1
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Yang Z, Zhou J, Li Z, Guo J, Fang L, Xiao X, Xiao S. Identification of whole-cell dsRNA-binding proteins by phase separation. RNA Biol 2024; 21:32-45. [PMID: 39115224 PMCID: PMC11312991 DOI: 10.1080/15476286.2024.2386498] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Revised: 07/19/2024] [Accepted: 07/25/2024] [Indexed: 08/11/2024] Open
Abstract
Interactions between double-stranded RNA (dsRNA) and proteins play an important role in cellular homeostasis by regulating the editing, stability, and splicing of intracellular RNA. The identification of dsRNA-binding proteins (dsRBPs) is key; however, it has long been challenging to purify dsRBPs from cells. In this study, we developed a novel method, dsRBPC (dsRNA-binding protein capture), to purify cellular dsRBPs based on classic phase separation purification procedures. A global dsRNA-binding proteome of LLC-PK1 cells was obtained, and we identified 1326 dsRBPs, including 1303 putative novel dsRBPs. Functional analyses suggested that these enriched dsRBPs are mainly associated with rRNA processing, RNA splicing, transcriptional regulation, and nucleocytoplasmic transport. We also found that the ARM (armadillo/beta-catenin-like repeats) motif is a previously unknown dsRNA-binding domain, as demonstrated by biochemical experiments. Collectively, this study provides a useful approach for dsRBP identification and the discovery of a global dsRNA-binding proteome to comprehensively map the dsRNA - protein interaction network.
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Affiliation(s)
- Zhixiang Yang
- National Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
- The Key Laboratory of Preventive Veterinary Medicine in Hubei Province, Cooperative Innovation Center for Sustainable Pig Production, Wuhan, China
| | - Junwei Zhou
- National Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
- The Key Laboratory of Preventive Veterinary Medicine in Hubei Province, Cooperative Innovation Center for Sustainable Pig Production, Wuhan, China
| | - Zhuang Li
- National Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
- The Key Laboratory of Preventive Veterinary Medicine in Hubei Province, Cooperative Innovation Center for Sustainable Pig Production, Wuhan, China
| | - Jiahui Guo
- National Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
- The Key Laboratory of Preventive Veterinary Medicine in Hubei Province, Cooperative Innovation Center for Sustainable Pig Production, Wuhan, China
| | - Liurong Fang
- National Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
- The Key Laboratory of Preventive Veterinary Medicine in Hubei Province, Cooperative Innovation Center for Sustainable Pig Production, Wuhan, China
| | - Xun Xiao
- National Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
- The Key Laboratory of Preventive Veterinary Medicine in Hubei Province, Cooperative Innovation Center for Sustainable Pig Production, Wuhan, China
| | - Shaobo Xiao
- National Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
- The Key Laboratory of Preventive Veterinary Medicine in Hubei Province, Cooperative Innovation Center for Sustainable Pig Production, Wuhan, China
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2
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Manjunath L, Oh S, Ortega P, Bouin A, Bournique E, Sanchez A, Martensen PM, Auerbach AA, Becker JT, Seldin M, Harris RS, Semler BL, Buisson R. APOBEC3B drives PKR-mediated translation shutdown and protects stress granules in response to viral infection. Nat Commun 2023; 14:820. [PMID: 36781883 PMCID: PMC9925369 DOI: 10.1038/s41467-023-36445-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Accepted: 01/31/2023] [Indexed: 02/15/2023] Open
Abstract
Double-stranded RNA produced during viral replication and transcription activates both protein kinase R (PKR) and ribonuclease L (RNase L), which limits viral gene expression and replication through host shutoff of translation. In this study, we find that APOBEC3B forms a complex with PABPC1 to stimulate PKR and counterbalances the PKR-suppressing activity of ADAR1 in response to infection by many types of viruses. This leads to translational blockage and the formation of stress granules. Furthermore, we show that APOBEC3B localizes to stress granules through the interaction with PABPC1. APOBEC3B facilitates the formation of protein-RNA condensates with stress granule assembly factor (G3BP1) by protecting mRNA associated with stress granules from RNAse L-induced RNA cleavage during viral infection. These results not only reveal that APOBEC3B is a key regulator of different steps of the innate immune response throughout viral infection but also highlight an alternative mechanism by which APOBEC3B can impact virus replication without editing viral genomes.
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Affiliation(s)
- Lavanya Manjunath
- Department of Biological Chemistry, School of Medicine, University of California Irvine, Irvine, CA, USA
- Center for Virus Research, University of California Irvine, Irvine, CA, USA
- Center for Epigenetics and Metabolism, Chao Family Comprehensive Cancer Center, University of California Irvine, Irvine, CA, USA
| | - Sunwoo Oh
- Department of Biological Chemistry, School of Medicine, University of California Irvine, Irvine, CA, USA
- Center for Virus Research, University of California Irvine, Irvine, CA, USA
- Center for Epigenetics and Metabolism, Chao Family Comprehensive Cancer Center, University of California Irvine, Irvine, CA, USA
| | - Pedro Ortega
- Department of Biological Chemistry, School of Medicine, University of California Irvine, Irvine, CA, USA
- Center for Virus Research, University of California Irvine, Irvine, CA, USA
- Center for Epigenetics and Metabolism, Chao Family Comprehensive Cancer Center, University of California Irvine, Irvine, CA, USA
| | - Alexis Bouin
- Center for Virus Research, University of California Irvine, Irvine, CA, USA
- Department of Microbiology & Molecular Genetics, School of Medicine, University of California Irvine, Irvine, CA, USA
| | - Elodie Bournique
- Department of Biological Chemistry, School of Medicine, University of California Irvine, Irvine, CA, USA
- Center for Virus Research, University of California Irvine, Irvine, CA, USA
- Center for Epigenetics and Metabolism, Chao Family Comprehensive Cancer Center, University of California Irvine, Irvine, CA, USA
| | - Ambrocio Sanchez
- Department of Biological Chemistry, School of Medicine, University of California Irvine, Irvine, CA, USA
- Center for Virus Research, University of California Irvine, Irvine, CA, USA
- Center for Epigenetics and Metabolism, Chao Family Comprehensive Cancer Center, University of California Irvine, Irvine, CA, USA
| | - Pia Møller Martensen
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus C, Denmark
| | - Ashley A Auerbach
- Department of Biochemistry and Structural Biology, University of Texas Health San Antonio, San Antonio, TX, USA
- Institute for Molecular Virology, University of Minnesota - Twin Cities, Minneapolis, MN, USA
| | - Jordan T Becker
- Institute for Molecular Virology, University of Minnesota - Twin Cities, Minneapolis, MN, USA
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota - Twin Cities, Minneapolis, MN, USA
| | - Marcus Seldin
- Department of Biological Chemistry, School of Medicine, University of California Irvine, Irvine, CA, USA
- Center for Epigenetics and Metabolism, Chao Family Comprehensive Cancer Center, University of California Irvine, Irvine, CA, USA
| | - Reuben S Harris
- Department of Biochemistry and Structural Biology, University of Texas Health San Antonio, San Antonio, TX, USA
- Howard Hughes Medical Institute, University of Texas Health San Antonio, San Antonio, TX, USA
| | - Bert L Semler
- Center for Virus Research, University of California Irvine, Irvine, CA, USA
- Department of Microbiology & Molecular Genetics, School of Medicine, University of California Irvine, Irvine, CA, USA
| | - Rémi Buisson
- Department of Biological Chemistry, School of Medicine, University of California Irvine, Irvine, CA, USA.
- Center for Virus Research, University of California Irvine, Irvine, CA, USA.
- Center for Epigenetics and Metabolism, Chao Family Comprehensive Cancer Center, University of California Irvine, Irvine, CA, USA.
- Department of Pharmaceutical Sciences, School of Pharmacy & Pharmaceutical Sciences, University of California Irvine, Irvine, CA, USA.
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3
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Hu SB, Heraud-Farlow J, Sun T, Liang Z, Goradia A, Taylor S, Walkley CR, Li JB. ADAR1p150 Prevents MDA5 and PKR Activation via Distinct Mechanisms to Avert Fatal Autoinflammation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.01.25.525475. [PMID: 36747811 PMCID: PMC9900771 DOI: 10.1101/2023.01.25.525475] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Effective immunity requires the innate immune system to distinguish foreign (non-self) nucleic acids from cellular (self) nucleic acids. Cellular double-stranded RNAs (dsRNAs) are edited by the RNA editing enzyme ADAR1 to prevent their dsRNA structure pattern being recognized as viral dsRNA by cytoplasmic dsRNA sensors including MDA5, PKR and ZBP1. A loss of ADAR1-mediated RNA editing of cellular dsRNA activates MDA5. However, additional RNA editing-independent functions of ADAR1 have been proposed, but a specific mechanism has not been delineated. We now demonstrate that the loss of ADAR1-mediated RNA editing specifically activates MDA5, while loss of the cytoplasmic ADAR1p150 isoform or its dsRNA binding activity enabled PKR activation. Deleting both MDA5 and PKR resulted in complete rescue of the embryonic lethality of Adar1p150 -/- mice to adulthood, contrasting with the limited or no rescue by removing MDA5, PKR or ZBP1 alone, demonstrating that this is a species conserved function of ADAR1p150. Our findings demonstrate that MDA5 and PKR are the primary in vivo effectors of fatal autoinflammation following the loss of ADAR1p150.
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4
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Kang YG, Kim J, Lee K, Choe JY, Dua P, Lee DK. Retinoic Acid-Inducible Gene I-Mediated Innate Immune Stimulation by Chemically Synthesized Long Double-Stranded RNAs Is Structure and Sequence Dependent. Nucleic Acid Ther 2022; 32:321-332. [PMID: 35263174 DOI: 10.1089/nat.2021.0104] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Double-stranded RNAs (dsRNAs) longer than 30 bp have not been considered desirable RNA interference (RNAi) triggering structures in mammalian cells as they nonspecifically activate innate immune response. However, in earlier studies, not only dsRNA length but also 5'-triphosphate moiety produced by in vitro transcription might have affected the stimulation of innate immune system. Herein, using chemically synthesized long dsRNAs without 5'-triphosphate, we elucidated direct relationship between length of dsRNAs and innate immune stimulation. First, we found that blunt-ended, chemically synthesized 38/40-60 bp-long dsRNAs induced retinoic acid-inducible gene I (RIG-I)-mediated innate immune response, which was suppressed by the introduction of the 2-nt 3' overhang structure. Surprisingly, we discovered that RIG-I activation by these long dsRNAs is also sequence dependent, and the sequence composition at dsRNA termini is important for RIG-I activation. In addition, we identified that long dsRNAs over 38 bp could elicit single- or dual-target gene silencing in a Dicer-independent manner. Taken together, our findings may serve as guidelines to develop an immunostimulatory RNAi trigger to exploit host's innate immune system, as well as a specific dual-gene targeting RNAi therapeutics platform without nonspecific innate immune stimulation by RIG-I.
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Affiliation(s)
- Young Gyu Kang
- Department of Chemistry, Sungkyunkwan University, Suwon, Korea.,OliX Pharmaceuticals, Inc., Suwon, Korea
| | - Jaejin Kim
- Department of Chemistry, Sungkyunkwan University, Suwon, Korea
| | - Kyeongmin Lee
- Department of Chemistry, Sungkyunkwan University, Suwon, Korea
| | - Jeong Yong Choe
- Department of Chemistry, Sungkyunkwan University, Suwon, Korea.,OliX Pharmaceuticals, Inc., Suwon, Korea
| | - Pooja Dua
- OliX Pharmaceuticals, Inc., Suwon, Korea
| | - Dong Ki Lee
- Department of Chemistry, Sungkyunkwan University, Suwon, Korea.,OliX Pharmaceuticals, Inc., Suwon, Korea
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5
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Guillemin A, Kumar A, Wencker M, Ricci EP. Shaping the Innate Immune Response Through Post-Transcriptional Regulation of Gene Expression Mediated by RNA-Binding Proteins. Front Immunol 2022; 12:796012. [PMID: 35087521 PMCID: PMC8787094 DOI: 10.3389/fimmu.2021.796012] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Accepted: 12/13/2021] [Indexed: 12/20/2022] Open
Abstract
Innate immunity is the frontline of defense against infections and tissue damage. It is a fast and semi-specific response involving a myriad of processes essential for protecting the organism. These reactions promote the clearance of danger by activating, among others, an inflammatory response, the complement cascade and by recruiting the adaptive immunity. Any disequilibrium in this functional balance can lead to either inflammation-mediated tissue damage or defense inefficiency. A dynamic and coordinated gene expression program lies at the heart of the innate immune response. This expression program varies depending on the cell-type and the specific danger signal encountered by the cell and involves multiple layers of regulation. While these are achieved mainly via transcriptional control of gene expression, numerous post-transcriptional regulatory pathways involving RNA-binding proteins (RBPs) and other effectors play a critical role in its fine-tuning. Alternative splicing, translational control and mRNA stability have been shown to be tightly regulated during the innate immune response and participate in modulating gene expression in a global or gene specific manner. More recently, microRNAs assisting RBPs and post-transcriptional modification of RNA bases are also emerging as essential players of the innate immune process. In this review, we highlight the numerous roles played by specific RNA-binding effectors in mediating post-transcriptional control of gene expression to shape innate immunity.
