101
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Ng CS, Kato H, Fujita T. Fueling Type I Interferonopathies: Regulation and Function of Type I Interferon Antiviral Responses. J Interferon Cytokine Res 2019; 39:383-392. [PMID: 30897023 DOI: 10.1089/jir.2019.0037] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
In conjunction with the development of genome-wide technology, numerous studies have revealed the importance of regulatory mechanisms to avoid the onset of autoimmunity. In this, protein regulators and the newly identified low-abundant RNA species participate in the regulation of type I interferon (IFN-I) and proinflammatory genes induced by innate immune sensors. In this review, we briefly look into some of the autoimmune diseases profiled by dysregulations of IFN-I signaling and the regulatory mechanisms critical for immunological homeostasis.
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Affiliation(s)
- Chen Seng Ng
- 1 Institute for Quantitative and Computational Biosciences, Immunology and Molecular Genetics, University of California, Los Angeles, California.,2 Department of Microbiology, Immunology and Molecular Genetics, University of California, Los Angeles, California
| | - Hiroki Kato
- 3 Institute of Cardiovascular Immunology, University Hospitals, University of Bonn, Bonn, Germany
| | - Takashi Fujita
- 4 Laboratory of Molecular Genetics, Institute for Frontier Life and Medical Sciences, Kyoto University, Kyoto, Japan.,5 Laboratory of Molecular and Cellular Immunology, Graduate School of Biostudies, Kyoto University, Kyoto, Japan
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102
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Fang M, Yang Y, Wang N, Wang A, He Y, Wang J, Jiang Y, Deng Z. Genome-wide analysis of long non-coding RNA expression profile in porcine circovirus 2-infected intestinal porcine epithelial cell line by RNA sequencing. PeerJ 2019; 7:e6577. [PMID: 30863688 PMCID: PMC6408913 DOI: 10.7717/peerj.6577] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2018] [Accepted: 02/05/2019] [Indexed: 12/17/2022] Open
Abstract
Porcine circovirus-associated disease (PCVAD), which is induced by porcine circovirus type 2 (PCV2), is responsible for severe economic losses. Recently, the role of noncoding RNAs, and in particular microRNAs, in PCV2 infection has received great attention. However, the role of long noncoding RNA (lncRNA) in PCV2 infection is unclear. Here, for the first time, we describe the expression profiles of lncRNAs in an intestinal porcine epithelial cell line (IPEC-J2) after PCV2 infection, and analyze the features of differently expressed lncRNAs and their potential target genes. After strict filtering of approximately 150 million reads, we identified 13,520 lncRNAs, including 199 lncRNAs that were differentially expressed in non-infected and PCV2-infected cells. Furthermore, trans analysis found lncRNA-regulated target genes enriched for specific Gene Ontology terms (P < 0.05), such as DNA binding, RNA binding, and transcription factor activity, which are closely associated with PCV2 infection. In addition, we analyzed the predicted target genes of differentially expressed lncRNAs, including SOD2, TNFAIP3, and ARG1, all of which are involved in infectious diseases. Our study identifies many candidate lncRNAs involved in PCV2 infection and provides new insight into the mechanisms underlying the pathogenesis of PCVAD.
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Affiliation(s)
- Manxin Fang
- Hunan Agricultural University, Hunan Provincial Key Laboratory of Protein Engineering in Animal Vaccines, Changsha, Hunan, China
| | - Yi Yang
- Hunan Agricultural University, Hunan Provincial Key Laboratory of Protein Engineering in Animal Vaccines, Changsha, Hunan, China
| | - Naidong Wang
- Hunan Agricultural University, Hunan Provincial Key Laboratory of Protein Engineering in Animal Vaccines, Changsha, Hunan, China
| | - Aibing Wang
- Hunan Agricultural University, Hunan Provincial Key Laboratory of Protein Engineering in Animal Vaccines, Changsha, Hunan, China
| | - Yanfeng He
- Hunan Agricultural University, Hunan Provincial Key Laboratory of Protein Engineering in Animal Vaccines, Changsha, Hunan, China
| | - Jiaoshun Wang
- Hunan Agricultural University, Hunan Provincial Key Laboratory of Protein Engineering in Animal Vaccines, Changsha, Hunan, China
| | - You Jiang
- Hunan Agricultural University, Hunan Provincial Key Laboratory of Protein Engineering in Animal Vaccines, Changsha, Hunan, China
| | - Zhibang Deng
- Hunan Agricultural University, Hunan Provincial Key Laboratory of Protein Engineering in Animal Vaccines, Changsha, Hunan, China
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103
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Gupta P, Peter S, Jung M, Lewin A, Hemmrich-Stanisak G, Franke A, von Kleist M, Schütte C, Einspanier R, Sharbati S, Bruegge JZ. Analysis of long non-coding RNA and mRNA expression in bovine macrophages brings up novel aspects of Mycobacterium avium subspecies paratuberculosis infections. Sci Rep 2019; 9:1571. [PMID: 30733564 PMCID: PMC6367368 DOI: 10.1038/s41598-018-38141-x] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2018] [Accepted: 12/18/2018] [Indexed: 12/12/2022] Open
Abstract
Paratuberculosis is a major disease in cattle that severely affects animal welfare and causes huge economic losses worldwide. Development of alternative diagnostic methods is of urgent need to control the disease. Recent studies suggest that long non-coding RNAs (lncRNAs) play a crucial role in regulating immune function and may confer valuable information about the disease. However, their role has not yet been investigated in cattle with respect to infection towards Paratuberculosis. Therefore, we investigated the alteration in genomic expression profiles of mRNA and lncRNA in bovine macrophages in response to Paratuberculosis infection using RNA-Seq. We identified 397 potentially novel lncRNA candidates in macrophages of which 38 were differentially regulated by the infection. A total of 820 coding genes were also significantly altered by the infection. Co-expression analysis of lncRNAs and their neighbouring coding genes suggest regulatory functions of lncRNAs in pathways related to immune response. For example, this included protein coding genes such as TNIP3, TNFAIP3 and NF-κB2 that play a role in NF-κB2 signalling, a pathway associated with immune response. This study advances our understanding of lncRNA roles during Paratuberculosis infection.
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Affiliation(s)
- Pooja Gupta
- Department of Mathematics and Informatics, Freie Universität Berlin, Berlin, Germany. .,Department of Mathematics for Life and Materials Sciences, Zuse Institute Berlin, Berlin, Germany.
| | - Sarah Peter
- Institute for the Reproduction of Farm Animals Schönow Inc, Bernau, Germany
| | - Markus Jung
- Institute for the Reproduction of Farm Animals Schönow Inc, Bernau, Germany
| | - Astrid Lewin
- Robert Koch-Institute, Department Infectious Diseases, Berlin, Germany
| | | | - Andre Franke
- Institute of Clinical Molecular Biology, Christian-Albrechts-University Kiel, Kiel, Germany
| | - Max von Kleist
- Department of Mathematics and Informatics, Freie Universität Berlin, Berlin, Germany
| | - Christof Schütte
- Department of Mathematics and Informatics, Freie Universität Berlin, Berlin, Germany.,Department of Mathematics for Life and Materials Sciences, Zuse Institute Berlin, Berlin, Germany
| | - Ralf Einspanier
- Institute of Veterinary Biochemistry, Department of Veterinary Medicine, Freie Universität Berlin, Berlin, Germany
| | - Soroush Sharbati
- Institute of Veterinary Biochemistry, Department of Veterinary Medicine, Freie Universität Berlin, Berlin, Germany
| | - Jennifer Zur Bruegge
- Institute of Veterinary Biochemistry, Department of Veterinary Medicine, Freie Universität Berlin, Berlin, Germany
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104
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Mariotti B, Servaas NH, Rossato M, Tamassia N, Cassatella MA, Cossu M, Beretta L, van der Kroef M, Radstake TRDJ, Bazzoni F. The Long Non-coding RNA NRIR Drives IFN-Response in Monocytes: Implication for Systemic Sclerosis. Front Immunol 2019; 10:100. [PMID: 30804934 PMCID: PMC6371048 DOI: 10.3389/fimmu.2019.00100] [Citation(s) in RCA: 53] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2018] [Accepted: 01/14/2019] [Indexed: 12/23/2022] Open
Abstract
TLR4 activation initiates a signaling cascade leading to the production of type I IFNs and of the downstream IFN-stimulated genes (ISGs). Recently, a number of IFN-induced long non-coding RNAs (lncRNAs) that feed-back regulate the IFN response have been identified. Dysregulation of this process, collectively known as the "Interferon (IFN) Response," represents a common molecular basis in the development of autoimmune and autoinflammatory disorders. Concurrently, alteration of lncRNA profile has been described in several type I IFN-driven autoimmune diseases. In particular, both TLR activation and the upregulation of ISGs in peripheral blood mononuclear cells have been identified as possible contributors to the pathogenesis of systemic sclerosis (SSc), a connective tissue disease characterized by vascular abnormalities, immune activation, and fibrosis. However, hitherto, a potential link between specific lncRNA and the presence of a type I IFN signature remains unclear in SSc. In this study, we identified, by RNA sequencing, a group of lncRNAs related to the IFN and anti-viral response consistently modulated in a type I IFN-dependent manner in human monocytes in response to TLR4 activation by LPS. Remarkably, these lncRNAs were concurrently upregulated in a total of 46 SSc patients in different stages of their disease as compared to 18 healthy controls enrolled in this study. Among these lncRNAs, Negative Regulator of the IFN Response (NRIR) was found significantly upregulated in vivo in SSc monocytes, strongly correlating with the IFN score of SSc patients. Weighted Gene Co-expression Network Analysis showed that NRIR-specific modules, identified in the two datasets, were enriched in "type I IFN" and "viral response" biological processes. Protein coding genes common to the two distinct NRIR modules were selected as putative NRIR target genes. Fifteen in silico-predicted NRIR target genes were experimentally validated in NRIR-silenced monocytes. Remarkably, induction of CXCL10 and CXCL11, two IFN-related chemokines associated with SSc pathogenesis, was reduced in NRIR-knockdown monocytes, while their plasmatic level was increased in SSc patients. Collectively, our data show that NRIR affects the expression of ISGs and that dysregulation of NRIR in SSc monocytes may account, at least in part, for the type I IFN signature present in SSc patients.
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Affiliation(s)
- Barbara Mariotti
- General Pathology Section, Department of Medicine, University of Verona, Verona, Italy
| | - Nila Hendrika Servaas
- Department of Rheumatology and Clinical Immunology, University Medical Center Utrecht, Utrecht, Netherlands
- Laboratory of Translational Immunology, University Medical Center Utrecht, Utrecht, Netherlands
| | - Marzia Rossato
- Department of Rheumatology and Clinical Immunology, University Medical Center Utrecht, Utrecht, Netherlands
- Laboratory of Translational Immunology, University Medical Center Utrecht, Utrecht, Netherlands
- Department of Biotechnology, University of Verona, Verona, Italy
| | - Nicola Tamassia
- General Pathology Section, Department of Medicine, University of Verona, Verona, Italy
| | - Marco A. Cassatella
- General Pathology Section, Department of Medicine, University of Verona, Verona, Italy
| | - Marta Cossu
- Department of Rheumatology and Clinical Immunology, University Medical Center Utrecht, Utrecht, Netherlands
- Laboratory of Translational Immunology, University Medical Center Utrecht, Utrecht, Netherlands
| | - Lorenzo Beretta
- Scleroderma Unit, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico di Milano, Referral Center for Systemic Autoimmune Diseases, Milan, Italy
| | - Maarten van der Kroef
- Department of Rheumatology and Clinical Immunology, University Medical Center Utrecht, Utrecht, Netherlands
- Laboratory of Translational Immunology, University Medical Center Utrecht, Utrecht, Netherlands
| | - Timothy R. D. J. Radstake
- Department of Rheumatology and Clinical Immunology, University Medical Center Utrecht, Utrecht, Netherlands
- Laboratory of Translational Immunology, University Medical Center Utrecht, Utrecht, Netherlands
| | - Flavia Bazzoni
- General Pathology Section, Department of Medicine, University of Verona, Verona, Italy
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105
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More S, Zhu Z, Lin K, Huang C, Pushparaj S, Liang Y, Sathiaseelan R, Yang X, Liu L. Long non-coding RNA PSMB8-AS1 regulates influenza virus replication. RNA Biol 2019; 16:340-353. [PMID: 30669933 DOI: 10.1080/15476286.2019.1572448] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022] Open
Abstract
Long non-coding RNAs (lncRNAs) are a new arm of gene regulatory mechanism as discovered by sequencing techniques and follow-up functional studies. There are only few studies on lncRNAs as related to gene expression regulation and anti-viral activity during influenza virus infection. We sought to identify and characterize lncRNAs involved in influenza virus replication. Using RNA sequencing analysis, we found that 1,912 lncRNAs were significantly changed in human lung epithelial A549 cells infected with influenza A/Puerto Rico/8/34. Gene ontology analysis on neighboring genes of these lncRNAs revealed that the genes involved in type I interferon signaling and cellular response were highly enriched. Seven selected up-regulated lncRNAs (AC015849.2, RP-1-7H24.1, PSMB8-AS1, CTD-2639E6.9, PSOR1C3, AC007283.5 and RP11-670E13.5) were verified by real-time PCR. These lncRNAs were also induced by other two influenza H1N1 virus strains (A/WSN/1933 and A/Oklahoma/3052/09) and interferon β1. Repression of PSMB8 antisense RNA 1 (PSMB8-AS1) using CRISPR interference reduced viral mRNA and protein levels as well as the release of progeny influenza virus particles. Our study suggests that lncRNA PSMB8-AS1 could be a new host factor target for developing antiviral therapy against influenza virus infection.
