1
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Genetically modified pigs are protected from classical swine fever virus. PLoS Pathog 2018; 14:e1007193. [PMID: 30543715 PMCID: PMC6292579 DOI: 10.1371/journal.ppat.1007193] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2018] [Accepted: 10/31/2018] [Indexed: 01/01/2023] Open
Abstract
Classical swine fever (CSF) caused by classical swine fever virus (CSFV) is one of the most detrimental diseases, and leads to significant economic losses in the swine industry. Despite efforts by many government authorities to stamp out the disease from national pig populations, the disease remains widespread. Here, antiviral small hairpin RNAs (shRNAs) were selected and then inserted at the porcine Rosa26 (pRosa26) locus via a CRISPR/Cas9-mediated knock-in strategy. Finally, anti-CSFV transgenic (TG) pigs were produced by somatic nuclear transfer (SCNT). Notably, in vitro and in vivo viral challenge assays further demonstrated that these TG pigs could effectively limit the replication of CSFV and reduce CSFV-associated clinical signs and mortality, and disease resistance could be stably transmitted to the F1-generation. Altogether, our work demonstrated that RNA interference (RNAi) technology combining CRISPR/Cas9 technology offered the possibility to produce TG animal with improved resistance to viral infection. The use of these TG pigs can reduce CSF-related economic losses and this antiviral strategy may be useful for future antiviral research. Classical swine fever (CSF), caused by classical swine fever virus (CSFV), and is a highly contagious, often fatal porcine disease that causes significant economic losses. Due to the economic importance of this virus to the pig industry, the biology and pathogenesis of CSFV have been investigated extensively. Despite efforts by many government authorities to stamp out the disease from national pig populations, the disease remains widespread, and it is only a matter of time before the virus is reintroduced and the next round of disease outbreaks occurs. These findings highlight the necessity and urgency for developing effective approaches to eradicate the challenging CSFV. In this study, we successfully produced anti-CSFV TG pigs by combining RNAi technology and CRISPR/Cas9 technologies, and viral challenge results confirmed that these TG pigs could effectively limit the replication of CSFV in vivo and in vitro. Additionally, we confirmed that the disease resistance traits in the TG founders were stably transmitted to their F1-generation offspring. Altogether, our work reported the combinational application of CRISPR/Cas9 and RNA interference (RNAi) technology in the generation of anti-CSFV TG pigs, it provided an alternative strategy to change the virus. The results of this study suggested that these TG pigs offered potential benefits over commercial vaccination and reduced CSFV-related economic losses.
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2
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Sun G, Riggs AD. A Simple and Cost-Effective Approach for In Vitro Production of Sliced siRNAs as Potent Triggers for RNAi. MOLECULAR THERAPY. NUCLEIC ACIDS 2017; 8:345-355. [PMID: 28918034 PMCID: PMC5537206 DOI: 10.1016/j.omtn.2017.07.008] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/20/2016] [Revised: 07/08/2017] [Accepted: 07/09/2017] [Indexed: 12/25/2022]
Abstract
We have studied the molecular properties of in-vitro-transcribed sliced small interfering RNAs (tsli-siRNAs) as an alternative RNAi agent for chemically synthesized siRNA. We describe here a simple and cost-effective procedure for high-purity production of tsli-siRNA using bacteriophage T7 RNA polymerases. tsli-siRNAs exhibit potent gene knockdown effects, with efficacy comparable with that of chemically synthesized sli-siRNAs and classical siRNAs. Furthermore, we found that it is very easy to prepare potent tsli-siRNAs with modified bases, such as 2′-fluorine- or biotin-16-modified tsli-siRNAs. tsli-siRNAs can cause a mild innate immune response, which can be easily eliminated by alkaline phosphatase treatment. On the other hand, this feature, which can be useful as a trigger of the innate immune response, can be enhanced by polynucleotide kinase treatment. Because of the simplicity of preparation and purification, the procedure presented here could be useful for the production of RNAi or immunostimulatory reagents.
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Affiliation(s)
- Guihua Sun
- Department of Diabetes Complications & Metabolism, Diabetes & Metabolism Research Institute, Beckman Research Institute, City of Hope, 1500 E. Duarte Road, Duarte, CA 91010, USA.
| | - Arthur D Riggs
- Department of Diabetes Complications & Metabolism, Diabetes & Metabolism Research Institute, Beckman Research Institute, City of Hope, 1500 E. Duarte Road, Duarte, CA 91010, USA.
