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de Reuver R, Maelfait J. Novel insights into double-stranded RNA-mediated immunopathology. Nat Rev Immunol 2024; 24:235-249. [PMID: 37752355 DOI: 10.1038/s41577-023-00940-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/24/2023] [Indexed: 09/28/2023]
Abstract
Recent progress in human and mouse genetics has transformed our understanding of the molecular mechanisms by which recognition of self double-stranded RNA (self-dsRNA) causes immunopathology. Novel mouse models recapitulate loss-of-function mutations in the RNA editing enzyme ADAR1 that are found in patients with Aicardi-Goutières syndrome (AGS) - a monogenic inflammatory disease associated with increased levels of type I interferon. Extensive analyses of the genotype-phenotype relationships in these mice have now firmly established a causal relationship between increased intracellular concentrations of endogenous immunostimulatory dsRNA and type I interferon-driven immunopathology. Activation of the dsRNA-specific immune sensor MDA5 perpetuates the overproduction of type I interferons, and chronic engagement of the interferon-inducible innate immune receptors PKR and ZBP1 by dsRNA drives immunopathology by activating an integrated stress response or by inducing excessive cell death. Biochemical and genetic data support a role for the p150 isoform of ADAR1 in the cytosol in suppressing the spontaneous, pathological response to self-dsRNA.
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Affiliation(s)
- Richard de Reuver
- VIB-UGent Center for Inflammation Research, Ghent, Belgium
- Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium
| | - Jonathan Maelfait
- VIB-UGent Center for Inflammation Research, Ghent, Belgium.
- Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium.
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2
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Roy A, Ghosh A. Epigenetic Restriction Factors (eRFs) in Virus Infection. Viruses 2024; 16:183. [PMID: 38399958 PMCID: PMC10892949 DOI: 10.3390/v16020183] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2023] [Revised: 01/23/2024] [Accepted: 01/24/2024] [Indexed: 02/25/2024] Open
Abstract
The ongoing arms race between viruses and their hosts is constantly evolving. One of the ways in which cells defend themselves against invading viruses is by using restriction factors (RFs), which are cell-intrinsic antiviral mechanisms that block viral replication and transcription. Recent research has identified a specific group of RFs that belong to the cellular epigenetic machinery and are able to restrict the gene expression of certain viruses. These RFs can be referred to as epigenetic restriction factors or eRFs. In this review, eRFs have been classified into two categories. The first category includes eRFs that target viral chromatin. So far, the identified eRFs in this category include the PML-NBs, the KRAB/KAP1 complex, IFI16, and the HUSH complex. The second category includes eRFs that target viral RNA or, more specifically, the viral epitranscriptome. These epitranscriptomic eRFs have been further classified into two types: those that edit RNA bases-adenosine deaminase acting on RNA (ADAR) and pseudouridine synthases (PUS), and those that covalently modify viral RNA-the N6-methyladenosine (m6A) writers, readers, and erasers. We delve into the molecular machinery of eRFs, their role in limiting various viruses, and the mechanisms by which viruses have evolved to counteract them. We also examine the crosstalk between different eRFs, including the common effectors that connect them. Finally, we explore the potential for new discoveries in the realm of epigenetic networks that restrict viral gene expression, as well as the future research directions in this area.
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Affiliation(s)
- Arunava Roy
- Department of Molecular Medicine, University of South Florida, Tampa, FL 33612, 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. Mol Cell 2023; 83:3869-3884.e7. [PMID: 37797622 DOI: 10.1016/j.molcel.2023.09.018] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2023] [Revised: 07/14/2023] [Accepted: 09/12/2023] [Indexed: 10/07/2023]
Abstract
Effective immunity requires the innate immune system to distinguish foreign nucleic acids from cellular ones. Cellular double-stranded RNAs (dsRNAs) are edited by the RNA-editing enzyme ADAR1 to evade being recognized as viral dsRNA by cytoplasmic dsRNA sensors, including MDA5 and PKR. The loss of ADAR1-mediated RNA editing of cellular dsRNA activates MDA5. 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, whereas 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 or PKR alone. 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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Affiliation(s)
- Shi-Bin Hu
- Department of Genetics, Stanford University, Stanford, CA 94305, USA
| | - Jacki Heraud-Farlow
- St. Vincent's Institute of Medical Research, Fitzroy, VIC 3065, Australia; Department of Medicine, Eastern Hill Precinct, Melbourne Medical School, University of Melbourne, Fitzroy, VIC 3065, Australia
| | - Tao Sun
- Department of Genetics, Stanford University, Stanford, CA 94305, USA
| | - Zhen Liang
- St. Vincent's Institute of Medical Research, Fitzroy, VIC 3065, Australia; Department of Medicine, Eastern Hill Precinct, Melbourne Medical School, University of Melbourne, Fitzroy, VIC 3065, Australia
| | - Ankita Goradia
- St. Vincent's Institute of Medical Research, Fitzroy, VIC 3065, Australia
| | - Scott Taylor
- St. Vincent's Institute of Medical Research, Fitzroy, VIC 3065, Australia
| | - Carl R Walkley
- St. Vincent's Institute of Medical Research, Fitzroy, VIC 3065, Australia; Department of Medicine, Eastern Hill Precinct, Melbourne Medical School, University of Melbourne, Fitzroy, VIC 3065, Australia.
| | - Jin Billy Li
- Department of Genetics, Stanford University, Stanford, CA 94305, USA.
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Datta R, Adamska JZ, Bhate A, Li JB. A-to-I RNA editing by ADAR and its therapeutic applications: From viral infections to cancer immunotherapy. WILEY INTERDISCIPLINARY REVIEWS. RNA 2023; 15:e1817. [PMID: 37718249 PMCID: PMC10947335 DOI: 10.1002/wrna.1817] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/11/2023] [Revised: 08/29/2023] [Accepted: 08/29/2023] [Indexed: 09/19/2023]
Abstract
ADAR deaminases catalyze adenosine-to-inosine (A-to-I) editing on double-stranded RNA (dsRNA) substrates that regulate an umbrella of biological processes. One of the two catalytically active ADAR enzymes, ADAR1, plays a major role in innate immune responses by suppression of RNA sensing pathways which are orchestrated through the ADAR1-dsRNA-MDA5 axis. Unedited immunogenic dsRNA substrates are potent ligands for the cellular sensor MDA5. Upon activation, MDA5 leads to the induction of interferons and expression of hundreds of interferon-stimulated genes with potent antiviral activity. In this way, ADAR1 acts as a gatekeeper of the RNA sensing pathway by striking a fine balance between innate antiviral responses and prevention of autoimmunity. Reduced editing of immunogenic dsRNA by ADAR1 is strongly linked to the development of common autoimmune and inflammatory diseases. In viral infections, ADAR1 exhibits both antiviral and proviral effects. This is modulated by both editing-dependent and editing-independent functions, such as PKR antagonism. Several A-to-I RNA editing events have been identified in viruses, including in the insidious viral pathogen, SARS-CoV-2 which regulates viral fitness and infectivity, and could play a role in shaping viral evolution. Furthermore, ADAR1 is an attractive target for immuno-oncology therapy. Overexpression of ADAR1 and increased dsRNA editing have been observed in several human cancers. Silencing ADAR1, especially in cancers that are refractory to immune checkpoint inhibitors, is a promising therapeutic strategy for cancer immunotherapy in conjunction with epigenetic therapy. The mechanistic understanding of dsRNA editing by ADAR1 and dsRNA sensing by MDA5 and PKR holds great potential for therapeutic applications. This article is categorized under: RNA Processing > RNA Editing and Modification RNA in Disease and Development > RNA in Disease.
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Affiliation(s)
- Rohini Datta
- Department of Genetics, Stanford University, Stanford, CA 94305, USA
| | - Julia Z Adamska
- Department of Genetics, Stanford University, Stanford, CA 94305, USA
| | - Amruta Bhate
- Department of Genetics, Stanford University, Stanford, CA 94305, USA
| | - Jin Billy Li
- Department of Genetics, Stanford University, Stanford, CA 94305, USA
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Zhao Q, Zhang R, Qiao C, Miao Y, Yuan Y, Zheng H. Ubiquitination network in the type I IFN-induced antiviral signaling pathway. Eur J Immunol 2023; 53:e2350384. [PMID: 37194705 DOI: 10.1002/eji.202350384] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2023] [Revised: 04/14/2023] [Accepted: 05/16/2023] [Indexed: 05/18/2023]
Abstract
Type I IFN (IFN-I) is the body's first line of defense against pathogen infection. IFN-I can induce cellular antiviral responses and therefore plays a key role in driving antiviral innate and adaptive immunity. Canonical IFN-I signaling activates the Janus kinase (JAK)/signal transducer and activator of transcription (STAT) pathway, which induces the expression of IFN-stimulated genes and eventually establishes a complex antiviral state in the cells. Ubiquitin is a ubiquitous cellular molecule for protein modifications, and the ubiquitination modifications of protein have been recognized as one of the key modifications that regulate protein levels and/or signaling activation. Despite great advances in understanding the ubiquitination regulation of many signaling pathways, the mechanisms by which protein ubiquitination regulates IFN-I-induced antiviral signaling have not been explored until very recently. This review details the current understanding of the regulatory network of ubiquitination that critically controls the IFN-I-induced antiviral signaling pathway from three main levels, including IFN-I receptors, IFN-I-induced cascade signals, and effector IFN-stimulated genes.
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Affiliation(s)
- Qian Zhao
- International Institute of Infection and Immunity, Institutes of Biology and Medical Sciences, Soochow University, Suzhou, China
- Jiangsu Key Laboratory of Infection and Immunity, Soochow University, Suzhou, China
| | - Renxia Zhang
- International Institute of Infection and Immunity, Institutes of Biology and Medical Sciences, Soochow University, Suzhou, China
- Jiangsu Key Laboratory of Infection and Immunity, Soochow University, Suzhou, China
| | - Caixia Qiao
- International Institute of Infection and Immunity, Institutes of Biology and Medical Sciences, Soochow University, Suzhou, China
- Jiangsu Key Laboratory of Infection and Immunity, Soochow University, Suzhou, China
| | - Ying Miao
- International Institute of Infection and Immunity, Institutes of Biology and Medical Sciences, Soochow University, Suzhou, China
- Jiangsu Key Laboratory of Infection and Immunity, Soochow University, Suzhou, China
| | - Yukang Yuan
- International Institute of Infection and Immunity, Institutes of Biology and Medical Sciences, Soochow University, Suzhou, China
- Jiangsu Key Laboratory of Infection and Immunity, Soochow University, Suzhou, China
| | - Hui Zheng
- International Institute of Infection and Immunity, Institutes of Biology and Medical Sciences, Soochow University, Suzhou, China
- Jiangsu Key Laboratory of Infection and Immunity, Soochow University, Suzhou, China
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6
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Shi S, Chen S, Wang M, Guo B, He Y, Chen H. Clinical relevance of RNA editing profiles in lung adenocarcinoma. Front Genet 2023; 14:1084869. [PMID: 36999050 PMCID: PMC10043753 DOI: 10.3389/fgene.2023.1084869] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Accepted: 02/27/2023] [Indexed: 03/12/2023] Open
Abstract
Background: Lung adenocarcinoma (LUAD) is the most frequently occurring lung cancer worldwide, with increasing death rates. It belongs to the non-small cell lung cancer (NSCLC) type and has a strong association with previous smoking history. Growing evidence has demonstrated the significance of adenosine-to-inosine RNA editing (ATIRE) dysregulation in cancer. The aim of the present study was to evaluate ATIRE events that might be clinically useful or tumorigenic.Methods: To explore survival-related ATIRE events in LUAD, its ATIRE profiles, gene expression data, and corresponding patients’ clinical information were downloaded from the Cancer Genome Atlas (TCGA) and the synapse database. We evaluated 10441 ATIRE in 440 LUAD patients from the TCGA database. ATIRE profiles were merged with TCGA survival data. We selected prognostic ATIRE sites, using a univariate Cox analysis (p < 0.001). Cox proportional hazards regression and lasso regression analysis were used to determine survival-related ATIRE sites, create risk ratings for those sites, and build a prognostic model and a nomogram for assessing overall survival (OS). Six ATIRE sites were used in the prognostic model construction and patients were randomly divided into a validation cohort (n = 176) and a training cohort (n = 264). The “Pheatmap” program was used to create risk curves that included risk score, survival time, and expression of ATIRE sites. We also determined the clinical prediction model’s discrimination. The decision curve analysis and the 1-, 2-, and 3-year corrective curves were simultaneously used to evaluate the nomogram. We also evaluated the relationship between the amount of ATIRE sites and host gene expression and the impact of ATIRE expression on transcriptome expression.Results: The pyroglutamyl-peptidase I (PGPEP1) chr19:18476416A > I, ankyrin repeat domain 36B pseudogene 1 (ANKRD36BP1) (dist = 3,795), T-box transcription factor (TBX19) (dist = 29815) chr1:168220463A > I, Syntrophin Beta 2 (SNTB2) chr16:69338598A > I, hook microtubule-tethering protein 3 (HOOK3) chr8:42883441A > I, NADH dehydrogenase flavoprotein 3 (NDUFV3) chr21:44329452A > I, and FK506-binding protein 11 (FKBP11) chr12:49316769A > I were used in the prognostic model construction. High levels of risk score were significantly associated with worse OS and progression-free survival. Tumour stage and risk score were related to OS in LUAD patients. The predictors were among the prognostic nomogram model’s risk score, age, gender, and tumor stage. The calibration plot and C-index (0.718) demonstrated the significant accuracy of nomogram’s predictions. ATIRE level was markedly elevated in tumor tissues and was highly variable between patients.Conclusion: Events involving ATIRE in LUAD were highly functional and clinically relevant. The RNA editing-based model provides a solid framework for further investigation of the functions of RNA editing in non-coding areas and may be used as a unique method for predicting LUAD survival.