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Affiliation(s)
- Sunil More
- a Oklahoma Center for Respiratory and Infectious Diseases , Oklahoma State University , Stillwater , OK , USA.,b The Lundberg-Kienlen Lung Biology and Toxicology Laboratory, Department of Physiological Sciences , Oklahoma State University , Stillwater , OK , USA
| | - Zhengyu Zhu
- a Oklahoma Center for Respiratory and Infectious Diseases , Oklahoma State University , Stillwater , OK , USA.,b The Lundberg-Kienlen Lung Biology and Toxicology Laboratory, Department of Physiological Sciences , Oklahoma State University , Stillwater , OK , USA
| | - Kong Lin
- a Oklahoma Center for Respiratory and Infectious Diseases , Oklahoma State University , Stillwater , OK , USA.,b The Lundberg-Kienlen Lung Biology and Toxicology Laboratory, Department of Physiological Sciences , Oklahoma State University , Stillwater , OK , USA
| | - Chaoqun Huang
- a Oklahoma Center for Respiratory and Infectious Diseases , Oklahoma State University , Stillwater , OK , USA.,b The Lundberg-Kienlen Lung Biology and Toxicology Laboratory, Department of Physiological Sciences , Oklahoma State University , Stillwater , OK , USA
| | - Samuel Pushparaj
- a Oklahoma Center for Respiratory and Infectious Diseases , Oklahoma State University , Stillwater , OK , USA.,b The Lundberg-Kienlen Lung Biology and Toxicology Laboratory, Department of Physiological Sciences , Oklahoma State University , Stillwater , OK , USA
| | - Yurong Liang
- a Oklahoma Center for Respiratory and Infectious Diseases , Oklahoma State University , Stillwater , OK , USA.,b The Lundberg-Kienlen Lung Biology and Toxicology Laboratory, Department of Physiological Sciences , Oklahoma State University , Stillwater , OK , USA
| | - Roshini Sathiaseelan
- a Oklahoma Center for Respiratory and Infectious Diseases , Oklahoma State University , Stillwater , OK , USA.,b The Lundberg-Kienlen Lung Biology and Toxicology Laboratory, Department of Physiological Sciences , Oklahoma State University , Stillwater , OK , USA
| | - Xiaoyun Yang
- a Oklahoma Center for Respiratory and Infectious Diseases , Oklahoma State University , Stillwater , OK , USA.,b The Lundberg-Kienlen Lung Biology and Toxicology Laboratory, Department of Physiological Sciences , Oklahoma State University , Stillwater , OK , USA
| | - Lin Liu
- a Oklahoma Center for Respiratory and Infectious Diseases , Oklahoma State University , Stillwater , OK , USA.,b The Lundberg-Kienlen Lung Biology and Toxicology Laboratory, Department of Physiological Sciences , Oklahoma State University , Stillwater , OK , USA
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106
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Wang P. The Opening of Pandora's Box: An Emerging Role of Long Noncoding RNA in Viral Infections. Front Immunol 2019; 9:3138. [PMID: 30740112 PMCID: PMC6355698 DOI: 10.3389/fimmu.2018.03138] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2018] [Accepted: 12/19/2018] [Indexed: 12/31/2022] Open
Abstract
Emerging evidence has proved that long noncoding RNAs (lncRNAs) participate in various physiological and pathological processes. Recent evidence has demonstrated that lncRNAs are crucial regulators of virus infections and antiviral immune responses. Upon viral infections, significant changes take place at the transcriptional level and the majority of the expression modifications occur in lncRNAs from both the host and viral genomes with dynamic regulatory courses. These lncRNAs exert diverse effects. Some are antiviral either through directly inhibiting viral infections or through stimulating antiviral immune responses, while others are pro-viral through directly promoting virus replication or through influencing cellular status, such as suppressing antiviral mechanisms. Consequently, these dynamic regulations lead to disparate pathophysiological outcomes and clinical manifestations. This review will focus on the roles of lncRNAs in viral infection and antiviral responses, summarize expression patterns of both host- and virally derived lncRNAs, describe their acting stages and modes of action, discuss challenges and novel concepts, and propose solutions and perspectives. Research into lncRNA will help identify novel viral infection-related regulators and design preventative and therapeutic strategies against virus-related diseases and immune disorders.
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Affiliation(s)
- Pin Wang
- National Key Laboratory of Medical Immunology and Institute of Immunology, Second Military Medical University, Shanghai, China
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107
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Profumo V, Forte B, Percio S, Rotundo F, Doldi V, Ferrari E, Fenderico N, Dugo M, Romagnoli D, Benelli M, Valdagni R, Dolfini D, Zaffaroni N, Gandellini P. LEADeR role of miR-205 host gene as long noncoding RNA in prostate basal cell differentiation. Nat Commun 2019; 10:307. [PMID: 30659180 PMCID: PMC6338800 DOI: 10.1038/s41467-018-08153-2] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2017] [Accepted: 12/19/2018] [Indexed: 01/26/2023] Open
Abstract
Though miR-205 function has been largely characterized, the nature of its host gene, MIR205HG, is still completely unknown. Here, we show that only lowly expressed alternatively spliced MIR205HG transcripts act as de facto pri-miRNAs, through a process that involves Drosha to prevent unfavorable splicing and directly mediate miR-205 excision. Notably, MIR205HG-specific processed transcripts revealed to be functional per se as nuclear long noncoding RNA capable of regulating differentiation of human prostate basal cells through control of the interferon pathway. At molecular level, MIR205HG directly binds the promoters of its target genes, which have an Alu element in proximity of the Interferon-Regulatory Factor (IRF) binding site, and represses their transcription likely buffering IRF1 activity, with the ultimate effect of preventing luminal differentiation. As MIR205HG functions autonomously from (albeit complementing) miR-205 in preserving the basal identity of prostate epithelial cells, it warrants reannotation as LEADeR (Long Epithelial Alu-interacting Differentiation-related RNA). miR-205 is known to have context-dependent tumor suppressive or oncogenic roles. Here, the authors report the host gene of miR-205, MIR205HG as a nuclear lincRNA that maintains the basal identity of prostate cell and prevents luminal cell differentiation via the repression of interferon responsive genes.
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Affiliation(s)
- Valentina Profumo
- Department of Applied Research and Technological Development, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, 20133, Italy
| | - Barbara Forte
- Department of Applied Research and Technological Development, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, 20133, Italy
| | - Stefano Percio
- Department of Applied Research and Technological Development, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, 20133, Italy
| | - Federica Rotundo
- Department of Applied Research and Technological Development, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, 20133, Italy
| | - Valentina Doldi
- Department of Applied Research and Technological Development, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, 20133, Italy
| | - Elena Ferrari
- Department of Applied Research and Technological Development, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, 20133, Italy
| | - Nicola Fenderico
- Oncode Institute and Department of Cell Biology, Centre for Molecular Medicine, University Medical Centre Utrecht, Utrecht, 3584 CX, The Netherlands
| | - Matteo Dugo
- Department of Applied Research and Technological Development, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, 20133, Italy
| | - Dario Romagnoli
- Centre for Integrative Biology, University of Trento, Trento, 38123, Italy
| | - Matteo Benelli
- Centre for Integrative Biology, University of Trento, Trento, 38123, Italy
| | - Riccardo Valdagni
- Department of Oncology and Hemato-oncology, University of Milan, Milan, 20133, Italy.,Prostate Cancer Program, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, 20133, Italy.,Radiation Oncology 1, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, 20133, Italy
| | - Diletta Dolfini
- Department of Biosciences, University of Milan, Milan, 20133, Italy
| | - Nadia Zaffaroni
- Department of Applied Research and Technological Development, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, 20133, Italy
| | - Paolo Gandellini
- Department of Applied Research and Technological Development, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, 20133, Italy.
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108
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Wang M, Jiang S, Wu W, Yu F, Chang W, Li P, Wang K. Non-coding RNAs Function as Immune Regulators in Teleost Fish. Front Immunol 2018; 9:2801. [PMID: 30546368 PMCID: PMC6279911 DOI: 10.3389/fimmu.2018.02801] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2018] [Accepted: 11/13/2018] [Indexed: 12/13/2022] Open
Abstract
Non-coding RNAs (ncRNAs) are functional RNA molecules that are transcribed from DNA but not translated into proteins. ncRNAs function as key regulators of gene expression and chromatin modification. Recently, the functional role of ncRNAs in teleost fish has been extensively studied. Teleost fish are a highly diverse group among the vertebrate lineage. Fish are also important in terms of aquatic ecosystem, food production and human life, being the source of animal proteins worldwide and models of biomedical research. However, teleost fish always suffer from the invasion of infectious pathogens including viruses and bacteria, which has resulted in a tremendous economic loss to the fishing industry worldwide. Emerging evidence suggests that ncRNAs, especially miRNAs and lncRNAs, may serve as important regulators in cytokine and chemokine signaling, antigen presentation, complement and coagulation cascades, and T cell response in teleost fish. In this review, we summarize current knowledge and understanding of the roles of both miRNAs and lncRNAs in immune regulation in teleost fish. Molecular mechanism insights into the function of ncRNAs in fish immune response may contribute to the development of potential biomarkers and therapeutic targets for the prevention and treatment of fish diseases.
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Affiliation(s)
- Man Wang
- Institute for Translational Medicine, Medical College of Qingdao University, Qingdao, China
| | - Shuai Jiang
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
| | - Wei Wu
- Institute for Translational Medicine, Medical College of Qingdao University, Qingdao, China
| | - Fei Yu
- Institute for Translational Medicine, Medical College of Qingdao University, Qingdao, China
| | - Wenguang Chang
- Institute for Translational Medicine, Medical College of Qingdao University, Qingdao, China
| | - Peifeng Li
- Institute for Translational Medicine, Medical College of Qingdao University, Qingdao, China
| | - Kun Wang
- Institute for Translational Medicine, Medical College of Qingdao University, Qingdao, China
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109
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Ji S, Zhu M, Zhang J, Cai Y, Zhai X, Wang D, Li G, Su S, Zhou J. Microarray analysis of lncRNA expression in rabies virus infected human neuroblastoma cells. INFECTION GENETICS AND EVOLUTION 2018; 67:88-100. [PMID: 30391720 DOI: 10.1016/j.meegid.2018.10.027] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/24/2018] [Revised: 10/30/2018] [Accepted: 10/31/2018] [Indexed: 02/06/2023]
Abstract
Rabies, caused by the rabies virus (RABV), is the oldest known zoonotic infectious disease. Although the molecular mechanisms of RABV pathogenesis have been investigated extensively, the interactions between host and RABV are not clearly understood. It is now known that long non-coding RNAs (lncRNAs) participate in various physiological and pathological processes, but their possible roles in the host response to RABV infection remain to be elucidated. To better understand the pathogenesis of RABV, RNAs from RABV-infected and uninfected human neuroblastoma cells (SK-N-SH) were analyzed using human lncRNA microarrays. We identified 896 lncRNAs and 579 mRNAs that were differentially expressed after infection, indicating a potential role for lncRNAs in the immune response to RABV. Differentially expressed RNAs were examined using Gene Ontology (GO) analysis and were tentatively assigned to biological pathways using the Kyoto Encyclopedia of Genes and Genomes (KEGG). A lncRNA-mRNA-transcription factor co-expression network was constructed to relate lncRNAs to regulatory factors and pathways that may be important in virus-host interactions. The network analysis suggests that E2F4, TAF7 and several lncRNAs function as transcriptional regulators in various signaling pathways. This study is the first global analysis of lncRNA and mRNA co-expression during RABV infection, provides deeper insight into the mechanism of RABV pathogenesis, and reveals promising candidate for future investigation.
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Affiliation(s)
- Senlin Ji
- MOE Joint International Research Laboratory of Animal Health and Food Safety, Engineering Laboratory of Animal Immunity of Jiangsu Province, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China
| | - Mengyan Zhu
- MOE Joint International Research Laboratory of Animal Health and Food Safety, Engineering Laboratory of Animal Immunity of Jiangsu Province, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China
| | - Junyan Zhang
- MOE Joint International Research Laboratory of Animal Health and Food Safety, Engineering Laboratory of Animal Immunity of Jiangsu Province, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China
| | - Yuchen Cai
- MOE Joint International Research Laboratory of Animal Health and Food Safety, Engineering Laboratory of Animal Immunity of Jiangsu Province, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China
| | - Xiaofeng Zhai
- MOE Joint International Research Laboratory of Animal Health and Food Safety, Engineering Laboratory of Animal Immunity of Jiangsu Province, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China
| | - Dong Wang
- China Institute of Veterina Drug Control, China
| | - Gairu Li
- MOE Joint International Research Laboratory of Animal Health and Food Safety, Engineering Laboratory of Animal Immunity of Jiangsu Province, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China
| | - Shuo Su
- MOE Joint International Research Laboratory of Animal Health and Food Safety, Engineering Laboratory of Animal Immunity of Jiangsu Province, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China.
| | - Jiyong Zhou
- MOE Joint International Research Laboratory of Animal Health and Food Safety, Engineering Laboratory of Animal Immunity of Jiangsu Province, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China; Key Laboratory of Animal Virology of Ministry of Agriculture, Zhejiang University, Hangzhou 310058, China; Collaborative Innovation Center and State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, First Affiliated Hospital, Zhejiang University, Hangzhou 310003, China.
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110
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Menard KL, Haskins BE, Colombo AP, Denkers EY. Toxoplasma gondii Manipulates Expression of Host Long Noncoding RNA during Intracellular Infection. Sci Rep 2018; 8:15017. [PMID: 30301916 PMCID: PMC6177471 DOI: 10.1038/s41598-018-33274-5] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2018] [Accepted: 09/26/2018] [Indexed: 12/16/2022] Open
Abstract
Long noncoding RNA (lncRNA) are non-protein-coding transcripts greater than 200 nucleotides that regulate gene expression. The field of transcriptomics is only beginning to understand the role of lncRNA in host defense. Little is known about the role of lncRNA in the response to infection by intracellular pathogens such as Toxoplasma gondii. Using a microarray, we examined the differential expression of 35,923 lncRNAs and 24,881 mRNAs in mouse bone-marrow-derived macrophages during infection with high- and low-virulence T. gondii strains. We found that 1,522 lncRNA molecules were differentially regulated during infection with the high-virulence Type I strain, versus 528 with the less-virulent Type II strain. Of these lncRNAs, 282 were co-regulated with a nearby or overlapping mRNA–including approximately 60 mRNAs with immune-related functions. We validated the microarray for 4 lncRNAs and 4 mRNAs using qRT-PCR. Using deletion strains of T. gondii, we found that the secretory kinase ROP16 controls upregulation of lncRNAs Csf1-lnc and Socs2-lnc, demonstrating that the parasite directly manipulates host lncRNA expression. Given the number of regulated lncRNAs and the magnitude of the expression changes, we hypothesize that these molecules constitute both an additional regulatory layer in the host response to infection and a target for manipulation by T. gondii.
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Affiliation(s)
- Kayla L Menard
- Department of Biology and Center for Evolutionary and Theoretical Immunology, University of New Mexico, Albuquerque, NM, 87131, USA
| | - Breanne E Haskins
- Department of Biology and Center for Evolutionary and Theoretical Immunology, University of New Mexico, Albuquerque, NM, 87131, USA
| | | | - Eric Y Denkers
- Department of Biology and Center for Evolutionary and Theoretical Immunology, University of New Mexico, Albuquerque, NM, 87131, USA.
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111
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Transduction with Lentiviral Vectors Altered the Expression Profile of Host MicroRNAs. J Virol 2018; 92:JVI.00503-18. [PMID: 29997205 DOI: 10.1128/jvi.00503-18] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2018] [Accepted: 06/22/2018] [Indexed: 01/07/2023] Open
Abstract
RNA interference (RNAi) is widely used in gene knockdown analysis and as a tool to screen host genes involved in viral infection. Owing to the limitations of transducing cells with synthetic small interfering RNAs (siRNAs), lentiviral short hairpin RNA (shRNA) vectors are more widely used. However, we found that stable transduction with lentiviral shRNA vectors inhibited hepatitis C virus (HCV) propagation in human hepatoma cells. We found by microRNA (miRNA) microarray analysis that this inhibition was induced by the alteration of host miRNA expression. In addition to one miRNA (miR-196b-5p) previously reported to be involved in HCV infection, other miRNAs (miR-216a-5p, -216b-5p, 217, and -30b-5p) were found to influence HCV infection in this study. Further studies suggested that this effect was independent of the transcription of shRNAs. The lentiviral vector itself and the integration site of the lentiviral vector might determine the change in miRNA expression. Moreover, the upregulation of JUN contributed to the dysregulation of miR-216a-5p, -216b-5p, and -217 in stably transduced cells. Although the changes in miRNA expression were beneficial for inhibiting HCV infection in our study, this off-target effect should be considered when transduction with lentiviral vectors is performed for other purposes, especially in therapy.IMPORTANCE We found that stable transduction with lentiviral shRNA was able to nonspecifically inhibit HCV infection by the dysregulation of host miRNAs. Previous studies showed that the overexpression of shRNAs oversaturated the host miRNA pathways to inhibit HCV infection. In contrast, the miRNA machinery was not affected in our study. Knockout studies suggested that the nonspecific effect was independent of the transcription of shRNAs. The lentiviral vector itself and the integration sites in the host genome determined the changes in miRNAs. Stable transduction with lentiviral vectors was able to increase the expression of JUN, which in turn upregulated miR-216a-5p, miR-216b-5p, and miR-217. miR-216a-5p and miR-216b-5p might inhibit HCV by suppressing the host autophagic machinery. Our study suggested a novel nonspecific effect of lentiviral vectors, and this side effect should be considered when transduction with lentiviral vectors is performed for other purposes, especially in therapy.