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3
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Wang W, Fromm M. Sphingolipids are required for efficient triacylglycerol loss in conjugated linoleic Acid treated adipocytes. PLoS One 2015; 10:e0119005. [PMID: 25906159 PMCID: PMC4407960 DOI: 10.1371/journal.pone.0119005] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2014] [Accepted: 01/13/2015] [Indexed: 11/19/2022] Open
Abstract
Conjugated linoleic acid (CLA) reduces adiposity in human and mouse adipocytes. This outcome is achieved through a variety of biological responses including increased energy expenditure and fatty acid oxidation, increased inflammation, repression of fatty acid biosynthesis, attenuated glucose transport, and apoptosis. In the current study, profiling of 261 metabolites was conducted to gain new insights into the biological pathways responding to CLA in 3T3-L1 adipocytes. Sphinganine and sphingosine levels were observed to be highly elevated in CLA treated adipocytes. Exogenous chemicals that increased endogenous ceramide levels decreased lipid levels in adipocytes, and activated AMP-activated protein kinase (AMPK) as well as NF-κB, both of which are typically activated in CLA treated adipocytes. Concurrent inhibition of ceramide de novo biosynthesis and recycling from existing sphingolipid pools attenuated the lipid lowering effect normally associated with responses to CLA, implicating ceramides as an important component of the lipid lowering response in CLA treated adipocytes.
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Affiliation(s)
- Wei Wang
- Department of Animal Science, University of Nebraska, Lincoln, Nebraska, United States of America
| | - Michael Fromm
- Center for Biotechnology, University of Nebraska, Lincoln, Nebraska, United States of America
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4
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Reyes-Darias JA, Berzal-Herranz A. Detection of immune response activation by exogenous nucleic acids by a multiplex RT-PCR method. Mol Cell Probes 2014; 28:181-5. [PMID: 24602599 DOI: 10.1016/j.mcp.2014.02.005] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2013] [Revised: 02/12/2014] [Accepted: 02/21/2014] [Indexed: 02/05/2023]
Abstract
Transfection of mammalian cells or in vivo administration of nucleic acids can induce inflammatory cytokines and/or interferon response, which could significantly influence the ex vivo or in vivo applications of gene-targeting strategies based on nucleic acids. Further induction of the interferon and inflammatory related stress responses may result in off-target effects and toxicity. This work describes an original one-step multiplex reverse transcription polymerase chain reaction procedure, which allows testing the induction of interferon and proinflamatory related responses by nucleic acids in the cell system of choice. The developed procedure has been tested on mammalian cells transfected with ssRNA, dsRNA, enzymatically synthesized siRNA and synthetic oligodesoxyribonucleotides containing unmethylated cytosine-guanosine motifs. This procedure is a rapid and convenient screening assay that could be used routinely in both the clinical and the research laboratory to validate the stimulation of the immune system on mammalian cells by nucleic acids.
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Affiliation(s)
- José A Reyes-Darias
- Instituto de Parasitología y Biomedicina "López-Neyra", CSIC (IPBLN-CSIC), PTS Granada, Avda. del Conocimiento s/n, Armilla, 18016 Granada, Spain
| | - Alfredo Berzal-Herranz
- Instituto de Parasitología y Biomedicina "López-Neyra", CSIC (IPBLN-CSIC), PTS Granada, Avda. del Conocimiento s/n, Armilla, 18016 Granada, Spain.
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5
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Wang R, Teng C, Spangler J, Wang J, Huang F, Guo YL. Mouse embryonic stem cells have underdeveloped antiviral mechanisms that can be exploited for the development of mRNA-mediated gene expression strategy. Stem Cells Dev 2013; 23:594-604. [PMID: 24219369 DOI: 10.1089/scd.2013.0417] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
We have recently reported that mouse embryonic stem cells (mESCs) are deficient in expressing type I interferons (IFN) when exposed to viral infection and double-stranded RNA. In this study, we extended our investigation and demonstrated that single-stranded RNA and protein-encoding mRNA can induce strong IFN expression and cytotoxicity in fibroblasts and epithelial cells, but none of the effects associated with these antiviral responses were observed in mESCs. Our results provided additional data to support the conclusion that mESCs are intrinsically deficient in antiviral responses. While our findings represent a novel feature of mESCs that in itself is important for understanding innate immunity development, we exploited this property to develop a novel mRNA-mediated gene expression cell model. Direct introduction of synthetic mRNA to express desired genes has been shown as an effective alternative to DNA/viral vector-based gene expression. However, a major biological challenge is that a synthetic mRNA is detected as a viral RNA analog by the host cell, resulting in a series of adverse effects associated with antiviral responses. We demonstrate that the lack of antiviral responses in mESCs effectively avoids this problem. mESCs can tolerate repeated transfection and effectively express proteins from their synthetic mRNA with expected biological functions, as demonstrated by the expression of green fluorescent protein and the transcription factor Etv2. Therefore, mRNA-based gene expression could be developed into a novel ESC differentiation strategy that avoids safety concerns associated with viral/DNA-based vectors in regenerative medicine.