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Affiliation(s)
- Anissa Guillemin
- LBMC, Laboratoire de Biologie et Modelisation de la Cellule, Université de Lyon, ENS de Lyon, Universite Claude Bernard Lyon 1, CNRS, UMR 5239, INSERM, U1293, Lyon, France
| | - Anuj Kumar
- CRCL, Centre de Recherche en Cancérologie de Lyon, INSERM U1052, CNRS UMR 5286, Lyon, France
| | - Mélanie Wencker
- LBMC, Laboratoire de Biologie et Modelisation de la Cellule, Université de Lyon, ENS de Lyon, Universite Claude Bernard Lyon 1, CNRS, UMR 5239, INSERM, U1293, Lyon, France
- CIRI, Centre International de Recherche en Infectiologie, Université de Lyon, ENS de Lyon, CNRS, UMR 5308, INSERM, Lyon, France
| | - Emiliano P. Ricci
- LBMC, Laboratoire de Biologie et Modelisation de la Cellule, Université de Lyon, ENS de Lyon, Universite Claude Bernard Lyon 1, CNRS, UMR 5239, INSERM, U1293, Lyon, France
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6
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Lee HC, Fu CY, Lin CY, Hu JR, Huang TY, Lo KY, Tsai HY, Sheu JC, Tsai HJ. Poly(U)-specific endoribonuclease ENDOU promotes translation of human CHOP mRNA by releasing uORF element-mediated inhibition. EMBO J 2021; 40:e104123. [PMID: 33511665 PMCID: PMC8167367 DOI: 10.15252/embj.2019104123] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2019] [Revised: 11/18/2020] [Accepted: 11/30/2020] [Indexed: 12/24/2022] Open
Abstract
Upstream open reading frames (uORFs) are known to negatively affect translation of the downstream ORF. The regulatory proteins involved in relieving this inhibition are however poorly characterized. In response to cellular stress, eIF2α phosphorylation leads to an inhibition of global protein synthesis, while translation of specific factors such as CHOP is induced. We analyzed a 105‐nt inhibitory uORF in the transcript of human CHOP (huORFchop) and found that overexpression of the zebrafish or human ENDOU poly(U)‐endoribonuclease (Endouc or ENDOU‐1, respectively) increases CHOP mRNA translation also in the absence of stress. We also found that Endouc/ENDOU‐1 binds and cleaves the huORFchop transcript at position 80G‐81U, which induces CHOP translation independently of phosphorylated eIF2α. However, both ENDOU and phospho‐eIF2α are nonetheless required for maximal translation of CHOP mRNA. Increased levels of ENDOU shift a huORFchop reporter as well as endogenous CHOP transcripts from the monosome to polysome fraction, indicating an increase in translation. Furthermore, we found that the uncapped truncated huORFchop‐69‐105‐nt transcript contains an internal ribosome entry site (IRES), facilitating translation of the cleaved transcript. Therefore, we propose a model where ENDOU‐mediated transcript cleavage positively regulates CHOP translation resulting in increased CHOP protein levels upon stress. Specifically, CHOP transcript cleavage changes the configuration of huORFchop thereby releasing its inhibition and allowing the stalled ribosomes to resume translation of the downstream ORF.
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Affiliation(s)
- Hung-Chieh Lee
- Institute of Biomedical Sciences, Mackay Medical College, New Taipei City, Taiwan
| | - Chuan-Yang Fu
- Institute of Biomedical Sciences, Mackay Medical College, New Taipei City, Taiwan
| | - Cheng-Yung Lin
- Institute of Biomedical Sciences, Mackay Medical College, New Taipei City, Taiwan
| | - Jia-Rung Hu
- Institute of Molecular and Cellular Biology, National Taiwan University, Taipei, Taiwan
| | - Ting-Ying Huang
- Institute of Molecular and Cellular Biology, National Taiwan University, Taipei, Taiwan
| | - Kai-Yin Lo
- Department of Agricultural Chemistry, National Taiwan University, Taipei, Taiwan
| | - Hsin-Yue Tsai
- Institute of Molecular Medicine, School of Medicine, National Taiwan University, Taipei, Taiwan
| | - Jin-Chuan Sheu
- Liver Disease Prevention and Treatment Research Foundation, Taipei, Taiwan
| | - Huai-Jen Tsai
- Institute of Biomedical Sciences, Mackay Medical College, New Taipei City, Taiwan.,Institute of Molecular and Cellular Biology, National Taiwan University, Taipei, Taiwan.,Department of Life Science, Fu Jen Catholic University, New Taipei, Taiwan
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7
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Markiewicz L, Drazkowska K, Sikorski PJ. Tricks and threats of RNA viruses - towards understanding the fate of viral RNA. RNA Biol 2021; 18:669-687. [PMID: 33618611 PMCID: PMC8078519 DOI: 10.1080/15476286.2021.1875680] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2020] [Revised: 12/22/2020] [Accepted: 01/09/2021] [Indexed: 12/24/2022] Open
Abstract
Human innate cellular defence pathways have evolved to sense and eliminate pathogens, of which, viruses are considered one of the most dangerous. Their relatively simple structure makes the identification of viral invasion a difficult task for cells. In the course of evolution, viral nucleic acids have become one of the strongest and most reliable early identifiers of infection. When considering RNA virus recognition, RNA sensing is the central mechanism in human innate immunity, and effectiveness of this sensing is crucial for triggering an appropriate antiviral response. Although human cells are armed with a variety of highly specialized receptors designed to respond only to pathogenic viral RNA, RNA viruses have developed an array of mechanisms to avoid being recognized by human interferon-mediated cellular defence systems. The repertoire of viral evasion strategies is extremely wide, ranging from masking pathogenic RNA through end modification, to utilizing sophisticated techniques to deceive host cellular RNA degrading enzymes, and hijacking the most basic metabolic pathways in host cells. In this review, we aim to dissect human RNA sensing mechanisms crucial for antiviral immune defences, as well as the strategies adopted by RNA viruses to avoid detection and degradation by host cells. We believe that understanding the fate of viral RNA upon infection, and detailing the molecular mechanisms behind virus-host interactions, may be helpful for developing more effective antiviral strategies; which are urgently needed to prevent the far-reaching consequences of widespread, highly pathogenic viral infections.
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8
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Sadeq S, Al-Hashimi S, Cusack CM, Werner A. Endogenous Double-Stranded RNA. Noncoding RNA 2021; 7:15. [PMID: 33669629 PMCID: PMC7930956 DOI: 10.3390/ncrna7010015] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2021] [Revised: 02/15/2021] [Accepted: 02/17/2021] [Indexed: 02/07/2023] Open
Abstract
The birth of long non-coding RNAs (lncRNAs) is closely associated with the presence and activation of repetitive elements in the genome. The transcription of endogenous retroviruses as well as long and short interspersed elements is not only essential for evolving lncRNAs but is also a significant source of double-stranded RNA (dsRNA). From an lncRNA-centric point of view, the latter is a minor source of bother in the context of the entire cell; however, dsRNA is an essential threat. A viral infection is associated with cytoplasmic dsRNA, and endogenous RNA hybrids only differ from viral dsRNA by the 5' cap structure. Hence, a multi-layered defense network is in place to protect cells from viral infections but tolerates endogenous dsRNA structures. A first line of defense is established with compartmentalization; whereas endogenous dsRNA is found predominantly confined to the nucleus and the mitochondria, exogenous dsRNA reaches the cytoplasm. Here, various sensor proteins recognize features of dsRNA including the 5' phosphate group of viral RNAs or hybrids with a particular length but not specific nucleotide sequences. The sensors trigger cellular stress pathways and innate immunity via interferon signaling but also induce apoptosis via caspase activation. Because of its central role in viral recognition and immune activation, dsRNA sensing is implicated in autoimmune diseases and used to treat cancer.
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Affiliation(s)
| | | | | | - Andreas Werner
- Biosciences Institute, Medical School, Newcastle University, Newcastle upon Tyne NE2 4HH, UK; (S.S.); (S.A.-H.); (C.M.C.)
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9
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Roca Suarez AA, Testoni B, Baumert TF, Lupberger J. Nucleic Acid-Induced Signaling in Chronic Viral Liver Disease. Front Immunol 2021; 11:624034. [PMID: 33613561 PMCID: PMC7892431 DOI: 10.3389/fimmu.2020.624034] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Accepted: 12/21/2020] [Indexed: 12/12/2022] Open
Abstract
A hallmark for the development and progression of chronic liver diseases is the persistent dysregulation of signaling pathways related to inflammatory responses, which eventually promotes the development of hepatic fibrosis, cirrhosis and hepatocellular carcinoma (HCC). The two major etiological agents associated with these complications in immunocompetent patients are hepatitis B virus (HBV) and hepatitis C virus (HCV), accounting for almost 1.4 million liver disease-associated deaths worldwide. Although both differ significantly from the point of their genomes and viral life cycles, they exert not only individual but also common strategies to divert innate antiviral defenses. Multiple virus-modulated pathways implicated in stress and inflammation illustrate how chronic viral hepatitis persistently tweaks host signaling processes with important consequences for liver pathogenesis. The following review aims to summarize the molecular events implicated in the sensing of viral nucleic acids, the mechanisms employed by HBV and HCV to counter these measures and how the dysregulation of these cellular pathways drives the development of chronic liver disease and the progression toward HCC.
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MESH Headings
- Carcinoma, Hepatocellular/immunology
- Carcinoma, Hepatocellular/mortality
- Carcinoma, Hepatocellular/pathology
- DNA, Viral/immunology
- Hepacivirus/immunology
- Hepatitis B virus/immunology
- Hepatitis B, Chronic/immunology
- Hepatitis B, Chronic/mortality
- Hepatitis B, Chronic/pathology
- Hepatitis C, Chronic/immunology
- Hepatitis C, Chronic/mortality
- Hepatitis C, Chronic/pathology
- Humans
- Liver Neoplasms/immunology
- Liver Neoplasms/mortality
- Liver Neoplasms/pathology
- RNA, Viral/immunology
- Signal Transduction/immunology
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Affiliation(s)
- Armando Andres Roca Suarez
- INSERM, U1110, Institut de Recherche sur les Maladies Virales et Hépatiques, Strasbourg, France
- Université de Strasbourg, Strasbourg, France
- INSERM U1052, CNRS UMR-5286, Cancer Research Center of Lyon (CRCL), Lyon, France
- University of Lyon, Université Claude-Bernard (UCBL), Lyon, France
| | - Barbara Testoni
- INSERM U1052, CNRS UMR-5286, Cancer Research Center of Lyon (CRCL), Lyon, France
- University of Lyon, Université Claude-Bernard (UCBL), Lyon, France
| | - Thomas F. Baumert
- INSERM, U1110, Institut de Recherche sur les Maladies Virales et Hépatiques, Strasbourg, France
- Université de Strasbourg, Strasbourg, France
- Institut Hospitalo-Universitaire, Pôle Hépato-digestif, Nouvel Hôpital Civil, Strasbourg, France
- Institut Universitaire de France (IUF), Paris, France
| | - Joachim Lupberger
- INSERM, U1110, Institut de Recherche sur les Maladies Virales et Hépatiques, Strasbourg, France
- Université de Strasbourg, Strasbourg, France
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10
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Asthana V, Stern BS, Tang Y, Bugga P, Li A, Ferguson A, Asthana A, Bao G, Drezek RA. Development of a Novel Class of Self-Assembling dsRNA Cancer Therapeutics: A Proof-of-Concept Investigation. MOLECULAR THERAPY-ONCOLYTICS 2020; 18:419-431. [PMID: 32913891 PMCID: PMC7452102 DOI: 10.1016/j.omto.2020.07.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/01/2020] [Accepted: 07/28/2020] [Indexed: 10/26/2022]
Abstract
Cancer has proven to be an extremely difficult challenge to treat. Several fundamental issues currently underlie cancer treatment, including differentiating self from nonself, functional coupling of the recognition and therapeutic components of various therapies, and the propensity of cancerous cells to develop resistance to common treatment modalities via evolutionary pressure. Given these limitations, there is an increasing need to develop an all-encompassing therapeutic that can uniquely target malignant cells, decouple recognition from treatment, and overcome evolutionarily driven cancer resistance. We describe herein a new class of programmable self-assembling double-stranded RNA (dsRNA)-based cancer therapeutics that uniquely targets aberrant genetic sequences and in a functionally decoupled manner, undergoes oncogenic RNA-activated displacement (ORAD), initiating a therapeutic cascade that induces apoptosis and immune activation. As a proof of concept, we show that RNA strands targeting the EWS/Fli1 fusion gene in Ewing sarcoma cells that are end blocked with phosphorothioate bonds and additionally sealed with a 2'-deoxyuridine (2'-U)-modified DNA protector can be used to induce specific and potent killing of cells containing the target oncogenic sequence but not wild type.