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112
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Cui YH, Song XL, Hu ZX, Yang G, Li ZJ, Pan HW. Transcriptional Profile and Integrative Analyses of Long Noncoding RNAs in Primary Human Corneal Epithelial Cells in Response to HSV-1 Infection. Curr Eye Res 2018; 43:1422-1431. [PMID: 30032655 DOI: 10.1080/02713683.2018.1504085] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
PURPOSE Long noncoding RNAs (lncRNAs) have been demonstrated to have important regulatory functions in diverse cellular processes; however, the role of lncRNAs in the pathogenesis of herpes simplex keratitis (HSK) remains poorly understood. METHODS Primary human corneal epithelial cells (HCECs) were infected with herpes simplex virus-1 (HSV-1) and the total RNAs extracted from both the infected group and the mock-infected group subjected to microarray analysis to identify the differential expression of lncRNAs and mRNAs. We also performed bioinformatic analysis including gene ontology (GO) analysis, pathway analysis and co-expression network analysis. RESULTS Compared with mock-infected group, the expression of thousands of lncRNAs and mRNAs were significantly changed, and the microarray results were validated by qRT-PCR. The most enriched GOs targeted by up-regulated transcripts were defense response, intrinsic component of plasma membrane and cytokine activity,and the most enriched GOs targeted by the down-regulated transcripts were cellular metabolic process, intracellular part and poly (A) RNA binding. Pathway analysis indicated that the most correlated pathways for up- and down-regulated transcripts were cytokine-cytokine receptor interaction and RNA transport, respectively. CONCLUSIONS Our study identified the genome-wide profile of lncRNAs and mRNAs expression in primary corneal epithelial cells with HSV-1 infection. These transcriptomic data together with subsequent bioinformatic analysis will provide us with novel clue to the insight into molecular mechanism and potential therapeutic targets of HSK. Further studies are expected to verify the potentially functional genes and pathways and explore the critical lncRNAs. ABBREVIATIONS Long noncoding RNAs: lncRNAs; herpes simplex virus-1: HSV-1; herpes simplex virus keratitis: HSK; human corneal epithelial cells: HCECs.
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Affiliation(s)
- Yu-Hong Cui
- a Guangzhou Institute of Cardiovascular Disease, The Second Affiliated Hospital of Guangzhou Medical University; School of Basic Medical Sciences , Guangzhou Medical University , Guangzhou , China.,b Department of public health and preventive medicine , Jinan University , Guangzhou , China
| | - Xi-Ling Song
- c Institute of Ophthalmology, School of Medicine , Jinan University , Guangzhou , China
| | - Zi-Xuan Hu
- c Institute of Ophthalmology, School of Medicine , Jinan University , Guangzhou , China
| | - Guang Yang
- c Institute of Ophthalmology, School of Medicine , Jinan University , Guangzhou , China
| | - Zhi-Jie Li
- d Department of Histology and Embryology , School of Basic Medical Sciences, Guangzhou Medical University , Guangzhou , China
| | - Hong-Wei Pan
- c Institute of Ophthalmology, School of Medicine , Jinan University , Guangzhou , China.,d Department of Histology and Embryology , School of Basic Medical Sciences, Guangzhou Medical University , Guangzhou , China
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113
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Long Noncoding RNA ITPRIP-1 Positively Regulates the Innate Immune Response through Promotion of Oligomerization and Activation of MDA5. J Virol 2018; 92:JVI.00507-18. [PMID: 29899107 DOI: 10.1128/jvi.00507-18] [Citation(s) in RCA: 55] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2018] [Accepted: 06/03/2018] [Indexed: 02/08/2023] Open
Abstract
Emerging evidence indicates that long noncoding RNAs (lncRNAs) regulate various biological processes, especially innate and adaptive immunity. However, the relationship between lncRNAs and the interferon (IFN) pathway remains largely unknown. Here, we report that lncRNA ITPRIP-1 (lncITPRIP-1) is involved in viral infection and plays a crucial role in the virus-triggered IFN signaling pathway through the targeting of melanoma differentiation-associated gene 5 (MDA5). LncITPRIP-1 can be induced by viral infection, which is not entirely dependent on the IFN signal. Besides, there is no coding potential found in the lncITPRIP-1 transcript. LncITPRIP-1 binds to the C terminus of MDA5, and it possesses the ability to boost the oligomerization of both the full length and the 2 caspase activation and recruitment domains of MDA5 in a K63-linked polyubiquitination-independent manner. Amazingly, we also found that MDA5 can suppress hepatitis C virus (HCV) replication independently of IFN signaling through its C-terminal-deficient domain bound to viral RNA, in which lncITPRIP-1 plays a role as an assistant. In addition, the expression of lncITPRIP-1 is highly consistent with MDA5 expression, indicating that lncITPRIP-1 may function as a cofactor of MDA5. All the data suggest that lncITPRIP-1 enhances the innate immune response to viral infection through the promotion of oligomerization and activation of MDA5. Our study discovers the first lncRNA ITPRIP-1 involved in MDA5 activation.IMPORTANCE Hepatitis C virus infection is a global health issue, and there is still no available vaccine, which makes it urgent to reveal the underlying mechanisms of HCV and host factors. Although RIG-I has been recognized as the leading cytoplasmic sensor against HCV for a long time, recent findings that MDA5 regulates the IFN response to HCV have emerged. Our work validates the significant role of MDA5 in IFN signaling and HCV infection and proposes the first lncRNA inhibiting HCV replication by promoting the activation of MDA5 and mediating the association between MDA5 and HCV RNA, the study of which may shed light on the MDA5 function and treatment for hepatitis C patients. Our suggested model of how lncITPRIP-1 orchestrates signal transduction for IFN production illustrates the essential role of lncRNAs in virus elimination.
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Ali A, Al-Tobasei R, Kenney B, Leeds TD, Salem M. Integrated analysis of lncRNA and mRNA expression in rainbow trout families showing variation in muscle growth and fillet quality traits. Sci Rep 2018; 8:12111. [PMID: 30108261 PMCID: PMC6092380 DOI: 10.1038/s41598-018-30655-8] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2018] [Accepted: 08/04/2018] [Indexed: 02/07/2023] Open
Abstract
Muscle yield and quality traits are important for the aquaculture industry and consumers. Genetic selection for these traits is difficult because they are polygenic and result from multifactorial interactions. To study the genetic architecture of these traits, phenotypic characterization of whole body weight (WBW), muscle yield, fat content, shear force and whiteness were measured in ~500 fish representing 98 families from a growth-selected line. RNA-Seq was used to sequence the muscle transcriptome of different families exhibiting divergent phenotypes for each trait. We have identified 240 and 1,280 differentially expressed (DE) protein-coding genes and long noncoding RNAs (lncRNAs), respectively, in fish families exhibiting contrasting phenotypes. Expression of many DE lncRNAs (n = 229) was positively correlated with overlapping, neighboring or distantly located protein-coding genes (n = 1,030), resulting in 3,392 interactions. Three DE antisense lncRNAs were co-expressed with sense genes known to impact muscle quality traits. Forty-four DE lncRNAs had potential sponge functions to miRNAs that affect muscle quality traits. This study (1) defines muscle quality associated protein-coding and noncoding genes and (2) provides insight into non-coding RNAs involvement in regulating growth and fillet quality traits in rainbow trout.
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Affiliation(s)
- Ali Ali
- Department of Biology and Molecular Biosciences Program, Middle Tennessee State University, Murfreesboro, TN, 37132, USA
| | - Rafet Al-Tobasei
- Computational Science Program, Middle Tennessee State University, Murfreesboro, TN, 37132, USA.,Department of Biostatistics, University of Alabama at Birmingham, Birmingham, AL, 35294-0022, USA
| | - Brett Kenney
- Division of Animal and Nutritional Science, West Virginia University, Morgantown, WV, 26506-6108, USA
| | - Timothy D Leeds
- The National Center for Cool and Cold Water Aquaculture, USDA Agricultural Research Service, Kearneysville, WV, 25430, USA
| | - Mohamed Salem
- Department of Biology and Molecular Biosciences Program, Middle Tennessee State University, Murfreesboro, TN, 37132, USA. .,Computational Science Program, Middle Tennessee State University, Murfreesboro, TN, 37132, USA.
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Valadkhan S, Plasek LM. Long Non-Coding RNA-Mediated Regulation of the Interferon Response: A New Perspective on a Familiar Theme. Pathog Immun 2018. [PMID: 30135954 PMCID: PMC6101671 DOI: 10.20411/pai.v3i1.252] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
The interferon (IFN) response is a critical and ubiquitous component of the innate immune response to pathogens. Detailed studies in the last decades have elucidated the function of a large number of proteins that mediate the complex signaling pathways and gene expression programs involved in the interferon response. The recent discovery of the long non-coding RNAs (lncRNAs) as a new category of cellular effectors has led to studies aiming to understand the role of these transcripts in the IFN response. Several high throughput studies have shown that a large number of lncRNAs are differentially expressed following IFN stimulation and/or viral infections. In-depth study of a very small fraction of the identified lncRNAs has revealed critical roles for this class of transcripts in the regulation of multiple steps of the IFN response, and pointed to the presence of an extensive RNA-mediated regulatory network during the antiviral response. As the vast majority of the identified potential regulatory lncRNAs remain unstudied, it is highly likely that future studies will reveal a completely new perspective on the regulation of the IFN response, with lncRNA- and protein-mediated regulatory networks coordinating the duration, magnitude, and character of this aspect of the innate immune response. In addition to providing a more complete picture of the IFN response, these studies will likely identify new therapeutic targets that in the long term may impact the therapeutic options available against microbial infections and diseases of the immune system.
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Affiliation(s)
- Saba Valadkhan
- Department of Molecular Biology and Microbiology, Case Western Reserve University School of Medicine, Cleveland, Ohio
| | - Leah M Plasek
- Department of Molecular Biology and Microbiology, Case Western Reserve University School of Medicine, Cleveland, Ohio
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El-Diwany R, Soliman M, Sugawara S, Breitwieser F, Skaist A, Coggiano C, Sangal N, Chattergoon M, Bailey JR, Siliciano RF, Blankson JN, Ray SC, Wheelan SJ, Thomas DL, Balagopal A. CMPK2 and BCL-G are associated with type 1 interferon-induced HIV restriction in humans. SCIENCE ADVANCES 2018; 4:eaat0843. [PMID: 30083606 PMCID: PMC6070316 DOI: 10.1126/sciadv.aat0843] [Citation(s) in RCA: 45] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/22/2018] [Accepted: 06/19/2018] [Indexed: 05/14/2023]
Abstract
Type 1 interferons (IFN) are critical for host control of HIV and simian immunodeficiency virus. However, it is unknown which of the hundreds of interferon-stimulated genes (ISGs) restrict HIV in vivo. We sequenced RNA from cells that support HIV replication (activated CD4+ T cells) in 19 HIV-infected people before and after interferon-α2b (IFN-α2b) injection. IFN-α2b administration reduced plasma HIV RNA and induced mRNA expression in activated CD4+ T cells: The IFN-α2b-induced change of each mRNA was compared to the change in plasma HIV RNA. Of 99 ISGs, 13 were associated in magnitude with plasma HIV RNA decline. In addition to well-known restriction factors among the 13 ISGs, two novel genes, CMPK2 and BCL-G, were identified and confirmed for their ability to restrict HIV in vitro: The effect of IFN on HIV restriction in culture was attenuated with RNA interference to CMPK2, and overexpression of BCL-G diminished HIV replication. These studies reveal novel antiviral molecules that are linked with IFN-mediated restriction of HIV in humans.
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Affiliation(s)
- Ramy El-Diwany
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Mary Soliman
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Sho Sugawara
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Florian Breitwieser
- Center for Computational Biology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Alyza Skaist
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Candelaria Coggiano
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Neel Sangal
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Michael Chattergoon
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Justin R. Bailey
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Robert F. Siliciano
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- Howard Hughes Medical Institute, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Joel N. Blankson
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Stuart C. Ray
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Sarah J. Wheelan
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - David L. Thomas
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Ashwin Balagopal
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
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Lnc-ISG20 Inhibits Influenza A Virus Replication by Enhancing ISG20 Expression. J Virol 2018; 92:JVI.00539-18. [PMID: 29899085 DOI: 10.1128/jvi.00539-18] [Citation(s) in RCA: 61] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2018] [Accepted: 05/31/2018] [Indexed: 02/06/2023] Open
Abstract
Long noncoding RNAs (lncRNAs) are involved in many aspects of cellular processes, including the antiviral immune response. To identify influenza A virus (IAV)-related lncRNAs, we performed RNA deep sequencing to compare the profiles of lncRNAs in A549 and HEK293T cells with or without IAV infection. We identified an IAV-upregulated lncRNA named lnc-ISG20 because it shares most of its sequence with ISG20. We found that lnc-ISG20 is an interferon-stimulated gene similar to ISG20. Overexpression of lnc-ISG20 inhibited IAV replication, while lnc-ISG20 knockdown favored viral replication, suggesting that lnc-ISG20 is inhibitory to IAV replication. Further study indicated that overexpression of lnc-ISG20 enhances ISG20 protein levels, while knockdown of lnc-ISG20 reduces ISG20 protein levels in A549 cells induced with poly(I·C) and Sendai virus. We demonstrated that lnc-ISG20 inhibits IAV replication in an ISG20-dependent manner. As lnc-ISG20 did not affect the mRNA level of ISG20, we postulated that lnc-ISG20 may function as endogenous RNA competing with ISG20 to enhance its translation. Indeed, we identified that microRNA 326 (miR-326) is a mutual microRNA for both ISG20 and lnc-ISG20 that targets the 3' untranslated region of ISG20 mRNA to inhibit its translation. We confirmed that lnc-ISG20 can bind miR-326, which in turn decreased the amount of miR-326 bound to ISG20 mRNA. In conclusion, we identified that the IAV-upregulated lnc-ISG20 is a novel interferon-stimulated gene that elicits its inhibitory effect on IAV replication by enhancing ISG20 expression. We demonstrated that lnc-ISG20 functions as a competitive endogenous RNA to bind miR-326 to reduce its inhibition of ISG20 translation. Our results revealed the mechanism by which lnc-ISG20 inhibits IAV replication.IMPORTANCE The replication of influenza A virus is regulated by host factors. However, the mechanisms by which lncRNAs regulate IAV infection are not well understood. We identified that lnc-ISG20 is upregulated during IAV infection and is also an interferon-stimulated gene. We demonstrated that lnc-ISG20 can enhance ISG20 expression, which in turn inhibits IAV replication. Our studies indicate that lnc-ISG20 functions as a competing endogenous RNA that binds miR-326 and reduces its inhibitory effect on ISG20. Taken together, our findings reveal the mechanistic details of lnc-ISG20 negatively regulating IAV replication. These findings indicate that lnc-ISG20 plays an important role during the host antiviral immune response.
