1
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Wang Q, Wang J, Xu Y, Li Z, Wang B, Li Y. The Interaction of Influenza A NS1 and Cellular TRBP Protein Modulates the Function of RNA Interference Machinery. Front Microbiol 2022; 13:859420. [PMID: 35558132 PMCID: PMC9087287 DOI: 10.3389/fmicb.2022.859420] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Accepted: 03/29/2022] [Indexed: 11/24/2022] Open
Abstract
Influenza A virus (IAV), one of the most prevalent respiratory diseases, causes pandemics around the world. The multifunctional non-structural protein 1 (NS1) of IAV is a viral antagonist that suppresses host antiviral response. However, the mechanism by which NS1 modulates the RNA interference (RNAi) pathway remains unclear. Here, we identified interactions between NS1 proteins of Influenza A/PR8/34 (H1N1; IAV-PR8) and Influenza A/WSN/1/33 (H1N1; IAV-WSN) and Dicer’s cofactor TAR-RNA binding protein (TRBP). We found that the N-terminal RNA binding domain (RBD) of NS1 and the first two domains of TRBP protein mediated this interaction. Furthermore, two amino acid residues (Arg at position 38 and Lys at position 41) in NS1 were essential for the interaction. We generated TRBP knockout cells and found that NS1 instead of NS1 mutants (two-point mutations within NS1, R38A/K41A) inhibited the process of microRNA (miRNA) maturation by binding with TRBP. PR8-infected cells showed masking of short hairpin RNA (shRNA)-mediated RNAi, which was not observed after mutant virus-containing NS1 mutation (R38A/K41A, termed PR8/3841) infection. Moreover, abundant viral small interfering RNAs (vsiRNAs) were detected in vitro and in vivo upon PR8/3841 infection. We identify, for the first time, the interaction between NS1 and TRBP that affects host RNAi machinery.
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Affiliation(s)
- Qi Wang
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai, China.,CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Jiaxin Wang
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai, China.,CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Yan Xu
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai, China.,CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Zhe Li
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai, China
| | - Binbin Wang
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai, China.,CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Yang Li
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
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2
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Shiohama Y, Fujita R, Sonokawa M, Hisano M, Kotake Y, Krstic-Demonacos M, Demonacos C, Kashiwazaki G, Kitayama T, Fujii M. Elimination of Off-Target Effect by Chemical Modification of 5′-End of Small Interfering RNA. Nucleic Acid Ther 2022; 32:438-447. [DOI: 10.1089/nat.2021.0068] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Affiliation(s)
- Yasuo Shiohama
- Environmental and Biological Information Group, Tropical Biosphere Research Centre, University of the Ryukyus, Nishihara, Japan
| | - Ryosuke Fujita
- Department of Biological & Environmental Chemistry, School of Humanity Oriented Science and Technology, Kindai University, Iizuka, Japan
| | - Maika Sonokawa
- Department of Biological & Environmental Chemistry, School of Humanity Oriented Science and Technology, Kindai University, Iizuka, Japan
| | - Masaaki Hisano
- Department of Biological & Environmental Chemistry, School of Humanity Oriented Science and Technology, Kindai University, Iizuka, Japan
| | - Yojiro Kotake
- Department of Biological & Environmental Chemistry, School of Humanity Oriented Science and Technology, Kindai University, Iizuka, Japan
| | - Marija Krstic-Demonacos
- School of Science, Engineering and Environment, University of Salford, Salford, United Kingdom
| | - Constantinos Demonacos
- Division of Pharmacy and Optometry, Faculty of Biology Medicine and Health, School of Health Science, University of Manchester, Manchester, United Kingdom
| | - Gengo Kashiwazaki
- Department of Advanced Bioscience, Faculty of Agriculture, Kindai University, Nara, Japan
| | - Takashi Kitayama
- Department of Advanced Bioscience, Faculty of Agriculture, Kindai University, Nara, Japan
| | - Masayuki Fujii
- Department of Biological & Environmental Chemistry, School of Humanity Oriented Science and Technology, Kindai University, Iizuka, Japan
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3
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Rodriguez-Salazar CA, Recalde-Reyes DP, Bedoya JP, Padilla-Sanabria L, Castaño-Osorio JC, Giraldo MI. In Vitro Inhibition of Replication of Dengue Virus Serotypes 1-4 by siRNAs Bound to Non-Toxic Liposomes. Viruses 2022; 14:339. [PMID: 35215929 PMCID: PMC8875542 DOI: 10.3390/v14020339] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Revised: 01/29/2022] [Accepted: 02/05/2022] [Indexed: 12/04/2022] Open
Abstract
Dengue virus is a ssRNA+ flavivirus, which produces the dengue disease in humans. Currently, no specific treatment exists. siRNAs regulate gene expression and have been used systematically to silence viral genomes; however, they require controlled release. Liposomes show favorable results encapsulating siRNA for gene silencing. The objective herein was to design and evaluate in vitro siRNAs bound to liposomes that inhibit DENV replication. siRNAs were designed against DENV1-4 from conserved regions using siDirect2.0 and Web-BLOCK-iT™ RNAiDesigner; the initial in vitro evaluation was carried out through transfection into HepG2 cells. siRNA with silencing capacity was encapsulated in liposomes composed of D-Lin-MC3-DMA, DSPC, Chol. Cytotoxicity, hemolysis, pro-inflammatory cytokine release and antiviral activity were evaluated using plaque assay and RT-qPCR. A working concentration of siRNA was established at 40 nM. siRNA1, siRNA2, siRNA3.1, and siRNA4 were encapsulated in liposomes, and their siRNA delivery through liposomes led to a statistically significant decrease in viral titers, yielded no cytotoxicity or hemolysis and did not stimulate release of pro-inflammatory cytokines. Finally, liposomes were designed with siRNA against DENV, which proved to be safe in vitro.
