Mantovani
- School
of Pharmacy, University of Nottingham, Boots Science Building, University
Park, Nottingham NG7 2RD, U.K
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7
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Sajeesh S, Lee TY, Kim JK, Son DS, Hong SW, Kim S, Yun WS, Kim S, Chang C, Li C, Lee DK. Efficient intracellular delivery and multiple-target gene silencing triggered by tripodal RNA based nanoparticles: a promising approach in liver-specific RNAi delivery. J Control Release 2014; 196:28-36. [PMID: 25251899 DOI: 10.1016/j.jconrel.2014.09.016] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2014] [Revised: 08/17/2014] [Accepted: 09/16/2014] [Indexed: 02/07/2023]
Abstract
RNA interference (RNAi) triggering oligonucleotides in unconventional structural format can offer advantages over conventional small interfering RNA (siRNA), enhanced cellular delivery and improved target gene silencing. With this concept, we present a well-defined tripodal-interfering RNA (tiRNA) structure that can induce simultaneous silencing of multiple target genes with improved potency. The tiRNA structure, formed by the complementary association of three single-stranded RNA units, was optimized for improved gene silencing efficacy. When combined with cationic polymers such as linear polyethyleneimine (PEI), tiRNA assembled to form a stable nano-structured complex through electrostatic interactions and induced stronger RNAi response over conventional siRNA-PEI complex. In combination with a liver-targeting delivery system, tripodal nucleic acid structure demonstrated enhanced fluorescent accumulation in mouse liver compared to standard duplex nucleic acid format. Tripodal RNA structure complexed with galactose-modified PEI could generate effective RNAi-mediated gene silencing effect on experimental mice models. Our studies demonstrate that optimized tiRNA structural format with appropriate polymeric carriers have immense potential to become an RNAi-based platform suitable for multi-target gene silencing.
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Affiliation(s)
- S Sajeesh
- Global Research Laboratory for RNAi Medicine, Department of Chemistry, Sungkyunkwan University, Suwon 440-746, Korea
| | - Tae Yeon Lee
- Global Research Laboratory for RNAi Medicine, Department of Chemistry, Sungkyunkwan University, Suwon 440-746, Korea
| | - Joon Ki Kim
- Global Research Laboratory for RNAi Medicine, Department of Chemistry, Sungkyunkwan University, Suwon 440-746, Korea
| | - Da Seul Son
- Global Research Laboratory for RNAi Medicine, Department of Chemistry, Sungkyunkwan University, Suwon 440-746, Korea
| | - Sun Woo Hong
- Global Research Laboratory for RNAi Medicine, Department of Chemistry, Sungkyunkwan University, Suwon 440-746, Korea
| | - Soohyun Kim
- Department of Chemistry, Sungkyunkwan University, Suwon 440-746, Korea
| | - Wan Soo Yun
- Department of Chemistry, Sungkyunkwan University, Suwon 440-746, Korea
| | - Soyoun Kim
- Department of Medical Biotechnology, Dongguk University, Seoul 100-715, Korea
| | | | - Chiang Li
- Skip Ackerman Center for Molecular Therapeutics, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA
| | - Dong-ki Lee
- Global Research Laboratory for RNAi Medicine, Department of Chemistry, Sungkyunkwan University, Suwon 440-746, Korea.
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8
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Maruyama H, Nakashima Y, Shuto S, Matsuda A, Ito Y, Abe H. An intracellular buildup reaction of active siRNA species from short RNA fragments. Chem Commun (Camb) 2014; 50:1284-7. [PMID: 24365776 DOI: 10.1039/c3cc47529h] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Here we report a new strategy for the buildup reaction of active siRNA species from short RNA fragments in living cells using a chemical ligation reaction. This strategy could decrease undesired immune responses and provide more latitude for RNAi technology in the design and concentration of introduced RNA compared to traditional siRNA methods.
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Affiliation(s)
- Hideto Maruyama
- Nano Medical Engineering Laboratory, RIKEN, 2-1, Hirosawa, Wako-Shi, Saitama 351-0198, Japan.
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9
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Effect of the guide strand 3′-end structure on the gene-silencing potency of asymmetric siRNA. Biochem J 2014; 461:427-34. [DOI: 10.1042/bj20140407] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
This paper describes the effect of the guide strand 3′-end structure on the gene-silencing potency of asymmetric siRNAs and demonstrates the molecular basis of the enhanced potency of the asymmetric siRNA with a 21 nt guide strand composed solely of RNA.