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Affiliation(s)
- Ruoxing Wang
- 1 Department of Biological Sciences, The University of Southern Mississippi , Hattiesburg, Mississippi
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6
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Schlee M. Master sensors of pathogenic RNA - RIG-I like receptors. Immunobiology 2013; 218:1322-35. [PMID: 23896194 PMCID: PMC7114584 DOI: 10.1016/j.imbio.2013.06.007] [Citation(s) in RCA: 176] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2013] [Revised: 05/27/2013] [Accepted: 06/05/2013] [Indexed: 12/25/2022]
Abstract
Initiating the immune response to invading pathogens, the innate immune system is constituted of immune receptors (pattern recognition receptors, PRR) that sense microbe-associated molecular patterns (MAMPs). Detection of pathogens triggers intracellular defense mechanisms, such as the secretion of cytokines or chemokines to alarm neighboring cells and attract or activate immune cells. The innate immune response to viruses is mostly based on PRRs that detect the unusual structure, modification or location of viral nucleic acids. Most of the highly pathogenic and emerging viruses are RNA genome-based viruses, which can give rise to zoonotic and epidemic diseases or cause viral hemorrhagic fever. As viral RNA is located in the same compartment as host RNA, PRRs in the cytosol have to discriminate between viral and endogenous RNA by virtue of their structure or modification. This challenging task is taken on by the homologous cytosolic DExD/H-box family helicases RIG-I and MDA5, which control the innate immune response to most RNA viruses. This review focuses on the molecular basis for RIG-I like receptor (RLR) activation by synthetic and natural ligands and will discuss controversial ligand definitions.
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Affiliation(s)
- Martin Schlee
- Institute of Clinical Chemistry and Clinical Pharmacology, University Hospital Bonn, 53105 Bonn, Germany.
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Jiang S, Wang W, Miner J, Fromm M. Cross regulation of sirtuin 1, AMPK, and PPARγ in conjugated linoleic acid treated adipocytes. PLoS One 2012; 7:e48874. [PMID: 23155420 PMCID: PMC3498327 DOI: 10.1371/journal.pone.0048874] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2012] [Accepted: 10/02/2012] [Indexed: 02/04/2023] Open
Abstract
Trans-10, cis-12 conjugated linoleic acid (t10c12 CLA) reduces triglyceride (TG) levels in adipocytes through multiple pathways, with AMP-activated protein kinase (AMPK) generally facilitating, and peroxisome proliferator-activated receptor γ (PPARγ) generally opposing these reductions. Sirtuin 1 (SIRT1), a histone/protein deacetylase that affects energy homeostasis, often functions coordinately with AMPK, and is capable of binding to PPARγ, thereby inhibiting its activity. This study investigated the role of SIRT1 in the response of 3T3-L1 adipocytes to t10c12 CLA by testing the following hypotheses: 1) SIRT1 is functionally required for robust TG reduction; and 2) SIRT1, AMPK, and PPARγ cross regulate each other. These experiments were performed by using activators, inhibitors, or siRNA knockdowns that affected these pathways in t10c12 CLA-treated 3T3-L1 adipocytes. Inhibition of SIRT1 amounts or activity using siRNA, sirtinol, nicotinamide, or etomoxir attenuated the amount of TG loss, while SIRT1 activator SRT1720 increased the TG loss. SRT1720 increased AMPK activity while sirtuin-specific inhibitors decreased AMPK activity. Reciprocally, an AMPK inhibitor reduced SIRT1 activity. Treatment with t10c12 CLA increased PPARγ phosphorylation in an AMPK-dependent manner and increased the amount of PPARγ bound to SIRT1. Reciprocally, a PPARγ agonist attenuated AMPK and SIRT1 activity levels. These results indicated SIRT1 increased TG loss and that cross regulation between SIRT1, AMPK, and PPARγ occurred in 3T3-L1 adipocytes treated with t10c12 CLA.