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Affiliation(s)
- Carlos Andrés Rodriguez-Salazar
- Center of Biomedical Research, Faculty of Health Sciences, Universidad del Quindío, Armenia 630003, Colombia; (D.P.R.-R.); (J.P.B.); (L.P.-S.); (J.C.C.-O.)
- Molecular Biology and Virology Laboratory, Faculty of Medicine and Health Sciences, Corporación Universitaria Empresarial Alexander Von Humboldt, Armenia 630003, Colombia
| | - Delia Piedad Recalde-Reyes
- Center of Biomedical Research, Faculty of Health Sciences, Universidad del Quindío, Armenia 630003, Colombia; (D.P.R.-R.); (J.P.B.); (L.P.-S.); (J.C.C.-O.)
- Molecular Biology and Virology Laboratory, Faculty of Medicine and Health Sciences, Corporación Universitaria Empresarial Alexander Von Humboldt, Armenia 630003, Colombia
| | - Juan Pablo Bedoya
- Center of Biomedical Research, Faculty of Health Sciences, Universidad del Quindío, Armenia 630003, Colombia; (D.P.R.-R.); (J.P.B.); (L.P.-S.); (J.C.C.-O.)
| | - Leonardo Padilla-Sanabria
- Center of Biomedical Research, Faculty of Health Sciences, Universidad del Quindío, Armenia 630003, Colombia; (D.P.R.-R.); (J.P.B.); (L.P.-S.); (J.C.C.-O.)
| | - Jhon Carlos Castaño-Osorio
- Center of Biomedical Research, Faculty of Health Sciences, Universidad del Quindío, Armenia 630003, Colombia; (D.P.R.-R.); (J.P.B.); (L.P.-S.); (J.C.C.-O.)
| | - Maria Isabel Giraldo
- Department of Microbiology, Immunology University of Texas Medical Branch, Galveston, TX 77555, USA
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4
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Kitamura Y, Kandeel M, Kondo T, Tanaka A, Makino Y, Miyamoto N, Shibata A, Ikeda M, Kitade Y. Sulfonamide antibiotics inhibit RNAi by binding to human Argonaute protein 2 PAZ. Bioorg Med Chem Lett 2020; 30:127637. [PMID: 33132114 DOI: 10.1016/j.bmcl.2020.127637] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2020] [Revised: 10/14/2020] [Accepted: 10/18/2020] [Indexed: 02/06/2023]
Abstract
We found that sulfisomidine, a sulfonamide antibiotic, potently binds to the Piwi/Argonaute/Zwille (PAZ) domain of human Argonaute protein 2 and inhibits RNA interference (RNAi). To elucidate the effect on RNAi of strong affinity of the 3'-ends in small interfering RNA (siRNA) to the PAZ domain, chemically modified siRNAs bearing sulfisomidine at the 3'-end were synthesized.
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Affiliation(s)
- Yoshiaki Kitamura
- Department of Chemistry and Biomolecular Science, Faculty of Engineering, Gifu University, 1-1 Yanagido, Gifu 501-1193, Japan.
| | - Mahmoud Kandeel
- Department of Physiology, Biochemistry and Pharmacology, Faculty of Veterinary Medicine, King Faisal University, Al-Hofuf, Al-Ahsa 31982, Saudi Arabia; Department of Pharmacology, Faculty of Veterinary Medicine, Kafrelshikh University, Kafrelshikh 33516, Egypt
| | - Tomoya Kondo
- Department of Chemistry and Biomolecular Science, Faculty of Engineering, Gifu University, 1-1 Yanagido, Gifu 501-1193, Japan
| | - Akihiro Tanaka
- Department of Chemistry and Biomolecular Science, Faculty of Engineering, Gifu University, 1-1 Yanagido, Gifu 501-1193, Japan
| | - Yohei Makino
- Department of Chemistry and Biomolecular Science, Faculty of Engineering, Gifu University, 1-1 Yanagido, Gifu 501-1193, Japan
| | - Noriko Miyamoto
- Department of Applied Chemistry, Faculty of Engineering, Aichi Institute of Technology, 1247 Yachigusa, Yakusa-cho, Toyota, Aichi 470-0392, Japan
| | - Aya Shibata
- Department of Chemistry and Biomolecular Science, Faculty of Engineering, Gifu University, 1-1 Yanagido, Gifu 501-1193, Japan
| | - Masato Ikeda
- Department of Chemistry and Biomolecular Science, Faculty of Engineering, Gifu University, 1-1 Yanagido, Gifu 501-1193, Japan; United Graduate School of Drug Discovery and Medical Information Sciences, Gifu University, 1-1 Yanagido, Gifu 501-1193, Japan; Center for Highly Advanced Integration of Nano and Life Sciences, Gifu University (G-CHAIN), 1-1 Yanagido, Gifu 501-1193, Japan; Institute of Nano-Life-Systems, Institute of Innovation for Future Society, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi 464-8603, Japan; Institute for Glyco-core Research (iGCORE), Tokai National Higher Education and Research System, Furo-cho, Chikusa-ku, Nagoya, Aichi 464-8603, Japan
| | - Yukio Kitade
- Department of Chemistry and Biomolecular Science, Faculty of Engineering, Gifu University, 1-1 Yanagido, Gifu 501-1193, Japan; Department of Applied Chemistry, Faculty of Engineering, Aichi Institute of Technology, 1247 Yachigusa, Yakusa-cho, Toyota, Aichi 470-0392, Japan.
