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Hepatitis C Virus Evades Interferon Signaling by Suppressing Long Noncoding RNA Linc-Pint Involving C/EBP-β. J Virol 2021; 95:e0095221. [PMID: 34160260 PMCID: PMC8354323 DOI: 10.1128/jvi.00952-21] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
Hepatitis C virus (HCV) regulates many cellular genes in modulating the host immune system for benefit of viral replication and long-term persistence in a host for chronic infection. Long noncoding RNAs (lncRNAs) play an important role in the regulation of many important cellular processes, including immune responses. We recently reported that HCV infection downregulates lncRNA Linc-Pint (long intergenic non-protein-coding RNA p53-induced transcript) expression, although the mechanism of repression and functional consequences are not well understood. In this study, we demonstrate that HCV infection of hepatocytes transcriptionally reduces Linc-Pint expression through CCAAT/enhancer binding protein β (C/EBP-β). Subsequently, we observed that the overexpression of Linc-Pint significantly upregulates interferon alpha (IFN-α) and IFN-β expression in HCV-replicating hepatocytes. Using unbiased proteomics, we identified that Linc-Pint associates with DDX24, which enables RIP1 to interact with IFN-regulatory factor 7 (IRF7) of the IFN signaling pathway. We furthermore observed that IFN-α14 promoter activity was enhanced in the presence of Linc-Pint. Together, these results demonstrated that Linc-Pint acts as a positive regulator of host innate immune responses, especially IFN signaling. HCV-mediated downregulation of Linc-Pint expression appears to be one of the mechanisms by which HCV may evade innate immunity for long-term persistence and chronicity. IMPORTANCE The mechanism by which lncRNA regulates the host immune response during HCV infection is poorly understood. We observed that Linc-Pint was transcriptionally downregulated by HCV. Using a chromatin immunoprecipitation (ChIP) assay, we showed inhibition of transcription factor C/EBP-β binding to the Linc-Pint promoter in the presence of HCV infection. We further identified that Linc-Pint associates with DDX24 for immunomodulatory function. The overexpression of Linc-Pint reduces DDX24 expression, which in turn results in the disruption of DDX24-RIP1 complex formation and the activation of IRF7. The induction of IFN-α14 promoter activity in the presence of Linc-Pint further confirms our observation. Together, our results suggest that Linc-Pint acts as a positive regulator of host innate immune responses. Downregulation of Linc-Pint expression by HCV helps in escaping the innate immune system for the development of chronicity.
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2
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Zhao P, Malik S, Xing S. Epigenetic Mechanisms Involved in HCV-Induced Hepatocellular Carcinoma (HCC). Front Oncol 2021; 11:677926. [PMID: 34336665 PMCID: PMC8320331 DOI: 10.3389/fonc.2021.677926] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2021] [Accepted: 06/28/2021] [Indexed: 12/19/2022] Open
Abstract
Hepatocellular carcinoma (HCC), is the third leading cause of cancer-related deaths, which is largely caused by virus infection. About 80% of the virus-infected people develop a chronic infection that eventually leads to liver cirrhosis and hepatocellular carcinoma (HCC). With approximately 71 million HCV chronic infected patients worldwide, they still have a high risk of HCC in the near future. However, the mechanisms of carcinogenesis in chronic HCV infection have not been still fully understood, which involve a complex epigenetic regulation and cellular signaling pathways. Here, we summarize 18 specific gene targets and different signaling pathways involved in recent findings. With these epigenetic alterations requiring histone modifications and DNA hyper or hypo-methylation of these specific genes, the dysregulation of gene expression is also associated with different signaling pathways for the HCV life cycle and HCC. These findings provide a novel insight into a correlation between HCV infection and HCC tumorigenesis, as well as potentially preventable approaches. Hepatitis C virus (HCV) infection largely causes hepatocellular carcinoma (HCC) worldwide with 3 to 4 million newly infected cases diagnosed each year. It is urgent to explore its underlying molecular mechanisms for therapeutic treatment and biomarker discovery. However, the mechanisms of carcinogenesis in chronic HCV infection have not been still fully understood, which involve a complex epigenetic regulation and cellular signaling pathways. Here, we summarize 18 specific gene targets and different signaling pathways involved in recent findings. With these epigenetic alterations requiring histone modifications and DNA hyper or hypo-methylation of these specific genes, the dysregulation of gene expression is also associated with different signaling pathways for the HCV life cycle and HCC. These findings provide a novel insight into a correlation between HCV infection and HCC tumorigenesis, as well as potentially preventable approaches.