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Affiliation(s)
- Shan Jiang
- Department of Molecular Genetics, University of Texas Southwestern Medical Center, Dallas, Texas, United States of America
| | - Wei Wang
- Department of Animal Science, University of Nebraska, Lincoln, Nebraska, United States of America
| | - Jess Miner
- Department of Animal Science, University of Nebraska, Lincoln, Nebraska, United States of America
| | - Michael Fromm
- Center for Biotechnology, University of Nebraska, Lincoln, Nebraska, United States of America
- * E-mail:
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8
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Kabilova TO, Meschaninova MI, Venyaminova AG, Nikolin VP, Zenkova MA, Vlassov VV, Chernolovskaya EL. Short Double-Stranded RNA with Immunostimulatory Activity: Sequence Dependence. Nucleic Acid Ther 2012; 22:196-204. [DOI: 10.1089/nat.2011.0328] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Affiliation(s)
- Tatyana O. Kabilova
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Science (SB RAS), Novosibirsk, Russia
| | - Mariya I. Meschaninova
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Science (SB RAS), Novosibirsk, Russia
| | - Alya G. Venyaminova
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Science (SB RAS), Novosibirsk, Russia
| | - Valery P. Nikolin
- Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Science (SB RAS), Novosibirsk, Russia
| | - Marina A. Zenkova
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Science (SB RAS), Novosibirsk, Russia
| | - Valentin V. Vlassov
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Science (SB RAS), Novosibirsk, Russia
| | - Elena L. Chernolovskaya
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Science (SB RAS), Novosibirsk, Russia
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9
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Chiappinelli KB, Haynes BC, Brent MR, Goodfellow PJ. Reduced DICER1 elicits an interferon response in endometrial cancer cells. Mol Cancer Res 2012; 10:316-25. [PMID: 22252463 DOI: 10.1158/1541-7786.mcr-11-0520] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
DICER1 is essential for the generation of mature miRNAs and other short noncoding RNAs. Several lines of investigation implicate DICER1 as a tumor suppressor. Reduced DICER1 levels and changes in miRNA abundance have been associated with aggressive tumor phenotypes. The global effects of reduced DICER1 on mRNA transcript abundance in tumor cells remain largely unknown. We used short hairpin RNA to stably knock down DICER1 in endometrial cancer cell lines to begin to determine how reduced DICER1 activity contributes to tumor phenotypes. DICER1 knockdown did not affect cell proliferation but caused enhanced cell migration and growth in soft agar. miRNA and mRNA profiling in KLE cells revealed overall decreases in miRNA levels and changes in the relative abundance of many mRNAs. One of the most striking changes in mRNA levels was the upregulation of IFN-stimulated genes (ISG), the majority of which lack known miRNA target sequences. IFNβ, a key upstream regulator of the IFN response, was significantly increased in DICER1 knockdowns in the AN3CA, Ishikawa, and KLE endometrial cancer cell lines and in the normal endometrial cell line EM-E6/E7/TERT. IFNβ secreted in media from KLE and EM-E6/E7/TERT shDcr cells was sufficient to activate an IFN response in HT29 cells. The reduced miRNA processing in DICER1 knockdowns was associated with increases in pre-miRNAs in the cytoplasm. Our findings suggest that elevated pre-miRNA levels trigger the IFN response to double-stranded RNA. We thus report a novel effect of reduced DICER1 function in cancer cells.
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Affiliation(s)
- Katherine B Chiappinelli
- Department of Surgery, Division of Gynecologic Oncology, Washington University School of Medicine, 660 South Euclid Avenue, Saint Louis, MO 63110, USA.
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10
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Abstract
The RIG-I-like receptors (RLRs) RIG-I, MDA5, and LGP2 play a major role in pathogen sensing of RNA virus infection to initiate and modulate antiviral immunity. The RLRs detect viral RNA ligands or processed self RNA in the cytoplasm to trigger innate immunity and inflammation and to impart gene expression that serves to control infection. Importantly, RLRs cooperate in signaling crosstalk networks with Toll-like receptors and other factors to impart innate immunity and to modulate the adaptive immune response. RLR regulation occurs at a variety of levels ranging from autoregulation to ligand and cofactor interactions and posttranslational modifications. Abberant RLR signaling or dysregulation of RLR expression is now implicated in the development of autoimmune diseases. Understanding the processes of RLR signaling and response will provide insights to guide RLR-targeted therapeutics for antiviral and immune-modifying applications.