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5
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Komori C, Takahashi T, Nakano Y, Ui-Tei K. TRBP-Dicer interaction may enhance HIV-1 TAR RNA translation via TAR RNA processing, repressing host-cell apoptosis. Biol Open 2020; 9:bio050435. [PMID: 32051109 PMCID: PMC7055394 DOI: 10.1242/bio.050435] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2019] [Accepted: 02/03/2020] [Indexed: 12/24/2022] Open
Abstract
The transactivating response (TAR) RNA-binding protein (TRBP) has been identified as a double-stranded RNA (dsRNA)-binding protein, which associates with a stem-loop region known as the TAR element in human immunodeficiency virus-1 (HIV-1). However, TRBP is also known to be an enhancer of RNA silencing, interacting with Dicer, an enzyme that belongs to the RNase III family. Dicer cleaves long dsRNA into small dsRNA fragments called small interfering RNA or microRNA (miRNA) to mediate RNA silencing. During HIV-1 infection, TAR RNA-mediated translation is suppressed by the secondary structure of 5'UTR TAR RNA. However, TRBP binding to TAR RNA relieves its inhibitory action of translation and Dicer processes HIV-1 TAR RNA to generate TAR miRNA. However, whether the interaction between TRBP and Dicer is necessary for TAR RNA translation or TAR miRNA processing remains unclear. In this study, we constructed TRBP mutants that were unable to interact with Dicer by introducing mutations into amino acid residues necessary for the interaction. Furthermore, we established cell lines expressing such TRBP mutants. Then, we revealed that the TRBP-Dicer interaction is essential for both the TAR-containing RNA translation and the TAR miRNA processing in HIV-1.
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Affiliation(s)
- Chiaki Komori
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Hongo, Tokyo 113-0033, Japan
| | - Tomoko Takahashi
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Hongo, Tokyo 113-0033, Japan
| | - Yuko Nakano
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Hongo, Tokyo 113-0033, Japan
| | - Kumiko Ui-Tei
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Hongo, Tokyo 113-0033, Japan
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwano-ha, Chiba 277-8561, Japan
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6
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Mutual Regulation of RNA Silencing and the IFN Response as an Antiviral Defense System in Mammalian Cells. Int J Mol Sci 2020; 21:ijms21041348. [PMID: 32079277 PMCID: PMC7072894 DOI: 10.3390/ijms21041348] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2019] [Revised: 02/14/2020] [Accepted: 02/15/2020] [Indexed: 12/20/2022] Open
Abstract
RNA silencing is a posttranscriptional gene silencing mechanism directed by endogenous small non-coding RNAs called microRNAs (miRNAs). By contrast, the type-I interferon (IFN) response is an innate immune response induced by exogenous RNAs, such as viral RNAs. Endogenous and exogenous RNAs have typical structural features and are recognized accurately by specific RNA-binding proteins in each pathway. In mammalian cells, both RNA silencing and the IFN response are induced by double-stranded RNAs (dsRNAs) in the cytoplasm, but have long been considered two independent pathways. However, recent reports have shed light on crosstalk between the two pathways, which are mutually regulated by protein–protein interactions triggered by viral infection. This review provides brief overviews of RNA silencing and the IFN response and an outline of the molecular mechanism of their crosstalk and its biological implications. Crosstalk between RNA silencing and the IFN response may reveal a novel antiviral defense system that is regulated by miRNAs in mammalian cells.
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7
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Takahashi T, Nakano Y, Onomoto K, Yoneyama M, Ui-Tei K. Virus Sensor RIG-I Represses RNA Interference by Interacting with TRBP through LGP2 in Mammalian Cells. Genes (Basel) 2018; 9:genes9100511. [PMID: 30347765 PMCID: PMC6210652 DOI: 10.3390/genes9100511] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2018] [Revised: 10/16/2018] [Accepted: 10/17/2018] [Indexed: 12/22/2022] Open
Abstract
Exogenous double-stranded RNAs (dsRNAs) similar to viral RNAs induce antiviral RNA silencing or RNA interference (RNAi) in plants or invertebrates, whereas interferon (IFN) response is induced through activation of virus sensor proteins including Toll like receptor 3 (TLR3) or retinoic acid-inducible gene I (RIG-I) like receptors (RLRs) in mammalian cells. Both RNA silencing and IFN response are triggered by dsRNAs. However, the relationship between these two pathways has remained unclear. Laboratory of genetics and physiology 2 (LGP2) is one of the RLRs, but its function has remained unclear. Recently, we reported that LGP2 regulates endogenous microRNA-mediated RNA silencing by interacting with an RNA silencing enhancer, TAR-RNA binding protein (TRBP). Here, we investigated the contribution of other RLRs, RIG-I and melanoma-differentiation-associated gene 5 (MDA5), in the regulation of RNA silencing. We found that RIG-I, but not MDA5, also represses short hairpin RNA (shRNA)-induced RNAi by type-I IFN. Our finding suggests that RIG-I, but not MDA5, interacts with TRBP indirectly through LGP2 to function as an RNAi modulator in mammalian cells.
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Affiliation(s)
- Tomoko Takahashi
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo 113-0033, Japan.
| | - Yuko Nakano
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo 113-0033, Japan.
| | - Koji Onomoto
- Division of Molecular Immunology, Medical Mycology Research Center, Chiba University, Chiba 260-8673, Japan.
| | - Mitsutoshi Yoneyama
- Division of Molecular Immunology, Medical Mycology Research Center, Chiba University, Chiba 260-8673, Japan.
| | - Kumiko Ui-Tei
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo 113-0033, Japan.
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Chiba 277-8561, Japan.