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Affiliation(s)
- Si Shi
- The Respiratory Department, The Second Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang, China
| | - Shibin Chen
- Medical Research Center, Beijing Chao-Yang Hospital, Capital Medical University, Beijing, China
| | - Menghang Wang
- The Respiratory Department, The Second Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang, China
| | - Bingchen Guo
- Department of Cardiology, The first Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang, China
| | - Yaowu He
- The Respiratory Department, The Second Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang, China
| | - Hong Chen
- The Respiratory Department, The Second Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang, China
- *Correspondence: Hong Chen,
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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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8
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Zhang K, Wang S, Chen T, Tu Z, Huang X, Zang G, Wu C, Fan X, Liu J, Tian Y, Cheng Y, Lu N, Zhang G. ADAR1p110 promotes Enterovirus D68 replication through its deaminase domain and inhibition of PKR pathway. Virol J 2022; 19:222. [PMID: 36550502 PMCID: PMC9773460 DOI: 10.1186/s12985-022-01952-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2022] [Accepted: 12/09/2022] [Indexed: 12/24/2022] Open
Abstract
BACKGROUND Severe respiratory and neurological diseases caused by human enterovirus D68 (EV-D68) pose a serious threat to public health, and there are currently no effective drugs and vaccines. Adenosine deaminase acting on RNA1 (ADAR1) has diverse biological functions in various viral infections, but its role in EV-D68 infections remains undetermined. METHODS Rhabdomyosarcoma (RD) and human embryonic kidney 293 T (293 T) cells, and HeLa cells were used to evaluate the expression level of ADAR1 upon EV-D68 (Fermon strain) and human parainfluenza virus type 3 (HPIV3; NIH47885) infection, respectively. Knockdown through silencing RNA (siRNA) and overexpression of either ADAR1p110 or ADAR1p150 in cells were used to determine the function of the two proteins after viral infection. ADAR1p110 double-stranded RNA binding domains (dsRBDs) deletion mutation was generated using a seamless clone kit. The expression of ADAR1, EV-D68 VP1, and HPIV3 hemagglutinin-neuraminidase (HN) proteins was identified using western blotting. The median tissue culture infectious dose (TCID50) was applied to detect viral titers. The transcription level of EV-D68 mRNA was analyzed using reverse transcription-quantitative PCR (RT-qPCR) and the viral 5'-untranslated region (5'-UTR)-mediated translation was analyzed using a dual luciferase reporter system. CONCLUSION We found that the transcription and expression of ADAR1 was inhibited upon EV-D68 infection. RNA interference of endogenous ADAR1 decreased VP1 protein expression and viral titers, while overexpression of ADAR1p110, but not ADAR1p150, facilitated viral replication. Immunofluorescence assays showed that ADAR1p110 migrated from the nucleus to the cytoplasm after EV-D68 infection. Further, ADAR1p110 lost its pro-viral ability after mutations of the active sites in the deaminase domain, and 5'-UTR sequencing of the viral genome revealed that ADAR1p110 likely plays a role in EV-D68 RNA editing. In addition, after ADAR1 knockdown, the levels of both phosphorylated double-stranded RNA dependent protein kinase (p-PKR) and phosphorylated eukaryotic initiation factor 2α (p-eIF2α) increased. Attenuated translation activity of the viral genome 5'-UTR was also observed in the dual-luciferase reporter assay. Lastly, the deletion of ADAR1p110 dsRBDs increased the level of p-PKR, which correlated with a decreased VP1 expression, indicating that the promotion of EV-D68 replication by ADAR1p110 is also related to the inhibition of PKR activation by its dsRBDs. Our study illustrates that ADAR1p110 is a novel pro-viral factor of EV-D68 replication and provides a theoretical basis for EV-D68 antiviral research.
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Affiliation(s)
- Kehan Zhang
- grid.203458.80000 0000 8653 0555Pathogen Biology and Immunology Laboratory and Laboratory of Tissue and Cell Biology, Experimental Teaching and Management Center, Chongqing Medical University, Chongqing, China ,grid.203458.80000 0000 8653 0555Department of the First Clinical Medicine, Chongqing Medical University, Chongqing, China
| | - Siyuan Wang
- grid.203458.80000 0000 8653 0555Department of the First Clinical Medicine, Chongqing Medical University, Chongqing, China
| | - Tingting Chen
- grid.203458.80000 0000 8653 0555Pathogen Biology and Immunology Laboratory and Laboratory of Tissue and Cell Biology, Experimental Teaching and Management Center, Chongqing Medical University, Chongqing, China
| | - Zeng Tu
- grid.203458.80000 0000 8653 0555Department of Pathogen Biology, Basic Medical School, Chongqing Medical University, Chongqing, China
| | - Xia Huang
- grid.203458.80000 0000 8653 0555Department of the First Clinical Medicine, Chongqing Medical University, Chongqing, China
| | - Guangchao Zang
- grid.203458.80000 0000 8653 0555Pathogen Biology and Immunology Laboratory and Laboratory of Tissue and Cell Biology, Experimental Teaching and Management Center, Chongqing Medical University, Chongqing, China
| | - Chun Wu
- Chongqing Better Biotechnology LLC, Chongqing, China
| | - Xinyue Fan
- grid.203458.80000 0000 8653 0555Department of the First Clinical Medicine, Chongqing Medical University, Chongqing, China
| | - Jia Liu
- grid.203458.80000 0000 8653 0555Pathogen Biology and Immunology Laboratory and Laboratory of Tissue and Cell Biology, Experimental Teaching and Management Center, Chongqing Medical University, Chongqing, China
| | - Yunbo Tian
- Quality Management Section, Chongqing Blood Center, Chongqing, China
| | - Yong Cheng
- Monitoring On Terrestrial Wildlife-Borne Infectious Diseases, Jinggangshan National Nature Reserve of Jiangxi Province, Ji’an, Jiangxi China
| | - Nan Lu
- grid.203458.80000 0000 8653 0555Department of Pathogen Biology, Basic Medical School, Chongqing Medical University, Chongqing, China
| | - Guangyuan Zhang
- grid.203458.80000 0000 8653 0555Pathogen Biology and Immunology Laboratory and Laboratory of Tissue and Cell Biology, Experimental Teaching and Management Center, Chongqing Medical University, Chongqing, China
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Xiang R, Liu Y, Fan L, Jiang B, Wang F. RNA adenosine deaminase (ADAR1) alleviates high-fat diet-induced nonalcoholic fatty liver disease by inhibiting NLRP3 inflammasome. J Transl Med 2022; 102:1088-1100. [PMID: 36775349 DOI: 10.1038/s41374-022-00805-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2021] [Revised: 04/13/2022] [Accepted: 05/06/2022] [Indexed: 12/26/2022] Open
Abstract
Nonalcoholic fatty liver disease (NAFLD) is a chronic inflammatory disease in which nucleotide-binding domain of leucine-rich repeat protein 3 (NLRP3) inflammasome plays an important role. The present research was aimed to explore the protective function of ADAR1, an RNA editing enzyme, against inflammatory damages in high-fat diet (HFD)-induced NAFLD through inhibiting NLRP3 inflammasome and subsequent inflammation. A total of 30 patients with NAFLD were investigated, and ADAR1 mRNA expression in peripheral blood monocytes surveyed. The in vivo study used lentivirus to explore the function of ADAR1 overexpression in the HFD-induced mouse model of NAFLD. The in vitro study used lentivirus and siRNA to explore the function of ADAR1 on the NLRP3 inflammasome activation in THP-1 cells. Results shown that the ADAR1 expression was upregulated in NAFLD patients in comparison to healthy controls. In vivo, the upregulation of ADAR1 impaired NLRP3 inflammasome activation and alleviated liver disease in HFD mice in comparison to the control group. Moreover, ADAR1 overexpression attenuated NLRP3 inflammasome in lipopolysaccharide (LPS)+ palmitic acid (PA)-induced THP-1 cells, while ADAR1 knockdown increased the NLRP3 inflammasome activation. Furthermore, we speculated that c-Jun may participate in ADAR1's inhibition of NLRP3 inflammasome. Our results suggested that ADAR1 is a potential treatment target for NAFLD via regulating the activation of NLRP3 inflammasome.
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Affiliation(s)
- Rong Xiang
- The Endocrinology Department of the Third Xiangya Hospital, Central South University, Changsha, Hunan Province, China.,Department of Cell Biology, School of Life Sciences, Central South University, Changsha, 410013, China.,Hunan Key Laboratory of Medical Genetics, Central South University, Changsha, 410078, China.,Hunan Key Laboratory of Animal for Human Disease, School of Life Sciences, Central South University, Changsha, China
| | - Yuxing Liu
- The Endocrinology Department of the Third Xiangya Hospital, Central South University, Changsha, Hunan Province, China.,Department of Cell Biology, School of Life Sciences, Central South University, Changsha, 410013, China
| | - Liangliang Fan
- Department of Cell Biology, School of Life Sciences, Central South University, Changsha, 410013, China.,Hunan Key Laboratory of Medical Genetics, Central South University, Changsha, 410078, China.,Hunan Key Laboratory of Animal for Human Disease, School of Life Sciences, Central South University, Changsha, China
| | - Boyue Jiang
- Department of Cell Biology, School of Life Sciences, Central South University, Changsha, 410013, China
| | - Fang Wang
- The Endocrinology Department of the Third Xiangya Hospital, Central South University, Changsha, Hunan Province, China. .,Hunan Key Laboratory of Animal for Human Disease, School of Life Sciences, Central South University, Changsha, China.
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10
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Diallo MA, Pirotte S, Hu Y, Morvan L, Rakus K, Suárez NM, PoTsang L, Saneyoshi H, Xu Y, Davison A, Tompa P, Sussman J, Vanderplasschen A. A fish herpesvirus highlights functional diversities among Zα domains related to phase separation induction and A-to-Z conversion. Nucleic Acids Res 2022; 51:806-830. [PMID: 36130731 PMCID: PMC9881149 DOI: 10.1093/nar/gkac761] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Revised: 08/18/2022] [Accepted: 08/25/2022] [Indexed: 02/06/2023] Open
Abstract
Zalpha (Zα) domains bind to left-handed Z-DNA and Z-RNA. The Zα domain protein family includes cellular (ADAR1, ZBP1 and PKZ) and viral (vaccinia virus E3 and cyprinid herpesvirus 3 (CyHV-3) ORF112) proteins. We studied CyHV-3 ORF112, which contains an intrinsically disordered region and a Zα domain. Genome editing of CyHV-3 indicated that the expression of only the Zα domain of ORF112 was sufficient for normal viral replication in cell culture and virulence in carp. In contrast, its deletion was lethal for the virus. These observations revealed the potential of the CyHV-3 model as a unique platform to compare the exchangeability of Zα domains expressed alone in living cells. Attempts to rescue the ORF112 deletion by a broad spectrum of cellular, viral, and artificial Zα domains showed that only those expressing Z-binding activity, the capacity to induce liquid-liquid phase separation (LLPS), and A-to-Z conversion, could rescue viral replication. For the first time, this study reports the ability of some Zα domains to induce LLPS and supports the biological relevance of dsRNA A-to-Z conversion mediated by Zα domains. This study expands the functional diversity of Zα domains and stimulates new hypotheses concerning the mechanisms of action of proteins containing Zα domains.
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Affiliation(s)
| | | | - Yunlong Hu
- Department of Infectious and Parasitic Diseases, Immunology-Vaccinology, University of Liège, Liège B-4000, Belgium
| | - Léa Morvan
- Department of Infectious and Parasitic Diseases, Immunology-Vaccinology, University of Liège, Liège B-4000, Belgium
| | - Krzysztof Rakus
- Department of Infectious and Parasitic Diseases, Immunology-Vaccinology, University of Liège, Liège B-4000, Belgium,Department of Evolutionary Immunology, Institute of Zoology and Biomedical Research, Faculty of Biology, Jagiellonian University, Krakow 30387, Poland
| | - Nicolás M Suárez
- MRC-University of Glasgow Centre for Virus Research, Glasgow G61 1QH, UK
| | - Lee PoTsang
- Department of Infectious and Parasitic Diseases, Immunology-Vaccinology, University of Liège, Liège B-4000, Belgium,Department of Aquaculture, National Taiwan Ocean University, Keelung 202, Taiwan
| | - Hisao Saneyoshi
- Department of Medical Sciences, Division of Chemistry, University of Miyazaki, Miyazaki 889-1692, Japan
| | - Yan Xu
- Department of Medical Sciences, Division of Chemistry, University of Miyazaki, Miyazaki 889-1692, Japan
| | - Andrew J Davison
- MRC-University of Glasgow Centre for Virus Research, Glasgow G61 1QH, UK
| | - Peter Tompa
- VIB-VUB Center for Structural Biology, Vrije Universiteit Brussel, Brussel B-1050, Belgium
| | - Joel L Sussman
- Department of Chemical and Structural Biology, Weizmann Institute of Science, Rehovot 7610001, Israel
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11
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Chan CP, Jin DY. Cytoplasmic RNA sensors and their interplay with RNA-binding partners in innate antiviral response: theme and variations. RNA (NEW YORK, N.Y.) 2022; 28:449-477. [PMID: 35031583 PMCID: PMC8925969 DOI: 10.1261/rna.079016.121] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Sensing of pathogen-associated molecular patterns including viral RNA by innate immunity represents the first line of defense against viral infection. In addition to RIG-I-like receptors and NOD-like receptors, several other RNA sensors are known to mediate innate antiviral response in the cytoplasm. Double-stranded RNA-binding protein PACT interacts with prototypic RNA sensor RIG-I to facilitate its recognition of viral RNA and induction of host interferon response, but variations of this theme are seen when the functions of RNA sensors are modulated by other RNA-binding proteins to impinge on antiviral defense, proinflammatory cytokine production and cell death programs. Their discrete and coordinated actions are crucial to protect the host from infection. In this review, we will focus on cytoplasmic RNA sensors with an emphasis on their interplay with RNA-binding partners. Classical sensors such as RIG-I will be briefly reviewed. More attention will be brought to new insights on how RNA-binding partners of RNA sensors modulate innate RNA sensing and how viruses perturb the functions of RNA-binding partners.