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10
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Sajeesh S, Lee TY, Hong SW, Dua P, Choe JY, Kang A, Yun WS, Song C, Park SH, Kim S, Li C, Lee DK. Long dsRNA-Mediated RNA Interference and Immunostimulation: A Targeted Delivery Approach Using Polyethyleneimine Based Nano-Carriers. Mol Pharm 2014; 11:872-84. [DOI: 10.1021/mp400541z] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- S. Sajeesh
- Global
Research Laboratory for RNAi Medicine, Department of Chemistry, Sungkyunkwan University, Suwon 440-746, Republic of Korea
| | - Tae Yeon Lee
- Global
Research Laboratory for RNAi Medicine, Department of Chemistry, Sungkyunkwan University, Suwon 440-746, Republic of Korea
| | - Sun Woo Hong
- Global
Research Laboratory for RNAi Medicine, Department of Chemistry, Sungkyunkwan University, Suwon 440-746, Republic of Korea
| | - Pooja Dua
- Global
Research Laboratory for RNAi Medicine, Department of Chemistry, Sungkyunkwan University, Suwon 440-746, Republic of Korea
| | - Jeong Yong Choe
- Global
Research Laboratory for RNAi Medicine, Department of Chemistry, Sungkyunkwan University, Suwon 440-746, Republic of Korea
| | - Aeyeon Kang
- Department
of Chemistry, Sungkyunkwan University, Suwon 440-746, Republic of Korea
| | - Wan Soo Yun
- Department
of Chemistry, Sungkyunkwan University, Suwon 440-746, Republic of Korea
| | - Changsik Song
- Department
of Chemistry, Sungkyunkwan University, Suwon 440-746, Republic of Korea
| | - Sung Ha Park
- Department
of Physics, Sungkyunkwan University, Suwon 440-746, Republic of Korea
| | - Soyoun Kim
- Department
of Medical Biotechnology, Dongguk University, Seoul 100-715, Republic of Korea
| | - Chiang Li
- Department
of Gastroenterology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts 02215, United States
| | - Dong-ki Lee
- Global
Research Laboratory for RNAi Medicine, Department of Chemistry, Sungkyunkwan University, Suwon 440-746, Republic of Korea
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11
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In vitro antiviral activity of circular triple helix forming oligonucleotide RNA towards Feline Infectious Peritonitis virus replication. BIOMED RESEARCH INTERNATIONAL 2014; 2014:654712. [PMID: 24707494 PMCID: PMC3950953 DOI: 10.1155/2014/654712] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/28/2013] [Revised: 01/02/2014] [Accepted: 01/14/2014] [Indexed: 02/06/2023]
Abstract
Feline Infectious Peritonitis (FIP) is a severe fatal immune-augmented disease in cat population. It is caused by FIP virus (FIPV), a virulent mutant strain of Feline Enteric Coronavirus (FECV). Current treatments and prophylactics are not effective. The in vitro antiviral properties of five circular Triple-Helix Forming Oligonucleotide (TFO) RNAs (TFO1 to TFO5), which target the different regions of virulent feline coronavirus (FCoV) strain FIPV WSU 79-1146 genome, were tested in FIPV-infected Crandell-Rees Feline Kidney (CRFK) cells. RT-qPCR results showed that the circular TFO RNAs, except TFO2, inhibit FIPV replication, where the viral genome copy numbers decreased significantly by 5-fold log10 from 1014 in the virus-inoculated cells to 109 in the circular TFO RNAs-transfected cells. Furthermore, the binding of the circular TFO RNA with the targeted viral genome segment was also confirmed using electrophoretic mobility shift assay. The strength of binding kinetics between the TFO RNAs and their target regions was demonstrated by NanoITC assay. In conclusion, the circular TFOs have the potential to be further developed as antiviral agents against FIPV infection.