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8
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Takahashi T, Nakano Y, Onomoto K, Murakami F, Komori C, Suzuki Y, Yoneyama M, Ui-Tei K. LGP2 virus sensor regulates gene expression network mediated by TRBP-bound microRNAs. Nucleic Acids Res 2018; 46:9134-9147. [PMID: 29939295 PMCID: PMC6158488 DOI: 10.1093/nar/gky575] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2018] [Revised: 06/07/2018] [Accepted: 06/14/2018] [Indexed: 12/24/2022] Open
Abstract
Here we show that laboratory of genetics and physiology 2 (LGP2) virus sensor protein regulates gene expression network of endogenous genes mediated by TAR-RNA binding protein (TRBP)-bound microRNAs (miRNAs). TRBP is an enhancer of RNA silencing, and functions to recruit precursor-miRNAs (pre-miRNAs) to Dicer that processes pre-miRNA into mature miRNA. Viral infection activates the antiviral innate immune response in mammalian cells. Retinoic acid-inducible gene I (RIG-I)-like receptors (RLRs), including RIG-I, melanoma-differentiation-associated gene 5 (MDA5), and LGP2, function as cytoplasmic virus sensor proteins during viral infection. RIG-I and MDA5 can distinguish between different types of RNA viruses to produce antiviral cytokines, including type I interferon. However, the role of LGP2 is controversial. We found that LGP2 bound to the double-stranded RNA binding sites of TRBP, resulting in inhibition of pre-miRNA binding and recruitment by TRBP. Furthermore, although it is unclear whether TRBP binds to specific pre-miRNA, we found that TRBP bound to particular pre-miRNAs with common structural characteristics. Thus, LGP2 represses specific miRNA activities by interacting with TRBP, resulting in selective regulation of target genes. Our findings show that a novel function of LGP2 is to modulate RNA silencing, indicating the crosstalk between RNA silencing and RLR signaling in mammalian cells.
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Affiliation(s)
- Tomoko Takahashi
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo 113-0033, Japan
| | - Yuko Nakano
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo 113-0033, Japan
| | - Koji Onomoto
- Division of Molecular Immunology, Medical Mycology Research Center, Chiba University, Chiba 260-8673, Japan
| | - Fuminori Murakami
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Chiba 277-8561, Japan
| | - Chiaki Komori
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo 113-0033, Japan
| | - Yutaka Suzuki
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Chiba 277-8561, Japan
| | - Mitsutoshi Yoneyama
- Division of Molecular Immunology, Medical Mycology Research Center, Chiba University, Chiba 260-8673, Japan
| | - Kumiko Ui-Tei
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo 113-0033, Japan
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Chiba 277-8561, Japan
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9
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Ye J, Wang J, Zhang N, Liu Y, Tan L, Xu L. Expression of TARBP1 protein in human non-small-cell lung cancer and its prognostic significance. Oncol Lett 2018; 15:7182-7190. [PMID: 29731880 PMCID: PMC5920659 DOI: 10.3892/ol.2018.8202] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2017] [Accepted: 02/27/2018] [Indexed: 12/22/2022] Open
Abstract
The aim of the present study was to investigate the expression of transactivation response RNA-binding protein (TARBP)1 and its clinical significance in human non-small-cell lung cancer (NSCLC). TARBP1 expression at the mRNA level was detected by reverse transcription-quantitative polymerase chain reaction (RT-qPCR) in 10 NSCLC tissues and paired adjacent normal tissues. TARBP1 protein expression was analyzed in 90 paraffin-embedded NSCLC tissue samples and paired adjacent normal tissues by immunohistochemistry. Statistical analyses were performed to assess the clinicopathological significance of TARBP1 expression. The expression of TARBP1 mRNA was higher in the 10 NSCLC samples than in the paired adjacent non-tumor tissues (P=0.0017). In the paraffin-embedded tissue samples, the expression level of TARBP1 was higher in the cancer tissues than in the adjacent non-cancerous tissues. TARBP1 expression was detected in 76.67% (69/90) of the NSCLC samples and in 22.22% (20/90) of the adjacent normal lung tissues (P<0.001). The expression of TARBP1 was significantly associated with histological grade (P<0.001), clinical stage (P=0.024) and pathological type (P<0.001), along with a decreased overall survival (OS) rate (P<0.001). On multivariate analysis, the expression of TARBP1 was an independent prognostic factor for hazard ratio (OS, 2.729; 95% confidence interval, 1.471-5.061; P=0.003). TARBP1 is overexpressed in NSCLC, and the expression of TARBP1 is associated with pathological grade, clinical stage and pathological type. Thus, TARBP1 may be an independent prognostic marker in patients with NSCLC.