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Affiliation(s)
- Pin Zhao
- Guandong Key Laboratory for Biomedical Measurements and Ultrasound Imaging, School of Biomedical Engineering, Shenzhen University Health Science Center, Shenzhen, China
| | - Samiullah Malik
- Department of Pathogen Biology, Shenzhen University Health Science Center, Shenzhen, China
| | - Shaojun Xing
- Department of Pathogen Biology, Shenzhen University Health Science Center, Shenzhen, China
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3
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Ranjbar R, Behjatfar M, Teimouri A, Aghaie Fard A, Maniati M, Taheri-Anganeh M. Long non-coding RNAs and microorganism-associated cancers. Cell Biochem Funct 2021; 39:844-853. [PMID: 34227160 DOI: 10.1002/cbf.3657] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2021] [Revised: 06/17/2021] [Accepted: 06/25/2021] [Indexed: 12/26/2022]
Abstract
Cancerous cells are abnormal cells characterized by aberrant growth and proliferation, which can involve various types of cells and tissues. Through numerous signalling pathways, many mechanisms are involved in cells that keep them normal. These signalling pathways are tightly set by different proteins whose expression is regulated by a large number of factors. In other words, when a regulating factor does not act properly or undergoes a change in its function or expression, the result will be that the subordinate gene and subsequently the related protein will show deranged expression and activity. This leads to disordered signalling pathways which bring about uncontrolled proliferation in cells. One of the most significant factors in adjusting the expression of genes is noncoding RNAs. It should be noted that all underlying causes initiating malignancy try to alter the main regulatory factors in cellular processes and gene expression and direct the cell to an unregulated state. Microorganisms have been identified as one of the important elements to direct normal cells to abnormality. That is, they probably agitate the malignant traits through manipulating significant factors such as ncRNAs in given cells using their own or host-related factors. The present study is aimed at examining how the long noncoding RNAs are involved in microorganism-mediated cancers.
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Affiliation(s)
- Reza Ranjbar
- Molecular Biology Research Center, Systems Biology and Poisonings Institute, Baqiyatallah University of Medical Sciences, Tehran, Iran
| | - Mojtaba Behjatfar
- Department of Electrical Engineering, Kazeroon Branch, Islamic Azad University, Kazeroon, Iran
| | - Ali Teimouri
- Student Research Committee, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Arad Aghaie Fard
- Department of Hematology, Faculty of Medical Sciences, Tarbiat Modares University, Tehran, Iran
| | - Mahmood Maniati
- English Department, School of Medicine, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
| | - Mortaza Taheri-Anganeh
- Department of Medical Biotechnology, School of Advanced Medical Sciences and Technologies, Shiraz University of Medical Sciences, Shiraz, Iran
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4
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Plasek LM, Valadkhan S. lncRNAs in T lymphocytes: RNA regulation at the heart of the immune response. Am J Physiol Cell Physiol 2021; 320:C415-C427. [PMID: 33296288 PMCID: PMC8294623 DOI: 10.1152/ajpcell.00069.2020] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Genome-wide analyses in the last decade have uncovered the presence of a large number of long non-protein-coding transcripts that show highly tissue- and state-specific expression patterns. High-throughput sequencing analyses in diverse subsets of immune cells have revealed a complex and dynamic expression pattern for these long noncoding RNAs (lncRNAs) that correlate with the functional states of immune cells. Although the vast majority of lncRNAs expressed in immune cells remain unstudied, functional studies performed on a small subset have indicated that their state-specific expressions pattern frequently has a regulatory impact on the function of immune cells. In vivo and in vitro studies have pointed to the involvement of lncRNAs in a wide variety of cellular processes, including both the innate and adaptive immune response through mechanisms ranging from epigenetic and transcriptional regulation to sequestration of functional molecules in subcellular compartments. This review will focus mainly on the role of lncRNAs in CD4+ and CD8+ T cells, which play pivotal roles in adaptive immunity. Recent studies have pointed to key physiological functions for lncRNAs during several developmental and functional stages of the life cycle of lymphocytes. Although lncRNAs play important physiological roles in lymphocytic response to antigenic stimulation, differentiation into effector cells, and secretion of cytokines, their dysregulated expression can promote or sustain pathological states such as autoimmunity, chronic inflammation, cancer, and viremia. This, together with their highly cell type-specific expression patterns, makes lncRNAs ideal therapeutic targets and underscores the need for additional studies into the role of these understudied transcripts in adaptive immune response.