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Affiliation(s)
- Chi-Ping Chan
- School of Biomedical Sciences and State Key Laboratory of Liver Research, Faculty of Medicine Building, Pokfulam, Hong Kong
| | - Dong-Yan Jin
- School of Biomedical Sciences and State Key Laboratory of Liver Research, Faculty of Medicine Building, Pokfulam, Hong Kong
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12
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Dutta N, Deb I, Sarzynska J, Lahiri A. Inosine and its methyl derivatives: Occurrence, biogenesis, and function in RNA. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2022; 169-170:21-52. [PMID: 35065168 DOI: 10.1016/j.pbiomolbio.2022.01.001] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/11/2021] [Revised: 12/11/2021] [Accepted: 01/11/2022] [Indexed: 05/21/2023]
Abstract
Inosine is one of the most common post-transcriptional modifications. Since its discovery, it has been noted for its ability to contribute to non-Watson-Crick interactions within RNA. Rapidly accumulating evidence points to the widespread generation of inosine through hydrolytic deamination of adenosine to inosine by different classes of adenosine deaminases. Three naturally occurring methyl derivatives of inosine, i.e., 1-methylinosine, 2'-O-methylinosine and 1,2'-O-dimethylinosine are currently reported in RNA modification databases. These modifications are expected to lead to changes in the structure, folding, dynamics, stability and functions of RNA. The importance of the modifications is indicated by the strong conservation of the modifying enzymes across organisms. The structure, binding and catalytic mechanism of the adenosine deaminases have been well-studied, but the underlying mechanism of the catalytic reaction is not very clear yet. Here we extensively review the existing data on the occurrence, biogenesis and functions of inosine and its methyl derivatives in RNA. We also included the structural and thermodynamic aspects of these modifications in our review to provide a detailed and integrated discussion on the consequences of A-to-I editing in RNA and the contribution of different structural and thermodynamic studies in understanding its role in RNA. We also highlight the importance of further studies for a better understanding of the mechanisms of the different classes of deamination reactions. Further investigation of the structural and thermodynamic consequences and functions of these modifications in RNA should provide more useful information about their role in different diseases.
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Affiliation(s)
- Nivedita Dutta
- Department of Biophysics, Molecular Biology and Bioinformatics, University of Calcutta, 92, Acharya Prafulla Chandra Road, Kolkata, 700009, West Bengal, India
| | - Indrajit Deb
- Department of Biophysics, Molecular Biology and Bioinformatics, University of Calcutta, 92, Acharya Prafulla Chandra Road, Kolkata, 700009, West Bengal, India
| | - Joanna Sarzynska
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704, Poznan, Poland
| | - Ansuman Lahiri
- Department of Biophysics, Molecular Biology and Bioinformatics, University of Calcutta, 92, Acharya Prafulla Chandra Road, Kolkata, 700009, West Bengal, India.
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13
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Tong J, Zhang W, Chen Y, Yuan Q, Qin NN, Qu G. The Emerging Role of RNA Modifications in the Regulation of Antiviral Innate Immunity. Front Microbiol 2022; 13:845625. [PMID: 35185855 PMCID: PMC8851159 DOI: 10.3389/fmicb.2022.845625] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2021] [Accepted: 01/10/2022] [Indexed: 12/15/2022] Open
Abstract
Posttranscriptional modifications have been implicated in regulation of nearly all biological aspects of cellular RNAs, from stability, translation, splicing, nuclear export to localization. Chemical modifications also have been revealed for virus derived RNAs several decades before, along with the potential of their regulatory roles in virus infection. Due to the dynamic changes of RNA modifications during virus infection, illustrating the mechanisms of RNA epigenetic regulations remains a challenge. Nevertheless, many studies have indicated that these RNA epigenetic marks may directly regulate virus infection through antiviral innate immune responses. The present review summarizes the impacts of important epigenetic marks on viral RNAs, including N6-methyladenosine (m6A), 5-methylcytidine (m5C), 2ʹ-O-methylation (2ʹ-O-Methyl), and a few uncanonical nucleotides (A-to-I editing, pseudouridine), on antiviral innate immunity and relevant signaling pathways, while highlighting the significance of antiviral innate immune responses during virus infection.
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Affiliation(s)
- Jie Tong
- College of Life Sciences, Hebei University, Baoding, China.,Institute of Life Sciences and Green Development, Hebei University, Baoding, China
| | - Wuchao Zhang
- College of Veterinary Medicine, Hebei Agricultural University, Baoding, China
| | - Yuran Chen
- College of Life Sciences, Hebei University, Baoding, China.,Institute of Life Sciences and Green Development, Hebei University, Baoding, China
| | - Qiaoling Yuan
- College of Life Sciences, Hebei University, Baoding, China.,Institute of Life Sciences and Green Development, Hebei University, Baoding, China
| | - Ning-Ning Qin
- College of Life Sciences, Hebei University, Baoding, China.,Institute of Life Sciences and Green Development, Hebei University, Baoding, China
| | - Guosheng Qu
- College of Life Sciences, Hebei University, Baoding, China.,Institute of Life Sciences and Green Development, Hebei University, Baoding, China
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14
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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: 3] [Impact Index Per Article: 1.5] [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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15
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Liao GR, Tseng YY, Tseng CY, Lo CY, Hsu WL. The orf virus (ORFV) protein OV20.0 interacts with the microprocessor complex subunit DGCR8 to regulate miRNA biogenesis and ORFV infection. FEBS Lett 2021; 595:2897-2908. [PMID: 34778960 DOI: 10.1002/1873-3468.14231] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2021] [Revised: 10/15/2021] [Accepted: 11/03/2021] [Indexed: 02/01/2023]
Abstract
Cellular double-stranded RNA-binding proteins (DRBPs) play important roles in the regulation of innate immune responses and microRNA (miRNA) biogenesis. The current study aimed to understand whether OV20.0, a DRBP of orf virus (ORFV), is involved in cellular RNA biogenesis via association with host DRBPs. We found that OV20.0 interacts with DiGeorge syndrome critical region 8 (DGCR8), a subunit of the miRNA processor complex, and binds to primary- and precursor-miRNA. Additionally, OV20.0 regulates DGCR8 expression in multiple ways, including through interaction with the DGCR8 protein and binding to DGCR8 mRNA. Lastly, our data show that DGCR8 plays an antiviral role against ORFV infection, whereas it is beneficial for influenza virus propagation, indicating that the underlying mechanisms could be diverse among different viruses.
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Affiliation(s)
- Guan-Ru Liao
- Graduate Institute of Microbiology and Public Health, National Chung Hsing University, Taichung, Taiwan
| | - Yeu-Yang Tseng
- WHO Collaborating Centre for Reference and Research on Influenza, VIDRL, Peter Doherty Institute for Infection and Immunity, University of Melbourne, Victoria, Australia
| | - Ching-Yu Tseng
- Graduate Institute of Microbiology and Public Health, National Chung Hsing University, Taichung, Taiwan
| | - Chen-Yu Lo
- Graduate Institute of Veterinary Pathobiology, National Chung Hsing University, Taichung, Taiwan
| | - Wei-Li Hsu
- Graduate Institute of Microbiology and Public Health, National Chung Hsing University, Taichung, Taiwan
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16
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Piontkivska H, Wales-McGrath B, Miyamoto M, Wayne ML. ADAR Editing in Viruses: An Evolutionary Force to Reckon with. Genome Biol Evol 2021; 13:evab240. [PMID: 34694399 PMCID: PMC8586724 DOI: 10.1093/gbe/evab240] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/21/2021] [Indexed: 02/06/2023] Open
Abstract
Adenosine Deaminases that Act on RNA (ADARs) are RNA editing enzymes that play a dynamic and nuanced role in regulating transcriptome and proteome diversity. This editing can be highly selective, affecting a specific site within a transcript, or nonselective, resulting in hyperediting. ADAR editing is important for regulating neural functions and autoimmunity, and has a key role in the innate immune response to viral infections, where editing can have a range of pro- or antiviral effects and can contribute to viral evolution. Here we examine the role of ADAR editing across a broad range of viral groups. We propose that the effect of ADAR editing on viral replication, whether pro- or antiviral, is better viewed as an axis rather than a binary, and that the specific position of a given virus on this axis is highly dependent on virus- and host-specific factors, and can change over the course of infection. However, more research needs to be devoted to understanding these dynamic factors and how they affect virus-ADAR interactions and viral evolution. Another area that warrants significant attention is the effect of virus-ADAR interactions on host-ADAR interactions, particularly in light of the crucial role of ADAR in regulating neural functions. Answering these questions will be essential to developing our understanding of the relationship between ADAR editing and viral infection. In turn, this will further our understanding of the effects of viruses such as SARS-CoV-2, as well as many others, and thereby influence our approach to treating these deadly diseases.
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Affiliation(s)
- Helen Piontkivska
- Department of Biological Sciences, Kent State University, Ohio, USA
- School of Biomedical Sciences, Kent State University, Ohio, USA
- Brain Health Research Institute, Kent State University, Ohio, USA
| | | | - Michael Miyamoto
- Department of Biology, University of Florida, Gainesville, Florida, USA
| | - Marta L Wayne
- Department of Biology, University of Florida, Gainesville, Florida, USA
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17
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Liao GR, Tseng YY, Tseng CY, Huang YP, Tsai CH, Liu HP, Hsu WL. K160 in the RNA-binding domain of the orf virus virulence factor OV20.0 is critical for its functions in counteracting host antiviral defense. FEBS Lett 2021; 595:1721-1733. [PMID: 33909294 DOI: 10.1002/1873-3468.14099] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Revised: 04/09/2021] [Accepted: 04/22/2021] [Indexed: 11/10/2022]
Abstract
The OV20.0 virulence factor of orf virus antagonizes host antiviral responses. One mechanism through which it functions is by inhibiting activation of the dsRNA-activated protein kinase R (PKR) by sequestering dsRNA and by physically interacting with PKR. Sequence alignment indicated that several key residues critical for dsRNA binding were conserved in OV20.0, and their contribution to OV20.O function was investigated in this study. We found that residues F141, K160, and R164 were responsible for the dsRNA-binding ability of OV20.0. Interestingly, mutation at K160 (K160A) diminished the OV20.0-PKR interaction and further reduced the inhibitory effect of OV20.0 on PKR activation. Nevertheless, OV20.0 homodimerization was not influenced by K160A. The contribution of the dsRNA-binding domain and K160 to the suppression of RNA interference by OV20.0 was further demonstrated in plants. In summary, K160 is essential for the function of OV20.0, particularly its interaction with dsRNA and PKR that ultimately contributes to the suppression of PKR activation.
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Affiliation(s)
- Guan-Ru Liao
- Graduate Institute of Microbiology and Public Health, National Chung Hsing University, Taichung, Taiwan
| | - Yeu-Yang Tseng
- WHO Collaborating Centre for Reference and Research on Influenza, VIDRL, Peter Doherty Institute for Infection and Immunity, University of Melbourne, Australia
| | - Ching-Yu Tseng
- Graduate Institute of Microbiology and Public Health, National Chung Hsing University, Taichung, Taiwan
| | - Ying-Ping Huang
- Graduate Institute of Biotechnology, National Chung Hsing University, Taichung, Taiwan
| | - Ching-Hsiu Tsai
- Graduate Institute of Biotechnology, National Chung Hsing University, Taichung, Taiwan
| | - Hao-Ping Liu
- Department of Veterinary Medicine, National Chung Hsing University, Taichung, Taiwan
| | - Wei-Li Hsu
- Graduate Institute of Microbiology and Public Health, National Chung Hsing University, Taichung, Taiwan
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18
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Abstract
C6 deamination of adenosine (A) to inosine (I) in double-stranded RNA (dsRNA) is catalyzed by a family of enzymes known as ADARs (adenosine deaminases acting on RNA) encoded by three genes in mammals. Alternative promoters and splicing produce two ADAR1 proteins, an interferon-inducible cytoplasmic p150 and a constitutively expressed p110 that like ADAR2 is a nuclear enzyme. ADAR3 lacks deaminase activity. A-to-I editing occurs with both viral and cellular RNAs. Deamination activity is dependent on dsRNA substrate structure and regulatory RNA-binding proteins and ranges from highly site selective with hepatitis D RNA and glutamate receptor precursor messenger RNA (pre-mRNA) to hyperediting of measles virus and polyomavirus transcripts and cellular inverted Alu elements. Because I base-pairs as guanosine instead of A, editing can alter mRNA decoding, pre-mRNA splicing, and microRNA silencing. Editing also alters dsRNA structure, thereby suppressing innate immune responses including interferon production and action. Expected final online publication date for the Annual Review of Virology, Volume 8 is September 2021. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
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Affiliation(s)
- Christian K Pfaller
- Division of Veterinary Medicine, Paul-Ehrlich-Institute, Langen 63225, Germany
| | - Cyril X George
- Department of Molecular, Cellular, and Developmental Biology, University of California, Santa Barbara, California 93106, USA;
| | - Charles E Samuel
- Department of Molecular, Cellular, and Developmental Biology, University of California, Santa Barbara, California 93106, USA;
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19
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Abstract
The innate immune receptors in higher organisms have evolved to detect molecular signatures associated with pathogenic infection and trigger appropriate immune response. One common class of molecules utilized by the innate immune system for self vs. nonself discrimination is RNA, which is ironically present in all forms of life. To avoid self-RNA recognition, the innate immune sensors have evolved sophisticated discriminatory mechanisms that involve cellular RNA metabolic machineries. Posttranscriptional RNA modification and editing represent one such mechanism that allows cells to chemically tag the host RNAs as "self" and thus tolerate the abundant self-RNA molecules. In this chapter, we discuss recent advances in our understanding of the role of RNA editing/modification in the modulation of immune signaling pathways, and application of RNA editing/modification in RNA-based therapeutics and cancer immunotherapies.