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118
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Qiu L, Wang T, Tang Q, Li G, Wu P, Chen K. Long Non-coding RNAs: Regulators of Viral Infection and the Interferon Antiviral Response. Front Microbiol 2018; 9:1621. [PMID: 30072977 PMCID: PMC6060254 DOI: 10.3389/fmicb.2018.01621] [Citation(s) in RCA: 56] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2018] [Accepted: 06/28/2018] [Indexed: 11/13/2022] Open
Abstract
Interferons (IFNs) are a family of cytokines providing a robust first line of host innate defense against pathogenic infection, and have now been part of the standard treatment for viral infection. However, IFN based therapy can best be described as modestly effective. Long non-coding RNAs (lncRNAs) are a novel class of non-protein-coding RNAs that are capable of regulating gene expression at different levels, including chromatin, transcription, post-transcription, and translation. Recently, lncRNAs are found to be deregulated upon viral infection or IFN treatment, and some of them can modulate viral infection in an IFN-dependent or -independent manner. Due to the crucial roles of lncRNAs in viral infection and the IFN antiviral response, the modulation of specific lncRNAs may be involved to increase the IFN antiviral response and improve the clinical result of IFN-based therapy. In this review, we summarize lncRNAs that are deregulated by viral infection, with special focus on the functions and underlying mechanisms of some essential lncRNAs, and discuss their roles in viral infection and the antiviral response of IFN.
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Affiliation(s)
- Lipeng Qiu
- Institute of Life Sciences, Jiangsu University, Zhenjiang, China
| | - Tao Wang
- Institute of Life Sciences, Jiangsu University, Zhenjiang, China
| | - Qi Tang
- Institute of Life Sciences, Jiangsu University, Zhenjiang, China
| | - Guohui Li
- Institute of Life Sciences, Jiangsu University, Zhenjiang, China
| | - Peng Wu
- Institute of Life Sciences, Jiangsu University, Zhenjiang, China
| | - Keping Chen
- Institute of Life Sciences, Jiangsu University, Zhenjiang, China
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119
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Wu H, Yao R, Yu S, Chen H, Cai J, Peng S, Pang X, Sun X, Zhang Y, Zhang J. Transcriptome analysis identifies the potential roles of long non‐coding RNAs during parainfluenza virus infection. FEBS Lett 2018; 592:2444-2457. [DOI: 10.1002/1873-3468.13166] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2018] [Revised: 06/11/2018] [Accepted: 06/15/2018] [Indexed: 11/11/2022]
Affiliation(s)
- Haoming Wu
- Department of Immunology School of Basic Medical Sciences Key Laboratory of Medical Immunology Ministry of Health (Peking University) Peking University Health Science Center Beijing China
| | - Ran‐Ran Yao
- Department of Immunology School of Basic Medical Sciences Key Laboratory of Medical Immunology Ministry of Health (Peking University) Peking University Health Science Center Beijing China
| | - Shuang‐Shuang Yu
- Department of Immunology School of Basic Medical Sciences Key Laboratory of Medical Immunology Ministry of Health (Peking University) Peking University Health Science Center Beijing China
| | - Hong‐Yan Chen
- Department of Immunology School of Basic Medical Sciences Key Laboratory of Medical Immunology Ministry of Health (Peking University) Peking University Health Science Center Beijing China
| | - Juan Cai
- Department of Immunology School of Basic Medical Sciences Key Laboratory of Medical Immunology Ministry of Health (Peking University) Peking University Health Science Center Beijing China
| | - Shu‐Jie Peng
- Department of Immunology School of Basic Medical Sciences Key Laboratory of Medical Immunology Ministry of Health (Peking University) Peking University Health Science Center Beijing China
| | - Xue‐Wen Pang
- Department of Immunology School of Basic Medical Sciences Key Laboratory of Medical Immunology Ministry of Health (Peking University) Peking University Health Science Center Beijing China
| | - Xiu‐Yuan Sun
- Department of Immunology School of Basic Medical Sciences Key Laboratory of Medical Immunology Ministry of Health (Peking University) Peking University Health Science Center Beijing China
| | - Yu Zhang
- Department of Immunology School of Basic Medical Sciences Key Laboratory of Medical Immunology Ministry of Health (Peking University) Peking University Health Science Center Beijing China
| | - Jun Zhang
- Department of Immunology School of Basic Medical Sciences Key Laboratory of Medical Immunology Ministry of Health (Peking University) Peking University Health Science Center Beijing China
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A naturally occurring antiviral ribonucleotide encoded by the human genome. Nature 2018; 558:610-614. [PMID: 29925952 PMCID: PMC6026066 DOI: 10.1038/s41586-018-0238-4] [Citation(s) in RCA: 184] [Impact Index Per Article: 30.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2017] [Accepted: 04/27/2018] [Indexed: 02/08/2023]
Abstract
Viral infections continue to represent major public health challenges, demanding enhanced mechanistic understanding of the processes contributing to viral lifecycles for the realization of new therapeutic strategies1. Viperin, a member of the radical S-adenosyl-L-methionine (SAM) superfamily of enzymes, is an interferon inducible protein implicated in inhibiting the replication of a remarkable range of RNA and DNA viruses, including dengue virus, West Nile virus, hepatitis C virus, influenza A virus, rabies virus2 and HIV3,4. Viperin has been suggested to elicit these broad antiviral activities through interactions with a large number of functionally unrelated host and viral proteins3,4. In contrast, herein, we demonstrate that viperin catalyzes the conversion of cytidine triphosphate (CTP) to 3′-deoxy-3′,4′-didehydro-CTP (ddhCTP), a previously undescribed biologically relevant molecule, via a SAM-dependent radical mechanism. We show that mammalian cells expressing viperin, and macrophages stimulated with IFN-α, produce substantial quantities of ddhCTP. We also establish that ddhCTP acts as a chain terminator for the RNA-dependent RNA-polymerases from multiple members of the flavivirus family, and present evidence that ddhCTP directly inhibits in vivo replication of ZIKA virus. These findings suggest a partially unifying mechanism, based on intrinsic catalytic/enzymatic properties, for the broad antiviral effects of viperin, which involves the generation of a naturally occurring replication chain terminator encoded by mammalian genomes.
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Li J, Li Z, Zheng W, Li X, Wang Z, Cui Y, Jiang X. PANDAR: a pivotal cancer-related long non-coding RNA in human cancers. MOLECULAR BIOSYSTEMS 2018; 13:2195-2201. [PMID: 28976505 DOI: 10.1039/c7mb00414a] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Long non-coding RNAs (lncRNAs), non-protein-coding RNAs that are more than 200 nucleotides in length, have been demonstrated to play a vital role in the pathophysiology of human diseases, particularly in tumorigenesis and progression of cancers. Dysregulation of lncRNAs, which serve as either oncogenes or tumor suppressor genes, is involved in diverse cellular processes, such as proliferation, dedifferentiation, migration, invasion and anti-apoptosis. Promoter of CDKN1A antisense DNA damage-activated RNA (PANDAR), which was recently found to manifest aberrant expression in various malignancies including non-small cell lung cancer, hepatocellular carcinoma, colorectal cancer and gastric cancer, is a novel cancer-related lncRNA. Deregulation of PANDAR contributes to tumorigenesis and progression of cancers, suggesting that PANDAR is likely to represent a viable biomarker and therapeutic target for human cancers. In this review, we summarize current evidence regarding the biological functions and mechanisms of PANDAR during tumor development.
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Affiliation(s)
- Jinglin Li
- Department of Hepatopancreatobiliary Surgery, Second Affiliated Hospital of Harbin Medical University, Harbin 150086, Heilongjiang, People's Republic of China.
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Isaac C, Patel TR, Zovoilis A. Non-coding RNAs in virology: an RNA genomics approach. Biotechnol Genet Eng Rev 2018; 34:90-106. [PMID: 29865927 DOI: 10.1080/02648725.2018.1471642] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Advances in sequencing technologies and bioinformatic analysis techniques have greatly improved our understanding of various classes of RNAs and their functions. Despite not coding for proteins, non-coding RNAs (ncRNAs) are emerging as essential biomolecules fundamental for cellular functions and cell survival. Interestingly, ncRNAs produced by viruses not only control the expression of viral genes, but also influence host cell regulation and circumvent host innate immune response. Correspondingly, ncRNAs produced by the host genome can play a key role in host-virus interactions. In this article, we will first discuss a number of types of viral and mammalian ncRNAs associated with viral infections. Subsequently, we also describe the new possibilities and opportunities that RNA genomics and next-generation sequencing technologies provide for studying ncRNAs in virology.
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Affiliation(s)
- Christopher Isaac
- a Department of Chemistry and Biochemistry , Alberta RNA Research and Training Institute, University of Lethbridge , Lethbridge , Canada
| | - Trushar R Patel
- a Department of Chemistry and Biochemistry , Alberta RNA Research and Training Institute, University of Lethbridge , Lethbridge , Canada.,b Department of Microbiology, Immunology and Infectious Diseases , Cumming School of Medicine, University of Calgary , Calgary , Canada.,c DiscoveryLab, Faculty of Medicine & Dentistry , University of Alberta , Edmonton , Canada
| | - Athanasios Zovoilis
- a Department of Chemistry and Biochemistry , Alberta RNA Research and Training Institute, University of Lethbridge , Lethbridge , Canada
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Abstract
Cytokines and long noncoding RNAs (lncRNAs) are intertwined in the regulatory circuit controlling immunity. lncRNA expression levels are altered following cytokine stimulation in a cell-type-specific fashion. lncRNAs, in turn, regulate the inducible expression of cytokines following immune activation. These studies position lncRNAs as important regulators of gene expression within the complex pathways of the immune system. Our understanding of the functions of lncRNAs is just beginning. Current methodologies for functionally understanding how these transcripts mediate their effects are unable to keep up with the speed of genomic outputs cataloging thousands of these novel genes. In this review, we highlight the interplay between cytokines and lncRNAs and speculate on the future utility of these genes as potential biomarkers and therapeutic targets for the treatment of inflammatory disorders.
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Affiliation(s)
- Susan Carpenter
- Department of Molecular, Cell and Developmental Biology, University of California, Santa Cruz, California 95064
| | - Katherine A Fitzgerald
- Program in Innate Immunity, Division of Infectious Diseases, University of Massachusetts Medical School, Worcester, Massachusetts 01655
- Centre for Molecular Inflammation Research, Department of Cancer Research and Molecular Medicine, NTNU, 7491 Trondheim, Norway
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Huang J, Li Y, Lu Z, Che Y, Sun S, Mao S, Lei Y, Zang R, Li N, Sun N, He J. Long non-coding RNA GAS5 is induced by interferons and plays an antitumor role in esophageal squamous cell carcinoma. Cancer Med 2018; 7:3157-3167. [PMID: 29745062 PMCID: PMC6051207 DOI: 10.1002/cam4.1524] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2018] [Revised: 04/02/2018] [Accepted: 04/05/2018] [Indexed: 01/01/2023] Open
Abstract
The long non-coding RNA GAS5 has been reported as a tumor suppressor in many cancers. However, its functions and mechanisms remain largely unknown in esophageal squamous cell carcinoma (ESCC). In this study, we found that GAS5 was over-expressed in ESCC tissue compared with that in normal esophageal tissue in a public database. Functional studies showed that GAS5 could inhibit ESCC cell proliferation, migration and invasion in vitro. Further analysis revealed that GAS5 was regulated by interferon (IFN) responses via the JAK-STAT pathway. Moreover, as an IFN-stimulated gene (ISG), GAS5 was a positive regulator of IFN responses. The feedback loop between GAS5 and the IFN signaling pathway plays an important antitumor role in ESCC, thus providing novel potential therapeutic targets.
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Affiliation(s)
- Jianbing Huang
- Department of Thoracic Surgery, National Cancer Center/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Yuan Li
- Department of Thoracic Surgery, National Cancer Center/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Zhiliang Lu
- Department of Thoracic Surgery, National Cancer Center/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Yun Che
- Department of Thoracic Surgery, National Cancer Center/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Shouguo Sun
- Department of Thoracic Surgery, National Cancer Center/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Shuangshuang Mao
- Department of Thoracic Surgery, National Cancer Center/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Yuanyuan Lei
- Department of Thoracic Surgery, National Cancer Center/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Ruochuan Zang
- Department of Thoracic Surgery, National Cancer Center/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Ning Li
- Department of Thoracic Surgery, National Cancer Center/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Nan Sun
- Department of Thoracic Surgery, National Cancer Center/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Jie He
- Department of Thoracic Surgery, National Cancer Center/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
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125
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Melbourne JK, Chase KA, Feiner B, Rosen C, Sharma RP. Long non-coding and endogenous retroviral RNA levels are associated with proinflammatory cytokine mRNA expression in peripheral blood cells: Implications for schizophrenia. Psychiatry Res 2018; 262:465-468. [PMID: 28942956 PMCID: PMC5851803 DOI: 10.1016/j.psychres.2017.09.025] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/21/2016] [Revised: 09/08/2017] [Accepted: 09/11/2017] [Indexed: 11/17/2022]
Abstract
Recent research indicates that the expression of long non-coding and endogenous retroviral RNAs is coordinated with the activity of immune molecules often dysregulated in schizophrenia. We measured the expression of TMEVPG1, NRON, HERV-W env and HERV-W gag in blood cells from participants with schizophrenia and controls. We report that a) expression levels of these non-coding RNAs are correlated with proinflammatory cytokine mRNA expression in all participants, b) HERV-W transcripts are negatively correlated with atypical antipsychotic use in participants with schizophrenia, and c) that these RNAs are transcribed in response to proinflammatory stimuli in a THP-1 monocyte cell line.
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Affiliation(s)
- Jennifer K Melbourne
- The Psychiatric Institute, University of Illinois at Chicago, 1601 W. Taylor St., Chicago, IL 60612, USA
| | - Kayla A Chase
- The Psychiatric Institute, University of Illinois at Chicago, 1601 W. Taylor St., Chicago, IL 60612, USA; University of California, Department of Psychiatry, 9500 Gilman Drive, MC 8505, La Jolla, San Diego, CA 92037, USA
| | - Benjamin Feiner
- The Psychiatric Institute, University of Illinois at Chicago, 1601 W. Taylor St., Chicago, IL 60612, USA
| | - Cherise Rosen
- The Psychiatric Institute, University of Illinois at Chicago, 1601 W. Taylor St., Chicago, IL 60612, USA
| | - Rajiv P Sharma
- The Psychiatric Institute, University of Illinois at Chicago, 1601 W. Taylor St., Chicago, IL 60612, USA; Jesse Brown Veterans Affairs Medical Center, 820 South Damen Avenue (M/C 151), Chicago, IL 60612, USA.