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Affiliation(s)
| | - Brett S Stern
- Department of Bioengineering, Rice University, Houston, TX 77030, USA
| | - Yuqi Tang
- Department of Bioengineering, Rice University, Houston, TX 77030, USA
| | - Pallavi Bugga
- Department of Bioengineering, Rice University, Houston, TX 77030, USA
| | - Ang Li
- Department of Bioengineering, Rice University, Houston, TX 77030, USA
| | - Adam Ferguson
- Department of Bioengineering, Rice University, Houston, TX 77030, USA
| | - Anantratn Asthana
- Department of Bioengineering, Rice University, Houston, TX 77030, USA
| | - Gang Bao
- Department of Bioengineering, Rice University, Houston, TX 77030, USA
| | - Rebekah A Drezek
- Department of Bioengineering, Rice University, Houston, TX 77030, USA
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11
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Tanaka H, Sakurai Y, Anindita J, Akita H. Development of lipid-like materials for RNA delivery based on intracellular environment-responsive membrane destabilization and spontaneous collapse. Adv Drug Deliv Rev 2020; 154-155:210-226. [PMID: 32650040 DOI: 10.1016/j.addr.2020.07.001] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Revised: 06/26/2020] [Accepted: 07/02/2020] [Indexed: 01/01/2023]
Abstract
Messenger RNA and small interfering RNA are attractive modalities for curing diseases by complementation or knock-down of proteins. For success of these RNAs, a drug delivery system (DDS) is required to control a pharmacokinetics, to enhance cellular uptake, to overcome biological membranes, and to release the cargo into the cytoplasm. Based on past research, developing nanoparticles that are neutrally charged have been the mainstream of their development. Also, the materials are further mounted with pH- and/or reducing environment-responsive units. In this review, we summarize progress made in the molecular design of these materials. We also focus on the importance of the hydrophobic scaffold for tissue/cell targeting, intracellular trafficking, and immune responses. As a practical example, the design concept of the SS-cleavable and pH-activated lipid-like material (ssPalm) and subsequent molecular modification tailored to the RNA-based medical application is discussed.
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12
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RNA Signaling in Pulmonary Arterial Hypertension-A Double-Stranded Sword. Int J Mol Sci 2020; 21:ijms21093124. [PMID: 32354189 PMCID: PMC7247700 DOI: 10.3390/ijms21093124] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2020] [Revised: 04/26/2020] [Accepted: 04/27/2020] [Indexed: 12/17/2022] Open
Abstract
Recognition of and response to pathogens and tissue injury is driven by the innate immune system via activation of pattern recognition receptors. One of the many patterns recognized is RNA and, while several receptors bind RNA, Toll-like receptor 3 (TLR3) is well placed for initial recognition of RNA molecules due to its localization within the endosome. There is a growing body of work describing a role for TLR3 in maintenance of vascular homeostasis. For example, TLR3 deficiency has been shown to play repair and remodeling roles in the systemic vasculature and in lung parenchyma. A hallmark of pulmonary arterial hypertension (PAH) is pulmonary vascular remodeling, yet drivers and triggers of this remodeling remain incompletely understood. Based on its role in the systemic vasculature, our group discovered reduced endothelial TLR3 expression in PAH and revealed a protective role for a TLR3 agonist in rodent models of pulmonary hypertension. This review will provide an overview of RNA signaling in the vasculature and how it relates to PAH pathobiology, including whether targeting double-stranded RNA signaling is a potential treatment option for PAH.
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13
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Ku J, Kim S, Park J, Kim TS, Kharbash R, Shin EC, Char K, Kim Y, Li S. Reactive Polymer Targeting dsRNA as Universal Virus Detection Platform with Enhanced Sensitivity. Biomacromolecules 2020; 21:2440-2454. [PMID: 32233463 DOI: 10.1021/acs.biomac.0c00379] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Reactive poly(pentafluorophenyl acrylate) (PPFPA)-grafted surfaces offer a versatile platform to immobilize biomolecules. Here, we utilize PPFPA-grafted surface and double-stranded RNA (dsRNA) recognizing J2 antibody to construct a universal virus detection platform with enhanced sensitivity. PPFPA on silicon substrates is prepared, and surface hydrophilicity is modulated by partial substitution of the pentafluorophenyl units with poly(ethylene glycol). Following dsRNA antibody immobilization, the prepared surfaces can distinguish long dsRNAs from single-stranded RNAs of the same length and short dsRNAs. As long dsRNAs are common byproducts of viral transcription/replication, these surfaces can detect the presence of different kinds of viruses without prior knowledge of their genomic sequences. To increase dsRNA detection sensitivity, a two-step method is devised where the captured dsRNAs are visualized with multiple fluorophore-tagged J2 antibodies. We show that the developed platform can differentiate foreign long dsRNAs from cellular dsRNAs and other biomolecules present in the cell lysate. Moreover, when tested against cells infected with hepatitis A or C viruses, both viruses are successfully detected using a single platform. Our study shows that the developed PPFPA platform immobilized with J2 antibody can serve as a primary diagnostic tool to determine the infection status for a wide range of viruses.
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Affiliation(s)
- Jayoung Ku
- Department of Chemical and Biomolecular Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141 South Korea.,KI for Health Science and Technology (KIHST), KAIST, Daejeon 34141 South Korea
| | - Sura Kim
- Department of Chemical and Biomolecular Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141 South Korea
| | - Jaemin Park
- Department of Chemical and Biomolecular Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141 South Korea
| | - Tae-Shin Kim
- Graduate School of Medical Science and Engineering, KAIST, Daejeon 34141 South Korea
| | - Raisa Kharbash
- Department of Chemical and Biomolecular Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141 South Korea.,KI for Health Science and Technology (KIHST), KAIST, Daejeon 34141 South Korea
| | - Eui-Cheol Shin
- Graduate School of Medical Science and Engineering, KAIST, Daejeon 34141 South Korea
| | - Kookheon Char
- School of Chemical and Biological Engineering, Seoul National University, Seoul 08826, South Korea
| | - Yoosik Kim
- Department of Chemical and Biomolecular Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141 South Korea.,KI for Health Science and Technology (KIHST), KAIST, Daejeon 34141 South Korea
| | - Sheng Li
- Department of Chemical and Biomolecular Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141 South Korea
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14
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Nguyen TA, Bieging-Rolett KT, Putoczki TL, Wicks IP, Attardi LD, Pang KC. SIDT2 RNA Transporter Promotes Lung and Gastrointestinal Tumor Development. iScience 2019; 20:14-24. [PMID: 31546103 PMCID: PMC6817685 DOI: 10.1016/j.isci.2019.09.009] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2018] [Revised: 08/20/2019] [Accepted: 09/05/2019] [Indexed: 02/07/2023] Open
Abstract
RNautophagy is a newly described type of selective autophagy whereby cellular RNAs are transported into lysosomes for degradation. This process involves the transmembrane protein SIDT2, which transports double-stranded RNA (dsRNA) across the endolysosomal membrane. We previously demonstrated that SIDT2 is a transcriptional target of p53, but its role in tumorigenesis, if any, is unclear. Unexpectedly, we show here that Sidt2−/− mice with concurrent oncogenic KrasG12D activation develop significantly fewer tumors than littermate controls in a mouse model of lung adenocarcinoma. Consistent with this observation, loss of SIDT2 also leads to enhanced survival and delayed tumor development in an Apcmin/+ mouse model of intestinal cancer. Within the intestine, Apcmin/+;Sidt2−/− mice display accumulation of dsRNA in association with increased phosphorylation of eIF2α and JNK as well as elevated rates of apoptosis. Taken together, our data demonstrate a role for SIDT2, and by extension RNautophagy, in promoting tumor development. Loss of the SIDT2 double-stranded RNA (dsRNA) transporter leads to accumulation of dsRNA in tissues is associated with increased apoptosis reduces tumor burden in mouse models of lung adenocarcinoma and intestinal cancer
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Affiliation(s)
- Tan A Nguyen
- The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia; Department of Medical Biology, University of Melbourne, Parkville, VIC, Australia
| | - Kathryn T Bieging-Rolett
- Department of Radiation Oncology, Stanford University School of Medicine, Stanford, CA, USA; Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
| | - Tracy L Putoczki
- The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia; Department of Medical Biology, University of Melbourne, Parkville, VIC, Australia
| | - Ian P Wicks
- The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia; Department of Medical Biology, University of Melbourne, Parkville, VIC, Australia
| | - Laura D Attardi
- Department of Radiation Oncology, Stanford University School of Medicine, Stanford, CA, USA; Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
| | - Ken C Pang
- The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia; Murdoch Children's Research Institute, Parkville, VIC, Australia; Department of Paediatrics, University of Melbourne, Parkville, VIC, Australia; Department of Psychiatry, University of Melbourne, Parkville, VIC, Australia.
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15
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Safran SA, Eckert DM, Leslie EA, Bass BL. PKR activation by noncanonical ligands: a 5'-triphosphate requirement versus antisense contamination. RNA (NEW YORK, N.Y.) 2019; 25:1192-1201. [PMID: 31239298 PMCID: PMC6800522 DOI: 10.1261/rna.071910.119] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/08/2019] [Accepted: 06/20/2019] [Indexed: 05/16/2023]
Abstract
Protein kinase RNA-activated (PKR) is an interferon-inducible kinase that is potently activated by long double-stranded RNA (dsRNA). In a previous study, we found that snoRNAs exhibit increased association with PKR in response to metabolic stress. While it was unclear if snoRNAs also activated PKR in cells, activation in vitro was observed. snoRNAs do not exhibit the double-stranded character typically required for activation of PKR, but some studies suggest such RNAs can activate PKR if triphosphorylated at the 5' terminus, or if they are able to form intermolecular dimers. To interrogate the mechanism of PKR activation by snoRNAs in vitro we focused on SNORD113. Using multiple methods for defining the 5'-phosphorylation state, we find that activation of PKR by SNORD113 does not require a 5'-triphosphate. Gel purification from a native gel followed by analysis using analytical ultracentrifugation showed that dimerization was also not responsible for activation. We isolated distinct conformers of SNORD113 from a native polyacrylamide gel and tracked the activating species to dsRNA formed from antisense RNA synthesized during in vitro transcription with T7 RNA polymerase. Similar studies with additional snoRNAs and small RNAs showed the generality of our results. Our studies suggest that a 5' triphosphate is not an activating ligand for PKR, and emphasize the insidious nature of antisense contamination.
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Affiliation(s)
- Sarah A Safran
- Department of Biochemistry, University of Utah, Salt Lake City, Utah 84112, USA
| | - Debra M Eckert
- Department of Biochemistry, University of Utah, Salt Lake City, Utah 84112, USA
| | - Evan A Leslie
- Department of Biochemistry, University of Utah, Salt Lake City, Utah 84112, USA
| | - Brenda L Bass
- Department of Biochemistry, University of Utah, Salt Lake City, Utah 84112, USA
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16
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Wang W, Tai W. RNA binding protein as monodisperse carriers for siRNA delivery. MEDICINE IN DRUG DISCOVERY 2019. [DOI: 10.1016/j.medidd.2019.100011] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022] Open
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17
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Mayo CB, Erlandsen H, Mouser DJ, Feinstein AG, Robinson VL, May ER, Cole JL. Structural Basis of Protein Kinase R Autophosphorylation. Biochemistry 2019; 58:2967-2977. [PMID: 31246429 DOI: 10.1021/acs.biochem.9b00161] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
The RNA-activated protein kinase, PKR, is a key mediator of the innate immunity response to viral infection. Viral double-stranded RNAs induce PKR dimerization and autophosphorylation. The PKR kinase domain forms a back-to-back dimer. However, intermolecular ( trans) autophosphorylation is not feasible in this arrangement. We have obtained PKR kinase structures that resolves this dilemma. The kinase protomers interact via the known back-to-back interface as well as a front-to-front interface that is formed by exchange of activation segments. Mutational analysis of the front-to-front interface support a functional role in PKR activation. Molecular dynamics simulations reveal that the activation segment is highly dynamic in the front-to-front dimer and can adopt conformations conducive to phosphoryl transfer. We propose a mechanism where back-to-back dimerization induces a conformational change that activates PKR to phosphorylate a "substrate" kinase docked in a front-to-front geometry. This mechanism may be relevant to related kinases that phosphorylate the eukaryotic initiation factor eIF2α.
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18
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Lee YS, Kunkeaw N, Lee YS. Protein kinase R and its cellular regulators in cancer: An active player or a surveillant? WILEY INTERDISCIPLINARY REVIEWS-RNA 2019; 11:e1558. [PMID: 31231984 DOI: 10.1002/wrna.1558] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/09/2019] [Revised: 05/24/2019] [Accepted: 05/28/2019] [Indexed: 12/12/2022]
Abstract
Protein kinase R (PKR), originally known as an antiviral protein, senses various stresses as well as pathogen-driven double-stranded RNAs. Thereby activated PKR provokes diverse downstream events, including eIF2α phosphorylation and nuclear factor kappa-light-chain-enhancer of activated B cells activation. Consequently, PKR induces apoptosis and inflammation, both of which are highly important in cancer as much as its original antiviral role. Therefore, cellular proteins and RNAs should tightly control PKR activity. PKR and its regulators are often dysregulated in cancer and it is undoubted that such dysregulation contributes to tumorigenesis. However, PKR's precise role in cancer is still in debate, due to incomprehensible and even contradictory data. In this review, we introduce important cellular PKR regulators and discuss about their roles in cancer. Among them, we pay particular attention to nc886, a PKR repressor noncoding RNA that has been identified relatively recently, because its expression pattern in cancer can explain interesting yet obscure oncologic aspects of PKR. Based on nc886 and its regulation of PKR, we have proposed a tumor surveillance model, which reconciles contradictory data about PKR in cancer. This article is categorized under: Regulatory RNAs/RNAi/Riboswitches > Regulatory RNAs RNA Interactions with Proteins and Other Molecules > Protein-RNA Interactions: Functional Implications.