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Affiliation(s)
- Jingmei Ye
- Department of Blood Transfusion, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong 510230, P.R. China
| | - Jiani Wang
- Breast Cancer Center, The Third Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong 510630, P.R. China
| | - Nana Zhang
- Department of Pathology, The Third Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong 510630, P.R. China
| | - Yu Liu
- Breast Cancer Center, The Third Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong 510630, P.R. China
| | - Li Tan
- Department of Hematology, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong 510230, P.R. China
| | - Lihua Xu
- Department of Hematology, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong 510230, P.R. China.,Guangdong Key Laboratory of Urology, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong 510230, P.R. China
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10
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Nagaya Y, Kitamura Y, Shibata A, Ikeda M, Akao Y, Kitade Y. Introduction of 2- O -benzyl abasic nucleosides to the 3′-overhang regions of siRNAs greatly improves nuclease resistance. Bioorg Med Chem Lett 2017; 27:5454-5456. [DOI: 10.1016/j.bmcl.2017.10.070] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2017] [Revised: 10/26/2017] [Accepted: 10/27/2017] [Indexed: 02/01/2023]
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11
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Paces J, Nic M, Novotny T, Svoboda P. Literature review of baseline information to support the risk assessment of RNAi‐based GM plants. ACTA ACUST UNITED AC 2017. [PMCID: PMC7163844 DOI: 10.2903/sp.efsa.2017.en-1246] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Jan Paces
- Institute of Molecular Genetics of the Academy of Sciences of the Czech Republic (IMG)
| | | | | | - Petr Svoboda
- Institute of Molecular Genetics of the Academy of Sciences of the Czech Republic (IMG)
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12
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Utilizing Selected Di- and Trinucleotides of siRNA to Predict RNAi Activity. COMPUTATIONAL AND MATHEMATICAL METHODS IN MEDICINE 2017; 2017:5043984. [PMID: 28243313 PMCID: PMC5294759 DOI: 10.1155/2017/5043984] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/25/2016] [Accepted: 12/15/2016] [Indexed: 02/04/2023]
Abstract
Small interfering RNAs (siRNAs) induce posttranscriptional gene silencing in various organisms. siRNAs targeted to different positions of the same gene show different effectiveness; hence, predicting siRNA activity is a crucial step. In this paper, we developed and evaluated a powerful tool named “siRNApred” with a new mixed feature set to predict siRNA activity. To improve the prediction accuracy, we proposed 2-3NTs as our new features. A Random Forest siRNA activity prediction model was constructed using the feature set selected by our proposed Binary Search Feature Selection (BSFS) algorithm. Experimental data demonstrated that the binding site of the Argonaute protein correlates with siRNA activity. “siRNApred” is effective for selecting active siRNAs, and the prediction results demonstrate that our method can outperform other current siRNA activity prediction methods in terms of prediction accuracy.
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13
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Xu X, Li Z, Zhao X, Keen L, Kong X. Calcium phosphate nanoparticles-based systems for siRNA delivery. Regen Biomater 2016; 3:187-95. [PMID: 27252888 PMCID: PMC4881614 DOI: 10.1093/rb/rbw010] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2015] [Revised: 01/11/2016] [Accepted: 01/19/2016] [Indexed: 12/15/2022] Open
Abstract
Despite the enormous therapeutic potential of siRNA as a treatment strategy, the delivery is still a problem due to unfavorable biodistribution profiles and poor intracellular bioavailability. Calcium phosphate (CaP) co-precipitate has been used for nearly 40 years for in vitro transfection due to its non-toxic nature and simplicity of preparation. The surface charge of CaP will be tuned into positive by surface modification, which is important for siRNA loading and crossing cell membrane without enzymatic degradation. The new siRNA carrier system will also promote the siRNA escape from lysosome to achieve siRNA sustained delivery and high-efficiency silence. In this review, we focus on the current research activity in the development of CaP nanoparticles for siRNA delivery. These nanoparticles are mainly classified into lipid coated, polymer coated and various other types for discussion.
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Affiliation(s)
- Xiaochun Xu
- Institute of Biomaterials and Marine Biological Resources, College of Life Sciences, Zhejiang Sci-Tech University, Hangzhou 310018, China
| | - Zehao Li
- Institute of Biomaterials and Marine Biological Resources, College of Life Sciences, Zhejiang Sci-Tech University, Hangzhou 310018, China
| | - Xueqin Zhao
- Institute of Biomaterials and Marine Biological Resources, College of Life Sciences, Zhejiang Sci-Tech University, Hangzhou 310018, China
| | - Lawrence Keen
- Institute of Biomaterials and Marine Biological Resources, College of Life Sciences, Zhejiang Sci-Tech University, Hangzhou 310018, China
| | - Xiangdong Kong
- Institute of Biomaterials and Marine Biological Resources, College of Life Sciences, Zhejiang Sci-Tech University, Hangzhou 310018, China
- College of Materials and Textiles, Zhejiang Sci-Tech University, Hangzhou 310018, China
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14
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Kalantari R, Hicks JA, Li L, Gagnon KT, Sridhara V, Lemoff A, Mirzaei H, Corey DR. Stable association of RNAi machinery is conserved between the cytoplasm and nucleus of human cells. RNA (NEW YORK, N.Y.) 2016; 22:1085-98. [PMID: 27198507 PMCID: PMC4911916 DOI: 10.1261/rna.056499.116] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/02/2016] [Accepted: 04/25/2016] [Indexed: 05/25/2023]
Abstract
Argonaute 2 (AGO2), the catalytic engine of RNAi, is typically associated with inhibition of translation in the cytoplasm. AGO2 has also been implicated in nuclear processes including transcription and splicing. There has been little insight into AGO2's nuclear interactions or how they might differ relative to cytoplasm. Here we investigate the interactions of cytoplasmic and nuclear AGO2 using semi-quantitative mass spectrometry. Mass spectrometry often reveals long lists of candidate proteins, complicating efforts to rigorously discriminate true interacting partners from artifacts. We prioritized candidates using orthogonal analytical strategies that compare replicate mass spectra of proteins associated with Flag-tagged and endogenous AGO2. Interactions with TRNC6A, TRNC6B, TNRC6C, and AGO3 are conserved between nuclei and cytoplasm. TAR binding protein interacted stably with cytoplasmic AGO2 but not nuclear AGO2, consistent with strand loading in the cytoplasm. Our data suggest that interactions between functionally important components of RNAi machinery are conserved between the nucleus and cytoplasm but that accessory proteins differ. Orthogonal analysis of mass spectra is a powerful approach to streamlining identification of protein partners.