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126
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Boldanova T, Suslov A, Heim MH, Necsulea A. Transcriptional response to hepatitis C virus infection and interferon-alpha treatment in the human liver. EMBO Mol Med 2018; 9:816-834. [PMID: 28360091 PMCID: PMC5452008 DOI: 10.15252/emmm.201607006] [Citation(s) in RCA: 48] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Hepatitis C virus (HCV) is widely used to investigate host-virus interactions. Cellular responses to HCV infection have been extensively studied in vitro However, in human liver, interferon (IFN)-stimulated gene expression can mask direct transcriptional responses to infection. To better characterize the direct effects of HCV infection in vivo, we analyze the transcriptomes of HCV-infected patients lacking an activated endogenous IFN system. We show that expression changes observed in these patients predominantly reflect immune cell infiltrates rather than cell-intrinsic pathways. We also investigate the transcriptomes of patients with endogenous IFN activation, which paradoxically cannot eradicate viral infection. We find that most IFN-stimulated genes are induced by both recombinant IFN therapy and the endogenous IFN system, but with lower induction levels in the latter, indicating that the innate immune response in chronic hepatitis C is too weak to clear the virus. We show that coding and non-coding transcripts have different expression dynamics following IFN treatment. Several microRNA primary transcripts, including that of miR-122, are significantly down-regulated in response to IFN treatment, suggesting a new mechanism for IFN-induced expression fine-tuning.
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Affiliation(s)
- Tujana Boldanova
- Department of Biomedicine, University of Basel, Basel, Switzerland.,Division of Gastroenterology and Hepatology, University Hospital Basel, University of Basel, Basel, Switzerland
| | - Aleksei Suslov
- Department of Biomedicine, University of Basel, Basel, Switzerland
| | - Markus H Heim
- Department of Biomedicine, University of Basel, Basel, Switzerland .,Division of Gastroenterology and Hepatology, University Hospital Basel, University of Basel, Basel, Switzerland
| | - Anamaria Necsulea
- Laboratory of Developmental Genomics, School of Life Sciences, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
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127
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Valadkhan S, Fortes P. Regulation of the Interferon Response by lncRNAs in HCV Infection. Front Microbiol 2018; 9:181. [PMID: 29503633 PMCID: PMC5820368 DOI: 10.3389/fmicb.2018.00181] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2017] [Accepted: 01/26/2018] [Indexed: 12/24/2022] Open
Affiliation(s)
- Saba Valadkhan
- Department of Molecular Biology and Microbiology, Case Western Reserve University School of Medicine, Cleveland, OH, United States
- *Correspondence: Saba Valadkhan, Puri Fortes,
| | - Puri Fortes
- Center for Applied Medical Research, Department of Gene Therapy and Hepatology, Navarra Institute for Health Research (IdiSNA), University of Navarra, Pamplona, Spain
- *Correspondence: Saba Valadkhan, Puri Fortes,
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128
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Arimoto KI, Miyauchi S, Stoner SA, Fan JB, Zhang DE. Negative regulation of type I IFN signaling. J Leukoc Biol 2018; 103:1099-1116. [PMID: 29357192 DOI: 10.1002/jlb.2mir0817-342r] [Citation(s) in RCA: 69] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2017] [Revised: 12/15/2017] [Accepted: 12/19/2017] [Indexed: 12/15/2022] Open
Abstract
Type I IFNs (α, β, and others) are a family of cytokines that are produced in physiological conditions as well as in response to the activation of pattern recognition receptors. They are critically important in controlling the host innate and adaptive immune response to viral and some bacterial infections, cancer, and other inflammatory stimuli. However, dysregulation of type I IFN production or response can contribute to immune pathologies termed "interferonopathies", pointing to the importance of balanced activating signals with tightly regulated mechanisms of tuning this signaling. Here, we summarize the recent advances of how type I IFN production and response are controlled at multiple levels of the type I IFN signaling cascade.
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Affiliation(s)
- Kei-Ichiro Arimoto
- Moores UCSD Cancer Center, University of California San Diego, La Jolla, California, USA
| | - Sayuri Miyauchi
- Moores UCSD Cancer Center, University of California San Diego, La Jolla, California, USA
| | - Samuel A Stoner
- Moores UCSD Cancer Center, University of California San Diego, La Jolla, California, USA
| | - Jun-Bao Fan
- Moores UCSD Cancer Center, University of California San Diego, La Jolla, California, USA
| | - Dong-Er Zhang
- Moores UCSD Cancer Center, University of California San Diego, La Jolla, California, USA
- Division of Biological Sciences, University of California San Diego, La Jolla, California, USA
- Department of Pathology, University of California San Diego, La Jolla, California, USA
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129
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Shaw AE, Hughes J, Gu Q, Behdenna A, Singer JB, Dennis T, Orton RJ, Varela M, Gifford RJ, Wilson SJ, Palmarini M. Fundamental properties of the mammalian innate immune system revealed by multispecies comparison of type I interferon responses. PLoS Biol 2017; 15:e2004086. [PMID: 29253856 PMCID: PMC5747502 DOI: 10.1371/journal.pbio.2004086] [Citation(s) in RCA: 201] [Impact Index Per Article: 28.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2017] [Revised: 12/29/2017] [Accepted: 11/22/2017] [Indexed: 12/31/2022] Open
Abstract
The host innate immune response mediated by type I interferon (IFN) and the resulting up-regulation of hundreds of interferon-stimulated genes (ISGs) provide an immediate barrier to virus infection. Studies of the type I ‘interferome’ have mainly been carried out at a single species level, often lacking the power necessary to understand key evolutionary features of this pathway. Here, using a single experimental platform, we determined the properties of the interferomes of multiple vertebrate species and developed a webserver to mine the dataset. This approach revealed a conserved ‘core’ of 62 ISGs, including genes not previously associated with IFN, underscoring the ancestral functions associated with this antiviral host response. We show that gene expansion contributes to the evolution of the IFN system and that interferomes are shaped by lineage-specific pressures. Consequently, each mammal possesses a unique repertoire of ISGs, including genes common to all mammals and others unique to their specific species or phylogenetic lineages. An analysis of genes commonly down-regulated by IFN suggests that epigenetic regulation of transcription is a fundamental aspect of the IFN response. Our study provides a resource for the scientific community highlighting key paradigms of the type I IFN response. The type I interferon (IFN) response is triggered upon sensing of an incoming pathogen in an infected cell and results in the expression of hundreds of IFN-stimulated genes (ISGs, collectively referred to as ‘the interferome’). Studies on the interferome have been carried out mainly in human cells and therefore often lack the power to understand comparative evolutionary aspects of this critical pathway. In this study, we characterized the interferome in several animal species (including humans) using a single experimental framework. This approach allowed us to identify fundamental properties of the innate immune system. In particular, we revealed 62 ‘core’ ISGs, up-regulated in response to IFN in all vertebrates, highlighting the ancestral functions of the IFN system. In addition, we show that many genes repressed by the IFN response normally function as regulators of cell transcription. ISGs shared by multiple species have a higher propensity than other genes to exist as multiple copies in the genome. Importantly, we observed that genes have arisen as ISGs throughout evolution. Hence, every animal species possesses a unique repertoire of ISGs that includes core and lineage-specific genes. Collectively, our data provide a framework on which it will be possible to test the role of the IFN response in pathogen emergence and cross-species transmission.
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Affiliation(s)
- Andrew E. Shaw
- MRC-University of Glasgow Centre for Virus Research, Glasgow, United Kingdom
| | - Joseph Hughes
- MRC-University of Glasgow Centre for Virus Research, Glasgow, United Kingdom
| | - Quan Gu
- MRC-University of Glasgow Centre for Virus Research, Glasgow, United Kingdom
| | - Abdelkader Behdenna
- MRC-University of Glasgow Centre for Virus Research, Glasgow, United Kingdom
| | - Joshua B. Singer
- MRC-University of Glasgow Centre for Virus Research, Glasgow, United Kingdom
| | - Tristan Dennis
- MRC-University of Glasgow Centre for Virus Research, Glasgow, United Kingdom
| | - Richard J. Orton
- MRC-University of Glasgow Centre for Virus Research, Glasgow, United Kingdom
| | - Mariana Varela
- MRC-University of Glasgow Centre for Virus Research, Glasgow, United Kingdom
| | - Robert J. Gifford
- MRC-University of Glasgow Centre for Virus Research, Glasgow, United Kingdom
| | - Sam J. Wilson
- MRC-University of Glasgow Centre for Virus Research, Glasgow, United Kingdom
- * E-mail: (SJW); (MP)
| | - Massimo Palmarini
- MRC-University of Glasgow Centre for Virus Research, Glasgow, United Kingdom
- * E-mail: (SJW); (MP)
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130
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Chew CL, Conos SA, Unal B, Tergaonkar V. Noncoding RNAs: Master Regulators of Inflammatory Signaling. Trends Mol Med 2017; 24:66-84. [PMID: 29246760 DOI: 10.1016/j.molmed.2017.11.003] [Citation(s) in RCA: 131] [Impact Index Per Article: 18.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2017] [Revised: 11/13/2017] [Accepted: 11/14/2017] [Indexed: 12/15/2022]
Abstract
Inflammatory signaling underlies many diseases, from arthritis to cancer. Our understanding of inflammation has thus far been limited to the world of proteins, because we are only just beginning to understand the role that noncoding RNAs (ncRNA) might play. It is now clear that ncRNA do not constitute transcriptional 'noise' but instead harbor physiological functions in controlling signaling pathways. In this review, we cover the newly discovered mechanisms and functions of ncRNAs in the regulation of inflammatory signaling. We also describe advances in experimental techniques allowing this field of research to take root. These findings have opened new avenues for putative therapeutic intervention in inflammatory diseases, which may be seen translated into clinical outcomes in the future.
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Affiliation(s)
- Chen Li Chew
- Institute of Molecular and Cell Biology (IMCB), A*STAR (Agency for Science, Technology and Research), Singapore 138673, Singapore; These authors contributed equally
| | - Stephanie Ana Conos
- Institute of Molecular and Cell Biology (IMCB), A*STAR (Agency for Science, Technology and Research), Singapore 138673, Singapore; These authors contributed equally
| | - Bilal Unal
- Institute of Molecular and Cell Biology (IMCB), A*STAR (Agency for Science, Technology and Research), Singapore 138673, Singapore; Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore (NUS), Singapore 117597, Singapore
| | - Vinay Tergaonkar
- Institute of Molecular and Cell Biology (IMCB), A*STAR (Agency for Science, Technology and Research), Singapore 138673, Singapore; Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore (NUS), Singapore 117597, Singapore; Cancer Science Institute of Singapore, Singapore 117599, Singapore; Centre for Cancer Biology (University of South Australia and SA Pathology), Adelaide, SA 5000, Australia.
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131
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Nan Y, Wu C, Zhang YJ. Interplay between Janus Kinase/Signal Transducer and Activator of Transcription Signaling Activated by Type I Interferons and Viral Antagonism. Front Immunol 2017; 8:1758. [PMID: 29312301 PMCID: PMC5732261 DOI: 10.3389/fimmu.2017.01758] [Citation(s) in RCA: 93] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2017] [Accepted: 11/27/2017] [Indexed: 12/13/2022] Open
Abstract
Interferons (IFNs), which were discovered a half century ago, are a group of secreted proteins that play key roles in innate immunity against viral infection. The major signaling pathway activated by IFNs is the Janus kinase/signal transducer and activator of transcription (JAK/STAT) pathway, which leads to the expression of IFN-stimulated genes (ISGs), including many antiviral effectors. Viruses have evolved various strategies with which to antagonize the JAK/STAT pathway to influence viral virulence and pathogenesis. In recent years, notable progress has been made to better understand the JAK/STAT pathway activated by IFNs and antagonized by viruses. In this review, recent progress in research of the JAK/STAT pathway activated by type I IFNs, non-canonical STAT activation, viral antagonism of the JAK/STAT pathway, removing of the JAK/STAT antagonist from viral genome for attenuation, and the potential pathogenesis roles of tyrosine phosphorylation-independent non-canonical STATs activation during virus infection are discussed in detail. We expect that this review will provide new insight into the understanding the complexity of the interplay between JAK/STAT signaling and viral antagonism.
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Affiliation(s)
- Yuchen Nan
- Department of Preventive Veterinary Medicine, College of Veterinary Medicine, Northwest A&F University, Yangling, China.,Molecular Virology Laboratory, VA-MD Regional College of Veterinary Medicine, Maryland Pathogen Research Institute, University of Maryland, College Park, MD, United States
| | - Chunyan Wu
- Department of Preventive Veterinary Medicine, College of Veterinary Medicine, Northwest A&F University, Yangling, China
| | - Yan-Jin Zhang
- Molecular Virology Laboratory, VA-MD Regional College of Veterinary Medicine, Maryland Pathogen Research Institute, University of Maryland, College Park, MD, United States
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132
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Meng XY, Luo Y, Anwar MN, Sun Y, Gao Y, Zhang H, Munir M, Qiu HJ. Long Non-Coding RNAs: Emerging and Versatile Regulators in Host-Virus Interactions. Front Immunol 2017; 8:1663. [PMID: 29234324 PMCID: PMC5712331 DOI: 10.3389/fimmu.2017.01663] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2017] [Accepted: 11/13/2017] [Indexed: 12/21/2022] Open
Abstract
Long non-coding RNAs (lncRNAs) are a class of non-protein-coding RNA molecules, which are involved in various biological processes, including chromatin modification, cell differentiation, pre-mRNA transcription and splicing, protein translation, etc. During the last decade, increasing evidence has suggested the involvement of lncRNAs in both immune and antiviral responses as positive or negative regulators. The immunity-associated lncRNAs modulate diverse and multilayered immune checkpoints, including activation or repression of innate immune signaling components, such as interleukin (IL)-8, IL-10, retinoic acid inducible gene I, toll-like receptors 1, 3, and 8, and interferon (IFN) regulatory factor 7, transcriptional regulation of various IFN-stimulated genes, and initiation of the cell apoptosis pathways. Additionally, some virus-encoded lncRNAs facilitate viral replication through individually or synergistically inhibiting the host antiviral responses or regulating multiple steps of the virus life cycle. Moreover, some viruses are reported to hijack host-encoded lncRNAs to establish persistent infections. Based on these amazing discoveries, lncRNAs are an emerging hotspot in host–virus interactions. In this review, we summarized the current findings of the host- or virus-encoded lncRNAs and the underlying mechanisms, discussed their impacts on immune responses and viral replication, and highlighted their critical roles in host–virus interactions.
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Affiliation(s)
- Xing-Yu Meng
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, China
| | - Yuzi Luo
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, China
| | - Muhammad Naveed Anwar
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, China
| | - Yuan Sun
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, China
| | - Yao Gao
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, China
| | - Huawei Zhang
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, China
| | | | - Hua-Ji Qiu
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, China
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133
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Tang Y, Zhou T, Yu X, Xue Z, Shen N. The role of long non-coding RNAs in rheumatic diseases. Nat Rev Rheumatol 2017; 13:657-669. [PMID: 28978995 DOI: 10.1038/nrrheum.2017.162] [Citation(s) in RCA: 58] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Long non-coding RNAs (lncRNAs) have emerged as key epigenetic regulators that govern gene expression and influence multiple biological processes. Accumulating evidence demonstrates that lncRNAs have critical roles in immune cell development and function. In this Review, the molecular mechanisms of gene expression regulation by lncRNAs are described and current knowledge of the role of lncRNAs in immune regulation and inflammation are presented, highlighting strategies for defining the roles of lncRNAs in the pathogenesis of multiple rheumatic diseases. Finally, research progress in understanding the role of lncRNAs in rheumatic diseases is discussed.