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Affiliation(s)
- Yong Sun Lee
- Department of Cancer Biomedical Science, Graduate School of Cancer Science and Policy, National Cancer Center, Goyang, Korea
| | - Nawapol Kunkeaw
- Institute of Molecular Biosciences, Mahidol University, Nakhon Pathom, Thailand
| | - Yeon-Su Lee
- Division of Clinical Research, Research Institute, National Cancer Center, Goyang, Korea
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19
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Kaempfer R, Ilan L, Cohen-Chalamish S, Turgeman O, Namer LS, Osman F. Control of mRNA Splicing by Intragenic RNA Activators of Stress Signaling: Potential Implications for Human Disease. Front Genet 2019; 10:464. [PMID: 31139209 PMCID: PMC6527590 DOI: 10.3389/fgene.2019.00464] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2019] [Accepted: 04/30/2019] [Indexed: 11/13/2022] Open
Abstract
A critical step in the cellular stress response is transient activation of the RNA-dependent protein kinase PKR by double-helical RNA, resulting in down-regulation of protein synthesis through phosphorylation of the α chain of translation initiation factor eIF2, a major PKR substrate. However, intragenic elements of 100–200 nucleotides in length within primary transcripts of cellular genes, exemplified by the tumor necrosis factor (TNF)-α gene and fetal and adult globin genes, are capable of forming RNA structures that potently activate PKR and thereby strongly enhance mRNA splicing efficiency. By inducing nuclear eIF2α phosphorylation, these PKR activator elements enable highly efficient early spliceosome assembly yet do not impair translation of the mature spliced mRNA. The TNF-α RNA activator of PKR folds into a compact pseudoknot that is highly conserved within the phylogeny. Upon excision of β-globin first intron, the RNA activator of PKR, located in exon 1, is silenced through strand displacement by a short sequence within exon 2, restricting thereby the ability to activate PKR to the splicing process without impeding subsequent synthesis of β-globin essential for survival. This activator/silencer mechanism likewise controls splicing of α-globin pre-mRNA, but the exonic locations of PKR activator and silencer sequences are reversed, demonstrating evolutionary flexibility. Impaired splicing efficiency may underlie numerous human β-thalassemia mutations that map to the β-globin RNA activator of PKR or its silencer. Even where such mutations change the encoded amino acid sequence during subsequent translation, they carry the potential of first impairing PKR-dependent mRNA splicing or shutoff of PKR activation needed for optimal translation.
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Affiliation(s)
- Raymond Kaempfer
- Department of Biochemistry and Molecular Biology, The Institute for Medical Research Israel-Canada, The Hebrew University-Hadassah Medical School, Jerusalem, Israel
| | - Lena Ilan
- Department of Biochemistry and Molecular Biology, The Institute for Medical Research Israel-Canada, The Hebrew University-Hadassah Medical School, Jerusalem, Israel
| | - Smadar Cohen-Chalamish
- Department of Biochemistry and Molecular Biology, The Institute for Medical Research Israel-Canada, The Hebrew University-Hadassah Medical School, Jerusalem, Israel
| | - Orli Turgeman
- Department of Biochemistry and Molecular Biology, The Institute for Medical Research Israel-Canada, The Hebrew University-Hadassah Medical School, Jerusalem, Israel
| | - Lise Sarah Namer
- Department of Biochemistry and Molecular Biology, The Institute for Medical Research Israel-Canada, The Hebrew University-Hadassah Medical School, Jerusalem, Israel
| | - Farhat Osman
- Department of Biochemistry and Molecular Biology, The Institute for Medical Research Israel-Canada, The Hebrew University-Hadassah Medical School, Jerusalem, Israel
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20
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Kakiyama S, Tabara M, Nishibori Y, Moriyama H, Fukuhara T. Long DCL4-substrate dsRNAs efficiently induce RNA interference in plant cells. Sci Rep 2019; 9:6920. [PMID: 31061468 PMCID: PMC6502814 DOI: 10.1038/s41598-019-43443-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2018] [Accepted: 02/26/2019] [Indexed: 12/29/2022] Open
Abstract
RNA interference (RNAi) is induced by the direct transfer of double-stranded RNAs (dsRNAs) into protoplasts prepared from Arabidopsis thaliana seedlings. In this protoplast RNAi system, we compared the efficacies of various-sized dsRNAs (between 21 and 139 nucleotides [nt]) for inducing RNAi and assessed the dsRNA-cleaving activities of Dicer-like 3 (DCL3) and 4 (DCL4). After the direct transfer of dsRNAs into protoplasts, cleaved RNA products of 21 nt were detected from long 130- or 500-nt dsRNAs by DCL4 but not from 37-nt dsRNAs. These results indicate that DCL4 preferentially cleaves long dsRNAs in protoplasts, consistent with our previous biochemical data regarding the substrate specificity of DCL4. Direct transfer of long dsRNAs of approximately 130 nt into protoplasts induces RNAi much more effectively (by approximately 60- to 400-fold) than direct transfer of short 37-nt dsRNAs. Although transfer of 21-nt dsRNAs into protoplasts induced RNAi without DCL4 activity, the induction of RNAi was less effective (by approximately 0.01-fold) compared with long dsRNAs. These results indicate that cleavage of long dsRNAs exceeding 100 nt by DCL4 into 21-nt dsRNAs is essential for efficient induction of RNAi in plant cells.
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Affiliation(s)
- Sayaka Kakiyama
- Department of Applied Biological Sciences, Tokyo University of Agriculture and Technology, 3-5-8 Saiwaicho, Fuchu, Tokyo, 183-8509, Japan
| | - Midori Tabara
- Department of Applied Biological Sciences, Tokyo University of Agriculture and Technology, 3-5-8 Saiwaicho, Fuchu, Tokyo, 183-8509, Japan
| | - Yuki Nishibori
- Department of Applied Biological Sciences, Tokyo University of Agriculture and Technology, 3-5-8 Saiwaicho, Fuchu, Tokyo, 183-8509, Japan
| | - Hiromitsu Moriyama
- Department of Applied Biological Sciences, Tokyo University of Agriculture and Technology, 3-5-8 Saiwaicho, Fuchu, Tokyo, 183-8509, Japan
| | - Toshiyuki Fukuhara
- Department of Applied Biological Sciences, Tokyo University of Agriculture and Technology, 3-5-8 Saiwaicho, Fuchu, Tokyo, 183-8509, Japan. .,Institute of Global Innovation Research, Tokyo University of Agriculture and Technology, 3-5-8 Saiwaicho, Fuchu, Tokyo, 183-8509, Japan.
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21
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Schwartz SL, Conn GL. RNA regulation of the antiviral protein 2'-5'-oligoadenylate synthetase. WILEY INTERDISCIPLINARY REVIEWS-RNA 2019; 10:e1534. [PMID: 30989826 DOI: 10.1002/wrna.1534] [Citation(s) in RCA: 51] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/05/2019] [Revised: 03/12/2019] [Accepted: 03/14/2019] [Indexed: 12/25/2022]
Abstract
The innate immune system is a broad collection of critical intra- and extra-cellular processes that limit the infectivity of diverse pathogens. The 2'-5'-oligoadenylate synthetase (OAS) family of enzymes are important sensors of cytosolic double-stranded RNA (dsRNA) that play a critical role in limiting viral infection by activating the latent ribonuclease (RNase L) to halt viral replication and establish an antiviral state. Attesting to the importance of the OAS/RNase L pathway, diverse viruses have developed numerous distinct strategies to evade the effects of OAS activation. How OAS proteins are regulated by viral or cellular RNAs is not fully understood but several recent studies have provided important new insights into the molecular mechanisms of OAS activation by dsRNA. Other studies have revealed unanticipated features of RNA sequence and structure that strongly enhance activation of at least one OAS family member. While these discoveries represent important advances, they also underscore the fact that much remains to be learned about RNA-mediated regulation of the OAS/RNase L pathway. In particular, defining the full complement of RNA molecular signatures that activate OAS is essential to our understanding of how these proteins maximize their protective role against pathogens while still accurately discriminating host molecules to avoid inadvertent activation by cellular RNAs. A more complete knowledge of OAS regulation may also serve as a foundation for the development of novel antiviral therapeutic strategies and lead the way to a deeper understanding of currently unappreciated cellular functions of the OAS/RNase L pathway in the absence of infection. This article is categorized under: RNA in Disease and Development > RNA in Disease RNA Interactions with Proteins and Other Molecules > Protein-RNA Interactions: Functional Implications Translation > Translation Regulation.
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Affiliation(s)
- Samantha L Schwartz
- Department of Biochemistry, Emory University School of Medicine and Graduate Program in Biochemistry, Cell and Developmental Biology (BCDB), Atlanta, Georgia
| | - Graeme L Conn
- Department of Biochemistry, Emory University School of Medicine and Graduate Program in Biochemistry, Cell and Developmental Biology (BCDB), Atlanta, Georgia
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22
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Koul A, Deo S, Booy EP, Orriss GL, Genung M, McKenna SA. Impact of double-stranded RNA characteristics on the activation of human 2'-5'-oligoadenylate synthetase 2 (OAS2). Biochem Cell Biol 2019; 98:70-82. [PMID: 30965010 DOI: 10.1139/bcb-2019-0060] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Human 2'-5' oligoadenylate synthetases (OAS) are a family of interferon-inducible proteins that, upon activation by double-stranded RNA, polymerize ATP into 2'-5' linked oligoadenylates. In this study, we probed the RNA cofactor specificity of the two smallest isozymes, OAS1 and OAS2. First, we developed a strategy for the expression and purification of recombinant human OAS2 from eukaryotic cells and quantified the activity of the enzyme relative to OAS1 in vitro. We then confirmed that both OAS2 domains, as opposed to only the domain containing the canonical catalytic aspartic acid triad, are required for enzymatic activity. Enzyme kinetics of both OAS1 and OAS2 in the presence of a variety of RNA binding partners enabled characterization of the maximum reaction velocity and apparent RNA-protein affinity of activating RNAs. While in this study OAS1 can be catalytically activated by dsRNA of any length greater than 19 bp, OAS2 showed a marked increase in activity with increasing dsRNA length with a minimum requirement of 35 bp. Interestingly, activation of OAS2 was also more efficient when the dsRNA contained 3'-overhangs, despite no significant impact on binding affinity. Highly structured viral RNAs that are established OAS1 activators were not able to activate OAS2 enzymatic activity based on the lack of extended stretches of dsRNA of greater than 35 bp. Together these results may highlight distinct subsets of biological RNAs to which different human OAS isozymes respond.
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Affiliation(s)
- Amit Koul
- Department of Chemistry, University of Manitoba, Winnipeg, MB R3T 2N2, Canada
| | - Soumya Deo
- Alberta RNA Research and Training Institute, Department of Chemistry and Biochemistry, University of Lethbridge, Lethbridge, AB T1K 3M4, Canada
| | - Evan P Booy
- Department of Chemistry, University of Manitoba, Winnipeg, MB R3T 2N2, Canada
| | - George L Orriss
- Department of Chemistry, University of Manitoba, Winnipeg, MB R3T 2N2, Canada
| | - Matthew Genung
- Max Rady College of Medicine, Rady Faculty of Health Sciences, University of Manitoba, Winnipeg, MB, R3E 0W2, Canada
| | - Sean A McKenna
- Department of Chemistry, University of Manitoba, Winnipeg, MB R3T 2N2, Canada.,Department of Biochemistry and Medical Genetics, University of Manitoba, Winnipeg, MB R3T 2N2, Canada
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Abstract
Small silencing RNAs have provided powerful reverse genetics tools and have opened new areas of research. This introduction describes the use of RNAi to suppress expression of individual genes for loss-of-function analysis. It also summarizes methods for measuring specific and global changes in small RNA expression, as well as methods to inhibit the function of individual endogenous small RNA species such as miRNAs.
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24
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Wahid A, Hamzawy MA, Khalifa MMA, Gad GFM, Bekhit A, Abdelwahab SF. RNA protein kinase SNP at -226 C<T is a biomarker for the clearance of HCV among Egyptian patients. Immunol Invest 2019; 48:211-221. [PMID: 30080984 DOI: 10.1080/08820139.2018.1493496] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
BACKGROUND RNA-dependant protein kinase R (PKR) is a primary mediator in the defence mechanism of interferon against viral replication and pathogenesis during Hepatitis C virus (HCV) infection. In the present study, we have examined the role of Single Nucleotide Polymorphisms (SNPs) in the promoter region of PKR and the serum level of the same protein on the outcome of HCV-infected Egyptian patients. PATIENTS AND METHODS Genomic DNA was extracted from a total of 135 subjects, including 15 healthy controls, 40 HCV spontaneous resolvers (SRs), and 80 patients with chronic HCV infection. PKR genotyping was assessed using DNA sequencing. Finally, serum levels of PKR, TNF-α, INF-γ, and IL-10 were measured using ELISA technique. RESULTS Serum levels of PKR, TNF-α, and INF-γ showed a significant increase in SRs as compared to chronic HCV patients. On the other hand, serum levels of IL-10 were significantly higher in chronic HCV patients compared to SRs. The present study demonstrated two novel SNPs in the PKR promoter region: at -226 C/T and -141 C/G. The PKR SNP at -226 C < T correlated with HCV-infected patients (genotype 4a) outcome among Egyptians. Our data showed the unique presence of the TT genotype in SRs group (three patients: 7.5%) in PKR -226 C/T. Interestingly, subjects with the TT genotype were more likely to clear their HCV infection than those with the CC genotype. CONCLUSION Our work provides more detail about PKR gene polymorphism in HCV genotype 4a as a new clinical tool for anticipating HCV-4a infection outcome.