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Affiliation(s)
- Roya Kalantari
- Department of Pharmacology, Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA
| | - Jessica A Hicks
- Department of Pharmacology, Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA
| | - Liande Li
- Department of Pharmacology, Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA
| | - Keith T Gagnon
- Department of Biochemistry and Molecular Biology, Southern Illinois University, Carbondale, Illinois 62901, USA
| | - Viswanadham Sridhara
- Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA
| | - Andrew Lemoff
- Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA
| | - Hamid Mirzaei
- Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA
| | - David R Corey
- Department of Pharmacology, Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA
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15
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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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16
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Good ME, Begandt D, DeLalio LJ, Johnstone SR, Isakson BE. Small Interfering RNA-Mediated Connexin Gene Knockdown in Vascular Endothelial and Smooth Muscle Cells. Methods Mol Biol 2016; 1437:71-82. [PMID: 27207287 DOI: 10.1007/978-1-4939-3664-9_5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Global knockout of vascular connexins can result in premature/neonatal death, severe developmental complications, or compensatory up-regulation of different connexin isoforms. Thus, specific connexin gene knockdown using RNAi-mediated technologies is a technique that allows investigators to efficiently monitor silencing effects of single or multiple connexin gene products. The present chapter describes the transient knockdown of connexins in vitro and ex vivo for cells of the blood vessel wall. In detail, different transfection methods for primary endothelial cells and ex vivo thoracodorsal arteries are described. Essential controls for validating transfection efficiency as well as targeted gene knockdown are explained. These protocols provide researchers with the ability to modify connexin gene expression levels in a multitude of experimental setups.
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Affiliation(s)
- Miranda E Good
- Robert M. Berne Cardiovascular Research Center, University of Virginia School of Medicine, Charlottesville, VA, 22908, USA
| | - Daniela Begandt
- Robert M. Berne Cardiovascular Research Center, University of Virginia School of Medicine, Charlottesville, VA, 22908, USA
| | - Leon J DeLalio
- Robert M. Berne Cardiovascular Research Center, University of Virginia School of Medicine, Charlottesville, VA, 22908, USA.,Department of Pharmacology, University of Virginia School of Medicine, Charlottesville, VA, 22908, USA
| | - Scott R Johnstone
- Institute of Cardiovascular and Medical Sciences, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, UK
| | - Brant E Isakson
- Robert M. Berne Cardiovascular Research Center, University of Virginia School of Medicine, Charlottesville, VA, 22908, USA. .,Department of Molecular Physiology and Biological Physics, University of Virginia School of Medicine, Charlottesville, VA, 22908, USA.
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17
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Kamola PJ, Nakano Y, Takahashi T, Wilson PA, Ui-Tei K. The siRNA Non-seed Region and Its Target Sequences Are Auxiliary Determinants of Off-Target Effects. PLoS Comput Biol 2015; 11:e1004656. [PMID: 26657993 PMCID: PMC4676691 DOI: 10.1371/journal.pcbi.1004656] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2015] [Accepted: 11/16/2015] [Indexed: 01/06/2023] Open
Abstract
RNA interference (RNAi) is a powerful tool for post-transcriptional gene silencing. However, the siRNA guide strand may bind unintended off-target transcripts via partial sequence complementarity by a mechanism closely mirroring micro RNA (miRNA) silencing. To better understand these off-target effects, we investigated the correlation between sequence features within various subsections of siRNA guide strands, and its corresponding target sequences, with off-target activities. Our results confirm previous reports that strength of base-pairing in the siRNA seed region is the primary factor determining the efficiency of off-target silencing. However, the degree of downregulation of off-target transcripts with shared seed sequence is not necessarily similar, suggesting that there are additional auxiliary factors that influence the silencing potential. Here, we demonstrate that both the melting temperature (Tm) in a subsection of siRNA non-seed region, and the GC contents of its corresponding target sequences, are negatively correlated with the efficiency of off-target effect. Analysis of experimentally validated miRNA targets demonstrated a similar trend, indicating a putative conserved mechanistic feature of seed region-dependent targeting mechanism. These observations may prove useful as parameters for off-target prediction algorithms and improve siRNA ‘specificity’ design rules. Small interfering RNAs (siRNAs) are double stranded RNA molecules designed to perfectly match the sequence of a target gene and silence its expression. The function is exerted through the RNA interference (RNAi) pathway and has revolutionised biological research due to its ease-of-use and high potency. While siRNAs were initially believed to be highly specific, they have subsequently been observed to interact with other, unintended messenger RNAs. However, the mechanistic details of this process remain poorly understood, and there is a paucity of strategies and guidelines directed toward mitigating this issue. To address this potential safety liability, we performed a comprehensive analysis of sequence characteristics of siRNA duplexes and their target regions. Results from luciferase-reporter assays and global expression data confirmed previous observations that the siRNA seed region is the primary determinant for off-target gene recognition and binding. Furthermore, our analysis revealed the important contribution of siRNA non-seed region, and its corresponding target sequences, to the potency of off-target knockdown. Similar results were observed in an equivalent evaluation of the miRNA-targeting mechanism, suggesting that the correlating features arise through an evolutionary conserved mechanistic factor.