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Affiliation(s)
- Yuanjia Tang
- Shanghai Institute of Rheumatology, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 145 Shan Dong Road (c), Shanghai 200001, China.,Institute of Health Sciences, Shanghai Jiao Tong University School of Medicine and Shanghai Institutes for Biological Sciences (SIBS), University of Chinese Academy of Sciences, Chinese Academy of Sciences (CAS), 320 Yueyang Road, Shanghai, China
| | - Tian Zhou
- Shanghai Institute of Rheumatology, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 145 Shan Dong Road (c), Shanghai 200001, China
| | - Xiang Yu
- Shanghai Institute of Rheumatology, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 145 Shan Dong Road (c), Shanghai 200001, China
| | - Zhixin Xue
- Shanghai Institute of Rheumatology, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 145 Shan Dong Road (c), Shanghai 200001, China
| | - Nan Shen
- Shanghai Institute of Rheumatology, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 145 Shan Dong Road (c), Shanghai 200001, China.,Institute of Health Sciences, Shanghai Jiao Tong University School of Medicine and Shanghai Institutes for Biological Sciences (SIBS), University of Chinese Academy of Sciences, Chinese Academy of Sciences (CAS), 320 Yueyang Road, Shanghai, China.,State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Renji Hospital, 2200 Lane 25 Xietu Road, Shanghai, China.,Collaborative Innovation Centre for Translational Medicine, Shanghai Jiao Tong University School of Medicine, 197 Rui Jin Er Road, Shanghai, China.,Center for Autoimmune Genomics and Etiology (CAGE), Cincinnati Children's Hospital Medical Center, 3333 Burnet Avenue, Cincinnati, Ohio, USA
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134
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Li Y, Zhang H, Zhu B, Ashraf U, Chen Z, Xu Q, Zhou D, Zheng B, Song Y, Chen H, Ye J, Cao S. Microarray Analysis Identifies the Potential Role of Long Non-Coding RNA in Regulating Neuroinflammation during Japanese Encephalitis Virus Infection. Front Immunol 2017; 8:1237. [PMID: 29033949 PMCID: PMC5626832 DOI: 10.3389/fimmu.2017.01237] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2016] [Accepted: 09/19/2017] [Indexed: 01/31/2023] Open
Abstract
Japanese encephalitis virus (JEV) is the leading cause of epidemic encephalitis worldwide. JEV-induced neuroinflammation is characterized by profound neuronal cells damage accompanied by activation of glial cells. Albeit long non-coding RNAs (lncRNAs) have been emerged as important regulatory RNAs with profound effects on various biological processes, it is unknown how lncRNAs regulate JEV-induced inflammation. Here, using microarray approach, we identified 618 lncRNAs and 1,007 mRNAs differentially expressed in JEV-infected mice brain. The functional annotation analysis revealed that differentially regulated transcripts were predominantly involved in various signaling pathways related to host immune and inflammatory responses. The lncRNAs with their potential to regulate JEV-induced inflammatory response were identified by constructing the lncRNA-mRNA coexpression network. Furthermore, silencing of the two selected lncRNAs (E52329 and N54010) resulted in reducing the phosphorylation of JNK and MKK4, which are known to be involved during inflammatory response. Collectively, we first demonstrated the transcriptomic landscape of lncRNAs in mice brain infected with JEV and analyzed the coexpression network of differentially regulated lncRNAs and mRNAs during JEV infection. Our results provide a better understanding of the host response to JEV infection and suggest that the identified lncRNAs may be used as potential therapeutic targets for the management of Japanese encephalitis.
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Affiliation(s)
- Yunchuan Li
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China.,Laboratory of Animal Virology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China.,The Cooperative Innovation Center for Sustainable Pig Production, Huazhong Agricultural University, Wuhan, China
| | - Hao Zhang
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China.,Laboratory of Animal Virology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China.,The Cooperative Innovation Center for Sustainable Pig Production, Huazhong Agricultural University, Wuhan, China
| | - Bibo Zhu
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China.,Laboratory of Animal Virology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China.,The Cooperative Innovation Center for Sustainable Pig Production, Huazhong Agricultural University, Wuhan, China
| | - Usama Ashraf
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China.,Laboratory of Animal Virology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China.,The Cooperative Innovation Center for Sustainable Pig Production, Huazhong Agricultural University, Wuhan, China
| | - Zheng Chen
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China.,Laboratory of Animal Virology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China.,The Cooperative Innovation Center for Sustainable Pig Production, Huazhong Agricultural University, Wuhan, China
| | - Qiuping Xu
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China.,Laboratory of Animal Virology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China.,The Cooperative Innovation Center for Sustainable Pig Production, Huazhong Agricultural University, Wuhan, China
| | - Dengyuan Zhou
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China.,Laboratory of Animal Virology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China.,The Cooperative Innovation Center for Sustainable Pig Production, Huazhong Agricultural University, Wuhan, China
| | - Bohan Zheng
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China.,Laboratory of Animal Virology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China.,The Cooperative Innovation Center for Sustainable Pig Production, Huazhong Agricultural University, Wuhan, China
| | - Yunfeng Song
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China.,Laboratory of Animal Virology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China.,The Cooperative Innovation Center for Sustainable Pig Production, Huazhong Agricultural University, Wuhan, China
| | - Huanchun Chen
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China.,Laboratory of Animal Virology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China.,The Cooperative Innovation Center for Sustainable Pig Production, Huazhong Agricultural University, Wuhan, China
| | - Jing Ye
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China.,Laboratory of Animal Virology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China.,The Cooperative Innovation Center for Sustainable Pig Production, Huazhong Agricultural University, Wuhan, China
| | - Shengbo Cao
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China.,Laboratory of Animal Virology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China.,The Cooperative Innovation Center for Sustainable Pig Production, Huazhong Agricultural University, Wuhan, China
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135
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Barriocanal M, Fortes P. Long Non-coding RNAs in Hepatitis C Virus-Infected Cells. Front Microbiol 2017; 8:1833. [PMID: 29033906 PMCID: PMC5625025 DOI: 10.3389/fmicb.2017.01833] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2017] [Accepted: 09/06/2017] [Indexed: 12/13/2022] Open
Abstract
Hepatitis C virus (HCV) often leads to a chronic infection in the liver that may progress to steatosis, fibrosis, cirrhosis, and hepatocellular carcinoma (HCC). Several viral and cellular factors are required for a productive infection and for the development of liver disease. Some of these are long non-coding RNAs (lncRNAs) deregulated in infected cells. After HCV infection, the sequence and the structure of the viral RNA genome are sensed to activate interferon (IFN) synthesis and signaling pathways. These antiviral pathways regulate transcription of several cellular lncRNAs. Some of these are also deregulated in response to viral replication. Certain viral proteins and/or viral replication can activate transcription factors such as MYC, SP1, NRF2, or HIF1α that modulate the expression of additional cellular lncRNAs. Interestingly, several lncRNAs deregulated in HCV-infected cells described so far play proviral or antiviral functions by acting as positive or negative regulators of the IFN system, while others help in the development of liver cirrhosis and HCC. The study of the structure and mechanism of action of these lncRNAs may aid in the development of novel strategies to treat infectious and immune pathologies and liver diseases such as cirrhosis and HCC.
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Affiliation(s)
| | - Puri Fortes
- Department of Gene Therapy and Hepatology, Navarra Institute for Health Research (IdiSNA), Centro de Investigación Médica Aplicada, University of Navarra, Pamplona, Spain
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136
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Li J, Li Z, Zheng W, Li X, Wang Z, Cui Y, Jiang X. LncRNA-ATB: An indispensable cancer-related long noncoding RNA. Cell Prolif 2017; 50. [PMID: 28884871 DOI: 10.1111/cpr.12381] [Citation(s) in RCA: 141] [Impact Index Per Article: 20.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2017] [Accepted: 08/06/2017] [Indexed: 02/06/2023] Open
Abstract
OBJECTIVES Long non-coding RNAs (lncRNAs) are a group of non-protein-coding RNAs that are greater than 200 nucleotides in length. Increasing evidence indicates that lncRNAs, which may serve as either oncogenes or tumour suppressor genes, play a vital role in the pathophysiology of human diseases, especially in tumourigenesis and progression. Deregulation of lncRNAs impacts different cellular processes, such as proliferation, dedifferentiation, migration, invasion and anti-apoptosis. The aim of this review was to explore the molecular mechanism and clinical significance of long non-coding RNA-activated by transforming growth factor β (lncRNA-ATB) in various types of cancers. MATERIALS AND METHODS In this review, we summarize and analyze current studies concerning the biological functions and mechanisms of lncRNA-ATB in tumour development. The related studies were obtained through a systematic search of Pubmed, Web of Science, Embase and Cochrane Library. RESULTS Long non-coding RNAs-ATB is a novel cancer-related lncRNA that was recently found to exhibit aberrant expression in a variety of malignancies, including hepatocellular carcinoma, colorectal cancer, gastric cancer, and lung cancer. Dysregulation of lncRNA-ATB has been shown to contribute to proliferation, migration and invasion of cancer cells. Long non-coding RNAs-ATB promotes tumourigenesis and progression mainly through competitively binding miRNAs to induce epithelial-mesenchymal transition (EMT). CONCLUSIONS Long non-coding RNAs-ATB likely represents a feasible cancer biomarker or therapeutic target.
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Affiliation(s)
- Jinglin Li
- Department of Hepatopancreatobiliary Surgery, Second Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Zhenglong Li
- Department of Hepatopancreatobiliary Surgery, Second Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Wangyang Zheng
- Department of Hepatopancreatobiliary Surgery, Second Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Xinheng Li
- Department of Hepatopancreatobiliary Surgery, Second Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Zhidong Wang
- Department of Hepatopancreatobiliary Surgery, Second Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Yunfu Cui
- Department of Hepatopancreatobiliary Surgery, Second Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Xingming Jiang
- Department of Hepatopancreatobiliary Surgery, Second Affiliated Hospital of Harbin Medical University, Harbin, China
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137
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Selinger M, Wilkie GS, Tong L, Gu Q, Schnettler E, Grubhoffer L, Kohl A. Analysis of tick-borne encephalitis virus-induced host responses in human cells of neuronal origin and interferon-mediated protection. J Gen Virol 2017; 98:2043-2060. [PMID: 28786780 PMCID: PMC5817271 DOI: 10.1099/jgv.0.000853] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2017] [Accepted: 06/02/2017] [Indexed: 12/25/2022] Open
Abstract
Tick-borne encephalitis virus (TBEV) is a member of the genus Flavivirus. It can cause serious infections in humans that may result in encephalitis/meningoencephalitis. Although several studies have described the involvement of specific genes in the host response to TBEV infection in the central nervous system (CNS), the overall network remains poorly characterized. Therefore, we investigated the response of DAOY cells (human medulloblastoma cells derived from cerebellar neurons) to TBEV (Neudoerfl strain, Western subtype) infection to characterize differentially expressed genes by transcriptome analysis. Our results revealed a wide panel of interferon-stimulated genes (ISGs) and pro-inflammatory cytokines, including type III but not type I (or II) interferons (IFNs), which are activated upon TBEV infection, as well as a number of non-coding RNAs, including long non-coding RNAs. To obtain a broader view of the pathways responsible for eliciting an antiviral state in DAOY cells we examined the effect of type I and III IFNs and found that only type I IFN pre-treatment inhibited TBEV production. The cellular response to TBEV showed only partial overlap with gene expression changes induced by IFN-β treatment - suggesting a virus-specific signature - and we identified a group of ISGs that were highly up-regulated following IFN-β treatment. Moreover, a high rate of down-regulation was observed for a wide panel of pro-inflammatory cytokines upon IFN-β treatment. These data can serve as the basis for further studies of host-TBEV interactions and the identification of ISGs and/or lncRNAs with potent antiviral effects in cases of TBEV infection in human neuronal cells.
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Affiliation(s)
- Martin Selinger
- Institute of Parasitology, Biology Centre of the Academy of Sciences of the Czech Republic, Branišovská 31, 370 05 České Budějovice, Czech Republic
- Faculty of Science, University of South Bohemia in České Budějovice, Branišovská 31, 370 05 České Budějovice, Czech Republic
| | - Gavin S. Wilkie
- MRC-University of Glasgow Centre for Virus Research, Glasgow G61 1QH, Scotland, UK
| | - Lily Tong
- MRC-University of Glasgow Centre for Virus Research, Glasgow G61 1QH, Scotland, UK
| | - Quan Gu
- MRC-University of Glasgow Centre for Virus Research, Glasgow G61 1QH, Scotland, UK
| | - Esther Schnettler
- MRC-University of Glasgow Centre for Virus Research, Glasgow G61 1QH, Scotland, UK
- Present address: Bernhard Nocht Institute for Tropical Medicine, Bernhard-Nocht-Str. 74, 20359 Hamburg, Germany
| | - Libor Grubhoffer
- Institute of Parasitology, Biology Centre of the Academy of Sciences of the Czech Republic, Branišovská 31, 370 05 České Budějovice, Czech Republic
- Faculty of Science, University of South Bohemia in České Budějovice, Branišovská 31, 370 05 České Budějovice, Czech Republic
| | - Alain Kohl
- MRC-University of Glasgow Centre for Virus Research, Glasgow G61 1QH, Scotland, UK
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138
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Genome-wide analysis of long noncoding RNA profiling in PRRSV-infected PAM cells by RNA sequencing. Sci Rep 2017; 7:4952. [PMID: 28694521 PMCID: PMC5504012 DOI: 10.1038/s41598-017-05279-z] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2016] [Accepted: 05/26/2017] [Indexed: 12/27/2022] Open
Abstract
Porcine reproductive and respiratory syndrome (PRRS) is a major threat to the global swine industry and causes tremendous economic losses. Its causative agent, porcine reproductive and respiratory syndrome virus (PRRSV), primarily infects immune cells, such as porcine alveolar macrophages and dendritic cells. PRRSV infection results in immune suppression, antibody-dependent enhancement, and persistent infection. Highly pathogenic strains in China cause high fever and severe inflammatory responses in the lungs. However, the pathogenesis of PRRSV is still not fully understood. In this study, we analysed the long noncoding RNA (lncRNA) and mRNA expression profiles of the HP-PRRSV GSWW15 and the North American strain FL-12 in infected porcine alveolar macrophages (PAMs) at 12 and 24 hours post-infection. We predicted 12,867 novel lncRNAs, 299 of which were differentially expressed after viral infection. The Gene Ontology (GO) and Kyoto Encyclopaedia of Genes and Genomes (KEGG) analyses of the genes adjacent to lncRNAs showed that they were enriched in pathways related to viral infection and immune response, indicating that lncRNAs might play regulatory roles in virus-host interactions. Our study provided information about lncRNAs in the porcine immune system and offers new insights into the pathogenic mechanism of PRRSV infection and novel antiviral therapy development.