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Affiliation(s)
- Yueh-Ming Loo
- Department of Immunology, University of Washington School of Medicine, Seattle, WA 98195-7650, USA
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11
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Pongratz C, Yazdanpanah B, Kashkar H, Lehmann MJ, Kräusslich HG, Krönke M. Selection of potent non-toxic inhibitory sequences from a randomized HIV-1 specific lentiviral short hairpin RNA library. PLoS One 2010; 5:e13172. [PMID: 20949027 PMCID: PMC2951894 DOI: 10.1371/journal.pone.0013172] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2010] [Accepted: 09/08/2010] [Indexed: 12/30/2022] Open
Abstract
RNA interference (RNAi) has been considered as an efficient therapeutic approach against the human immunodeficiency virus type 1 (HIV-1). However, to establish a durable inhibition of HIV-1, multiple effective short hairpin RNAs (shRNAs) need to be stably expressed to prevent the emergence of viral escape variants. In this study, we engineered a randomized lentiviral H1-promoter driven shRNA-library against the viral genome. Potent HIV-1 specific shRNAs were selected by ganciclovir treatment of cell lines stably expressing the cDNA of Herpes Simplex Virus thymidine kinase (HSV-TK) fused to HIV-1 nucleotide sequences. More than 50% of 200 selected shRNAs inhibited an HIV-1 based luciferase reporter assay by more than 70%. Stable expression of some of those shRNAs in an HIV-1 permissive HeLa cell line inhibited infection of wild-type HIV-1 by more than 90%. The combination of a randomized shRNA-library directed against HIV-1 with a live cell selection procedure yielded non-toxic and highly efficient HIV-1 specific inhibitory sequences that could serve as valuable candidates for gene therapy studies.
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Affiliation(s)
- Carola Pongratz
- Institute for Medical Microbiology, Immunology and Hygiene, University Hospital Cologne, Cologne, Germany
- Cologne Excellence Cluster on Cellular Stress Responses in Aging Associated Diseases (CECAD) at the Institute for Genetics, University of Cologne, Cologne, Germany
| | - Benjamin Yazdanpanah
- Institute for Medical Microbiology, Immunology and Hygiene, University Hospital Cologne, Cologne, Germany
- Center for Molecular Medicine at the University of Cologne, Cologne, Germany
- * E-mail:
| | - Hamid Kashkar
- Institute for Medical Microbiology, Immunology and Hygiene, University Hospital Cologne, Cologne, Germany
- Cologne Excellence Cluster on Cellular Stress Responses in Aging Associated Diseases (CECAD) at the Institute for Genetics, University of Cologne, Cologne, Germany
- Center for Molecular Medicine at the University of Cologne, Cologne, Germany
| | - Maik J. Lehmann
- Department of Virology, University Hospital Heidelberg, Heidelberg, Germany
| | | | - Martin Krönke
- Institute for Medical Microbiology, Immunology and Hygiene, University Hospital Cologne, Cologne, Germany
- Cologne Excellence Cluster on Cellular Stress Responses in Aging Associated Diseases (CECAD) at the Institute for Genetics, University of Cologne, Cologne, Germany
- Center for Molecular Medicine at the University of Cologne, Cologne, Germany
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12
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Schlee M, Hartmann G. The chase for the RIG-I ligand--recent advances. Mol Ther 2010; 18:1254-62. [PMID: 20461060 PMCID: PMC2911265 DOI: 10.1038/mt.2010.90] [Citation(s) in RCA: 69] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2009] [Accepted: 04/05/2010] [Indexed: 12/14/2022] Open
Abstract
Multicellular organisms evolved efficient host-defense mechanisms to sense viruses and to block their replication and spread. Invertebrates and plants mainly rely on RNA interference (RNAi) for antiviral defense. In mammals, the initiation of antiviral defense mechanisms is largely based on the detection of viral nucleic acids by innate receptors: retinoic acid-inducible gene I (RIG-I)-like helicases (RLHs) and Toll-like receptors (TLRs). RLHs play a pivotal role in sensing viral RNA and DNA in the cytoplasm of cells. RLHs, like Dicer of the RNAi pathway, belong to the phylogenetically conserved DExD/H-box family of helicases. Unlike TLRs, RLHs are functional in all somatic cells. Activation of RIG-I triggers antiviral responses including type I interferon (IFN), inflammasome activation and proapoptotic signaling. Here, we provide a comprehensive overview of the current literature on the ligand structures detected by RIG-I, and conclude with the molecular definition of the RIG-I ligand: short double-stranded blunt-end 5'-triphosphate RNA. The recent information on the RIG-I ligand now allows the design of short double-stranded RNA (dsRNA) oligonucleotides that are ideally suited alone or in combination with small-interfering RNA (siRNA) for the treatment of viral infection and cancer.