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Affiliation(s)
- Piotr J. Kamola
- Department of Surgery and Cancer, Imperial College London, London, United Kingdom
- Safety Assessment, GlaxoSmithKline R&D, Ware, Hertfordshire, United Kingdom
- Computational Biology, GlaxoSmithKline R&D, Stevenage, Hertfordshire, United Kingdom
- Centre for Radiation, Chemical and Environmental Hazards, Public Health England, Harwell Science and Innovation Campus, United Kingdom
| | - Yuko Nakano
- Department of Biological Sciences, University of Tokyo, Bunkyo, Tokyo, Japan
| | - Tomoko Takahashi
- Department of Biological Sciences, University of Tokyo, Bunkyo, Tokyo, Japan
| | - Paul A. Wilson
- Computational Biology, GlaxoSmithKline R&D, Stevenage, Hertfordshire, United Kingdom
| | - Kumiko Ui-Tei
- Department of Biological Sciences, University of Tokyo, Bunkyo, Tokyo, Japan
- Department of Computational Biology and Medical Sciences, University of Tokyo, Kashiwa, Chiba, Japan
- * E-mail:
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18
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Synthesis of small interfering RNAs containing acetal-type nucleoside analogs at their 3′-ends and analysis of their silencing activity and their ability to bind to the Argonaute2 PAZ domain. Eur J Med Chem 2015; 103:460-72. [DOI: 10.1016/j.ejmech.2015.09.011] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2015] [Revised: 08/20/2015] [Accepted: 09/06/2015] [Indexed: 02/08/2023]
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19
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Moon SL, Dodd BJT, Brackney DE, Wilusz CJ, Ebel GD, Wilusz J. Flavivirus sfRNA suppresses antiviral RNA interference in cultured cells and mosquitoes and directly interacts with the RNAi machinery. Virology 2015; 485:322-9. [PMID: 26331679 DOI: 10.1016/j.virol.2015.08.009] [Citation(s) in RCA: 111] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2015] [Revised: 08/07/2015] [Accepted: 08/09/2015] [Indexed: 10/23/2022]
Abstract
Productive arbovirus infections require mechanisms to suppress or circumvent the cellular RNA interference (RNAi) pathway, a major antiviral response in mosquitoes. In this study, we demonstrate that two flaviviruses, Dengue virus and Kunjin virus, significantly repress siRNA-mediated RNAi in infected human cells as well as during infection of the mosquito vector Culex quinquefasciatus. Arthropod-borne flaviviruses generate a small structured non-coding RNA from the viral 3' UTR referred to as sfRNA. Analysis of infections with a mutant Kunjin virus that is unable to generate appreciable amounts of the major sfRNA species indicated that RNAi suppression was associated with the generation of the non-coding sfRNA. Co-immunoprecipitation of sfRNA with RNAi mediators Dicer and Ago2 suggest a model for RNAi suppression. Collectively, these data help to establish a clear role for sfRNA in RNAi suppression and adds to the emerging impact of viral long non-coding RNAs in modulating aspects of anti-viral immune processes.
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Affiliation(s)
- Stephanie L Moon
- Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, CO 80523, USA
| | - Benjamin J T Dodd
- Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, CO 80523, USA
| | - Doug E Brackney
- Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, CO 80523, USA
| | - Carol J Wilusz
- Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, CO 80523, USA
| | - Gregory D Ebel
- Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, CO 80523, USA
| | - Jeffrey Wilusz
- Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, CO 80523, USA.
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20
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Matsui M, Li L, Janowski BA, Corey DR. Reduced Expression of Argonaute 1, Argonaute 2, and TRBP Changes Levels and Intracellular Distribution of RNAi Factors. Sci Rep 2015; 5:12855. [PMID: 26242502 PMCID: PMC4525381 DOI: 10.1038/srep12855] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2015] [Accepted: 07/06/2015] [Indexed: 11/25/2022] Open
Abstract
Until recently, Argonaute 2 (AGO2) and other RNA factors were believed to be restricted to the cytoplasm of mammalian somatic cells. It is now becoming appreciated that RNAi factors can also be found in cell nuclei, but much remains to be learned about their transport, molecular recognition, and function. We find that siRNA-mediated reduction of AGO1 or AGO2 increases the proportion of AGO1 or AGO2 in cell nuclei. Inhibition of AGO1 expression led to increased AGO2 levels, while knockdown of AGO2 led to increased levels of AGO1. Blocking AGO1, AGO2, or TRBP expression changed expression levels and nuclear distribution of RNAi factors Dicer, TNRC6A (GW182), and TRBP. These data reveal the expression of RNAi proteins is mutually dependent and that perturbation can affect subcellular distribution of those factors inside cells.
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Affiliation(s)
- Masayuki Matsui
- Departments of Pharmacology and Biochemistry, University of Texas Southwestern Medical Center, Dallas, Texas, 75390-9041
| | - Liande Li
- Departments of Pharmacology and Biochemistry, University of Texas Southwestern Medical Center, Dallas, Texas, 75390-9041
| | - Bethany A Janowski
- Departments of Pharmacology and Biochemistry, University of Texas Southwestern Medical Center, Dallas, Texas, 75390-9041
| | - David R Corey
- Departments of Pharmacology and Biochemistry, University of Texas Southwestern Medical Center, Dallas, Texas, 75390-9041
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21
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Ye J, Wang J, Tan L, Yang S, Xu L, Wu X, Deng H, Tan H. Expression of protein TARBP1 in human hepatocellular carcinoma and its prognostic significance. INTERNATIONAL JOURNAL OF CLINICAL AND EXPERIMENTAL PATHOLOGY 2015; 8:9089-9096. [PMID: 26464651 PMCID: PMC4583883] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Received: 06/15/2015] [Accepted: 07/24/2015] [Indexed: 06/05/2023]
Abstract
OBJECTIVE The objective of this study was to analyze the expression of TARBP1 and its clinical significance in hepatocellular carcinoma (HCC). MATERIALS AND METHODS 90 patients with primary hepatocellular carcinoma were included in this study. The tumor and paired adjacent non-tumor tissues were collected. TARBP1 expression was assessed by quantitative real-time polymerase chain reaction and immunohistochemistry. Associations of TARBP1 expression with the clinicopathological features were analyzed, and prognosis of HCC patients was evaluated. RESULTS The result show the expression of TARBP1 mRNA in liver cancer tissues were higher than in the adjacent normal liver tissues in 10 paired samples (P=0.0015). Compared with adjacent normal liver tissues, overexpression of TARBP1 was detected in 61.1% (55/90) HCC patients. TARBP1 expression was associated with the AJCC tumor stage (P=0.004) and clinical stage (P=0.005), and decreased overall survival (P=0.002). In multivariate analysis, TARBP1 expression was an independent prognostic factor for overall survival (Hazard ratio [HR]=2.773, 95% confidence interval [CI] 1.542-4.985; P=0.019). CONCLUSIONS TARBP1 is up-regulated in HCC, and the expression of TARBP1 was associated with the pathological grading and clinical stage. TARBP1 maybe is an independent prognostic marker of HCC patients.