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12
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Hypoxia-Inducible Factor-1α and its Role in the Proliferation of Retinoblastoma Cells. Pathol Oncol Res 2013; 20:557-63. [DOI: 10.1007/s12253-013-9728-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/01/2013] [Accepted: 11/18/2013] [Indexed: 10/25/2022]
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13
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Nishimura Y, Mieda H, Ishii J, Ogino C, Fujiwara T, Kondo A. Targeting cancer cell-specific RNA interference by siRNA delivery using a complex carrier of affibody-displaying bio-nanocapsules and liposomes. J Nanobiotechnology 2013; 11:19. [PMID: 23800313 PMCID: PMC3699380 DOI: 10.1186/1477-3155-11-19] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2013] [Accepted: 06/18/2013] [Indexed: 12/12/2022] Open
Abstract
Background Small interfering RNA (siRNA) has attracted attention in the field of nucleic acid medicine as a RNA interference (RNAi) application that leads to gene silencing due to specific messenger RNA (mRNA) destruction. However, since siRNA is unstable in blood and unable to cross the cell membrane, encapsulation of siRNA into a carrier is required. Results In this study, we used a carrier that combined ZHER2-displaying bio-nanocapsule (derived from hepatitis B virus surface antigen) and liposomes in a complex in order to investigate the feasibility of effective and target-cell-specific RNAi applications. As a result, by observing RNAi only in HER2-expressing breast cancer cells, using our proposed methodology, we successfully demonstrated target-cell-specific delivery and effective function expression of siRNA. Conclusions These findings show that, in the field of nucleic acid medicine, ZHER2-BNC/LP can be a useful carrier for siRNA delivery, and could also become a useful tool for gene silencing and to accomplish protein knock-down.
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Affiliation(s)
- Yuya Nishimura
- Department of Chemical Science and Engineering, Graduate School of Engineering, Kobe University, 1-1 Rokkodai, Nada, Kobe 657-8501, Japan
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14
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Lee TY, Chang CI, Lee D, Hong SW, Shin C, Li CJ, Kim S, Haussecker D, Lee DK. RNA interference-mediated simultaneous silencing of four genes using cross-shaped RNA. Mol Cells 2013; 35:320-6. [PMID: 23563800 PMCID: PMC3887895 DOI: 10.1007/s10059-013-2316-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2012] [Revised: 02/21/2013] [Accepted: 03/06/2013] [Indexed: 12/17/2022] Open
Abstract
The structural flexibility of RNA interference (RNAi)-triggering nucleic acids suggests that the design of unconventional RNAi trigger structures with novel features is possible. Here, we report a cross-shaped RNA duplex structure, termed quadruple interfering RNA (qiRNA), with multiple target gene silencing activity. qiRNA triggers the simultaneous down-regulation of four cellular target genes via an RNAi mechanism. In addition, qiRNA shows enhanced intracellular delivery and target gene silencing over conventional siRNA when complexed with jetPEI, a linear polyethyleneimine (PEI). We also show that the long antisense strand of qiRNA is incorporated intact into an RNA-induced silencing complex (RISC). This novel RNA scaffold further expands the repertoire of RNAi-triggering molecular structures and could be used in the development of therapeutics for various diseases including viral infections and cancer.
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Affiliation(s)
- Tae Yeon Lee
- Global Research Laboratory for RNAi Medicine, Department of Chemistry, Sungkyunkwan University, Suwon 440-746,
Korea
| | - Chan Il Chang
- Global Research Laboratory for RNAi Medicine, Department of Chemistry, Sungkyunkwan University, Suwon 440-746,
Korea
- Skip Ackerman Center for Molecular Therapeutics, Beth Israel Deconness Medical Center, Harvard Medical School, Boston,
USA
- BMT Inc., Seoul 153-777,
Korea
| | - Dooyoung Lee
- Department of Agricultural Biotechnology, Seoul National University, Seoul 151-921,
Korea
| | - Sun Woo Hong
- Global Research Laboratory for RNAi Medicine, Department of Chemistry, Sungkyunkwan University, Suwon 440-746,
Korea
- Department of Medical Biotechnology, Dongguk University, Seoul 100-715,
Korea
| | - Chanseok Shin
- Department of Agricultural Biotechnology, Seoul National University, Seoul 151-921,
Korea
| | - Chiang J. Li
- Skip Ackerman Center for Molecular Therapeutics, Beth Israel Deconness Medical Center, Harvard Medical School, Boston,
USA
| | - Soyoun Kim
- Department of Medical Biotechnology, Dongguk University, Seoul 100-715,
Korea
| | - Dirk Haussecker
- Department of Medical Biotechnology, Dongguk University, Seoul 100-715,
Korea
| | - Dong-ki Lee
- Global Research Laboratory for RNAi Medicine, Department of Chemistry, Sungkyunkwan University, Suwon 440-746,
Korea
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15
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16
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Pan W, Bae SK, Shim EJ, Park SE, Lee SS, Park SJ, Yeo CW, Zhou HH, Shon JH, Shin JG. Effects of clopidogrel and clarithromycin on the disposition of sibutramine and its active metabolites M1 and M2 in relation to CYP2B6*6 polymorphism. Xenobiotica 2012; 43:211-8. [PMID: 22830954 DOI: 10.3109/00498254.2012.706722] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Plasma concentrations of sibutramine and its two active metabolites after single oral dose of sibutramine were determined in Korean healthy male subjects with different CYP2B6 genotypes (CYP2B6*1/*1, *1/*6 and *6/*6), either alone or after four-day pretreatment with clopidogrel or clarithromycin. The pretreatment with clopidogrel and clarithromycin raised the mean area under the concentration-time curve (AUC) of sibutramine by 163% and 255%, respectively. Co-administration of clarithromycin, combined with CYP2B6*6/*6 genotype, led to highest concentration of sibutramine. The molar sum AUC (M1 + M2) was raised by 35% in the clopidogrel phase but not significantly affected by clarithromycin or CYP2B6 genotype. The CYP2B6*6/*6 subjects in the clopidogrel phase showed the highest molar AUC (M1 + M2) among three genotype groups throughout the three phases. The exposure of sibutramine and its metabolites seemed to be associated with the CYP2B6 genotype. The treatment of clopidogrel significantly altered the disposition of active metabolites as well as sibutramine, but clarithromycin only affects the disposition of sibutramine. These results suggest that the perturbation of CYP2B6 activity may contribute to the inter-individual variation of sibutramine drug responses although the clinical relevance is remained to be established.