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Affiliation(s)
- Martin Schlee
- Institute of Clinical Chemistry and Pharmacology, University Hospital Bonn, Bonn, Germany
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13
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Olejniczak M, Galka P, Krzyzosiak WJ. Sequence-non-specific effects of RNA interference triggers and microRNA regulators. Nucleic Acids Res 2009; 38:1-16. [PMID: 19843612 PMCID: PMC2800214 DOI: 10.1093/nar/gkp829] [Citation(s) in RCA: 159] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
RNA reagents of diverse lengths and structures, unmodified or containing various chemical modifications are powerful tools of RNA interference and microRNA technologies. These reagents which are either delivered to cells using appropriate carriers or are expressed in cells from suitable vectors often cause unintended sequence-non-specific immune responses besides triggering intended sequence-specific silencing effects. This article reviews the present state of knowledge regarding the cellular sensors of foreign RNA, the signaling pathways these sensors mobilize and shows which specific features of the RNA reagents set the responsive systems on alert. The representative examples of toxic effects caused in the investigated cell lines and tissues by the RNAs of specific types and structures are collected and may be instructive for further studies of sequence-non-specific responses to foreign RNA in human cells.
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Affiliation(s)
- Marta Olejniczak
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, Poland
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14
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Schlee M, Roth A, Hornung V, Hagmann CA, Wimmenauer V, Barchet W, Coch C, Janke M, Mihailovic A, Wardle G, Juranek S, Kato H, Kawai T, Poeck H, Fitzgerald KA, Takeuchi O, Akira S, Tuschl T, Latz E, Ludwig J, Hartmann G. Recognition of 5' triphosphate by RIG-I helicase requires short blunt double-stranded RNA as contained in panhandle of negative-strand virus. Immunity 2009; 31:25-34. [PMID: 19576794 PMCID: PMC2824854 DOI: 10.1016/j.immuni.2009.05.008] [Citation(s) in RCA: 589] [Impact Index Per Article: 39.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2008] [Revised: 03/30/2009] [Accepted: 05/08/2009] [Indexed: 12/24/2022]
Abstract
Antiviral immunity is triggered by immunorecognition of viral nucleic acids. The cytosolic helicase RIG-I is a key sensor of viral infections and is activated by RNA containing a triphosphate at the 5' end. The exact structure of RNA activating RIG-I remains controversial. Here, we established a chemical approach for 5' triphosphate oligoribonucleotide synthesis and found that synthetic single-stranded 5' triphosphate oligoribonucleotides were unable to bind and activate RIG-I. Conversely, the addition of the synthetic complementary strand resulted in optimal binding and activation of RIG-I. Short double-strand conformation with base pairing of the nucleoside carrying the 5' triphosphate was required. RIG-I activation was impaired by a 3' overhang at the 5' triphosphate end. These results define the structure of RNA for full RIG-I activation and explain how RIG-I detects negative-strand RNA viruses that lack long double-stranded RNA but do contain blunt short double-stranded 5' triphosphate RNA in the panhandle region of their single-stranded genome.