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Affiliation(s)
- Ahmed Wahid
- a Department of Pharmacology and Toxicology, Faculty of Pharmacy , Alexandria University , Alexandria , Egypt
| | - Mustafa A Hamzawy
- b Department of Biochemistry, Faculty of Pharmacy , Minia University , Minia , Egypt
| | - Mohamad M A Khalifa
- c Department of Pharmacology, Faculty of Pharmacy , Minia University , Minia , Egypt
| | - Gamal F M Gad
- d Department of Microbiology and Immunology, Faculty of Pharmacy , Minia University , Minia , Egypt
| | - Amany Bekhit
- b Department of Biochemistry, Faculty of Pharmacy , Minia University , Minia , Egypt
| | - Sayed F Abdelwahab
- e Department of Microbiology and Immunology, Faculty of Medicine , Minia University , Minia , Egypt
- f Department of Microbiology , College of Pharmacy, Taif University , KSA
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25
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Wang K, Peng Y, Fu W, Shen Z, Han Z. Key factors determining variations in RNA interference efficacy mediated by different double-stranded RNA lengths in Tribolium castaneum. INSECT MOLECULAR BIOLOGY 2019; 28:235-245. [PMID: 30325555 DOI: 10.1111/imb.12546] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Double-stranded RNA (dsRNA) length may affect RNA interference (RNAi) efficacy. Herein, variation in RNAi efficacy associated with dsRNA molecular length was confirmed via comparison of knockdown results following dsRNA injection into Tribolium castaneum. Through in vitro experiments with T. castaneum midgut, dsRNA accumulation in the midgut, degradation by midgut homogenates and persistence in haemolymph after injection were tested to determine the causes of RNAi efficacy variation. The comparative efficacies of dsRNAs were 480 bp ≈ 240 bp > 120 bp > 60 bp >> 21 bp. The combined midgut dsRNA accumulation and midgut homogenate-induced degradation analyses suggested cellular uptake to be the key barrier for 21 bp dsRNA functioning, but was likely not the main determinant of the variation in longer dsRNAs' (≥60 bp) bioactivity. In vitro RNAi experiment with T. castaneum midgut showed that long dsRNAs all significantly depleted the expression of corresponding genes, suggesting little variation in intracellular RNAi machinery's affinity for different dsRNA lengths. In vivo haemolymph content dynamics of different dsRNAs following injection indicated higher persistence of longer dsRNAs. In addition, comparison of the in vivo and in vitro RNAi efficacy also indicated the importance of haemolymph degradation. Thus, the varied efficacy of long dsRNAs resulted from their degradation by nucleases, which varied with dsRNA length.
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Affiliation(s)
- K Wang
- Department of Entomology, College of Plant Protection, Nanjing Agricultural University/The Key Laboratory of Integrated Management of Crop Diseases and Pests (Ministry of Education), Nanjing, China
| | - Y Peng
- Department of Entomology, College of Plant Protection, Nanjing Agricultural University/The Key Laboratory of Integrated Management of Crop Diseases and Pests (Ministry of Education), Nanjing, China
| | - W Fu
- Department of Entomology, College of Plant Protection, Nanjing Agricultural University/The Key Laboratory of Integrated Management of Crop Diseases and Pests (Ministry of Education), Nanjing, China
| | - Z Shen
- Department of Entomology, College of Plant Protection, Nanjing Agricultural University/The Key Laboratory of Integrated Management of Crop Diseases and Pests (Ministry of Education), Nanjing, China
| | - Z Han
- Department of Entomology, College of Plant Protection, Nanjing Agricultural University/The Key Laboratory of Integrated Management of Crop Diseases and Pests (Ministry of Education), Nanjing, China
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Yamada KE, Eckhert CD. Boric Acid Activation of eIF2α and Nrf2 Is PERK Dependent: a Mechanism that Explains How Boron Prevents DNA Damage and Enhances Antioxidant Status. Biol Trace Elem Res 2019; 188:2-10. [PMID: 30196486 DOI: 10.1007/s12011-018-1498-4] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/12/2018] [Accepted: 08/28/2018] [Indexed: 02/06/2023]
Abstract
Boron is abundant in vegetables, nuts, legumes, and fruit and intake is associated with reduced risk of cancer and DNA damage and increased antioxidant status. Blood boric acid (BA) levels are approximately 10 μM BA in men at the mean US boron intake. Treatment of DU-145 human prostate cancer cells with 10 μM BA stimulates phosphorylation of elongation initiation factor 2α (eIF2α) at Ser51 leading to activation of the eIF2α/ATF4 pathway which activates the DNA damage-inducible protein GADD34. In the present study, we used MEF WT and MEF PERK (±) cells to test the hypothesis that BA-activated eIF2α phosphorylation requires protein kinase RNA-like endoplasmic reticulum kinase (PERK) and activates Nrf2 and the antioxidant response element (ARE). BA (10 μM) increased phosphorylation of eIF2α Ser51 in MEF WT cells at 1 h, but not in MEF Perk -/- cells exposed for as long as 6 h. GCN2 kinase-dependent phosphorylation of eIF2α Ser51 was activated in MEF PERK -/- cells by amino acid starvation. Nrf2 phosphorylation is PERK dependent and when activated is translocated from the cytoplasm to the nucleus where it acts as a transcription factor for ARE. DU-145 cells were treated with 10 μM BA and Nrf2 measured by immunofluorescence. Cytoplasmic Nrf2 was translocated to the nucleus at 1.5-2 h in DU-145 and MEF WT cells, but not MEF PERK -/- cells. Real-time PCR was used to measure mRNA levels of three ARE genes (HMOX-1, NQO1, and GCLC). Treatment with 10 μM BA increased the mRNA levels of all three genes at 1-4 h in DU-145 cells and HMOX1 and GCLC in MEF WT cells. These results extend the known boric acid signaling pathway to ARE-regulated genes. The BA signaling pathway can be expressed using the schematic [BA + cADPR → cADPR-BA → [[ER]i Ca2+↓] → 3 pathways: PERK/eIF2αP → pathways ATF4 and Nrf2; and [[ER]i Ca2+↓] → ER stress → ATF6 pathway. This signaling pathway provides a framework that links many of the molecular changes that underpin the biological effects of boron intake.
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Affiliation(s)
- Kristin E Yamada
- Interdepartmental Program in Molecular Toxicology, University of California, Los Angeles, 90095, CA, USA
| | - Curtis D Eckhert
- Interdepartmental Program in Molecular Toxicology, University of California, Los Angeles, 90095, CA, USA.
- Department of Environmental Health Sciences, Fielding School of Public Health, University of California, 650 Charles E. Young Dr., Los Angeles, CA, 90095, USA.
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27
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Binding of norharmane with RNA reveals two thermodynamically different binding modes with opposing heat capacity changes. J Colloid Interface Sci 2019; 538:587-596. [DOI: 10.1016/j.jcis.2018.12.011] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2018] [Revised: 11/26/2018] [Accepted: 12/03/2018] [Indexed: 02/01/2023]
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Raja MAG, Katas H, Amjad MW. Design, mechanism, delivery and therapeutics of canonical and Dicer-substrate siRNA. Asian J Pharm Sci 2019; 14:497-510. [PMID: 32104477 PMCID: PMC7032099 DOI: 10.1016/j.ajps.2018.12.005] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2018] [Revised: 12/07/2018] [Accepted: 12/24/2018] [Indexed: 12/12/2022] Open
Abstract
Upon the discovery of RNA interference (RNAi), canonical small interfering RNA (siRNA) has been recognized to trigger sequence-specific gene silencing. Despite the benefits of siRNAs as potential new drugs, there are obstacles still to be overcome, including off-target effects and immune stimulation. More recently, Dicer substrate siRNA (DsiRNA) has been introduced as an alternative to siRNA. Similarly, it also is proving to be potent and target-specific, while rendering less immune stimulation. DsiRNA is 25–30 nucleotides in length, and is further cleaved and processed by the Dicer enzyme. As with siRNA, it is crucial to design and develop a stable, safe, and efficient system for the delivery of DsiRNA into the cytoplasm of targeted cells. Several polymeric nanoparticle systems have been well established to load DsiRNA for in vitro and in vivo delivery, thereby overcoming a major hurdle in the therapeutic uses of DsiRNA. The present review focuses on a comparison of siRNA and DsiRNA on the basis of their design, mechanism, in vitro and in vivo delivery, and therapeutics.
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Affiliation(s)
- Maria Abdul Ghafoor Raja
- Department of Pharmaceutics, Faculty of Pharmacy, Northern Border University, Rafha 73211, Saudi Arabia
| | - Haliza Katas
- Centre for Drug Delivery Research, Faculty of Pharmacy, Universiti Kebangsaan Malaysia, Kuala Lumpur 50300, Malaysia
| | - Muhammad Wahab Amjad
- Department of Pharmaceutics, Faculty of Pharmacy, Northern Border University, Rafha 73211, Saudi Arabia
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Kim D, Kim H, Han S, Scatena M, Kim DH, Lee JB. Immunostimulatory Effects Triggered by Self-Assembled Microspheres with Tandem Repeats of Polymerized RNA Strands. Adv Healthc Mater 2019; 8:e1801395. [PMID: 30657652 DOI: 10.1002/adhm.201801395] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2018] [Revised: 01/08/2019] [Indexed: 12/19/2022]
Abstract
Self-assembled RNA particles have been exploited widely to maximize the therapeutic potential of RNA. However, the immune response via RNA particles is not fully understood. In addition, the investigation of the immunogenicity from RNA-based particles is required owing to inherent immunostimulatory effects of RNA for clinical translation. To examine the immune stimulating potency, rationally designed microsized RNA particles, called RNA microspheres (RMSs), are generated with single or double strands via rolling circle transcription. The RMSs show an exceptional stability in the presence of serum, while they are selectively degraded under endolysosomal conditions. With precisely controlled size, both RMSs are successfully taken up by macrophages. Unlike the nature of RNA fragments, RMSs induce only basal-level expression of inflammatory cytokines as well as type I interferon from macrophages, suggesting that RMSs are immunocompatible in the therapeutic dose range. Taken together, this study could help accelerate clinical translation and broaden the applicability of the self-assembled RNA-based particles without being limited by their potential immunotoxicity, while a systematic controllability study observing the release of RNA fragments from RMSs would provide self-assembled RNA-based structures with a great potential for immunomodulation.
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Affiliation(s)
- Dajeong Kim
- Department of Chemical Engineering; University of Seoul; Seoul 02504 Republic of Korea
| | - Hyejin Kim
- Department of Chemical Engineering; University of Seoul; Seoul 02504 Republic of Korea
- Department of Bioengineering; University of Washington; Seattle WA 98195 USA
| | - Sangwoo Han
- Department of Chemical Engineering; University of Seoul; Seoul 02504 Republic of Korea
| | - Marta Scatena
- Department of Bioengineering; University of Washington; Seattle WA 98195 USA
- Institute of Stem Cell and Regenerative Medicine; University of Washington; Seattle WA 98109 USA
| | - Deok-Ho Kim
- Department of Bioengineering; University of Washington; Seattle WA 98195 USA
- Institute of Stem Cell and Regenerative Medicine; University of Washington; Seattle WA 98109 USA
| | - Jong Bum Lee
- Department of Chemical Engineering; University of Seoul; Seoul 02504 Republic of Korea
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30
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Endornaviruses: persistent dsRNA viruses with symbiotic properties in diverse eukaryotes. Virus Genes 2019; 55:165-173. [DOI: 10.1007/s11262-019-01635-5] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2018] [Accepted: 01/07/2019] [Indexed: 10/27/2022]
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31
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Okamoto K, Rausch JW, Wakashin H, Fu Y, Chung JY, Dummer PD, Shin MK, Chandra P, Suzuki K, Shrivastav S, Rosenberg AZ, Hewitt SM, Ray PE, Noiri E, Le Grice SFJ, Hoek M, Han Z, Winkler CA, Kopp JB. APOL1 risk allele RNA contributes to renal toxicity by activating protein kinase R. Commun Biol 2018; 1:188. [PMID: 30417125 PMCID: PMC6220249 DOI: 10.1038/s42003-018-0188-2] [Citation(s) in RCA: 50] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2018] [Accepted: 10/03/2018] [Indexed: 01/09/2023] Open
Abstract
APOL1 risk alleles associate with chronic kidney disease in African Americans, but the mechanisms remain to be fully understood. We show that APOL1 risk alleles activate protein kinase R (PKR) in cultured cells and transgenic mice. This effect is preserved when a premature stop codon is introduced to APOL1 risk alleles, suggesting that APOL1 RNA but not protein is required for the effect. Podocyte expression of APOL1 risk allele RNA, but not protein, in transgenic mice induces glomerular injury and proteinuria. Structural analysis of the APOL1 RNA shows that the risk variants possess secondary structure serving as a scaffold for tandem PKR binding and activation. These findings provide a mechanism by which APOL1 variants damage podocytes and suggest novel therapeutic strategies.