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139
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Liu W, Ding C. Roles of LncRNAs in Viral Infections. Front Cell Infect Microbiol 2017; 7:205. [PMID: 28603696 PMCID: PMC5445353 DOI: 10.3389/fcimb.2017.00205] [Citation(s) in RCA: 77] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2017] [Accepted: 05/08/2017] [Indexed: 12/12/2022] Open
Abstract
Many proteins and signaling pathways participate in anti-viral host responses. Long non-coding RNAs (lncRNAs), a subset of non-coding RNAs greater than 200 nucleotides in length, have been recently described as critical regulators in viral infections. Accumulating research indicates that lncRNAs are important in the development and progression of infectious diseases. LncRNAs are not only involved in anti-viral responses, but in many different virus-host interactions, some of which may be beneficial to the virus. Here we review the current knowledge regarding host and viral lncRNAs and their roles in viral infections. In addition, the potential of using lncRNAs as diagnostic biomarkers is discussed.
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Affiliation(s)
- Weiwei Liu
- Avian infectious Department, Shanghai Veterinary Research Institute, Chinese Academy of Agricultural ScienceShanghai, China
| | - Chan Ding
- Avian infectious Department, Shanghai Veterinary Research Institute, Chinese Academy of Agricultural ScienceShanghai, China
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140
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Wróblewska A, Bernat A, Woziwodzka A, Markiewicz J, Romanowski T, Bielawski KP, Smiatacz T, Sikorska K. Interferon lambda polymorphisms associate with body iron indices and hepatic expression of interferon-responsive long non-coding RNA in chronic hepatitis C. Clin Exp Med 2017; 17:225-232. [PMID: 27125837 PMCID: PMC5403869 DOI: 10.1007/s10238-016-0423-4] [Citation(s) in RCA: 9] [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] [Received: 03/04/2016] [Accepted: 04/18/2016] [Indexed: 12/21/2022]
Abstract
Single nucleotide polymorphisms (SNPs) within DNA region containing interferon lambda 3 (IFNL3) and IFNL4 genes are prognostic factors of treatment response in chronic hepatitis C (CHC). Iron overload, frequently diagnosed in CHC, is associated with unfavorable disease course and a risk of carcinogenesis. Its etiology and relationship with the immune response in CHC are not fully explained. Our aim was to determine whether IFNL polymorphisms in CHC patients associate with body iron indices, and whether they are linked with hepatic expression of genes involved in iron homeostasis and IFN signaling. For 192 CHC patients, four SNPs within IFNL3-IFNL4 region (rs12979860, rs368234815, rs8099917, rs12980275) were genotyped. In 185 liver biopsies, histopathological analyses were performed. Expression of five mRNAs and three long non-coding RNAs (lncRNAs) was determined with qRT-PCR in 105 liver samples. Rs12979860 TT or rs8099917 GG genotypes as well as markers of serum and hepatocyte iron overload associated with higher activity of gamma-glutamyl transpeptidase and liver steatosis. The presence of two minor alleles in any of the tested SNPs predisposed to abnormally high serum iron concentration and correlated with higher hepatic expression of lncRNA NRIR. On the other hand, homozygosity in any major allele associated with higher viral load. Patients bearing rs12979860 CC genotype had lower hepatic expression of hepcidin (HAMP; P = 0.03). HAMP mRNA level positively correlated with serum iron indices and degree of hepatocyte iron deposits. IFNL polymorphisms influence regulatory pathways of cellular response to IFN and affect body iron balance in chronic hepatitis C virus infection.
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Affiliation(s)
- Anna Wróblewska
- Laboratory of Molecular Diagnostics, Intercollegiate Faculty of Biotechnology UG and MUG, Abrahama 58, 80-307, Gdańsk, Poland
| | - Agnieszka Bernat
- Laboratory of Molecular Diagnostics, Intercollegiate Faculty of Biotechnology UG and MUG, Abrahama 58, 80-307, Gdańsk, Poland
| | - Anna Woziwodzka
- Laboratory of Molecular Diagnostics, Intercollegiate Faculty of Biotechnology UG and MUG, Abrahama 58, 80-307, Gdańsk, Poland
| | - Joanna Markiewicz
- Department of Infectious Diseases, Pomeranian Center of Infectious Diseases, Smoluchowskiego 18, 80-214, Gdańsk, Poland
| | - Tomasz Romanowski
- Laboratory of Molecular Diagnostics, Intercollegiate Faculty of Biotechnology UG and MUG, Abrahama 58, 80-307, Gdańsk, Poland
| | - Krzysztof P Bielawski
- Laboratory of Molecular Diagnostics, Intercollegiate Faculty of Biotechnology UG and MUG, Abrahama 58, 80-307, Gdańsk, Poland
| | - Tomasz Smiatacz
- Department of Infectious Diseases, Medical University of Gdansk, Smoluchowskiego 18, 80-214, Gdańsk, Poland
| | - Katarzyna Sikorska
- Department of Infectious Diseases, Medical University of Gdansk, Smoluchowskiego 18, 80-214, Gdańsk, Poland.
- Department of Tropical Medicine and Epidemiology, Medical University of Gdansk, Powstania Styczniowego 9b, 81-519, Gdynia, Poland.
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141
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Ma H, Han P, Ye W, Chen H, Zheng X, Cheng L, Zhang L, Yu L, Wu X, Xu Z, Lei Y, Zhang F. The Long Noncoding RNA NEAT1 Exerts Antihantaviral Effects by Acting as Positive Feedback for RIG-I Signaling. J Virol 2017; 91:e02250-16. [PMID: 28202761 PMCID: PMC5391460 DOI: 10.1128/jvi.02250-16] [Citation(s) in RCA: 140] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2016] [Accepted: 02/07/2017] [Indexed: 11/20/2022] Open
Abstract
Hantavirus infection, which causes zoonotic diseases with a high mortality rate in humans, has long been a global public health concern. Over the past decades, accumulating evidence suggests that long noncoding RNAs (lncRNAs) play key regulatory roles in innate immunity. However, the involvement of host lncRNAs in hantaviral control remains uncharacterized. In this study, we identified the lncRNA NEAT1 as a vital antiviral modulator. NEAT1 was dramatically upregulated after Hantaan virus (HTNV) infection, whereas its downregulation in vitro or in vivo delayed host innate immune responses and aggravated HTNV replication. Ectopic expression of NEAT1 enhanced beta interferon (IFN-β) production and suppressed HTNV infection. Further investigation suggested that NEAT1 served as positive feedback for RIG-I signaling. HTNV infection activated NEAT1 transcription through the RIG-I-IRF7 pathway, whereas NEAT1 removed the transcriptional inhibitory effects of the splicing factor proline- and glutamine-rich protein (SFPQ) by relocating SFPQ to paraspeckles, thus promoting the expression of RIG-I and DDX60. RIG-I and DDX60 had synergic effects on IFN production. Taken together, our findings demonstrate that NEAT1 modulates the innate immune response against HTNV infection, providing another layer of information about the role of lncRNAs in controlling viral infections.IMPORTANCE Hantaviruses have attracted worldwide attention as archetypal emerging pathogens. Recently, increasing evidence has highlighted long noncoding RNAs (lncRNAs) as key regulators of innate immunity; however, their roles in hantavirus infection remain unknown. In the present work, a new unexplored function of lncRNA NEAT1 in controlling HTNV replication was found. NEAT1 promoted interferon (IFN) responses by acting as positive feedback for RIG-I signaling. This lncRNA was induced by HTNV through the RIG-I-IRF7 pathway in a time- and dose-dependent manner and promoted HTNV-induced IFN production by facilitating RIG-I and DDX60 expression. Intriguingly, NEAT1 relocated SFPQ and formed paraspeckles after HTNV infection, which might reverse inhibitive effects of SFPQ on the transcription of RIG-I and DDX60. To the best of our knowledge, this is the first study to address the regulatory role of the lncRNA NEAT1 in host innate immunity after HTNV infection. In summary, our findings provide additional insights regarding the role of lncRNAs in controlling viral infections.
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Affiliation(s)
- Hongwei Ma
- Department of Microbiology, Fourth Military Medical University, Xi'an, China
| | - Peijun Han
- Department of Microbiology, Fourth Military Medical University, Xi'an, China
| | - Wei Ye
- Department of Microbiology, Fourth Military Medical University, Xi'an, China
| | - Hesong Chen
- Department of Microbiology, Fourth Military Medical University, Xi'an, China
| | - Xuyang Zheng
- Center of Infectious Diseases, Tangdu Hospital, Fourth Military Medical University, Xi'an, China
| | - Linfeng Cheng
- Department of Microbiology, Fourth Military Medical University, Xi'an, China
| | - Liang Zhang
- Department of Microbiology, Fourth Military Medical University, Xi'an, China
| | - Lan Yu
- Department of Microbiology, Fourth Military Medical University, Xi'an, China
| | - Xing'an Wu
- Department of Microbiology, Fourth Military Medical University, Xi'an, China
| | - Zhikai Xu
- Department of Microbiology, Fourth Military Medical University, Xi'an, China
| | - Yingfeng Lei
- Department of Microbiology, Fourth Military Medical University, Xi'an, China
| | - Fanglin Zhang
- Department of Microbiology, Fourth Military Medical University, Xi'an, China
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142
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Chen K, Liu J, Cao X. Regulation of type I interferon signaling in immunity and inflammation: A comprehensive review. J Autoimmun 2017; 83:1-11. [PMID: 28330758 DOI: 10.1016/j.jaut.2017.03.008] [Citation(s) in RCA: 178] [Impact Index Per Article: 25.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2017] [Accepted: 03/15/2017] [Indexed: 01/14/2023]
Abstract
Type I interferons (IFNs) play essential roles in establishing and modulating host defense against microbial infection via induction of IFN-stimulated genes (ISGs) through Janus kinase (JAK)-signal transducer and activator of transcription (STAT) signaling pathway. However, dysregulation of IFNs production and function could also mediate immune pathogenesis such as inflammatory autoimmune diseases and infectious diseases via aberrantly activating inflammatory responses or improperly suppressing microbial controls. Thus, IFN responses need to be tightly regulated to achieve protective immunity against microbial infection while avoiding harmful toxicity caused by improper or prolonged IFN signaling. Multiple levels of cellular and molecular events act in a cooperated manner to regulate IFN responses, in especial, post-translational modification (PTMs) of signaling molecules and epigenetic modification of gene expression programs are two important mechanisms for regulation of IFN signaling and thus critical for orchestrating IFN-mediated host immune response to the complex pathogenic or environmental stimuli. Conventional PTMs such as phosphorylation and polyubiquitylation, as well as numerous other PTMs including acetylation, ISGylation, SUMOylation and methylation have been shown to potently modulate type I IFN signaling transduction via targeting distinct signaling steps or components. Moreover, epigenetic mechanisms, such as histone modification, DNA methylation, non-coding RNAs play critical roles in regulating chromatin structure and function, leading to flexible and dynamic gene expression patterns downstream type I IFN signaling. Herein, we summarize the recent advances in the PTMs and epigenetic mechanisms in regulation of type I IFN signaling and responses. The involvement of dysregulated IFN signaling in inflammatory and autoimmune diseases are also discussed.
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Affiliation(s)
- Kun Chen
- Institute of Immunology, Zhejiang University School of Medicine, Hangzhou 310058, China
| | - Juan Liu
- National Key Laboratory of Medical Immunology & Institute of Immunology, Second Military Medical University, Shanghai 200433, China
| | - Xuetao Cao
- Institute of Immunology, Zhejiang University School of Medicine, Hangzhou 310058, China; National Key Laboratory of Medical Immunology & Institute of Immunology, Second Military Medical University, Shanghai 200433, China; National Key Laboratory of Medical Molecular Biology, Department of Immunology & Center for Immunotherapy, Institute of Basic Medical Sciences, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing 100005, China.
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143
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Xu-Yang Z, Pei-Yu B, Chuan-Tao Y, Wei Y, Hong-Wei M, Kang T, Chun-Mei Z, Ying-Feng L, Xin W, Ping-Zhong W, Chang-Xing H, Xue-Fan B, Ying Z, Zhan-Sheng J. Interferon-Induced Transmembrane Protein 3 Inhibits Hantaan Virus Infection, and Its Single Nucleotide Polymorphism rs12252 Influences the Severity of Hemorrhagic Fever with Renal Syndrome. Front Immunol 2017; 7:535. [PMID: 28096800 PMCID: PMC5206578 DOI: 10.3389/fimmu.2016.00535] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2016] [Accepted: 11/14/2016] [Indexed: 11/17/2022] Open
Abstract
Hantaan virus (HTNV) causes hemorrhagic fever with renal syndrome (HFRS). Previous studies have identified interferon-induced transmembrane proteins (IFITMs) as an interferon-stimulated gene family. However, the role of IFITMs in HTNV infection is unclear. In this study, we observed that IFITM3 single nucleotide polymorphisms (SNP) rs12252 C allele and CC genotype associated with the disease severity and HTNV load in the plasma of HFRS patients. In vitro experiments showed that the truncated protein produced by the rs12252 C allele exhibited an impaired anti-HTNV activity. We also proved that IFITM3 was able to inhibit HTNV infection in both HUVEC and A549 cells by overexpression and RNAi assays, likely via a mechanism of inhibiting virus entry demonstrated by binding and entry assay. Localization of IFITM3 in late endosomes was also observed. In addition, we demonstrated that the transcription of IFITM3 is negatively regulated by an lncRNA negative regulator of interferon response (NRIR). Taken together, we conclude that IFITM3, negatively regulated by NRIR, inhibits HTNV infection, and its SNP rs12252 correlates with the plasma HTNV load and the disease severity of patients with HFRS.
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Affiliation(s)
- Zheng Xu-Yang
- Department of Infectious Diseases, Tangdu Hospital, Fourth Military Medical University , Xi'an , China
| | - Bian Pei-Yu
- Department of Infectious Diseases, Tangdu Hospital, Fourth Military Medical University , Xi'an , China
| | - Ye Chuan-Tao
- Department of Infectious Diseases, Tangdu Hospital, Fourth Military Medical University , Xi'an , China
| | - Ye Wei
- Department of Microbiology, Fourth Military Medical University , Xi'an , China
| | - Ma Hong-Wei
- Department of Microbiology, Fourth Military Medical University , Xi'an , China
| | - Tang Kang
- Department of Immunology, Fourth Military Medical University , Xi'an , China
| | - Zhang Chun-Mei
- Department of Immunology, Fourth Military Medical University , Xi'an , China
| | - Lei Ying-Feng
- Department of Microbiology, Fourth Military Medical University , Xi'an , China
| | - Wei Xin
- Department of Infectious Diseases, Tangdu Hospital, Fourth Military Medical University , Xi'an , China
| | - Wang Ping-Zhong
- Department of Infectious Diseases, Tangdu Hospital, Fourth Military Medical University , Xi'an , China
| | - Huang Chang-Xing
- Department of Infectious Diseases, Tangdu Hospital, Fourth Military Medical University , Xi'an , China
| | - Bai Xue-Fan
- Department of Infectious Diseases, Tangdu Hospital, Fourth Military Medical University , Xi'an , China
| | - Zhang Ying
- Department of Infectious Diseases, Tangdu Hospital, Fourth Military Medical University , Xi'an , China
| | - Jia Zhan-Sheng
- Department of Infectious Diseases, Tangdu Hospital, Fourth Military Medical University , Xi'an , China
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144
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Involvement of Host Non-Coding RNAs in the Pathogenesis of the Influenza Virus. Int J Mol Sci 2016; 18:ijms18010039. [PMID: 28035991 PMCID: PMC5297674 DOI: 10.3390/ijms18010039] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2016] [Revised: 12/11/2016] [Accepted: 12/19/2016] [Indexed: 12/19/2022] Open
Abstract
Non-coding RNAs (ncRNAs) are a new type of regulators that play important roles in various cellular processes, including cell growth, differentiation, survival, and apoptosis. ncRNAs, including small non-coding RNAs (e.g., microRNAs, small interfering RNAs) and long non-coding RNAs (lncRNAs), are pervasively transcribed in human and mammalian cells. Recently, it has been recognized that these ncRNAs are critically implicated in the virus-host interaction as key regulators of transcription or post-transcription during viral infection. Influenza A virus (IAV) is still a major threat to human health. Hundreds of ncRNAs are differentially expressed in response to infection with IAV, such as infection by pandemic H1N1 and highly pathogenic avian strains. There is increasing evidence demonstrating functional involvement of these regulatory microRNAs, vault RNAs (vtRNAs) and lncRNAs in pathogenesis of influenza virus, including a variety of host immune responses. For example, it has been shown that ncRNAs regulate activation of pattern recognition receptor (PRR)-associated signaling and transcription factors (nuclear factor κ-light-chain-enhancer of activated B cells, NF-κB), as well as production of interferons (IFNs) and cytokines, and expression of critical IFN-stimulated genes (ISGs). The vital functions of IAV-regulated ncRNAs either to against defend viral invasion or to promote progeny viron production are summarized in this review. In addition, we also highlight the potentials of ncRNAs as therapeutic targets and diagnostic biomarkers.