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Affiliation(s)
- Martin Schlee
- Institute of Clinical Chemistry and Pharmacology, University of Bonn, D-53127 Bonn, Germany
| | - Andreas Roth
- Institute of Clinical Chemistry and Pharmacology, University of Bonn, D-53127 Bonn, Germany
| | - Veit Hornung
- Division of Infectious Diseases and Immunology, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | | | - Vera Wimmenauer
- Institute of Clinical Chemistry and Pharmacology, University of Bonn, D-53127 Bonn, Germany
| | - Winfried Barchet
- Institute of Clinical Chemistry and Pharmacology, University of Bonn, D-53127 Bonn, Germany
| | - Christoph Coch
- Institute of Clinical Chemistry and Pharmacology, University of Bonn, D-53127 Bonn, Germany
| | - Markus Janke
- Institute of Clinical Chemistry and Pharmacology, University of Bonn, D-53127 Bonn, Germany
| | - Aleksandra Mihailovic
- Howard Hughes Medical Institute, Laboratory of RNA Biology, The Rockefeller Unversity, New York, NY 10021, USA
| | - Greg Wardle
- Howard Hughes Medical Institute, Laboratory of RNA Biology, The Rockefeller Unversity, New York, NY 10021, USA
| | - Stefan Juranek
- Howard Hughes Medical Institute, Laboratory of RNA Biology, The Rockefeller Unversity, New York, NY 10021, USA
| | - Hiroki Kato
- Department of Host Defense, Research Institute for Microbial Diseases, Osaka University, Suita, Osaka 565-0871, Japan
| | - Taro Kawai
- Department of Host Defense, Research Institute for Microbial Diseases, Osaka University, Suita, Osaka 565-0871, Japan
| | - Hendrik Poeck
- Institute of Clinical Chemistry and Pharmacology, University of Bonn, D-53127 Bonn, Germany
| | - Katherine A. Fitzgerald
- Division of Infectious Diseases and Immunology, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Osamu Takeuchi
- Department of Host Defense, Research Institute for Microbial Diseases, Osaka University, Suita, Osaka 565-0871, Japan
| | - Shizuo Akira
- Department of Host Defense, Research Institute for Microbial Diseases, Osaka University, Suita, Osaka 565-0871, Japan
| | - Thomas Tuschl
- Howard Hughes Medical Institute, Laboratory of RNA Biology, The Rockefeller Unversity, New York, NY 10021, USA
| | - Eicke Latz
- Division of Infectious Diseases and Immunology, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Janos Ludwig
- Institute of Clinical Chemistry and Pharmacology, University of Bonn, D-53127 Bonn, Germany
- Howard Hughes Medical Institute, Laboratory of RNA Biology, The Rockefeller Unversity, New York, NY 10021, USA
| | - Gunther Hartmann
- Institute of Clinical Chemistry and Pharmacology, University of Bonn, D-53127 Bonn, Germany
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Sugiyama R, Habu Y, Ohnari A, Miyano-Kurosaki N, Takaku H. RNA interference targeted to the conserved dimerization initiation site (DIS) of HIV-1 restricts virus escape mutation. J Biochem 2009; 146:481-9. [PMID: 19556221 PMCID: PMC7539327 DOI: 10.1093/jb/mvp093] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Short hairpin RNAs (shRNA) targeting viral or cellular genes can effectively inhibit human immunodeficiency virus type 1 (HIV-1) replication. This inhibition, however, may induce mutations in the targeted gene, leading to rapid escape from the shRNA-induced inhibition. We generated a lymphoid cell line that stably expressed a 19-bp shRNA targeting a well-conserved dimerization initiation site (DIS) of HIV-1, which strongly inhibited viral replication, thereby delaying virus escape. Furthermore, treatment of HIV-1 infection with DIS- and vif-shRNA combination therapy resulted in superior anti-viral responses compared to vif-shRNA monotherapy. Continuous challenge with HIV-1, however, generated virus mutants that could overcome the RNA interference restriction. Such anti-genes may be promising tools for HIV-1 gene therapy for HIV/acquired immunodeficiency syndrome.
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Affiliation(s)
- Ryuichi Sugiyama
- Department of Life and Environmental Science, Chiba Institute of Technology, 2-17-1 Tsudanuma, Narashino-shi, Chiba 275-0016, Japan
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Hajeri PB, Singh SK. siRNAs: their potential as therapeutic agents--Part I. Designing of siRNAs. Drug Discov Today 2009; 14:851-8. [PMID: 19540928 DOI: 10.1016/j.drudis.2009.06.001] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2009] [Accepted: 06/08/2009] [Indexed: 12/25/2022]
Abstract
RNA interference (RNAi) is a novel and essential biological process, as well as a powerful experimental tool with the potential to be used in therapeutic development. RNAi-based strategies have the capability of being able to be driven from bench to bedside. It is very important to develop the precise tools for designing the siRNAs to get the most efficient knockdown of the target genes and to reduce any off-target effects. In this review we have discussed the strategies and parameters required for effective siRNA designing and synthesis, based on already published literature.