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Affiliation(s)
- Koji Okamoto
- Kidney Disease Section, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, 9000 Rockville Pike, Bethesda, MD, 20892, USA
- Division of Nephrology, Endocrinology and Vascular Medicine, Department of Medicine, Tohoku University Hospital, 1-1 Seiryo-machi, Aoba-ku, Sendai, Miyagi, 980-8574, Japan
- Department of Nephrology, Endocrinology, Hemodialysis & Apheresis, University Hospital, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 133-8655, Japan
| | - Jason W Rausch
- Reverse Transcriptase Biochemistry Section, Basic Research Program, Frederick National Laboratory for Cancer Research, 1050 Boyle Street, Frederick, MD, 21702, USA
| | - Hidefumi Wakashin
- Kidney Disease Section, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, 9000 Rockville Pike, Bethesda, MD, 20892, USA
| | - Yulong Fu
- Children's National Health System, 111 Michigan Ave NW, Washington, DC, 20010, USA
| | - Joon-Yong Chung
- Experimental Pathology Lab, Laboratory of Pathology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, 9000 Rockville Pike, Bethesda, MD, 20892, USA
| | - Patrick D Dummer
- Kidney Disease Section, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, 9000 Rockville Pike, Bethesda, MD, 20892, USA
| | - Myung K Shin
- Merck Research Laboratories, Merck and Co., Inc., 2000 Galloping Hill Rd, Kenilworth, NJ, 07033, USA
| | - Preeti Chandra
- Division of Nephrology, Department of Medicine, University of Maryland School of Medicine, 655 W. Baltimore Street, Baltimore, MD, 21201, USA
| | - Kosuke Suzuki
- Division of Nephrology, Endocrinology and Vascular Medicine, Department of Medicine, Tohoku University Hospital, 1-1 Seiryo-machi, Aoba-ku, Sendai, Miyagi, 980-8574, Japan
| | - Shashi Shrivastav
- Kidney Disease Section, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, 9000 Rockville Pike, Bethesda, MD, 20892, USA
| | - Avi Z Rosenberg
- Department of Pathology, Johns Hopkins Medical Institutions, 720 Rutland Avenue, Baltimore, MD, 21287, USA
| | - Stephen M Hewitt
- Experimental Pathology Lab, Laboratory of Pathology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, 9000 Rockville Pike, Bethesda, MD, 20892, USA
| | - Patricio E Ray
- Children's National Health System, 111 Michigan Ave NW, Washington, DC, 20010, USA
| | - Eisei Noiri
- Department of Nephrology, Endocrinology, Hemodialysis & Apheresis, University Hospital, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 133-8655, Japan
| | - Stuart F J Le Grice
- Reverse Transcriptase Biochemistry Section, Basic Research Program, Frederick National Laboratory for Cancer Research, 1050 Boyle Street, Frederick, MD, 21702, USA
| | - Maarten Hoek
- Merck Research Laboratories, Merck and Co., Inc., 2000 Galloping Hill Rd, Kenilworth, NJ, 07033, USA
| | - Zhe Han
- Children's National Health System, 111 Michigan Ave NW, Washington, DC, 20010, USA
| | - Cheryl A Winkler
- Basic Research Laboratory, Center for Cancer Research, National Cancer Institute, Leidos Biomedical Research, Frederick National Laboratory, 8560 Progress Dr., Frederick, MD, 21702, USA
| | - Jeffrey B Kopp
- Kidney Disease Section, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, 9000 Rockville Pike, Bethesda, MD, 20892, USA.
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Kaempfer R, Namer LS, Osman F, Ilan L. Control of mRNA splicing by noncoding intragenic RNA elements that evoke a cellular stress response. Int J Biochem Cell Biol 2018; 105:20-23. [PMID: 30282053 DOI: 10.1016/j.biocel.2018.09.021] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2018] [Revised: 09/25/2018] [Accepted: 09/27/2018] [Indexed: 11/15/2022]
Abstract
Once activated by double-helical RNA, mammalian RNA-dependent stress protein kinase, PKR, phosphorylates its substrate, translation initiation factor eIF2α, to inhibit translation. eIF2α phosphorylation is critical for mounting a cellular stress response. We describe short, 100-200 nucleotide elements within cellular genes that, once transcribed, form RNA structures that potently activate PKR in the vicinity of the RNA and thereby tightly regulate gene expression in cis. Intragenic RNA activators of PKR can (a) attenuate translation of the encoded mRNA by activating PKR and inducing eIF2α phosphorylation, exemplified by the IFN-γ gene, or (b) greatly enhance mRNA splicing efficiency by activating PKR and inducing nuclear eIF2α phosphorylation, thus enabling efficient early spliceosome assembly, exemplified by the adult and fetal globin genes and the TNF-α gene that activates PKR through an RNA pseudoknot conserved from fish to humans. These opposite outcomes considerably extend the potential scope of gene regulation by these novel RNA elements.
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Affiliation(s)
- Raymond Kaempfer
- Department of Biochemistry and Molecular Biology, Faculty of Medicine, The Hebrew University, Jerusalem, Israel.
| | - Lise Sarah Namer
- Department of Biochemistry and Molecular Biology, Faculty of Medicine, The Hebrew University, Jerusalem, Israel
| | - Farhat Osman
- Department of Biochemistry and Molecular Biology, Faculty of Medicine, The Hebrew University, Jerusalem, Israel
| | - Lena Ilan
- Department of Biochemistry and Molecular Biology, Faculty of Medicine, The Hebrew University, Jerusalem, Israel
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33
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Meng L, Xu W, Zhu Y, Zhang N, Shao C, Liu Y, Chen S. Molecular characterization and expression analysis of strbp in Chinese tongue sole (Cynoglossus semilaevis). Theriogenology 2018; 118:225-232. [DOI: 10.1016/j.theriogenology.2018.06.001] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2017] [Revised: 05/31/2018] [Accepted: 06/01/2018] [Indexed: 12/11/2022]
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34
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Defining the Role of Stress Granules in Innate Immune Suppression by the Herpes Simplex Virus 1 Endoribonuclease VHS. J Virol 2018; 92:JVI.00829-18. [PMID: 29793959 DOI: 10.1128/jvi.00829-18] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2018] [Accepted: 05/16/2018] [Indexed: 12/20/2022] Open
Abstract
In response to virus-induced shutoff host protein synthesis, dynamic aggregates containing mRNA, RNA-binding proteins and translation factors termed stress granules (SGs) often accumulate within the cytoplasm. SGs typically form following phosphorylation and inactivation of the eukaryotic translation initiation factor 2α (eIF2α), a substrate of the double-stranded RNA (dsRNA)-activated kinase protein kinase R (PKR). The detection of innate immune sensors and effectors like PKR at SGs suggests a role in pathogen nucleic acid sensing. However, the functional importance of SGs in host innate responses is unclear and has primarily been examined in response to infection with select RNA viruses. During infection with the DNA virus herpes simplex virus 1 (HSV-1), the virus-encoded virion host shutoff (VHS) endoribonuclease is required to restrict interferon production, PKR activation, and SG formation, although the relationship between these activities remains incompletely understood. Here, we show that in cells infected with a VHS-deficient HSV-1 (ΔVHS) dsRNA accumulated and localized to SGs. Surprisingly, formation of dsRNA and its concentration at SGs was not required for beta interferon mRNA induction, indicating that suppression of type I interferon induction by VHS does not stem from its control of dsRNA accumulation. Instead, STING signaling downstream of cGMP-AMP synthase (cGAS)-dependent DNA sensing is required for beta interferon induction. In contrast, significantly less PKR activation is observed when SG assembly is disrupted by ISRIB, an inhibitor of phosphorylated eIF2α-mediated translation repression, or depleting SG scaffolding proteins G3BP1 or TIA1. This demonstrates that PKR activation is intimately linked to SG formation and that SGs form important hubs to potentiate PKR activation during infection.IMPORTANCE Formation of cytoplasmic stress granules that are enriched for innate immune sensors and effectors is suppressed during many viral infections. It is unclear, however, to what extent this is a side effect of viral efforts to maintain protein synthesis or intentional disruption of a hub for innate immune sensing. In this study, we utilize a herpes simplex virus 1 mutant lacking the RNA nuclease VHS which upon infection induces SGs, PKR activation, and beta interferon to address this question. We show that dsRNA is localized to SGs and that SGs can function to promote PKR activation in the context of a DNA virus infection, but we find no evidence to support their importance for interferon induction during HSV-1 infection.
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Lackey L, Coria A, Woods C, McArthur E, Laederach A. Allele-specific SHAPE-MaP assessment of the effects of somatic variation and protein binding on mRNA structure. RNA (NEW YORK, N.Y.) 2018; 24:513-528. [PMID: 29317542 PMCID: PMC5855952 DOI: 10.1261/rna.064469.117] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/06/2017] [Accepted: 01/04/2018] [Indexed: 05/22/2023]
Abstract
The impact of inherited and somatic mutations on messenger RNA (mRNA) structure remains poorly understood. Recent technological advances that leverage next-generation sequencing to obtain experimental structure data, such as SHAPE-MaP, can reveal structural effects of mutations, especially when these data are incorporated into structure modeling. Here, we analyze the ability of SHAPE-MaP to detect the relatively subtle structural changes caused by single-nucleotide mutations. We find that allele-specific sorting greatly improved our detection ability. Thus, we used SHAPE-MaP with a novel combination of clone-free robotic mutagenesis and allele-specific sorting to perform a rapid, comprehensive survey of noncoding somatic and inherited riboSNitches in two cancer-associated mRNAs, TPT1 and LCP1 Using rigorous thermodynamic modeling of the Boltzmann suboptimal ensemble, we identified a subset of mutations that change TPT1 and LCP1 RNA structure, with approximately 14% of all variants identified as riboSNitches. To confirm that these in vitro structures were biologically relevant, we tested how dependent TPT1 and LCP1 mRNA structures were on their environments. We performed SHAPE-MaP on TPT1 and LCP1 mRNAs in the presence or absence of cellular proteins and found that both mRNAs have similar overall folds in all conditions. RiboSNitches identified within these mRNAs in vitro likely exist under biological conditions. Overall, these data reveal a robust mRNA structural landscape where differences in environmental conditions and most sequence variants do not significantly alter RNA structural ensembles. Finally, predicting riboSNitches in mRNAs from sequence alone remains particularly challenging; these data will provide the community with benchmarks for further algorithmic development.
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Affiliation(s)
- Lela Lackey
- Department of Biology, University of North Carolina, Chapel Hill, North Carolina 27599, USA
| | - Aaztli Coria
- Department of Biology, University of North Carolina, Chapel Hill, North Carolina 27599, USA
| | - Chanin Woods
- Department of Biology, University of North Carolina, Chapel Hill, North Carolina 27599, USA
| | - Evonne McArthur
- School of Medicine, Vanderbilt University, Nashville, Tennessee 37232, USA
| | - Alain Laederach
- Department of Biology, University of North Carolina, Chapel Hill, North Carolina 27599, USA
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Namer LS, Osman F, Banai Y, Masquida B, Jung R, Kaempfer R. An Ancient Pseudoknot in TNF-α Pre-mRNA Activates PKR, Inducing eIF2α Phosphorylation that Potently Enhances Splicing. Cell Rep 2018; 20:188-200. [PMID: 28683312 DOI: 10.1016/j.celrep.2017.06.035] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2017] [Revised: 05/15/2017] [Accepted: 06/12/2017] [Indexed: 12/22/2022] Open
Abstract
Tumor necrosis factor alpha (TNF-α) is expressed promptly during inflammatory responses. Efficient TNF-α mRNA splicing is achieved through a 3' UTR element that activates RNA-dependent eIF2α protein kinase (PKR). The TNF-α RNA activator, we show, folds into a pseudoknot conserved from teleost fish to humans, critical for PKR activation and mRNA splicing. The pseudoknot constrains the RNA into two double-helical stacks having parallel axes, permitting facile PKR dimerization and trans-autophosphorylation needed for kinase activation. Mutations show that the PKR activator potently enhances splicing without inhibiting translation. eIF2α phosphorylation represses translation and is essential for coping with cellular stress, yet PKR-enabled TNF mRNA splicing depends strictly on eIF2α phosphorylation. Indeed, eIF2α phosphorylation at Serine51 is necessary and sufficient to achieve highly efficient splicing, extending its role from negative control of translation to positive control of splicing. This mechanism, operational in human peripheral blood mononuclear cells (PBMCs), links stress signaling to protective immunity through TNF mRNA splicing rendered efficient upon eIF2α phosphorylation.
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Affiliation(s)
- Lise Sarah Namer
- Department of Biochemistry and Molecular Biology, Institute of Medical Research Israel-Canada, The Hebrew University-Hadassah Medical School, Jerusalem 9112102, Israel
| | - Farhat Osman
- Department of Biochemistry and Molecular Biology, Institute of Medical Research Israel-Canada, The Hebrew University-Hadassah Medical School, Jerusalem 9112102, Israel
| | - Yona Banai
- Department of Biochemistry and Molecular Biology, Institute of Medical Research Israel-Canada, The Hebrew University-Hadassah Medical School, Jerusalem 9112102, Israel
| | - Benoît Masquida
- Génétique Moléculaire Génomique Microbiologie, CNRS-University of Strasbourg, Strasbourg 67084, France
| | - Rodrigo Jung
- Department of Biochemistry and Molecular Biology, Institute of Medical Research Israel-Canada, The Hebrew University-Hadassah Medical School, Jerusalem 9112102, Israel
| | - Raymond Kaempfer
- Department of Biochemistry and Molecular Biology, Institute of Medical Research Israel-Canada, The Hebrew University-Hadassah Medical School, Jerusalem 9112102, Israel.