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Affiliation(s)
- Wei Pan
- Department of Pharmacology and PharmacoGenomics, Research Center, Inje University College of Medicine, Busan, South Korea
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Fiszer A, Olejniczak M, Switonski PM, Wroblewska JP, Wisniewska-Kruk J, Mykowska A, Krzyzosiak WJ. An evaluation of oligonucleotide-based therapeutic strategies for polyQ diseases. BMC Mol Biol 2012; 13:6. [PMID: 22397573 PMCID: PMC3359213 DOI: 10.1186/1471-2199-13-6] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2011] [Accepted: 03/07/2012] [Indexed: 01/16/2023] Open
Abstract
Background RNA interference (RNAi) and antisense strategies provide experimental therapeutic agents for numerous diseases, including polyglutamine (polyQ) disorders caused by CAG repeat expansion. We compared the potential of different oligonucleotide-based strategies for silencing the genes responsible for several polyQ diseases, including Huntington's disease and two spinocerebellar ataxias, type 1 and type 3. The strategies included nonallele-selective gene silencing, gene replacement, allele-selective SNP targeting and CAG repeat targeting. Results Using the patient-derived cell culture models of polyQ diseases, we tested various siRNAs, and antisense reagents and assessed their silencing efficiency and allele selectivity. We showed considerable allele discrimination by several SNP targeting siRNAs based on a weak G-G or G-U pairing with normal allele and strong G-C pairing with mutant allele at the site of RISC-induced cleavage. Among the CAG repeat targeting reagents the strongest allele discrimination is achieved by miRNA-like functioning reagents that bind to their targets and inhibit their translation without substantial target cleavage. Also, morpholino analog performs well in mutant and normal allele discrimination but its efficient delivery to cells at low effective concentration still remains a challenge. Conclusions Using three cellular models of polyQ diseases and the same experimental setup we directly compared the performance of different oligonucleotide-based treatment strategies that are currently under development. Based on the results obtained by us and others we discussed the advantages and drawbacks of these strategies considering them from several different perspectives. The strategy aimed at nonallele-selective inhibiting of causative gene expression by targeting specific sequence of the implicated gene is the easiest to implement but relevant benefits are still uncertain. The gene replacement strategy that combines the nonallele-selective gene silencing with the expression of the exogenous normal allele is a logical extension of the former and it deserves to be explored further. Both allele-selective RNAi approaches challenge cellular RNA interference machinery to show its ability to discriminate between similar sequences differing in either single base substitutions or repeated sequence length. Although both approaches perform well in allele discrimination most of our efforts are focused on repeat targeting due to its potentially higher universality.