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Affiliation(s)
- Jingmei Ye
- Department of Blood Transfusion, The First Affiliated Hospital of Guangzhou Medical UniversityGuangzhou 510230, China
| | - Jiani Wang
- Breast Cancer Center, The Third Affiliated Hospital of Sun Yat-sen UniversityGuangzhou 510630, China
| | - Li Tan
- Department of Hematology, The First Affiliated Hospital of Guangzhou Medical UniversityGuangzhou 510230, China
| | - Shaojiang Yang
- Department of Hematology, The First People’s Hospital of FoshanFoshan 528000, China
| | - Lihua Xu
- Department of Hematology, The First Affiliated Hospital of Guangzhou Medical UniversityGuangzhou 510230, China
| | - Xiaohong Wu
- Department of Hematology, The First Affiliated Hospital of Guangzhou Medical UniversityGuangzhou 510230, China
| | - Huaifu Deng
- PET/CT Center, Department of Nuclear Medicine, The First Affiliated Hospital of Guangzhou Medical UniversityGuangzhou 510230, China
| | - Huo Tan
- Department of Hematology, The First Affiliated Hospital of Guangzhou Medical UniversityGuangzhou 510230, China
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22
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Ogata A, Ueno Y. Incorporation of an acyclic alkynyl nucleoside analog into siRNA improves silencing activity and nuclease resistance. Bioorg Med Chem Lett 2015; 25:2574-8. [PMID: 25956414 DOI: 10.1016/j.bmcl.2015.04.034] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2014] [Revised: 04/06/2015] [Accepted: 04/11/2015] [Indexed: 01/04/2023]
Abstract
In order to improve the silencing activity and nuclease resistance of small interfering RNA (siRNA), we designed and synthesized an acyclic thymidine analog containing 4-pentyne-1,2-diol instead of d-ribofuranose. The incorporation of this analog into siRNAs at specific positions in the strands was found to enhance the silencing activity of siRNAs and to increase the resistance of the siRNA to hydrolytic degradation by a 3' exonuclease.
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Affiliation(s)
- Aya Ogata
- United Graduate School of Agricultural Science, Gifu University, 1-1 Yanagido, Gifu 501-1193, Japan
| | - Yoshihito Ueno
- United Graduate School of Agricultural Science, Gifu University, 1-1 Yanagido, Gifu 501-1193, Japan; Faculty of Applied Biological Sciences, Gifu University, 1-1 Yanagido, Gifu 501-1193, Japan.
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23
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Burugu S, Daher A, Meurs EF, Gatignol A. HIV-1 translation and its regulation by cellular factors PKR and PACT. Virus Res 2014; 193:65-77. [PMID: 25064266 DOI: 10.1016/j.virusres.2014.07.014] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2014] [Revised: 07/13/2014] [Accepted: 07/14/2014] [Indexed: 12/24/2022]
Abstract
The synthesis of proteins from viral mRNA is the first step towards viral assembly. Viruses are dependent upon the cellular translation machinery to synthesize their own proteins. The synthesis of proteins from the human immunodeficiency virus (HIV) type 1 and 2 RNAs utilize several alternative mechanisms. The regulation of viral protein production requires a constant interplay between viral requirements and the cell response to viral infection. Among the antiviral cell responses, the interferon-induced RNA activated protein kinase, PKR, regulates the cellular and viral translation. During HIV-1 infection, PKR activation is highly regulated by viral and cellular factors. The cellular TAR RNA Binding Protein, TRBP, the Adenosine Deaminase acting on RNA, ADAR1, and the PKR Activator, PACT, play important roles. Recent data show that PACT changes its function from activator to inhibitor in HIV-1 infected cells. Therefore, HIV-1 has evolved to replicate in cells in which TRBP, ADAR1 and PACT prevent PKR activation to allow efficient viral protein synthesis. This proper translation will initiate the assembly of viral particles.
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Affiliation(s)
- Samantha Burugu
- Virus-cell Interactions Laboratory, Lady Davis Institute for Medical Research, Montréal, QC, Canada; Department of Microbiology and Immunology, McGill University, Montréal, QC, Canada
| | - Aïcha Daher
- Virus-cell Interactions Laboratory, Lady Davis Institute for Medical Research, Montréal, QC, Canada
| | - Eliane F Meurs
- Institut Pasteur, Department of Virology, Hepacivirus and Innate Immunity Unit, Paris, France
| | - Anne Gatignol
- Virus-cell Interactions Laboratory, Lady Davis Institute for Medical Research, Montréal, QC, Canada; Department of Microbiology and Immunology, McGill University, Montréal, QC, Canada; Department of Medicine, Division of Experimental Medicine, McGill University, Montréal, QC, Canada.
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