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Takahashi H, Kozhuharova A, Sharma H, Hirose M, Ohyama T, Fasolo F, Yamazaki T, Cotella D, Santoro C, Zucchelli S, Gustincich S, Carninci P. Identification of functional features of synthetic SINEUPs, antisense lncRNAs that specifically enhance protein translation. PLoS One 2018; 13:e0183229. [PMID: 29414979 PMCID: PMC5802440 DOI: 10.1371/journal.pone.0183229] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2017] [Accepted: 08/01/2017] [Indexed: 12/26/2022] Open
Abstract
SINEUPs are antisense long noncoding RNAs, in which an embedded SINE B2 element UP-regulates translation of partially overlapping target sense mRNAs. SINEUPs contain two functional domains. First, the binding domain (BD) is located in the region antisense to the target, providing specific targeting to the overlapping mRNA. Second, the inverted SINE B2 represents the effector domain (ED) and enhances translation. To adapt SINEUP technology to a broader number of targets, we took advantage of a high-throughput, semi-automated imaging system to optimize synthetic SINEUP BD and ED design in HEK293T cell lines. Using SINEUP-GFP as a model SINEUP, we extensively screened variants of the BD to map features needed for optimal design. We found that most active SINEUPs overlap an AUG-Kozak sequence. Moreover, we report our screening of the inverted SINE B2 sequence to identify active sub-domains and map the length of the minimal active ED. Our synthetic SINEUP-GFP screening of both BDs and EDs constitutes a broad test with flexible applications to any target gene of interest.
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Affiliation(s)
- Hazuki Takahashi
- RIKEN Center for Life Science Technologies, Division of Genomic Technologies, Yokohama, Kanagawa, Japan
| | - Ana Kozhuharova
- RIKEN Center for Life Science Technologies, Division of Genomic Technologies, Yokohama, Kanagawa, Japan
| | - Harshita Sharma
- RIKEN Center for Life Science Technologies, Division of Genomic Technologies, Yokohama, Kanagawa, Japan
| | - Masakazu Hirose
- RIKEN Center for Life Science Technologies, Division of Genomic Technologies, Yokohama, Kanagawa, Japan
| | - Takako Ohyama
- RIKEN Center for Life Science Technologies, Division of Structural and Synthetic Biology, Yokohama, Kanagawa, Japan
| | - Francesca Fasolo
- Area of Neuroscience, Scuola Internazionale Superiore di Studi Avanzati, Trieste, Italy
| | - Toshio Yamazaki
- RIKEN Center for Life Science Technologies, Division of Structural and Synthetic Biology, Yokohama, Kanagawa, Japan
| | - Diego Cotella
- Department of Health Sciences, Università del Piemonte Orientale, Novara, Italy
| | - Claudio Santoro
- Department of Health Sciences & IRCAD, Università del Piemonte Orientale, Novara, Italy
| | - Silvia Zucchelli
- Area of Neuroscience, Scuola Internazionale Superiore di Studi Avanzati, Trieste, Italy
- Department of Health Sciences, Università del Piemonte Orientale, Novara, Italy
| | - Stefano Gustincich
- Area of Neuroscience, Scuola Internazionale Superiore di Studi Avanzati, Trieste, Italy
- Department of Neuroscience and Brain Technologies, Istituto Italiano di Tecnologia, Genova, Italy
| | - Piero Carninci
- RIKEN Center for Life Science Technologies, Division of Genomic Technologies, Yokohama, Kanagawa, Japan
- TransSINE Technologies, Yokohama, Kanagawa, Japan
- * E-mail:
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Shirinfar B, Seema H, Ahmed N. Charged probes: turn-on selective fluorescence for RNA. Org Biomol Chem 2018; 16:164-168. [DOI: 10.1039/c7ob02423a] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Imidazolium-based charged fluorescent probes for the selective in vitro and in vivo recognition of RNA over other biomolecules.
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Affiliation(s)
| | - Humaira Seema
- Institute of Chemical Sciences
- University of Peshawar
- Pakistan
| | - Nisar Ahmed
- School of Chemistry
- Cardiff University
- Cardiff
- UK
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Abstract
Although the antiviral kinase PKR was originally characterized as a double-stranded RNA activated enzyme it can be stimulated by RNAs containing limited secondary structure. Single-stranded regions in such RNAs contribute to binding and activation but the mechanism is not understood. Here, we demonstrate that single-stranded RNAs bind to PKR with micromolar dissociation constants and can induce activation. Addition of a 5'-triphosphate slightly enhances binding affinity. Single-stranded RNAs also activate PKR constructs lacking the double-stranded RNA binding domain and bind to a basic region adjacent to the N-terminus of the kinase. However, the isolated kinase is not activated by and does not bind single-stranded RNA. Photocrosslinking measurements demonstrate that that the basic region interacts with RNA in the context of full length PKR. We propose that bivalent interactions with the double stranded RNA binding domain and the basic region underlie the ability of RNAs containing limited structure to activate PKR by enhancing binding affinity and thereby increasing the population of productive complexes containing two PKRs bound to a single RNA.
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40
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Ghatak S, Markwald RR, Hascall VC, Dowling W, Lottes RG, Baatz JE, Beeson G, Beeson CC, Perrella MA, Thannickal VJ, Misra S. Transforming growth factor β1 (TGFβ1) regulates CD44V6 expression and activity through extracellular signal-regulated kinase (ERK)-induced EGR1 in pulmonary fibrogenic fibroblasts. J Biol Chem 2017; 292:10465-10489. [PMID: 28389562 DOI: 10.1074/jbc.m116.752451] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2016] [Revised: 04/06/2017] [Indexed: 01/06/2023] Open
Abstract
The appearance of myofibroblasts is generally thought to be the underlying cause of the fibrotic changes that underlie idiopathic pulmonary fibrosis. However, the cellular/molecular mechanisms that account for the fibroblast-myofibroblast differentiation/activation in idiopathic pulmonary fibrosis remain poorly understood. We investigated the functional role of hyaluronan receptor CD44V6 (CD44 containing variable exon 6 (v6)) for differentiation of lung fibroblast to myofibroblast phenotype. Increased hyaluronan synthesis and CD44 expression have been detected in numerous fibrotic organs. Previously, we found that the TGFβ1/CD44V6 pathway is important in lung myofibroblast collagen-1 and α-smooth-muscle actin synthesis. Because increased EGR1 (early growth response-1) expression has been shown to appear very early and nearly coincident with the expression of CD44V6 found after TGFβ1 treatment, we investigated the mechanism(s) of regulation of CD44V6 expression in lung fibroblasts by TGFβ1. TGFβ1-mediated CD44V6 up-regulation was initiated through EGR1 via ERK-regulated transcriptional activation. We showed that TGFβ1-induced CD44V6 expression is through EGR1-mediated AP-1 (activator protein-1) activity and that the EGR1- and AP-1-binding sites in the CD44v6 promoter account for its responsiveness to TGFβ1 in lung fibroblasts. We also identified a positive-feedback loop in which ERK/EGR1 signaling promotes CD44V6 splicing and found that CD44V6 then sustains ERK signaling, which is important for AP-1 activity in lung fibroblasts. Furthermore, we identified that HAS2-produced hyaluronan is required for CD44V6 and TGFβRI co-localization and subsequent CD44V6/ERK1/EGR1 signaling. These results demonstrate a novel positive-feedback loop that links the myofibroblast phenotype to TGFβ1-stimulated CD44V6/ERK/EGR1 signaling.
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Affiliation(s)
- Shibnath Ghatak
- From the Department of Regenerative Medicine and Cell Biology, Medical University of South Carolina, Charleston, South Carolina 29425,
| | - Roger R Markwald
- From the Department of Regenerative Medicine and Cell Biology, Medical University of South Carolina, Charleston, South Carolina 29425
| | - Vincent C Hascall
- the Department of Biomedical Engineering, Cleveland Clinic, Cleveland, Ohio 44195
| | - William Dowling
- From the Department of Regenerative Medicine and Cell Biology, Medical University of South Carolina, Charleston, South Carolina 29425.,the College of Charleston, Charleston, South Carolina 29424
| | | | | | - Gyada Beeson
- Drug Discovery and Biomedical sciences, Medical University of South Carolina, Charleston, South Carolina 29425
| | - Craig C Beeson
- Drug Discovery and Biomedical sciences, Medical University of South Carolina, Charleston, South Carolina 29425
| | - Mark A Perrella
- the Division of Pulmonary and Critical Care Medicine, Department of Medicine, and the Department of Pediatric Newborn Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts 02115, and
| | - Victor J Thannickal
- the Division of Pulmonary, Allergy, and Critical Care Medicine, University of Alabama at Birmingham, Birmingham, Alabama 35294-0006
| | - Suniti Misra
- From the Department of Regenerative Medicine and Cell Biology, Medical University of South Carolina, Charleston, South Carolina 29425,
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41
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PKR activation and eIF2α phosphorylation mediate human globin mRNA splicing at spliceosome assembly. Cell Res 2017; 27:688-704. [PMID: 28374749 DOI: 10.1038/cr.2017.39] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2016] [Revised: 11/20/2016] [Accepted: 12/30/2016] [Indexed: 02/01/2023] Open
Abstract
Short elements in mammalian mRNA can control gene expression by activating the RNA-dependent protein kinase PKR that attenuates translation by phosphorylating cytoplasmic eukaryotic initiation factor 2α (eIF2α). We demonstrate a novel, positive role for PKR activation and eIF2α phosphorylation in human globin mRNA splicing. PKR localizes in splicing complexes and associates with splicing factor SC35. Splicing and early-stage spliceosome assembly on β-globin pre-mRNA depend strictly on activation of PKR by a codon-containing RNA fragment within exon 1 and on phosphorylation of nuclear eIF2α on Serine 51. Nonphosphorylatable mutant eIF2αS51A blocked β-globin mRNA splicing in cells and nuclear extract. Mutations of the β-globin RNA activator abrogated PKR activation and profoundly affected mRNA splicing efficiency. PKR depletion abrogated splicing and spliceosome assembly; recombinant PKR effectively restored splicing. Excision of the first intron of β-globin induces strand displacement within the RNA activator of PKR by a sequence from exon 2, a structural rearrangement that silences the ability of spliced β-globin mRNA to activate PKR. Thus, the ability to activate PKR is transient, serving solely to enable splicing. α-Globin pre-mRNA splicing is controlled likewise but positions of PKR activator and silencer are reversed, demonstrating evolutionary flexibility in how PKR activation regulates globin mRNA splicing through eIF2α phosphorylation.
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42
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Weng Y, Shi Y, Xia X, Zhou W, Wang H, Wang C. A multi-shRNA vector enhances the silencing efficiency of exogenous and endogenous genes in human cells. Oncol Lett 2017; 13:1553-1562. [PMID: 28454290 PMCID: PMC5403481 DOI: 10.3892/ol.2017.5672] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2015] [Accepted: 09/27/2016] [Indexed: 01/10/2023] Open
Abstract
RNA interference (RNAi) is a powerful technology for suppressing gene function. In most studies, small interfering RNAs (siRNAs) consist of one short hairpin RNA (shRNA) and, therefore, are often unable to achieve loss-of-function of their target genes. In the current study, an RNAi vector containing three shRNAs under the control of three RNA polymerase III U6 promoters was constructed. RNAi vectors containing one or two shRNAs were generated for comparisons. A pilot study targeting exogenously expressed DsRed in the HEK293 cell line revealed promising effects and a high selectivity for the multi-shRNA RNAi vector. Akt2 is constitutively expressed in cultured SKOV3 human ovarian cancer cells, and the multi-shRNA RNAi vector showed a strong efficiency for downregulating the expression of Akt2 in these cells, with no apparent interferon response. In addition, the Akt2-3shRNA vector, containing three shRNAs targeting Akt2, showed the best effect of all the shRNA vectors in reversing paclitaxel-induced resistance in SKOV3 cells. This study developed a widely applicable resource for enhancing the efficiency of gene silencing and a novel technique for performing complex loss-of-function screens in mammalian cells.