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Affiliation(s)
- Praveensingh B Hajeri
- Section of Infectious Diseases & Immunobiology, Centre for Cellular and Molecular Biology, Uppal Road, Hyderabad-500007, AP, India
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O’HARA STEVENP, MOTT JUSTINL, SPLINTER PATRICKL, GORES GREGORYJ, LARUSSO NICHOLASF. MicroRNAs: key modulators of posttranscriptional gene expression. Gastroenterology 2009; 136:17-25. [PMID: 19049808 PMCID: PMC3156441 DOI: 10.1053/j.gastro.2008.11.028] [Citation(s) in RCA: 73] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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Schlee M, Hartmann E, Coch C, Wimmenauer V, Janke M, Barchet W, Hartmann G. Approaching the RNA ligand for RIG-I? Immunol Rev 2009; 227:66-74. [PMID: 19120476 DOI: 10.1111/j.1600-065x.2008.00724.x] [Citation(s) in RCA: 62] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Innate and antigen-specific antiviral immunity are triggered by immunorecognition of viral nucleic acids. The helicase retinoic acid-inducible gene I (RIG-I) (also known as DDX58) is the key sensor of negative strand RNA viruses in the cytosol of cells. RNA containing a triphosphate at the 5'-end was shown to activate RIG-I, but the exact structure of RNA supporting 5'-triphosphate recognition, the requirement of a 5'-triphosphate group, as well as the existence of RNA structures detected by RIG-I in the absence of 5'-triphosphate remain controversial. Here, we revisit the literature on RIG-I and RIG-I ligands. The literature proposes at least six different RIG-I ligands: (i) single strand with a 5'-triphosphate, (ii) double-stranded RNA with a 5'-triphosphate, (iii) 5'-triphosphate single-stranded RNA with A- and U-rich 3'-sequences, (iv) double-stranded RNA of intermediate length (>300 and <2000 bp) without 5'-triphosphate, (v) blunt-end short double-stranded RNA (23-30 bp) without 5'-triphosphate, and (vi) short double-stranded RNA (23-30 bp) with 5'-monophosphate. RIG-I thus seems promiscuous for a variety of different RNA molecules, very similar to the Toll-like receptors, of which 10 family members are sufficient for the safe detection of the microbial cosmos. In the light of these outstanding publications, it seems an unlikely possibility that there is a fundamental shortcoming in the design of all studies. Looking closely, the only issue that comes to mind is the in vitro transcription technique used by all investigators without confirming the identity of RNA products. This technique, together with the different biological systems used, the lack of dose responses and of proper comparison of different published ligands and controls leave us with more questions than answers as to what the exact RIG-I ligand is, if in fact it exists.
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Affiliation(s)
- Martin Schlee
- Institute of Clinical Chemistry and Pharmacology, University Hospital Bonn, Bonn, Germany
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Li T, Koshy S, Folkesson HG. RNA interference for CFTR attenuates lung fluid absorption at birth in rats. Respir Res 2008; 9:55. [PMID: 18652671 PMCID: PMC2515309 DOI: 10.1186/1465-9921-9-55] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2008] [Accepted: 07/24/2008] [Indexed: 11/10/2022] Open
Abstract
Background Small interfering RNA (siRNA) against αENaC (α-subunit of the epithelial Na channel) and CFTR (cystic fibrosis transmembrane conductance regulator) was used to explore ENaC and CTFR function in newborn rat lungs. Methods Twenty-four hours after trans-thoracic intrapulmonary (ttip) injection of siRNA-generating plasmid DNA (pSi-0, pSi-4, or pSi-C2), we measured CFTR and ENaC expression, extravascular lung water, and mortality. Results αENaC and CFTR mRNA and protein decreased by ~80% and ~85%, respectively, following αENaC and CFTR silencing. Extravascular lung water and mortality increased after αENaC and CFTR-silencing. In pSi-C2-transfected isolated DLE cells there were attenuated CFTR mRNA and protein. In pSi-4-transfected DLE cells αENaC mRNA and protein were both reduced. Interestingly, CFTR-silencing also reduced αENaC mRNA and protein. αENaC silencing, on the other hand, only slightly reduced CFTR mRNA and protein. Conclusion Thus, ENaC and CFTR are both involved in the fluid secretion to absorption conversion around at birth.
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Affiliation(s)
- Tianbo Li
- Department of Integrative Medical Sciences, Northeastern Ohio Universities Colleges of Medicine and Pharmacy, Rootstown, OH 44272-0095, USA.
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