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Affiliation(s)
- Agnieszka Fiszer
- Laboratory of Molecular Biomedicine, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznan, Poland
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Affiliation(s)
- Dirk Haussecker
- Department of Medical Biotechnology, College of Natural Sciences, Dongguk University, Seoul, Korea
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19
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Chang CI, Lee TY, Yoo JW, Shin D, Kim M, Kim S, Lee DK. Branched, Tripartite-Interfering RNAs Silence Multiple Target Genes with Long Guide Strands. Nucleic Acid Ther 2012; 22:30-9. [DOI: 10.1089/nat.2011.0315] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Affiliation(s)
- Chan Il Chang
- Global Research Laboratory for RNAi Medicine, Department of Chemistry, Sungkyunkwan University, Suwon, Korea
- Skip Ackerman Center for Molecular Therapeutics, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts
| | - Tae Yeon Lee
- Global Research Laboratory for RNAi Medicine, Department of Chemistry, Sungkyunkwan University, Suwon, Korea
| | - Jae Wook Yoo
- Global Research Laboratory for RNAi Medicine, Department of Chemistry, Sungkyunkwan University, Suwon, Korea
| | | | - Meehyein Kim
- Korean Research Institute of Chemical Technology, Daejeon, Korea
| | - Soyoun Kim
- Department of Biomedical Engineering, Dongguk University, Seoul, Korea
| | - Dong-ki Lee
- Global Research Laboratory for RNAi Medicine, Department of Chemistry, Sungkyunkwan University, Suwon, Korea
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Abstract
RNA interference (RNAi) has been extensively employed for in vivo research since its use was first demonstrated in mammalian cells 10 years ago. Design rules have improved, and it is now routinely possible to obtain reagents that suppress expression of any gene desired. At the same time, increased understanding of the molecular basis of unwanted side effects has led to the development of chemical modification strategies that mitigate these concerns. Delivery remains the single greatest hurdle to widespread adoption of in vivo RNAi methods. However, exciting advances have been made and new delivery systems under development may help to overcome these barriers. This review discusses advances in RNAi biochemistry and biology that impact in vivo use and provides an overview of select publications that demonstrate interesting applications of these principles. Emphasis is placed on work with synthetic, small interfering RNAs (siRNAs) published since the first installment of this review which appeared in 2006.
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Jo SG, Hong SW, Yoo JW, Lee CH, Kim S, Kim S, Lee DK. Selection and optimization of asymmetric siRNA targeting the human c-MET gene. Mol Cells 2011; 32:543-8. [PMID: 22058018 PMCID: PMC3887682 DOI: 10.1007/s10059-011-0160-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2011] [Revised: 09/15/2011] [Accepted: 09/19/2011] [Indexed: 12/11/2022] Open
Abstract
The silencing of specific oncogenes via RNA interference (RNAi) holds great promise for the future of cancer therapy. RNAi is commonly carried out using small interfering RNA (siRNA) composed of a 19 bp duplex region with a 2-nucleotide overhang at each 3' end. This classical siRNA structure, however, can trigger non-specific effects, which has hampered the development of specific and safe RNAi therapeutics. Previously, we developed a novel siRNA structure, called asymmetric shorter-duplex siRNA (asiRNA), which did not cause the non-specific effects triggered by conventional siRNA, such as off-target gene silencing mediated by the sense strand. In this study, we first screened potent asiRNA molecules targeting the human c-MET gene, a promising anticancer target. Next, the activity of a selected asiRNA was further optimized by introducing a locked nucleic acid (LNA) to maximize the gene silencing potency. The optimized asiRNA targeted to c-MET may have potential as a specific and safe anticancer RNAi therapeutic.
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Affiliation(s)
- Seul-gi Jo
- Global Research Laboratory for RNAi Medicine, Department of Chemistry and Brain Korea 21 School of Chemical Materials Science, Sungkyunkwan University, Suwon 440-746, Korea
- These authors contributed equally to this work
| | - Sun Woo Hong
- Global Research Laboratory for RNAi Medicine, Department of Chemistry and Brain Korea 21 School of Chemical Materials Science, Sungkyunkwan University, Suwon 440-746, Korea
- Department of Biomedical Engineering, Dongguk University, Seoul 100-715, Korea
- These authors contributed equally to this work
| | - Jae Wook Yoo
- Global Research Laboratory for RNAi Medicine, Department of Chemistry and Brain Korea 21 School of Chemical Materials Science, Sungkyunkwan University, Suwon 440-746, Korea
| | - Chang Han Lee
- Global Research Laboratory for RNAi Medicine, Department of Chemistry and Brain Korea 21 School of Chemical Materials Science, Sungkyunkwan University, Suwon 440-746, Korea
| | - Sera Kim
- Global Research Laboratory for RNAi Medicine, Department of Chemistry and Brain Korea 21 School of Chemical Materials Science, Sungkyunkwan University, Suwon 440-746, Korea
| | - Soyoun Kim
- Department of Biomedical Engineering, Dongguk University, Seoul 100-715, Korea
| | - Dong-ki Lee
- Global Research Laboratory for RNAi Medicine, Department of Chemistry and Brain Korea 21 School of Chemical Materials Science, Sungkyunkwan University, Suwon 440-746, Korea
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