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Affiliation(s)
- Yanjie Weng
- Cancer Biology Research Center, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430030, P.R. China
| | - Ying Shi
- Cancer Biology Research Center, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430030, P.R. China
| | - Xi Xia
- Cancer Biology Research Center, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430030, P.R. China.,Department of Gynecology and Obstetrics, Affiliated Shenzhen Nanshan Hospital, Guangdong Medical College, Shenzhen, Guangdong 518052, P.R. China
| | - Wenjuan Zhou
- Cancer Biology Research Center, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430030, P.R. China
| | - Hongyan Wang
- Cancer Biology Research Center, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430030, P.R. China
| | - Changyu Wang
- Cancer Biology Research Center, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430030, P.R. China
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43
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Masuda T, Wan J, Yerrabelli A, Berlinicke C, Kallman A, Qian J, Zack DJ. Off Target, but Sequence-Specific, shRNA-Associated Trans-Activation of Promoter Reporters in Transient Transfection Assays. PLoS One 2016; 11:e0167867. [PMID: 27977714 PMCID: PMC5158200 DOI: 10.1371/journal.pone.0167867] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2016] [Accepted: 11/21/2016] [Indexed: 11/23/2022] Open
Abstract
Transient transfection promoter reporter assays are commonly used in the study of transcriptional regulation, and can be used to define and characterize both cis-acting regulatory sequences and trans-acting factors. In the process of using a variety of reporter assays designed to study regulation of the rhodopsin (rho) promoter, we discovered that rhodopsin promoter-driven reporter expression could be activated by certain species of shRNA in a gene-target-independent but shRNA sequence-specific manner, suggesting involvement of a specific shRNA associated pathway. Interestingly, the shRNA-mediated increase of rhodopsin promoter activity was synergistically enhanced by the rhodopsin transcriptional regulators CRX and NRL. Additionally, the effect was cell line-dependent, suggesting that this pathway requires the expression of cell-type specific factors. Since microRNA (miRNA) and interferon response-mediated processes have been implicated in RNAi off-target phenomena, we performed miRNA and gene expression profiling on cells transfected with shRNAs that do target a specific gene but have varied effects on rho reporter expression in order to identify transcripts whose expression levels are associated with shRNA induced rhodopsin promoter reporter activity. We identified a total of 50 miRNA species, and by microarray analysis, 320 protein-coding genes, some of which were predicted targets of the identified differentially expressed miRNAs, whose expression was altered in the presence of shRNAs that stimulated rhodopsin-promoter activity in a non-gene-targeting manner. Consistent with earlier studies on shRNA off-target effects, a number of interferon response genes were among those identified to be upregulated. Taken together, our results confirm the importance of considering off-target effects when interpreting data from RNAi experiments and extend prior results by focusing on the importance of including multiple and carefully designed controls in the design and analysis of the effects of shRNA on transient transfection-based transcriptional assays.
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Affiliation(s)
- Tomohiro Masuda
- Department of Ophthalmology, Wilmer Institute, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
| | - Jun Wan
- Department of Ophthalmology, Wilmer Institute, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
| | - Anitha Yerrabelli
- Department of Ophthalmology, Wilmer Institute, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
| | - Cindy Berlinicke
- Department of Ophthalmology, Wilmer Institute, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
| | - Alyssa Kallman
- Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
| | - Jiang Qian
- Department of Ophthalmology, Wilmer Institute, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
| | - Donald J. Zack
- Department of Ophthalmology, Wilmer Institute, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
- Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
- Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
- Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
- Institut de la Vision, University Pierre and Marie Curie, Paris, France
- * E-mail:
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Abstract
The discovery of an ever-expanding plethora of coding and non-coding RNAs with nodal and causal roles in the regulation of lung physiology and disease is reinvigorating interest in the clinical utility of the oligonucleotide therapeutic class. This is strongly supported through recent advances in nucleic acids chemistry, synthetic oligonucleotide delivery and viral gene therapy that have succeeded in bringing to market at least three nucleic acid-based drugs. As a consequence, multiple new candidates such as RNA interference modulators, antisense, and splice switching compounds are now progressing through clinical evaluation. Here, manipulation of RNA for the treatment of lung disease is explored, with emphasis on robust pharmacological evidence aligned to the five pillars of drug development: exposure to the appropriate tissue, binding to the desired molecular target, evidence of the expected mode of action, activity in the relevant patient population and commercially viable value proposition.
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Parlea L, Puri A, Kasprzak W, Bindewald E, Zakrevsky P, Satterwhite E, Joseph K, Afonin KA, Shapiro BA. Cellular Delivery of RNA Nanoparticles. ACS COMBINATORIAL SCIENCE 2016; 18:527-47. [PMID: 27509068 PMCID: PMC6345529 DOI: 10.1021/acscombsci.6b00073] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
RNA nanostructures can be programmed to exhibit defined sizes, shapes and stoichiometries from naturally occurring or de novo designed RNA motifs. These constructs can be used as scaffolds to attach functional moieties, such as ligand binding motifs or gene expression regulators, for nanobiology applications. This review is focused on four areas of importance to RNA nanotechnology: the types of RNAs of particular interest for nanobiology, the assembly of RNA nanoconstructs, the challenges of cellular delivery of RNAs in vivo, and the delivery carriers that aid in the matter. The available strategies for the design of nucleic acid nanostructures, as well as for formulation of their carriers, make RNA nanotechnology an important tool in both basic research and applied biomedical science.
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Affiliation(s)
- Lorena Parlea
- Gene Regulation and Chromosome Biology Laboratory, National Cancer Institute, Frederick, Maryland 21702, United States
| | - Anu Puri
- Gene Regulation and Chromosome Biology Laboratory, National Cancer Institute, Frederick, Maryland 21702, United States
| | - Wojciech Kasprzak
- Basic Science Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, Maryland 21702, United States
| | - Eckart Bindewald
- Basic Science Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, Maryland 21702, United States
| | - Paul Zakrevsky
- Gene Regulation and Chromosome Biology Laboratory, National Cancer Institute, Frederick, Maryland 21702, United States
| | - Emily Satterwhite
- Department of Chemistry, University of North Carolina at Charlotte, Charlotte, North Carolina 28223, United States
| | - Kenya Joseph
- Department of Chemistry, University of North Carolina at Charlotte, Charlotte, North Carolina 28223, United States
| | - Kirill A. Afonin
- Department of Chemistry, University of North Carolina at Charlotte, Charlotte, North Carolina 28223, United States
- Nanoscale Science Program, University of North Carolina at Charlotte, Charlotte North Carolina 28223, United States
- The Center for Biomedical Engineering and Science, University of North Carolina at Charlotte, Charlotte North Carolina 28223, United States
| | - Bruce A. Shapiro
- Gene Regulation and Chromosome Biology Laboratory, National Cancer Institute, Frederick, Maryland 21702, United States
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46
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Chemical and structural modifications of RNAi therapeutics. Adv Drug Deliv Rev 2016; 104:16-28. [PMID: 26549145 DOI: 10.1016/j.addr.2015.10.015] [Citation(s) in RCA: 98] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2015] [Revised: 10/14/2015] [Accepted: 10/23/2015] [Indexed: 12/25/2022]
Abstract
Small interfering RNA (siRNA), a 21-23nt double-stranded RNA responsible for post-transcriptional gene silencing, has attracted great interests as promising genomic drugs, due to its strong ability to silence target genes in a sequence-specific manner. Despite high silencing efficiency and on-target specificity, the clinical translation of siRNA has been hindered by its inherent features: poor intracellular delivery, limited blood stability, unpredictable immune responses and unwanted off-targeting effects. To overcome these hindrances, researchers have made various advances to modify siRNA itself and to improve its delivery. In this review paper, first we briefly discuss the innate properties and delivery barriers of siRNA. Then, we describe recent progress in (1) chemically and structurally modified siRNAs to solve their intrinsic problems and (2) siRNA delivery formulations including siRNA conjugates, polymerized siRNA, and nucleic acid-based nanoparticles to improve in vivo delivery.
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47
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Abstract
The ability to distinguish between self and nonself is the fundamental basis of the immune system in all organisms. The conceptual distinction between self and nonself, however, breaks down when it comes to endogenous retroviruses and other retroelements. While some retroelements retain the virus-like features including the capacity to replicate and reinvade the host genome, most have become inactive through mutations or host epigenetic silencing. And yet, accumulating evidence suggests that endogenous retroelements, both active and inactive, play important roles not only in pathogenesis of immune disorders, but also in proper functioning of the immune system. This review discusses the recent development in our understanding of the interaction between retroelements and the host innate immune system. In particular, it focuses on the impact of retroelement transcripts on the viral RNA sensors such as Toll-like receptors, RIG-I-like receptors, protein kinase R, and the inflammasomes.
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Affiliation(s)
- X Mu
- Harvard Medical School, Boston, MA, United States; Boston Children's Hospital, Boston, MA, United States
| | - S Ahmad
- Harvard Medical School, Boston, MA, United States; Boston Children's Hospital, Boston, MA, United States
| | - S Hur
- Harvard Medical School, Boston, MA, United States; Boston Children's Hospital, Boston, MA, United States.
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48
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Abstract
Immune sensing of foreign nucleic acids among abundant self nucleic acids is a hallmark of virus detection and antiviral defence. Efficient antiviral defence requires a balanced process of sensing foreign nucleic acids and ignoring self nucleic acids. This balance is accomplished by a multilevel, fail-safe system which combines immune sensing of pathogen-specific nucleic acid structures with specific labelling of self nucleic acids and nuclease-mediated degradation. Cellular localization of nucleic acids, nucleic acid secondary structure, nucleic acid sequence and chemical modification all contribute to selective recognition of foreign nucleic acids. Nucleic acid sensing occurs in immune cells and non-immune cells and results in antiviral responses that include the induction of antiviral effector proteins, the secretion of cytokines alarming neighbouring cells, the secretion of chemokines, which attract immune cells, and the induction of cell death. Vertebrate cells cannot completely avoid the occurrence of endogenous self nucleic acid structures with immunostimulatory properties. Therefore, additional mechanisms involving self-nucleic acid modification and nuclease-mediated degradation are necessary to diminish uncontrolled immune activation. Viruses have established sophisticated mechanisms to exploit and adopt endogenous tolerance mechanisms or to avoid the presentation of characteristic molecular features recognized by nucleic acid sensing receptors.
The detection of viruses by the immune system is mediated predominantly by the sensing of nucleic acids. Here, the authors review our current understanding of how this complex immune sensory system discriminates self from non-self nucleic acids to reliably detect pathogenic viruses, and discuss the future perspectives and implications for human disease. Innate immunity against pathogens relies on an array of immune receptors to detect molecular patterns that are characteristic of the pathogens, including receptors that are specialized in the detection of foreign nucleic acids. In vertebrates, nucleic acid sensing is the dominant antiviral defence pathway. Stimulation of nucleic acid receptors results in antiviral immune responses with the production of type I interferon (IFN), as well as the expression of IFN-stimulated genes, which encode molecules such as cell-autonomous antiviral effector proteins. This Review summarizes the tremendous progress that has been made in understanding how this sophisticated immune sensory system discriminates self from non-self nucleic acids in order to reliably detect pathogenic viruses.
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Affiliation(s)
- Martin Schlee
- Institute of Clinical Chemistry and Clinical Pharmacology, University Hospital, University of Bonn, Sigmund-Freud-Strasse 25, D-53127 Bonn, Germany
| | - Gunther Hartmann
- Institute of Clinical Chemistry and Clinical Pharmacology, University Hospital, University of Bonn, Sigmund-Freud-Strasse 25, D-53127 Bonn, Germany
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49
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Mayo CB, Wong CJ, Lopez PE, Lary JW, Cole JL. Activation of PKR by short stem-loop RNAs containing single-stranded arms. RNA (NEW YORK, N.Y.) 2016; 22:1065-75. [PMID: 27208315 PMCID: PMC4911914 DOI: 10.1261/rna.053348.115] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/16/2015] [Accepted: 04/19/2016] [Indexed: 05/22/2023]
Abstract
Protein kinase R (PKR) is a central component of the innate immunity antiviral pathway and is activated by dsRNA. PKR contains a C-terminal kinase domain and two tandem dsRNA binding domains. In the canonical activation model, binding of multiple PKR monomers to dsRNA enhances dimerization of the kinase domain, leading to enzymatic activation. A minimal dsRNA of 30 bp is required for activation. However, short (∼15 bp) stem-loop RNAs containing flanking single-stranded tails (ss-dsRNAs) are capable of activating PKR. Activation was reported to require a 5'-triphosphate. Here, we characterize the structural features of ss-dsRNAs that contribute to activation. We have designed a model ss-dsRNA containing 15-nt single-stranded tails and a 15-bp stem and made systematic truncations of the tail and stem regions. Autophosphorylation assays and analytical ultracentrifugation experiments were used to correlate activation and binding affinity. PKR activation requires both 5'- and 3'-single-stranded tails but the triphosphate is dispensable. Activation potency and binding affinity decrease as the ssRNA tails are truncated and activation is abolished in cases where the binding affinity is strongly reduced. These results indicate that the single-stranded regions bind to PKR and support a model where ss-dsRNA induced dimerization is required but not sufficient to activate the kinase. The length of the duplex regions in several natural RNA activators of PKR is below the minimum of 30 bp required for activation and similar interactions with single-stranded regions may contribute to PKR activation in these cases.
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Affiliation(s)
- Christopher B Mayo
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, Connecticut 06269, USA
| | - C Jason Wong
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, Connecticut 06269, USA
| | - Prisma E Lopez
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, Connecticut 06269, USA
| | - Jeffrey W Lary
- National Analytical Ultracentrifugation Facility, University of Connecticut, Storrs, Connecticut 06269, USA
| | - James L Cole
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, Connecticut 06269, USA Department of Chemistry, University of Connecticut, Storrs, Connecticut 06269, USA National Analytical Ultracentrifugation Facility, University of Connecticut, Storrs, Connecticut 06269, USA
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50
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Abstract
Short interfering RNAs (siRNAs) are as effective at targeting and silencing genes by RNA interference (RNAi) as long double-stranded RNAs (dsRNAs). siRNAs are widely used for assessing gene function in cultured mammalian cells or early developing vertebrate embryos. siRNAs are also promising reagents for developing gene-specific therapeutics. Specifically, the inhibition of HIV-1 replication is particularly well-suited to RNAi, as several stages of the viral life cycle and many viral and cellular genes can be targeted. The future success of this approach will depend on recent advances in siRNA-based silencing technologies.
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Affiliation(s)
- Hiroshi Takaku
- Department of Life & Environmental Sciences and High Technology Research Center, Chiba Institute of Technology, Chiba, Japan.
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