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20
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Viral pathogen-induced mechanisms to antagonize mammalian interferon (IFN) signaling pathway. Cell Mol Life Sci 2020; 78:1423-1444. [PMID: 33084946 PMCID: PMC7576986 DOI: 10.1007/s00018-020-03671-z] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Revised: 09/14/2020] [Accepted: 10/05/2020] [Indexed: 12/14/2022]
Abstract
Antiviral responses of interferons (IFNs) are crucial in the host immune response, playing a relevant role in controlling viralw infections. Three types of IFNs, type I (IFN-α, IFN-β), II (IFN-γ) and III (IFN-λ), are classified according to their receptor usage, mode of induction, biological activity and amino acid sequence. Here, we provide a comprehensive review of type I IFN responses and different mechanisms that viruses employ to circumvent this response. In the first part, we will give an overview of the different induction and signaling cascades induced in the cell by IFN-I after virus encounter. Next, highlights of some of the mechanisms used by viruses to counteract the IFN induction will be described. And finally, we will address different mechanism used by viruses to interference with the IFN signaling cascade and the blockade of IFN induced antiviral activities.
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21
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Abstract
Chemical modifications of viral RNA are an integral part of the viral life cycle and are present in most classes of viruses. To date, more than 170 RNA modifications have been discovered in all types of cellular RNA. Only a few, however, have been found in viral RNA, and the function of most of these has yet to be elucidated. Those few we have discovered and whose functions we understand have a varied effect on each virus. They facilitate RNA export from the nucleus, aid in viral protein synthesis, recruit host enzymes, and even interact with the host immune machinery. The most common methods for their study are mass spectrometry and antibody assays linked to next-generation sequencing. However, given that the actual amount of modified RNA can be very small, it is important to pair meticulous scientific methodology with the appropriate detection methods and to interpret the results with a grain of salt. Once discovered, RNA modifications enhance our understanding of viruses and present a potential target in combating them. This review provides a summary of the currently known chemical modifications of viral RNA, the effects they have on viral machinery, and the methods used to detect them.
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Affiliation(s)
- Jiří František Potužník
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Prague, Czech Republic
| | - Hana Cahová
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Prague, Czech Republic
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22
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Mutual Regulation of RNA Silencing and the IFN Response as an Antiviral Defense System in Mammalian Cells. Int J Mol Sci 2020; 21:ijms21041348. [PMID: 32079277 PMCID: PMC7072894 DOI: 10.3390/ijms21041348] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2019] [Revised: 02/14/2020] [Accepted: 02/15/2020] [Indexed: 12/20/2022] Open
Abstract
RNA silencing is a posttranscriptional gene silencing mechanism directed by endogenous small non-coding RNAs called microRNAs (miRNAs). By contrast, the type-I interferon (IFN) response is an innate immune response induced by exogenous RNAs, such as viral RNAs. Endogenous and exogenous RNAs have typical structural features and are recognized accurately by specific RNA-binding proteins in each pathway. In mammalian cells, both RNA silencing and the IFN response are induced by double-stranded RNAs (dsRNAs) in the cytoplasm, but have long been considered two independent pathways. However, recent reports have shed light on crosstalk between the two pathways, which are mutually regulated by protein–protein interactions triggered by viral infection. This review provides brief overviews of RNA silencing and the IFN response and an outline of the molecular mechanism of their crosstalk and its biological implications. Crosstalk between RNA silencing and the IFN response may reveal a novel antiviral defense system that is regulated by miRNAs in mammalian cells.
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23
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Zhou S, Yang C, Zhao F, Huang Y, Lin Y, Huang C, Ma X, Du J, Wang Y, Long G, He J, Liu C, Zhang P. Double-stranded RNA deaminase ADAR1 promotes the Zika virus replication by inhibiting the activation of protein kinase PKR. J Biol Chem 2019; 294:18168-18180. [PMID: 31636123 DOI: 10.1074/jbc.ra119.009113] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2019] [Revised: 10/03/2019] [Indexed: 12/14/2022] Open
Abstract
Zika virus (ZIKV) is a mosquito-borne flavivirus that has emerged as a threat to global health. The family of adenosine deaminases acting on dsRNA (ADARs) are human host factors important for the genetic diversity and evolution of ZIKV. Here, we further investigated the role of ADAR1 in ZIKV replication by utilizing CRISPR/Cas9-based gene editing and RNAi-based gene knockdown techniques. Both ADAR1 knockout and knockdown significantly reduced ZIKV RNA synthesis, protein levels, and viral titers in several human cell lines. Trans-complementation with the full-length ADAR1 form p150 or the shorter form p110 lacking the Zα domain restored viral replication levels suppressed by the ADAR1 knockout. Moreover, we observed that the nuclear p110 form was redistributed to the cytoplasm in response to ZIKV infection. ADAR1 was not involved in viral entry but promoted viral protein translation by impairing ZIKV-induced activation of protein kinase regulated by dsRNA (PKR). Of note, the RNA-editing activity of ADAR1 was not required to promote ZIKV replication. We also found that the proviral role of ADAR1 was partially mediated through its ability to suppress IFN production and PKR activation. Our work identifies ADAR1 as a proviral factor involved in ZIKV replication, suggesting that ADAR1 could be a potential antiviral target.
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Affiliation(s)
- Shili Zhou
- Department of Immunology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, China; Key Laboratory of Tropical Disease Control, Ministry of Education, Sun Yat-sen University, Guangzhou 510080, China
| | - Chao Yang
- Department of Neurosurgery, First Affiliated Hospital of Sun Yat-sen University, Guangzhou 510080, China
| | - Fanfan Zhao
- Key Laboratory of Molecular Virology and Immunology, Institut Pasteur of Shanghai, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Yanxia Huang
- Department of Immunology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, China; Key Laboratory of Tropical Disease Control, Ministry of Education, Sun Yat-sen University, Guangzhou 510080, China
| | - Yuxia Lin
- Department of Immunology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, China; Key Laboratory of Tropical Disease Control, Ministry of Education, Sun Yat-sen University, Guangzhou 510080, China
| | - Changbai Huang
- Department of Immunology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, China; Key Laboratory of Tropical Disease Control, Ministry of Education, Sun Yat-sen University, Guangzhou 510080, China
| | - Xiaocao Ma
- Department of Immunology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, China; Key Laboratory of Tropical Disease Control, Ministry of Education, Sun Yat-sen University, Guangzhou 510080, China
| | - Jingjie Du
- Department of Immunology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, China; Key Laboratory of Tropical Disease Control, Ministry of Education, Sun Yat-sen University, Guangzhou 510080, China
| | - Yi Wang
- Department of Immunology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, China; Key Laboratory of Tropical Disease Control, Ministry of Education, Sun Yat-sen University, Guangzhou 510080, China
| | - Gang Long
- Key Laboratory of Molecular Virology and Immunology, Institut Pasteur of Shanghai, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Junfang He
- Department of Immunology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, China; Key Laboratory of Tropical Disease Control, Ministry of Education, Sun Yat-sen University, Guangzhou 510080, China
| | - Chao Liu
- Department of Immunology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, China; Key Laboratory of Tropical Disease Control, Ministry of Education, Sun Yat-sen University, Guangzhou 510080, China.
| | - Ping Zhang
- Department of Immunology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, China; Key Laboratory of Tropical Disease Control, Ministry of Education, Sun Yat-sen University, Guangzhou 510080, China.
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24
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Lamers MM, van den Hoogen BG, Haagmans BL. ADAR1: "Editor-in-Chief" of Cytoplasmic Innate Immunity. Front Immunol 2019; 10:1763. [PMID: 31404141 PMCID: PMC6669771 DOI: 10.3389/fimmu.2019.01763] [Citation(s) in RCA: 123] [Impact Index Per Article: 24.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2019] [Accepted: 07/11/2019] [Indexed: 12/12/2022] Open
Abstract
Specialized receptors that recognize molecular patterns such as double stranded RNA duplexes-indicative of viral replication-are potent triggers of the innate immune system. Although their activation is beneficial during viral infection, RNA transcribed from endogenous mobile genetic elements may also act as ligands potentially causing autoimmunity. Recent advances indicate that the adenosine deaminase ADAR1 through RNA editing is involved in dampening the canonical antiviral RIG-I-like receptor-, PKR-, and OAS-RNAse L pathways to prevent autoimmunity. However, this inhibitory effect must be overcome during viral infections. In this review we discuss ADAR1's critical role in balancing immune activation and self-tolerance.
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25
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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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26
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Type I interferon signaling, regulation and gene stimulation in chronic virus infection. Semin Immunol 2019; 43:101277. [PMID: 31155227 DOI: 10.1016/j.smim.2019.05.001] [Citation(s) in RCA: 50] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/14/2019] [Revised: 05/21/2019] [Accepted: 05/24/2019] [Indexed: 12/12/2022]
Abstract
Type I Interferons (IFN-I) mediate numerous immune interactions during viral infections, from the establishment of an antiviral state to invoking and regulating innate and adaptive immune cells that eliminate infection. While continuous IFN-I signaling plays critical roles in limiting virus replication during both acute and chronic infections, sustained IFN-I signaling also leads to chronic immune activation, inflammation and, consequently, immune exhaustion and dysfunction. Thus, an understanding of the balance between the desirable and deleterious effects of chronic IFN-I signaling will inform our quest for IFN-based therapies for chronic viral infections as well as other chronic diseases, including cancer. As such the factors involved in induction, propagation and regulation of IFN-I signaling, from the initial sensing of viral nucleotides within the cell to regulatory downstream signaling factors and resulting IFN-stimulated genes (ISGs) have received significant research attention. This review summarizes recent work on IFN-I signaling in chronic infections, and provides an update on therapeutic approaches being considered to counter such infections.
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Bou-Nader C, Gordon JM, Henderson FE, Zhang J. The search for a PKR code-differential regulation of protein kinase R activity by diverse RNA and protein regulators. RNA (NEW YORK, N.Y.) 2019; 25:539-556. [PMID: 30770398 PMCID: PMC6467004 DOI: 10.1261/rna.070169.118] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
The interferon-inducible protein kinase R (PKR) is a key component of host innate immunity that restricts viral replication and propagation. As one of the four eIF2α kinases that sense diverse stresses and direct the integrated stress response (ISR) crucial for cell survival and proliferation, PKR's versatile roles extend well beyond antiviral defense. Targeted by numerous host and viral regulators made of RNA and proteins, PKR is subject to multiple layers of endogenous control and external manipulation, driving its rapid evolution. These versatile regulators include not only the canonical double-stranded RNA (dsRNA) that activates the kinase activity of PKR, but also highly structured viral, host, and artificial RNAs that exert a full spectrum of effects. In this review, we discuss our deepening understanding of the allosteric mechanism that connects the regulatory and effector domains of PKR, with an emphasis on diverse structured RNA regulators in comparison to their protein counterparts. Through this analysis, we conclude that much of the mechanistic details that underlie this RNA-regulated kinase await structural and functional elucidation, upon which we can then describe a "PKR code," a set of structural and chemical features of RNA that are both descriptive and predictive for their effects on PKR.