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145
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Paneru B, Al-Tobasei R, Palti Y, Wiens GD, Salem M. Differential expression of long non-coding RNAs in three genetic lines of rainbow trout in response to infection with Flavobacterium psychrophilum. Sci Rep 2016; 6:36032. [PMID: 27786264 PMCID: PMC5081542 DOI: 10.1038/srep36032] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2016] [Accepted: 10/10/2016] [Indexed: 12/15/2022] Open
Abstract
Bacterial cold-water disease caused by Flavobacterium psychrophilum is one of the major causes of mortality of salmonids. Three genetic lines of rainbow trout designated as ARS-Fp-R (resistant), ARS-Fp-C (control) and ARS-Fp-S (susceptible) have significant differences in survival rate following F. psychrophilum infection. Previous study identified transcriptome differences of immune-relevant protein-coding genes at basal and post infection levels among these genetic lines. Using RNA-Seq approach, we quantified differentially expressed (DE) long non-coding RNAs (lncRNAs) in response to F. psychrophilum challenge in these genetic lines. Pairwise comparison between genetic lines and different infection statuses identified 556 DE lncRNAs. A positive correlation existed between the number of the differentially regulated lncRNAs and that of the protein-coding genes. Several lncRNAs showed strong positive and negative expression correlation with their overlapped, neighboring and distant immune related protein-coding genes including complement components, cytokines, chemokines and several signaling molecules involved in immunity. The correlated expressions and genome-wide co-localization suggested that some lncRNAs may be involved in regulating immune-relevant protein-coding genes. This study provides the first evidence of lncRNA-mediated regulation of the anti-bacterial immune response in a commercially important aquaculture species and will likely help developing new genetic markers for rainbow trout disease resistance.
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Affiliation(s)
- Bam Paneru
- Department of Biology and Molecular Biosciences Program, Middle Tennessee State University, Murfreesboro, TN, 37132, U.S
| | - Rafet Al-Tobasei
- Computational Science Program, Middle Tennessee State University, Murfreesboro, TN 37132, U.S
| | - Yniv Palti
- The National Center for Cool and Cold Water Aquaculture, USDA Agricultural Research Service, Kearneysville, WV 25430, U.S
| | - Gregory D Wiens
- The National Center for Cool and Cold Water Aquaculture, USDA Agricultural Research Service, Kearneysville, WV 25430, U.S
| | - Mohamed Salem
- Department of Biology and Molecular Biosciences Program, Middle Tennessee State University, Murfreesboro, TN, 37132, U.S.,Computational Science Program, Middle Tennessee State University, Murfreesboro, TN 37132, U.S
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146
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Motterle A, Sanchez-Parra C, Regazzi R. Role of long non-coding RNAs in the determination of β-cell identity. Diabetes Obes Metab 2016; 18 Suppl 1:41-50. [PMID: 27615130 DOI: 10.1111/dom.12714] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/08/2016] [Accepted: 05/04/2016] [Indexed: 12/22/2022]
Abstract
Pancreatic β-cells are highly specialized cells committed to secrete insulin in response to changes in the level of nutrients, hormones and neurotransmitters. Chronic exposure to elevated concentrations of glucose, fatty acids or inflammatory mediators can result in modifications in β-cell gene expression that alter their functional properties. This can lead to the release of insufficient amount of insulin to cover the organism's needs, and thus to the development of diabetes mellitus. Although most of the studies carried out in the last decades to elucidate the causes of β-cell dysfunction under disease conditions have focused on protein-coding genes, we now know that insulin-secreting cells also contain thousands of molecules of RNA that do not encode polypeptides but play key roles in the acquisition and maintenance of a highly differentiated state. In this review, we will highlight the involvement of long non-coding RNAs (lncRNAs), a particular class of non-coding transcripts, in the differentiation of β-cells and in the regulation of their specialized tasks. We will also discuss the crosstalk between the activities of lncRNAs and microRNAs and present the emerging evidence of a potential contribution of particular lncRNAs to the development of both type 1 and type 2 diabetes.
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Affiliation(s)
- A Motterle
- Department of Fundamental Neurosciences, University of Lausanne, Lausanne, Switzerland.
| | - C Sanchez-Parra
- Department of Fundamental Neurosciences, University of Lausanne, Lausanne, Switzerland
| | - R Regazzi
- Department of Fundamental Neurosciences, University of Lausanne, Lausanne, Switzerland
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147
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Long noncoding RNA #32 contributes to antiviral responses by controlling interferon-stimulated gene expression. Proc Natl Acad Sci U S A 2016; 113:10388-93. [PMID: 27582466 DOI: 10.1073/pnas.1525022113] [Citation(s) in RCA: 65] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Despite the breadth of knowledge that exists regarding the function of long noncoding RNAs (lncRNAs) in biological phenomena, the role of lncRNAs in host antiviral responses is poorly understood. Here, we report that lncRNA#32 is associated with type I IFN signaling. The silencing of lncRNA#32 dramatically reduced the level of IFN-stimulated gene (ISG) expression, resulting in sensitivity to encephalomyocarditis virus (EMCV) infection. In contrast, the ectopic expression of lncRNA#32 significantly suppressed EMCV replication, suggesting that lncRNA#32 positively regulates the host antiviral response. We further demonstrated the suppressive function of lncRNA#32 in hepatitis B virus and hepatitis C virus infection. lncRNA#32 bound to activating transcription factor 2 (ATF2) and regulated ISG expression. Our results reveal a role for lncRNA#32 in host antiviral responses.
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148
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Li T, Li X, Zhu W, Wang H, Mei L, Wu S, Lin X, Han X. NF90 is a novel influenza A virus NS1-interacting protein that antagonizes the inhibitory role of NS1 on PKR phosphorylation. FEBS Lett 2016; 590:2797-810. [PMID: 27423063 DOI: 10.1002/1873-3468.12311] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2016] [Revised: 07/01/2016] [Accepted: 07/06/2016] [Indexed: 12/24/2022]
Abstract
NF90 is a novel host antiviral factor that regulates PKR activation and stress granule formation in influenza A virus (IAV)-infected cells, but the precise mechanisms by which it operates remain unclear. We identified NF90 as a novel interacting protein of IAV nonstructural protein 1 (NS1). The interaction was dependent on the RNA-binding properties of NS1. NS1 associated with NF90 and PKR simultaneously; however, the interaction between NF90 and PKR was restricted by NS1. Knockdown of NF90 promoted inhibition of PKR phosphorylation induced by NS1, while coexpression of NF90 impeded reduction of PKR phosphorylation and stress granule formation triggered by NS1. In summary, NF90 exerts its antiviral activity by antagonizing the inhibitory role of NS1 on PKR phosphorylation.
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Affiliation(s)
- Ting Li
- Chinese Academy of Inspection and Quarantine, Institute of Animal Quarantine, Chaoyang District, Beijing, China
| | - Xi Li
- Chinese Academy of Inspection and Quarantine, Institute of Animal Quarantine, Chaoyang District, Beijing, China
| | - WenFei Zhu
- National Institute for Viral Disease Control and Prevention, Collaboration Innovation Center for Diagnosis and Treatment of Infectious Diseases, Chinese Center for Disease Control and Prevention; Key Laboratory for Medical Virology, National Health and Family Planning Commission, Beijing, China
| | - HuiYu Wang
- Chinese Academy of Inspection and Quarantine, Institute of Animal Quarantine, Chaoyang District, Beijing, China
| | - Lin Mei
- Chinese Academy of Inspection and Quarantine, Institute of Animal Quarantine, Chaoyang District, Beijing, China
| | - ShaoQiang Wu
- Chinese Academy of Inspection and Quarantine, Institute of Animal Quarantine, Chaoyang District, Beijing, China
| | - XiangMei Lin
- Chinese Academy of Inspection and Quarantine, Institute of Animal Quarantine, Chaoyang District, Beijing, China
| | - XueQing Han
- Chinese Academy of Inspection and Quarantine, Institute of Animal Quarantine, Chaoyang District, Beijing, China
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149
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Sharma N, Singh SK. Implications of non-coding RNAs in viral infections. Rev Med Virol 2016; 26:356-68. [PMID: 27401792 DOI: 10.1002/rmv.1893] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2016] [Revised: 05/30/2016] [Accepted: 05/31/2016] [Indexed: 02/06/2023]
Abstract
The advances in RNA sequencing have unveiled various non-coding RNAs (ncRNAs), which modulate the gene expression. ncRNAs do not get translated into proteins. These include transfer RNAs, ribosomal RNAs, microRNA (miRNA), short interfering RNA, long non-coding RNA, piwi-interacting RNA and small nuclear RNA. ncRNAs regulate gene expression at various levels and control cellular machinery. miRNAs have been reported in plants, animals, several invertebrates and viruses. The miRNAs regulate the gene expression post-transcriptionally. Viral infection strongly influences the abundance and the distribution of miRNAs and other ncRNAs within the host cells. Viruses may encode their own miRNA, which help in the viral life cycle and other aspects of pathogenesis. Viruses are known to successfully modulate the expression pattern of ncRNAs. The ncRNA-based strategies adopted by viruses for their survival present a complex picture of host-virus interactions. Copyright © 2016 John Wiley & Sons, Ltd.
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Affiliation(s)
- Nikhil Sharma
- Laboratory of Neurovirology and Inflammation Biology, CSIR-Centre for Cellular and Molecular Biology (CCMB), Hyderabad, India
| | - Sunit K Singh
- Laboratory of Human Molecular Virology and Immunology, Molecular Biology Unit, Faculty of Medicine, Institute of Medical Sciences (IMS), Banaras Hindu University (BHU), Varanasi, India.
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150
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Pencik J, Pham HTT, Schmoellerl J, Javaheri T, Schlederer M, Culig Z, Merkel O, Moriggl R, Grebien F, Kenner L. JAK-STAT signaling in cancer: From cytokines to non-coding genome. Cytokine 2016; 87:26-36. [PMID: 27349799 DOI: 10.1016/j.cyto.2016.06.017] [Citation(s) in RCA: 155] [Impact Index Per Article: 19.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2016] [Accepted: 06/15/2016] [Indexed: 12/13/2022]
Abstract
In the past decades, studies of the Janus kinases (JAKs) and signal transducers and activators of transcription (STATs) signaling have uncovered highly conserved programs linking cytokine signaling to the regulation of essential cellular mechanisms such as proliferation, invasion, survival, inflammation and immunity. Inhibitors of the JAK/STAT pathway are used for treatment of autoimmune diseases, such as rheumatoid arthritis or psoriasis. Aberrant JAK/STAT signaling has been identified to contribute to cancer progression and metastatic development. Targeting of JAK/STAT pathway is currently one of the most promising therapeutic strategies in prostate cancer (PCa), hematopoietic malignancies and sarcomas. Notably, newly identified regulators of JAK/STAT signaling, the non-coding RNAs transcripts and their role as important targets and potential clinical biomarkers are highlighted in this review. In addition to the established role of the JAK/STAT signaling pathway in traditional cytokine signaling the non-coding RNAs add yet another layer of hidden regulation and function. Understanding the crosstalk of non-coding RNA with JAK/STAT signaling in cancer is of critical importance and may result in better patient stratification not only in terms of prognosis but also in the context of therapy.
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Affiliation(s)
- Jan Pencik
- Clinical Institute of Pathology, Medical University of Vienna, 1090 Vienna, Austria; Division of Nuclear Medicine, Department of Biomedical Imaging and Image-guided Therapy, 1090 Vienna, Austria; Ludwig Boltzmann Institute for Cancer Research, Medical University of Vienna, 1090 Vienna, Austria.
| | - Ha Thi Thanh Pham
- Ludwig Boltzmann Institute for Cancer Research, Medical University of Vienna, 1090 Vienna, Austria; Institute of Animal Breeding and Genetics, University of Veterinary Medicine Vienna, Medical University of Vienna, 1210 Vienna, Austria
| | - Johannes Schmoellerl
- Ludwig Boltzmann Institute for Cancer Research, Medical University of Vienna, 1090 Vienna, Austria
| | - Tahereh Javaheri
- Ludwig Boltzmann Institute for Cancer Research, Medical University of Vienna, 1090 Vienna, Austria; Institute of Animal Breeding and Genetics, University of Veterinary Medicine Vienna, Medical University of Vienna, 1210 Vienna, Austria
| | - Michaela Schlederer
- Clinical Institute of Pathology, Medical University of Vienna, 1090 Vienna, Austria; Ludwig Boltzmann Institute for Cancer Research, Medical University of Vienna, 1090 Vienna, Austria; Department for Pathology of Laboratory Animals, University of Veterinary Medicine Vienna, 1210 Vienna, Austria
| | - Zoran Culig
- Department of Urology, Medical University of Innsbruck, 6020 Innsbruck, Austria
| | - Olaf Merkel
- Clinical Institute of Pathology, Medical University of Vienna, 1090 Vienna, Austria
| | - Richard Moriggl
- Ludwig Boltzmann Institute for Cancer Research, Medical University of Vienna, 1090 Vienna, Austria; Institute of Animal Breeding and Genetics, University of Veterinary Medicine Vienna, Medical University of Vienna, 1210 Vienna, Austria
| | - Florian Grebien
- Ludwig Boltzmann Institute for Cancer Research, Medical University of Vienna, 1090 Vienna, Austria
| | - Lukas Kenner
- Clinical Institute of Pathology, Medical University of Vienna, 1090 Vienna, Austria; Ludwig Boltzmann Institute for Cancer Research, Medical University of Vienna, 1090 Vienna, Austria; Department for Pathology of Laboratory Animals, University of Veterinary Medicine Vienna, 1210 Vienna, Austria.
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