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Affiliation(s)
- Charles Bou-Nader
- Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, Bethesda, Maryland 20892, USA
| | - Jackson M Gordon
- Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, Bethesda, Maryland 20892, USA
| | - Frances E Henderson
- Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, Bethesda, Maryland 20892, USA
| | - Jinwei Zhang
- Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, Bethesda, Maryland 20892, USA
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28
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Rotavirus Induces Formation of Remodeled Stress Granules and P Bodies and Their Sequestration in Viroplasms To Promote Progeny Virus Production. J Virol 2018; 92:JVI.01363-18. [PMID: 30258011 DOI: 10.1128/jvi.01363-18] [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: 08/07/2018] [Accepted: 09/20/2018] [Indexed: 02/06/2023] Open
Abstract
Rotavirus replicates in unique virus-induced cytoplasmic inclusion bodies called viroplasms (VMs), the composition and structure of which have yet to be understood. Based on the analysis of a few proteins, earlier studies reported that rotavirus infection inhibits stress granule (SG) formation and disrupts P bodies (PBs). However, the recent demonstration that rotavirus infection induces cytoplasmic relocalization and colocalization with VMs of several nuclear hnRNPs and AU-rich element-binding proteins (ARE-BPs), which are known components of SGs and PBs, suggested the possibility of rotavirus-induced remodeling of SGs and PBs, prompting us to analyze a large number of the SG and PB components to understand the status of SGs and PBs in rotavirus-infected cells. Here we demonstrate that rotavirus infection induces molecular triage by selective exclusion of a few proteins of SGs (G3BP1 and ZBP1) and PBs (DDX6, EDC4, and Pan3) and sequestration of the remodeled/atypical cellular organelles, containing the majority of their components, in the VM. The punctate SG and PB structures are seen at about 4 h postinfection (hpi), coinciding with the appearance of small VMs, many of which fuse to form mature large VMs with progression of infection. By use of small interfering RNA (siRNA)-mediated knockdown and/or ectopic overexpression, the majority of the SG and PB components, except for ADAR1, were observed to inhibit viral protein expression and virus growth. In conclusion, this study demonstrates that VMs are highly complex supramolecular structures and that rotavirus employs a novel strategy of sequestration in the VM and harnessing of the remodeled cellular RNA recycling bins to promote its growth.IMPORTANCE Rotavirus is known to replicate in specialized virus-induced cytoplasmic inclusion bodies called viroplasms (VMs), but the composition and structure of VMs are not yet understood. Here we demonstrate that rotavirus interferes with normal SG and PB assembly but promotes formation of atypical SG-PB structures by selective exclusion of a few components and employs a novel strategy of sequestration of the remodeled SG-PB granules in the VMs to promote virus growth by modulating their negative influence on virus infection. Rotavirus VMs appear to be complex supramolecular structures formed by the union of the triad of viral replication complexes and remodeled SGs and PBs, as well as other host factors, and designed to promote productive virus infection. These observations have implications for the planning of future research with the aim of understanding the structure of the VM, the mechanism of morphogenesis of the virus, and the detailed roles of host proteins in rotavirus biology.
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Li J, Xie J, Liu S, Li X, Zhang D, Wang X, Jiang J, Hu W, Zhang Y, Jin B, Zhuang R, Yin W. ADAR1 attenuates allogeneic graft rejection by suppressing miR‐21 biogenesis in macrophages and promoting M2 polarization. FASEB J 2018; 32:5162-5173. [DOI: 10.1096/fj.201701449r] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Junjie Li
- Department of Emergency School of Basic Medical SciencesFourth Military Medical UniversityXi'anChina
| | - Jiangang Xie
- Department of Emergency School of Basic Medical SciencesFourth Military Medical UniversityXi'anChina
- Department of Plastic SurgeryXijing HospitalSchool of Basic Medical SciencesFourth Military Medical UniversityXi'anChina
| | - Shanshou Liu
- Department of Emergency School of Basic Medical SciencesFourth Military Medical UniversityXi'anChina
| | - Xiao Li
- Department of Hepatobiliary SurgerySchool of Basic Medical SciencesFourth Military Medical UniversityXi'anChina
| | - Dongliang Zhang
- Department of Plastic SurgeryXijing HospitalSchool of Basic Medical SciencesFourth Military Medical UniversityXi'anChina
- Transplant Immunology Laboratory and School of Basic Medical SciencesFourth Military Medical UniversityXi'anChina
| | - Xianqi Wang
- Department of Emergency School of Basic Medical SciencesFourth Military Medical UniversityXi'anChina
| | - Jinquan Jiang
- Department of Emergency School of Basic Medical SciencesFourth Military Medical UniversityXi'anChina
| | - Wei Hu
- Transplant Immunology Laboratory and School of Basic Medical SciencesFourth Military Medical UniversityXi'anChina
- Department of ImmunologySchool of Basic Medical SciencesFourth Military Medical UniversityXi'anChina
| | - Yuan Zhang
- Transplant Immunology Laboratory and School of Basic Medical SciencesFourth Military Medical UniversityXi'anChina
| | - Boquan Jin
- Department of ImmunologySchool of Basic Medical SciencesFourth Military Medical UniversityXi'anChina
| | - Ran Zhuang
- Transplant Immunology Laboratory and School of Basic Medical SciencesFourth Military Medical UniversityXi'anChina
- Department of ImmunologySchool of Basic Medical SciencesFourth Military Medical UniversityXi'anChina
| | - Wen Yin
- Department of Emergency School of Basic Medical SciencesFourth Military Medical UniversityXi'anChina
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30
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Radetskyy R, Daher A, Gatignol A. ADAR1 and PKR, interferon stimulated genes with clashing effects on HIV-1 replication. Cytokine Growth Factor Rev 2018; 40:48-58. [PMID: 29625900 DOI: 10.1016/j.cytogfr.2018.03.007] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2018] [Revised: 03/19/2018] [Accepted: 03/19/2018] [Indexed: 12/15/2022]
Abstract
The induction of hundreds of Interferon Stimulated Genes (ISGs) subsequent to virus infection generates an antiviral state that functions to restrict virus growth at multiple steps of their replication cycles. In the context of Human Immunodeficiency Virus-1 (HIV-1), ISGs also possess antiviral functions, but some ISGs show proapoptotic or proviral activity. One of the most studied ISGs, the RNA activated Protein Kinase (PKR), shuts down the viral protein synthesis upon activation. HIV-1 has evolved to evade its inhibition by PKR through viral and cellular mechanisms. One of the cellular mechanisms is the induction of another ISG, the Adenosine Deaminase acting on RNA 1 (ADAR1). ADAR1 promotes viral replication by acting as an RNA sensing inhibitor, by editing viral RNA and by inhibiting PKR. This review challenges the orthodox dogma of ISGs as antiviral proteins, by demonstrating that two ISGs have opposing and clashing effects on viral replication.
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Affiliation(s)
- Roman Radetskyy
- Laboratory of Virus-Cell Interactions, Lady Davis Institute for Medical Research, Canada; Department of Medicine, Division of Experimental Medicine, Canada
| | - Aïcha Daher
- Laboratory of Virus-Cell Interactions, Lady Davis Institute for Medical Research, Canada
| | - Anne Gatignol
- Laboratory of Virus-Cell Interactions, Lady Davis Institute for Medical Research, Canada; Department of Medicine, Division of Experimental Medicine, Canada; Department of Medicine, Division of Infectious Diseases, Canada; Department of Microbiology-Immunology, McGill University, Montréal, Québec, Canada.
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31
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Sooreshjani MA, Gursoy UK, Aryal UK, Sintim HO. Proteomic analysis of RAW macrophages treated with cGAMP or c-di-GMP reveals differentially activated cellular pathways. RSC Adv 2018; 8:36840-36851. [PMID: 35558957 PMCID: PMC9089301 DOI: 10.1039/c8ra04603d] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2018] [Accepted: 10/23/2018] [Indexed: 12/28/2022] Open
Abstract
Global and quantitative analysis of the proteome help to reveal how host cells sense invading bacteria and respond to bacterial signaling molecules. Here, we performed label free quantitative proteomic analysis of RAW macrophages treated with host-derived cGAMP and bacterial-derived c-di-GMP, in an attempt to identify cellular pathways impacted by these dinucleotides and determine if the host responds differentially to these two cyclic dinucleotides. We identified a total of 3811 proteins of which abundances of 404 proteins in cGAMP and 236 proteins in c-di-GMP treated cells were significantly different compared to the control. Many of the proteins that were strongly and commonly upregulated, such as interferon-induced proteins 47, 202 and 204 (Ifi47, Ifi202, Ifi204), ubiquitin-activating enzyme E7 (Uba7), interferon-induced protein with tetratricopeptide repeats 1, 2 or 3 (Ifit1, Ifit2, Ifit3), ubiquitin-like protein ISG15 (ISG15), might be due to the fact that both dinucleotides promote the production of interferons, which induce the expression of many proteins. However, there were also other proteins that were differentially affected by cGAMP or c-di-GMP treatment, including probable ATP-dependent RNA helicase DHX58 (Dhx58), nuclear autoantigen Sp-100 (Sp100), MARCKS-related protein (Marcksl1) and antigen peptide transporter 2 (Tap2). This is probably due to the differential levels of IFNs produced by the dinucleotides or may indicate that non-STING activation might also contribute to the host's response to c-di-GMP and cGAMP. Interestingly Trex1, a nuclease that degrades DNA (an activator of cGAS to produce cGAMP), was upregulated (3.22 fold) upon cGAMP treatment, hinting at a possible feedback loop to regulate cGAMP synthesis. These results lay a foundation for future studies to better characterize and understand the complex c-di-GMP and cGAMP signaling network. cGAMP modulates proteins involved in antigen presentation and inflammation.![]()
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Affiliation(s)
| | - Ulvi K. Gursoy
- Department of Periodontology
- Institute of Dentistry
- University of Turku
- Turku
- Finland
| | - Uma K. Aryal
- Purdue Proteomics Facility
- Bindley Bioscience Center
- Purdue University
- West Lafayette
- USA
| | - Herman O. Sintim
- Department of Chemistry
- Purdue University
- West Lafayette
- USA
- Department of Periodontology
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32
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RNA editing by ADAR1 regulates innate and antiviral immune functions in primary macrophages. Sci Rep 2017; 7:13339. [PMID: 29042669 PMCID: PMC5645456 DOI: 10.1038/s41598-017-13580-0] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2017] [Accepted: 09/25/2017] [Indexed: 12/24/2022] Open
Abstract
ADAR1-dependent A-to-I editing has recently been recognized as a key process for marking dsRNA as self, therefore, preventing innate immune activation and affecting the development and resolution of immune-mediated diseases and infections. Here, we have determined the role of ADAR1 as a regulator of innate immune activation and modifier of viral susceptibility in primary myeloid and lymphoid cells. We show that ADAR1 knockdown significantly enhanced interferon, cytokine and chemokine production in primary macrophages that function as antiviral paracrine factors, rendering them resistant to HIV-1 infection. ADAR1 knockdown induced deregulation of the RLRs-MAVS signaling pathway, by increasing MDA5, RIG-I, IRF7 and phospho-STAT1 expression, an effect that was partially rescued by pharmacological blockade of the pathway. In summary, our results demonstrate a role of ADAR1 in regulating innate immune function in primary macrophages, suggesting that macrophages may play an essential role in disease associated to ADAR1 dysfunction. We also show that viral inhibition is exclusively dependent on innate immune activation consequence of ADAR1 knockdown, pointing towards ADAR1 as a potential target to boost antiviral immune response.
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33
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Wang C, Zou J, Ma X, Wang E, Peng G. Mechanisms and implications of ADAR-mediated RNA editing in cancer. Cancer Lett 2017; 411:27-34. [PMID: 28974449 DOI: 10.1016/j.canlet.2017.09.036] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2017] [Revised: 09/20/2017] [Accepted: 09/21/2017] [Indexed: 12/11/2022]
Abstract
Adenosine deaminases acting on RNA (ADARs) are enzymes that catalyze the conversion of adenosine (A) to inosine (I) in double-stranded RNAs. Inosine exhibits similar properties as guanosine. As a result, A-to-I editing has a great impact on edited RNAs, not only affecting the base pairing properties, but also altering codons after translation. A-to-I editing are known to mediate and diversify transcripts. However, the overall biological effect of ADARs are still largely unknown. Aberrant ADAR activity and editing dysregulation are present in a variety of cancers, including hepatocellular carcinoma, chronic myelogenous leukemia, glioblastoma and melanoma. ADAR-mediated A-to-I editing can influence uncontrolled nucleotide changes, resulting in susceptibility of cells to developmental defects and potential carcinogenicity. A deeper understanding of the biological function of ADARs may provide mechanistic insights in the development of new cancer therapy. Here, we discuss recent advances in research on ADAR in detail including the structure and function of ADARs, the biochemistry of ADAR-mediated RNA editing, and the relevance of ADAR proteins in cancer.
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Affiliation(s)
- Chen Wang
- Department of Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Jun Zou
- Department of Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Xiangyi Ma
- Department of Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Edward Wang
- OncoMed Pharmaceuticals, Redwood City, CA 94063, USA
| | - Guang Peng
- Department of Clinical Cancer Prevention, MD Anderson Cancer Center, The University of Texas, Houston, TX 77030, USA.
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34
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Gonzales-van Horn SR, Sarnow P. Making the Mark: The Role of Adenosine Modifications in the Life Cycle of RNA Viruses. Cell Host Microbe 2017; 21:661-669. [PMID: 28618265 PMCID: PMC5555051 DOI: 10.1016/j.chom.2017.05.008] [Citation(s) in RCA: 62] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Viral epitranscriptomics is a newly emerging field that has identified unique roles for RNA modifications in modulating life cycles of RNA viruses. Despite the observation of a handful of modified viral RNAs five decades ago, very little was known about how these modifications regulate viral life cycles, until recently. Here we review the pro- and anti-viral effects of methyl-6-adenosine in distinct viral life cycles, the role of 2' O-methyl modifications in RNA stability and innate immune sensing, and functions of adenosine to inosine modifications in retroviral life cycles. With roles for over 100 modifications in RNA still unknown, this is a rapidly emerging field that is destined to suggest novel antiviral therapies.
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Affiliation(s)
- Sarah R Gonzales-van Horn
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Peter Sarnow
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA.
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35
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Paces J, Nic M, Novotny T, Svoboda P. Literature review of baseline information to support the risk assessment of RNAi‐based GM plants. ACTA ACUST UNITED AC 2017. [PMCID: PMC7163844 DOI: 10.2903/sp.efsa.2017.en-1246] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Jan Paces
- Institute of Molecular Genetics of the Academy of Sciences of the Czech Republic (IMG)
| | | | | | - Petr Svoboda
- Institute of Molecular Genetics of the Academy of Sciences of the Czech Republic (IMG)
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36
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Orecchini E, Doria M, Antonioni A, Galardi S, Ciafrè SA, Frassinelli L, Mancone C, Montaldo C, Tripodi M, Michienzi A. ADAR1 restricts LINE-1 retrotransposition. Nucleic Acids Res 2016; 45:155-168. [PMID: 27658966 PMCID: PMC5224506 DOI: 10.1093/nar/gkw834] [Citation(s) in RCA: 51] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2015] [Revised: 09/08/2016] [Accepted: 09/09/2016] [Indexed: 12/16/2022] Open
Abstract
Adenosine deaminases acting on RNA (ADARs) are involved in RNA editing that converts adenosines to inosines in double-stranded RNAs. ADAR1 was demonstrated to be functional on different viruses exerting either antiviral or proviral effects. Concerning HIV-1, several studies showed that ADAR1 favors viral replication. The aim of this study was to investigate the composition of the ADAR1 ribonucleoprotein complex during HIV-1 expression. By using a dual-tag affinity purification procedure in cells expressing HIV-1 followed by mass spectrometry analysis, we identified 14 non-ribosomal ADAR1-interacting proteins, most of which are novel. A significant fraction of these proteins were previously demonstrated to be associated to the Long INterspersed Element 1 (LINE1 or L1) ribonucleoparticles and to regulate the life cycle of L1 retrotransposons that continuously re-enter host-genome. Hence, we investigated the function of ADAR1 in the regulation of L1 activity. By using different cell-culture based retrotransposition assays in HeLa cells, we demonstrated a novel function of ADAR1 as suppressor of L1 retrotransposition. Apparently, this inhibitory mechanism does not occur through ADAR1 editing activity. Furthermore, we showed that ADAR1 binds the basal L1 RNP complex. Overall, these data support the role of ADAR1 as regulator of L1 life cycle.
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Affiliation(s)
- Elisa Orecchini
- Department of Biomedicine and Prevention, University of Rome 'Tor Vergata', Via Montpellier 1, Rome 00133, Italy
| | - Margherita Doria
- Laboratory of Immunoinfectivology, Bambino Gesù Children's Hospital, IRCCS, Piazza S. Onofrio 4, Rome 00165, Italy
| | - Ambra Antonioni
- Department of Biomedicine and Prevention, University of Rome 'Tor Vergata', Via Montpellier 1, Rome 00133, Italy
| | - Silvia Galardi
- Department of Biomedicine and Prevention, University of Rome 'Tor Vergata', Via Montpellier 1, Rome 00133, Italy
| | - Silvia Anna Ciafrè
- Department of Biomedicine and Prevention, University of Rome 'Tor Vergata', Via Montpellier 1, Rome 00133, Italy
| | - Loredana Frassinelli
- Department of Biomedicine and Prevention, University of Rome 'Tor Vergata', Via Montpellier 1, Rome 00133, Italy
| | - Carmine Mancone
- Istituto Pasteur-Fondazione Cenci Bolognetti, Department of Cellular Biotechnologies and Haematology, Sapienza University of Rome, Italy.,L. Spallanzani National Institute for Infectious Diseases, IRCCS, via Portuense 292, Rome 00149, Italy
| | - Claudia Montaldo
- L. Spallanzani National Institute for Infectious Diseases, IRCCS, via Portuense 292, Rome 00149, Italy
| | - Marco Tripodi
- Istituto Pasteur-Fondazione Cenci Bolognetti, Department of Cellular Biotechnologies and Haematology, Sapienza University of Rome, Italy.,L. Spallanzani National Institute for Infectious Diseases, IRCCS, via Portuense 292, Rome 00149, Italy
| | - Alessandro Michienzi
- Department of Biomedicine and Prevention, University of Rome 'Tor Vergata', Via Montpellier 1, Rome 00133, Italy
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37
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Liddicoat BJ, Chalk AM, Walkley CR. ADAR1, inosine and the immune sensing system: distinguishing self from non-self. WILEY INTERDISCIPLINARY REVIEWS-RNA 2015; 7:157-72. [PMID: 26692549 DOI: 10.1002/wrna.1322] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/23/2015] [Revised: 11/09/2015] [Accepted: 11/10/2015] [Indexed: 11/10/2022]
Abstract
The conversion of genomically encoded adenosine to inosine in dsRNA is termed as A-to-I RNA editing. This process is catalyzed by two of the three mammalian ADAR proteins (ADAR1 and ADAR2) both of which have essential functions for normal organismal homeostasis. The phenotype of ADAR2 deficiency can be primarily ascribed to a lack of site-selective editing of a single transcript in the brain. In contrast, the biology and substrates responsible for the Adar1(-/-) phenotype have remained more elusive. Several recent studies have identified that a feature of absence or reductions of ADAR1 activity, conserved across human and mouse models, is a profound activation of interferon-stimulated gene signatures and innate immune responses. Further analysis of this observation has lead to the conclusion that editing by ADAR1 is required to prevent activation of the cytosolic innate immune system, primarily focused on the dsRNA sensor MDA5 and leading to downstream signaling via MAVS. The delineation of this mechanism places ADAR1 at the interface between the cells ability to differentiate self- from non-self dsRNA. Based on MDA5 dsRNA recognition requisites, the mechanism indicates that the type of dsRNA must fulfil a particular structural characteristic, rather than a sequence-specific requirement. While additional studies are required to molecularly verify the genetic model, the observations to date collectively identify A-to-I editing by ADAR1 as a key modifier of the cellular response to endogenous dsRNA.
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Affiliation(s)
- Brian J Liddicoat
- St. Vincent's Institute of Medical Research, Fitzroy, Victoria, Australia.,Department of Medicine, St. Vincent's Hospital, University of Melbourne, Fitzroy, Victoria, Australia
| | - Alistair M Chalk
- St. Vincent's Institute of Medical Research, Fitzroy, Victoria, Australia.,Department of Medicine, St. Vincent's Hospital, University of Melbourne, Fitzroy, Victoria, Australia
| | - Carl R Walkley
- St. Vincent's Institute of Medical Research, Fitzroy, Victoria, Australia.,Department of Medicine, St. Vincent's Hospital, University of Melbourne, Fitzroy, Victoria, Australia
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38
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Cuadrado E, Booiman T, van Hamme JL, Jansen MH, van Dort KA, Vanderver A, Rice GI, Crow YJ, Kootstra NA, Kuijpers TW. ADAR1 Facilitates HIV-1 Replication in Primary CD4+ T Cells. PLoS One 2015; 10:e0143613. [PMID: 26629815 PMCID: PMC4667845 DOI: 10.1371/journal.pone.0143613] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2015] [Accepted: 11/06/2015] [Indexed: 01/09/2023] Open
Abstract
Unlike resting CD4+ T cells, activated CD4+T cells are highly susceptible to infection of human immunodeficiency virus 1 (HIV-1). HIV-1 infects T cells and macrophages without activating the nucleic acid sensors and the anti-viral type I interferon response. Adenosine deaminase acting on RNA 1 (ADAR1) is an RNA editing enzyme that displays antiviral activity against several RNA viruses. Mutations in ADAR1 cause the autoimmune disorder Aicardi-Goutieères syndrome (AGS). This disease is characterized by an inappropriate activation of the interferon-stimulated gene response. Here we show that HIV-1 replication, in ADAR1-deficient CD4+T lymphocytes from AGS patients, is blocked at the level of protein translation. Furthermore, viral protein synthesis block is accompanied by an activation of interferon-stimulated genes. RNA silencing of ADAR1 in Jurkat cells also inhibited HIV-1 protein synthesis. Our data support that HIV-1 requires ADAR1 for efficient replication in human CD4+T cells.
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Affiliation(s)
- Eloy Cuadrado
- Department of Experimental Immunology, Academic Medical Center (AMC), University of Amsterdam (UvA), Amsterdam, The Netherlands
- * E-mail:
| | - Thijs Booiman
- Department of Experimental Immunology, Academic Medical Center (AMC), University of Amsterdam (UvA), Amsterdam, The Netherlands
- Sanquin Research, Landsteiner Laboratory and Center for Infection and Immunity (CINIMA) at the Academic Medical Center of the University of Amsterdam, Amsterdam, The Netherlands
| | - John L. van Hamme
- Department of Experimental Immunology, Academic Medical Center (AMC), University of Amsterdam (UvA), Amsterdam, The Netherlands
- Sanquin Research, Landsteiner Laboratory and Center for Infection and Immunity (CINIMA) at the Academic Medical Center of the University of Amsterdam, Amsterdam, The Netherlands
| | - Machiel H. Jansen
- Department of Experimental Immunology, Academic Medical Center (AMC), University of Amsterdam (UvA), Amsterdam, The Netherlands
| | - Karel A. van Dort
- Department of Experimental Immunology, Academic Medical Center (AMC), University of Amsterdam (UvA), Amsterdam, The Netherlands
- Sanquin Research, Landsteiner Laboratory and Center for Infection and Immunity (CINIMA) at the Academic Medical Center of the University of Amsterdam, Amsterdam, The Netherlands
| | - Adeline Vanderver
- Center for Genetic Medicine Research, Children’s National Medical Center, Washington DC, United States of America
| | - Gillian I. Rice
- Manchester Centre for Genomic Medicine, University of Manchester, Manchester Academic Health Sciences Centre (MAHSC), Manchester, United Kingdom
| | - Yanick J. Crow
- Manchester Centre for Genomic Medicine, University of Manchester, Manchester Academic Health Sciences Centre (MAHSC), Manchester, United Kingdom
- INSERM UMR 1163, Laboratory of Neurogenetics and Neuroinflammation, Institut Imagine, Hôpital Necker, Paris, France
| | - Neeltje A. Kootstra
- Department of Experimental Immunology, Academic Medical Center (AMC), University of Amsterdam (UvA), Amsterdam, The Netherlands
- Sanquin Research, Landsteiner Laboratory and Center for Infection and Immunity (CINIMA) at the Academic Medical Center of the University of Amsterdam, Amsterdam, The Netherlands
| | - Taco W. Kuijpers
- Department of Experimental Immunology, Academic Medical Center (AMC), University of Amsterdam (UvA), Amsterdam, The Netherlands
- Emma Children’s Hospital, Dept of Pediatric Hematology, Immunology and Infectious disease, AMC, UvA, Amsterdam, The Netherlands
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George CX, John L, Samuel CE. An RNA editor, adenosine deaminase acting on double-stranded RNA (ADAR1). J Interferon Cytokine Res 2015; 34:437-46. [PMID: 24905200 DOI: 10.1089/jir.2014.0001] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Adenosine deaminase acting on RNA1 (ADAR1) catalyzes the C6 deamination of adenosine (A) to produce inosine (I) in regions of RNA with double-stranded (ds) character. This process is known as A-to-I RNA editing. Alternative promoters drive the expression of the Adar1 gene and alternative splicing gives rise to transcripts that encode 2 ADAR1 protein size isoforms. ADAR1 p150 is an interferon (IFN)-inducible dsRNA adenosine deaminase found in the cytoplasm and nucleus, whereas ADAR1 p110 is constitutively expressed and nuclear in localization. Dependent on the duplex structure of the dsRNA substrate, deamination of adenosine by ADAR can be either highly site-selective or nonspecific. A-to-I editing can alter the stability of RNA structures and the coding of RNA as I is read as G instead of A by ribosomes during mRNA translation and by polymerases during RNA replication. A-to-I editing is of broad physiologic significance. Both the production and the action of IFNs, and hence the subsequent interaction of viruses with their hosts, are among the processes affected by A-to-I editing.
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Affiliation(s)
- Cyril X George
- Department of Molecular, Cellular and Developmental Biology, University of California , Santa Barbara, California
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Nellimarla S, Mossman KL. Extracellular dsRNA: its function and mechanism of cellular uptake. J Interferon Cytokine Res 2015; 34:419-26. [PMID: 24905198 DOI: 10.1089/jir.2014.0002] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Double-stranded RNA (dsRNA) is arguably the most potent viral trigger of innate immune signaling. Its activity has been recognized for over 5 decades, first as a toxin, then as a central component of the interferon system, as an efficient activator of antiviral responses and an immunomodulator for therapeutic applications. Nucleic acid sensing is the main basis for antiviral defense systems throughout the diverse forms of life from bacteria to plants and animals. Pattern recognition receptors of the host defense system not only sense viral dsRNA as a pathogen-associated molecular pattern in infected cells, but also recognize circulating endogenous dsRNA, a nonmicrobial signal, as a danger-associated molecular pattern, often leading to autoimmunity. Despite the effects of extracellular viral and host dsRNA associated with infection and autoimmunity, respectively, the understanding of cellular mechanisms for its recognition and uptake has only been appreciated in recent years. This review presents an overview of this unique form of nucleic acid, addressing its roles in infection, autoimmunity, and host sensing mechanisms. The goal of this review is to highlight the novel findings with a focus on extracellular recognition and uptake by the cell.
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Affiliation(s)
- Srinivas Nellimarla
- 1 Department of Pathology and Molecular Medicine, McMaster Immunology Research Center, Michael DeGroote Institute for Infectious Disease Research, McMaster University , Hamilton, Ontario, Canada
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Double-stranded RNA-specific adenosine deaminase 1 (ADAR1) promotes EIAV replication and infectivity. Virology 2015; 476:364-371. [PMID: 25589239 DOI: 10.1016/j.virol.2014.12.038] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2014] [Revised: 10/23/2014] [Accepted: 12/23/2014] [Indexed: 12/23/2022]
Abstract
Adenosine deaminases that act on RNA (ADARs) have been reported to be functional on various viruses. ADAR1 may exhibit antiviral or proviral activity depending on the type of virus. Human immunodeficiency virus (HIV)-1 is the most well-studied lentivirus with respect to its interaction with ADAR1, and variable results have been reported. In this study, we demonstrated that equine ADAR1 (eADAR1) was a positive regulator of equine infectious anemia virus (EIAV), another lentivirus of the Retroviridae family. First, eADAR1 significantly promoted EIAV replication, and the enhancement of viral protein expression was associated with the long terminal repeat (LTR) and Rev response element (RRE) regions. Second, the RNA binding domain 1 of eADAR1 was essential only for enhancing LTR-mediated gene expression. Third, in contrast with APOBEC proteins, which have been shown to reduce lentiviral infectivity, eADAR1 increased the EIAV infectivity. This study indicated that eADAR1 was proviral rather than antiviral for EIAV.
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Cachat A, Alais S, Chevalier SA, Journo C, Fusil F, Dutartre H, Boniface A, Ko NL, Gessain A, Cosset FL, Suspène R, Vartanian JP, Mahieux R. ADAR1 enhances HTLV-1 and HTLV-2 replication through inhibition of PKR activity. Retrovirology 2014; 11:93. [PMID: 25389016 PMCID: PMC4245799 DOI: 10.1186/s12977-014-0093-9] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2014] [Accepted: 10/16/2014] [Indexed: 11/25/2022] Open
Abstract
Background The role of innate immunity in general and of type I interferon
(IFN-I) in particular in HTLV-1 pathogenesis is still a matter of debate.
ADAR1-p150 is an Interferon Stimulated Gene (ISG) induced by IFN-I that can edit
viral RNAs. We therefore investigated whether it could play the role of an
anti-HTLV factor. Results We demonstrate here that ADAR1 is also expressed in the absence of
IFN stimulation in activated primary T-lymphocytes that are the natural target of
this virus and in HTLV-1 or HTLV-2 chronically infected T-cells. ADAR1 expression
is also increased in primary lymphocytes obtained from HTLV-1 infected
individuals. We show that ADAR1 enhances HTLV-1 and HTLV-2 infection in
T-lymphocytes and that this proviral effect is independent from its editing
activity. ADAR1 expression suppresses IFN-α inhibitory effect on HTLV-1 and HTLV-2
and acts through the repression of PKR phosphorylation. Discussion This study demonstrates that two interferon stimulated genes, i.e.
PKR and ADAR1 have opposite effects on HTLV replication in
vivo. The balanced expression of those proteins could determine the
fate of the viral cycle in the course of infection. Electronic supplementary material The online version of this article (doi:10.1186/s12977-014-0093-9) contains supplementary material, which is available to authorized
users.
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Affiliation(s)
- Anne Cachat
- Equipe Oncogenèse Rétrovirale, Lyon, Cedex 07, France. .,Equipe labellisée "Ligue Nationale Contre le Cancer", Lyon, Cedex 07, France. .,Centre international de recherche en infectiologie, INSERM U1111 - CNRS UMR5308, Lyon, Cedex 07, France. .,Ecole Normale Supérieure de Lyon, 46 allée d'Italie, 69364, Lyon, Cedex 07, France. .,Université Lyon 1, LabEx ECOFECT - Eco-evolutionary dynamics of infectious diseases, 69364, Lyon, Cedex 07, France.
| | - Sandrine Alais
- Equipe Oncogenèse Rétrovirale, Lyon, Cedex 07, France. .,Equipe labellisée "Ligue Nationale Contre le Cancer", Lyon, Cedex 07, France. .,Centre international de recherche en infectiologie, INSERM U1111 - CNRS UMR5308, Lyon, Cedex 07, France. .,Ecole Normale Supérieure de Lyon, 46 allée d'Italie, 69364, Lyon, Cedex 07, France. .,Université Lyon 1, LabEx ECOFECT - Eco-evolutionary dynamics of infectious diseases, 69364, Lyon, Cedex 07, France.
| | - Sébastien Alain Chevalier
- Equipe Oncogenèse Rétrovirale, Lyon, Cedex 07, France. .,Equipe labellisée "Ligue Nationale Contre le Cancer", Lyon, Cedex 07, France. .,Centre international de recherche en infectiologie, INSERM U1111 - CNRS UMR5308, Lyon, Cedex 07, France. .,Ecole Normale Supérieure de Lyon, 46 allée d'Italie, 69364, Lyon, Cedex 07, France. .,Université Lyon 1, LabEx ECOFECT - Eco-evolutionary dynamics of infectious diseases, 69364, Lyon, Cedex 07, France.
| | - Chloé Journo
- Equipe Oncogenèse Rétrovirale, Lyon, Cedex 07, France. .,Equipe labellisée "Ligue Nationale Contre le Cancer", Lyon, Cedex 07, France. .,Centre international de recherche en infectiologie, INSERM U1111 - CNRS UMR5308, Lyon, Cedex 07, France. .,Ecole Normale Supérieure de Lyon, 46 allée d'Italie, 69364, Lyon, Cedex 07, France. .,Université Lyon 1, LabEx ECOFECT - Eco-evolutionary dynamics of infectious diseases, 69364, Lyon, Cedex 07, France.
| | - Floriane Fusil
- Centre international de recherche en infectiologie, INSERM U1111 - CNRS UMR5308, Lyon, Cedex 07, France. .,Ecole Normale Supérieure de Lyon, 46 allée d'Italie, 69364, Lyon, Cedex 07, France. .,Université Lyon 1, LabEx ECOFECT - Eco-evolutionary dynamics of infectious diseases, 69364, Lyon, Cedex 07, France. .,Equipe virus enveloppés, Lyon, Cedex 07, France.
| | - Hélène Dutartre
- Equipe Oncogenèse Rétrovirale, Lyon, Cedex 07, France. .,Equipe labellisée "Ligue Nationale Contre le Cancer", Lyon, Cedex 07, France. .,Centre international de recherche en infectiologie, INSERM U1111 - CNRS UMR5308, Lyon, Cedex 07, France. .,Ecole Normale Supérieure de Lyon, 46 allée d'Italie, 69364, Lyon, Cedex 07, France. .,Université Lyon 1, LabEx ECOFECT - Eco-evolutionary dynamics of infectious diseases, 69364, Lyon, Cedex 07, France.
| | - Adrien Boniface
- Equipe Oncogenèse Rétrovirale, Lyon, Cedex 07, France. .,Equipe labellisée "Ligue Nationale Contre le Cancer", Lyon, Cedex 07, France. .,Centre international de recherche en infectiologie, INSERM U1111 - CNRS UMR5308, Lyon, Cedex 07, France. .,Ecole Normale Supérieure de Lyon, 46 allée d'Italie, 69364, Lyon, Cedex 07, France. .,Université Lyon 1, LabEx ECOFECT - Eco-evolutionary dynamics of infectious diseases, 69364, Lyon, Cedex 07, France. .,Biology Department, Master Biosciences, Lyon, Cedex 07, France.
| | - Nga Ling Ko
- Unité d'épidémiologie et physiopathoglogie des virus oncogènes, Institut Pasteur, Paris, 75015, France.
| | - Antoine Gessain
- Unité d'épidémiologie et physiopathoglogie des virus oncogènes, Institut Pasteur, Paris, 75015, France.
| | - François-Loïc Cosset
- Centre international de recherche en infectiologie, INSERM U1111 - CNRS UMR5308, Lyon, Cedex 07, France. .,Ecole Normale Supérieure de Lyon, 46 allée d'Italie, 69364, Lyon, Cedex 07, France. .,Université Lyon 1, LabEx ECOFECT - Eco-evolutionary dynamics of infectious diseases, 69364, Lyon, Cedex 07, France. .,Equipe virus enveloppés, Lyon, Cedex 07, France.
| | - Rodolphe Suspène
- Unité de rétrovirologie moléculaire, Institut Pasteur, Paris, 75015, France.
| | | | - Renaud Mahieux
- Equipe Oncogenèse Rétrovirale, Lyon, Cedex 07, France. .,Equipe labellisée "Ligue Nationale Contre le Cancer", Lyon, Cedex 07, France. .,Centre international de recherche en infectiologie, INSERM U1111 - CNRS UMR5308, Lyon, Cedex 07, France. .,Ecole Normale Supérieure de Lyon, 46 allée d'Italie, 69364, Lyon, Cedex 07, France. .,Université Lyon 1, LabEx ECOFECT - Eco-evolutionary dynamics of infectious diseases, 69364, Lyon, Cedex 07, France.
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Burugu S, Daher A, Meurs EF, Gatignol A. HIV-1 translation and its regulation by cellular factors PKR and PACT. Virus Res 2014; 193:65-77. [PMID: 25064266 DOI: 10.1016/j.virusres.2014.07.014] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2014] [Revised: 07/13/2014] [Accepted: 07/14/2014] [Indexed: 12/24/2022]
Abstract
The synthesis of proteins from viral mRNA is the first step towards viral assembly. Viruses are dependent upon the cellular translation machinery to synthesize their own proteins. The synthesis of proteins from the human immunodeficiency virus (HIV) type 1 and 2 RNAs utilize several alternative mechanisms. The regulation of viral protein production requires a constant interplay between viral requirements and the cell response to viral infection. Among the antiviral cell responses, the interferon-induced RNA activated protein kinase, PKR, regulates the cellular and viral translation. During HIV-1 infection, PKR activation is highly regulated by viral and cellular factors. The cellular TAR RNA Binding Protein, TRBP, the Adenosine Deaminase acting on RNA, ADAR1, and the PKR Activator, PACT, play important roles. Recent data show that PACT changes its function from activator to inhibitor in HIV-1 infected cells. Therefore, HIV-1 has evolved to replicate in cells in which TRBP, ADAR1 and PACT prevent PKR activation to allow efficient viral protein synthesis. This proper translation will initiate the assembly of viral particles.
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Affiliation(s)
- Samantha Burugu
- Virus-cell Interactions Laboratory, Lady Davis Institute for Medical Research, Montréal, QC, Canada; Department of Microbiology and Immunology, McGill University, Montréal, QC, Canada
| | - Aïcha Daher
- Virus-cell Interactions Laboratory, Lady Davis Institute for Medical Research, Montréal, QC, Canada
| | - Eliane F Meurs
- Institut Pasteur, Department of Virology, Hepacivirus and Innate Immunity Unit, Paris, France
| | - Anne Gatignol
- Virus-cell Interactions Laboratory, Lady Davis Institute for Medical Research, Montréal, QC, Canada; Department of Microbiology and Immunology, McGill University, Montréal, QC, Canada; Department of Medicine, Division of Experimental Medicine, McGill University, Montréal, QC, Canada.
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Gleghorn ML, Maquat LE. 'Black sheep' that don't leave the double-stranded RNA-binding domain fold. Trends Biochem Sci 2014; 39:328-40. [PMID: 24954387 DOI: 10.1016/j.tibs.2014.05.003] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2014] [Revised: 05/19/2014] [Accepted: 05/19/2014] [Indexed: 12/28/2022]
Abstract
The canonical double-stranded RNA (dsRNA)-binding domain (dsRBD) is composed of an α1-β1-β2-β3-α2 secondary structure that folds in three dimensions to recognize dsRNA. Recently, structural and functional studies of divergent dsRBDs revealed adaptations that include intra- and/or intermolecular protein interactions, sometimes in the absence of detectable dsRNA-binding ability. We describe here how discrete dsRBD components can accommodate pronounced amino-acid sequence changes while maintaining the core fold. We exemplify the growing importance of divergent dsRBDs in mRNA decay by discussing Dicer, Staufen (STAU)1 and 2, trans-activation responsive RNA-binding protein (TARBP)2, protein activator of protein kinase RNA-activated (PKR) (PACT), DiGeorge syndrome critical region (DGCR)8, DEAH box helicase proteins (DHX) 9 and 30, and dsRBD-like fold-containing proteins that have ribosome-related functions. We also elaborate on the computational limitations to discovering yet-to-be-identified divergent dsRBDs.
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Affiliation(s)
- Michael L Gleghorn
- Department of Biochemistry and Biophysics, School of Medicine and Dentistry, University of Rochester, Rochester, NY 14642, USA; Center for RNA Biology, University of Rochester, Rochester, NY 14642, USA
| | - Lynne E Maquat
- Department of Biochemistry and Biophysics, School of Medicine and Dentistry, University of Rochester, Rochester, NY 14642, USA; Center for RNA Biology, University of Rochester, Rochester, NY 14642, USA.
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Abstract
Adenosine-to-inosine conversion (A-to-I editing), a posttranscriptional modification on RNA, contributes to extensive transcriptome diversity. A-to-I editing is a hydrolytic deamination process, catalyzed by adenosine deAminase acting on double-stranded RNA (ADAR) family of enzymes. ADARs are essential for normal mammalian development, and disturbance in RNA editing has been implicated in various pathologic disorders, including cancer. Thanks to next-generation sequencing, rich databases of transcriptome evolution for cancer development at the resolution of single nucleotide have been generated. Extensive bioinformatic analysis revealed a complex picture of RNA editing change during transformation. Cancer displayed global hypoediting of Alu-repetitive elements with gene-specific editing pattern. In particular, hepatocellular carcinoma editome is severely disrupted and characterized by hyper- and hypoediting of different genes, such as hyperedited AZIN1 (antizyme inhibitor 1) and FLNB (filamin B, β) and hypoedited COPA (coatomer protein complex, subunit α). In hepatocellular carcinoma, not only the recoding editing in exons, but also the editing in noncoding regions (e.g., Alu-repetitive elements and microRNA) displays such complex editing pattern with site-specific editing trend. In this review, we will discuss current research progress on the involvement of abnormal A-to-I editing in cancer development, more specifically on hepatocellular carcinoma.
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Affiliation(s)
- Lihua Qi
- Authors' Affiliations: Cancer Science Institute of Singapore, National University of Singapore, Singapore; and Harvard Stem Cell Institute, Harvard Medical School, Boston, Massachusetts
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Dominguez-Gutierrez PR, Ceribelli A, Satoh M, Sobel ES, Reeves WH, Chan EKL. Elevated signal transducers and activators of transcription 1 correlates with increased C-C motif chemokine ligand 2 and C-X-C motif chemokine 10 levels in peripheral blood of patients with systemic lupus erythematosus. Arthritis Res Ther 2014; 16:R20. [PMID: 24451065 PMCID: PMC3978614 DOI: 10.1186/ar4448] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2013] [Accepted: 01/14/2014] [Indexed: 02/09/2023] Open
Abstract
INTRODUCTION The present study examines the levels of recently reported biomarkers, adenosine deaminase acting on RNA (ADAR), C-C motif chemokine ligand 2 (CCL2), C-X-C motif chemokine 10 (CXCL10), signal transducers and activators of transcription 1 (STAT1), and miR-146a in systemic lupus erythematosus (SLE) patients over multiple visits. METHODS Peripheral blood leukocytes were collected from 65 healthy donors and 103 SLE patients, 60 of whom had samples from 2 or more visits. Total RNA was isolated and analyzed for the expression of mRNA and microRNA using Taqman real time PCR assays. Relative expression of I-IFN signature genes, chemokines, and miR-146a were determined by the ΔΔCT method. Results were correlated with clinical data and analyzed by Wilcoxon/Kruskal-Wallis test and Fisher's exact test. RESULTS Levels of ADAR, CCL2, CXCL10, and STAT1 in SLE were significantly elevated compared with the healthy controls (P <0.0001). ADAR, CCL2, and CXCL10 showed significant correlation with IFN score in both healthy donors (P <0.0033) and SLE patients (P <0.0001). In SLE patients, miR-146a level was not significantly different from healthy controls nor correlated to the IFN score. Two STAT1 populations were identified: a low STAT1 and a high STAT1 group. High STAT1 patient visits displayed higher (P ≤0.0020) levels of CCL2 and CXCL10 than the low STAT1 patient visits. STAT1 levels correlated with IFN score in low STAT1 group but not in high STAT1 group. More importantly, high STAT1 levels appeared as an enhancer of CCL2 and CXCL10 as indicated by the significantly stronger correlation of CCL2 and CXCL10 with IFN score in high STAT1 patient visits relative to low STAT1 patient visits. CONCLUSION Our data indicate a novel role for STAT1 in the pathogenesis of SLE as an expression enhancer of CCL2 and CXCL10 in SLE patients with high levels of STAT1. Future study is needed to examine the exact role of STAT1 in the etiology of SLE.
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Affiliation(s)
- Paul R Dominguez-Gutierrez
- Department of Oral Biology, University of Florida, P.O. Box 100424, 1395 Center Drive, Gainesville, FL 32610-0424, USA
- Current address: Department of Urology, University of Florida, 1600 SW Archer Road, Gainesville, FL 32610-0247, USA
| | - Angela Ceribelli
- Department of Oral Biology, University of Florida, P.O. Box 100424, 1395 Center Drive, Gainesville, FL 32610-0424, USA
- Current address: Rheumatology and Clinical Immunology, Humanitas Clinical and Research Center, Via A. Manzoni 56, 20089 Rozzano, Italy
- Current address: BIOMETRA Department, University of Milan, Milan, Italy
| | - Minoru Satoh
- Division of Rheumatology and Clinical Immunology, Department of Medicine, University of Florida, P.O. Box 100221, 1600 SW Archer Rd, Gainesville, FL 32610-0221, USA
- School of Health Sciences, University of Occupational and Environmental Health, Japan, 1-1 Isei-ga-oka, Yahata-nishi-ku, Kitakyushu, Fukuoka 807-8555, Japan
| | - Eric S Sobel
- Division of Rheumatology and Clinical Immunology, Department of Medicine, University of Florida, P.O. Box 100221, 1600 SW Archer Rd, Gainesville, FL 32610-0221, USA
| | - Westley H Reeves
- Division of Rheumatology and Clinical Immunology, Department of Medicine, University of Florida, P.O. Box 100221, 1600 SW Archer Rd, Gainesville, FL 32610-0221, USA
| | - Edward KL Chan
- Department of Oral Biology, University of Florida, P.O. Box 100424, 1395 Center Drive, Gainesville, FL 32610-0424, USA
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Clerzius G, Shaw E, Daher A, Burugu S, Gélinas JF, Ear T, Sinck L, Routy JP, Mouland AJ, Patel RC, Gatignol A. The PKR activator, PACT, becomes a PKR inhibitor during HIV-1 replication. Retrovirology 2013; 10:96. [PMID: 24020926 PMCID: PMC3848765 DOI: 10.1186/1742-4690-10-96] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2012] [Accepted: 09/06/2013] [Indexed: 11/29/2022] Open
Abstract
Background HIV-1 translation is modulated by the activation of the interferon (IFN)-inducible Protein Kinase RNA-activated (PKR). PKR phosphorylates its downstream targets, including the alpha subunit of the eukaryotic translation Initiation Factor 2 (eIF2α), which decreases viral replication. The PKR Activator (PACT) is known to activate PKR after a cellular stress. In lymphocytic cell lines, HIV-1 activates PKR only transiently and not when cells replicate the virus at high levels. The regulation of this activation is due to a combination of viral and cellular factors that have been only partially identified. Results PKR is transiently induced and activated in peripheral blood mononuclear cells after HIV-1 infection. The addition of IFN reduces viral replication, and induces both the production and phosphorylation of PKR. In lymphocytic Jurkat cells infected by HIV-1, a multiprotein complex around PKR contains the double-stranded RNA binding proteins (dsRBPs), adenosine deaminase acting on RNA (ADAR)1 and PACT. In HEK 293T cells transfected with an HIV-1 molecular clone, PACT unexpectedly inhibited PKR and eIF2α phosphorylation and increased HIV-1 protein expression and virion production in the presence of either endogenous PKR alone or overexpressed PKR. The comparison between different dsRBPs showed that ADAR1, TAR RNA Binding Protein (TRBP) and PACT inhibit PKR and eIF2α phosphorylation in HIV-infected cells, whereas Staufen1 did not. Individual or a combination of short hairpin RNAs against PACT or ADAR1 decreased HIV-1 protein expression. In the astrocytic cell line U251MG, which weakly expresses TRBP, PACT mediated an increased HIV-1 protein expression and a decreased PKR phosphorylation. In these cells, a truncated PACT, which constitutively activates PKR in non-infected cells showed no activity on either PKR or HIV-1 protein expression. Finally, PACT and ADAR1 interact with each other in the absence of RNAs. Conclusion In contrast to its previously described activity, PACT contributes to PKR dephosphorylation during HIV-1 replication. This activity is in addition to its heterodimer formation with TRBP and could be due to its binding to ADAR1. HIV-1 has evolved to replicate in cells with high levels of TRBP, to induce the expression of ADAR1 and to change the function of PACT for PKR inhibition and increased replication.
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Affiliation(s)
- Guerline Clerzius
- Lady Davis Institute for Medical Research, 3999 Côte Ste Catherine, Montréal, QC H3T 1E2, Canada.
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48
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Nallagatla SR, Jones CN, Ghosh SKB, Sharma SD, Cameron CE, Spremulli LL, Bevilacqua PC. Native tertiary structure and nucleoside modifications suppress tRNA's intrinsic ability to activate the innate immune sensor PKR. PLoS One 2013; 8:e57905. [PMID: 23483938 PMCID: PMC3587421 DOI: 10.1371/journal.pone.0057905] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2012] [Accepted: 01/28/2013] [Indexed: 11/17/2022] Open
Abstract
Interferon inducible protein kinase PKR is an essential component of innate immunity. It is activated by long stretches of dsRNA and provides the first line of host defense against pathogens by inhibiting translation initiation in the infected cell. Many cellular and viral transcripts contain nucleoside modifications and/or tertiary structure that could affect PKR activation. We have previously demonstrated that a 5'-end triphosphate-a signature of certain viral and bacterial transcripts-confers the ability of relatively unstructured model RNA transcripts to activate PKR to inhibit translation, and that this activation is abrogated by certain modifications present in cellular RNAs. In order to understand the biological implications of native RNA tertiary structure and nucleoside modifications on PKR activation, we study here the heavily modified cellular tRNAs and the unmodified or the lightly modified mitochondrial tRNAs (mt-tRNA). We find that both a T7 transcript of yeast tRNA(Phe) and natively extracted total bovine liver mt-tRNA activate PKR in vitro, whereas native E. coli, bovine liver, yeast, and wheat tRNA(Phe) do not, nor do a variety of base- or sugar-modified T7 transcripts. These results are further supported by activation of PKR by a natively folded T7 transcript of tRNA(Phe)in vivo supporting the importance of tRNA modification in suppressing PKR activation in cells. We also examine PKR activation by a T7 transcript of the A14G pathogenic mutant of mt-tRNA(Leu), which is known to dimerize, and find that the misfolded dimeric form activates PKR in vitro while the monomeric form does not. Overall, the in vitro and in vivo findings herein indicate that tRNAs have an intrinsic ability to activate PKR and that nucleoside modifications and native RNA tertiary folding may function, at least in part, to suppress such activation, thus serving to distinguish self and non-self tRNA in innate immunity.
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Affiliation(s)
- Subba Rao Nallagatla
- Department of Chemistry and Center for RNA Molecular Biology, The Pennsylvania State University, University Park, PA, USA
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Learning from the messengers: innate sensing of viruses and cytokine regulation of immunity - clues for treatments and vaccines. Viruses 2013; 5:470-527. [PMID: 23435233 PMCID: PMC3640511 DOI: 10.3390/v5020470] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2012] [Revised: 01/22/2013] [Accepted: 01/23/2013] [Indexed: 12/14/2022] Open
Abstract
Virus infections are a major global public health concern, and only via substantial knowledge of virus pathogenesis and antiviral immune responses can we develop and improve medical treatments, and preventive and therapeutic vaccines. Innate immunity and the shaping of efficient early immune responses are essential for control of viral infections. In order to trigger an efficient antiviral defense, the host senses the invading microbe via pattern recognition receptors (PRRs), recognizing distinct conserved pathogen-associated molecular patterns (PAMPs). The innate sensing of the invading virus results in intracellular signal transduction and subsequent production of interferons (IFNs) and proinflammatory cytokines. Cytokines, including IFNs and chemokines, are vital molecules of antiviral defense regulating cell activation, differentiation of cells, and, not least, exerting direct antiviral effects. Cytokines shape and modulate the immune response and IFNs are principle antiviral mediators initiating antiviral response through induction of antiviral proteins. In the present review, I describe and discuss the current knowledge on early virus–host interactions, focusing on early recognition of virus infection and the resulting expression of type I and type III IFNs, proinflammatory cytokines, and intracellular antiviral mediators. In addition, the review elucidates how targeted stimulation of innate sensors, such as toll-like receptors (TLRs) and intracellular RNA and DNA sensors, may be used therapeutically. Moreover, I present and discuss data showing how current antimicrobial therapies, including antibiotics and antiviral medication, may interfere with, or improve, immune response.
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The multiple functions of TRBP, at the hub of cell responses to viruses, stress, and cancer. Microbiol Mol Biol Rev 2013; 76:652-66. [PMID: 22933564 DOI: 10.1128/mmbr.00012-12] [Citation(s) in RCA: 69] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
The TAR RNA binding protein (TRBP) has emerged as a key player in many cellular processes. First identified as a cellular protein that facilitates the replication of human immunodeficiency virus, TRBP has since been shown to inhibit the activation of protein kinase R (PKR), a protein involved in innate immune responses and the cellular response to stress. It also binds to the PKR activator PACT and regulates its function. TRBP also contributes to RNA interference as an integral part of the minimal RNA-induced silencing complex with Dicer and Argonaute proteins. Due to its multiple functions in the cell, TRBP is involved in oncogenesis when its sequence is mutated or its expression is deregulated. The depletion or overexpression of TRBP results in malignancy, suggesting that the balance of TRBP expression is key to normal cellular function. These studies show that TRBP is multifunctional and mediates cross talk between different pathways. Its activities at the molecular level impact the cellular function from normal development to cancer and the response to infections.
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