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5
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Abstract
Recent studies have identified host long noncoding RNAs (lncRNAs) as key regulators of
host-virus interactions during viral infection. The influenza A virus (IAV) remains a
serious threat to public health and economic stability. It is well known that thousands of
lncRNAs are differentially expressed upon IAV infection, some of which regulate IAV
infection by modulating the host innate immune response, affecting cellular metabolism, or
directly interacting with viral proteins. Some of these lncRNAs appear to be required for
IAV infection, but the molecular mechanisms are not completely elucidated. In this review,
we summarize the roles of host lncRNAs in regulating IAV infection and provide an overview
of the lncRNA-mediated regulatory network. The goal of this review is to stimulate further
research on the function of both well-established and newly discovered lncRNAs in IAV
infection.
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Affiliation(s)
- Jing Wang
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical School, Beijing, People's Repbulic of People's Republic of China
| | - Shan Cen
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical School, Beijing, People's Repbulic of People's Republic of China.,CAMS Key Laboratory of Antiviral Drug Research, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, People's Repbulic of People's Republic of China.,Beijing Friendship Hospital, Capital Medical University, Beijing, People's Repbulic of People's Republic of China
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6
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Mazahery C, Valadkhan S, Levine AD. Transcriptomic Analysis Reveals Receptor Subclass-Specific Immune Regulation of CD8 + T Cells by Opioids. Immunohorizons 2020; 4:420-429. [PMID: 32675085 DOI: 10.4049/immunohorizons.2000019] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2020] [Accepted: 06/29/2020] [Indexed: 11/19/2022] Open
Abstract
Opioid peptides are released at sites of injury, and their cognate G protein-coupled opioid receptors (OR) are expressed on immune cells. Exposure of human circulating CD8+ T cells to selective OR agonists differentially regulates thousands of genes. Gene set enrichment analysis reveals that μ-OR more strongly regulates cellular processes than δ-OR. In TCR naive T cells, triggering μ-OR exhibits stimulatory and inhibitory patterns, yet when administered prior to TCR cross-linking, a μ-OR agonist inhibits activation. μ-OR, but not δ-OR, signaling is linked to upregulation of lipid, cholesterol, and steroid hormone biosynthesis, suggesting lipid regulation is a mechanism for immune suppression. Lipid rafts are cholesterol-rich, liquid-ordered membrane domains that function as a nexus for the initiation of signal transduction from surface receptors, including TCR and μ-OR. We therefore propose that μ-OR-specific inhibition of TCR responses in human CD8+ T cells may be mediated through alterations in lipid metabolism and membrane structure.
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Affiliation(s)
- Claire Mazahery
- Department of Pathology, Case Western Reserve University, Cleveland, OH 44106
| | - Saba Valadkhan
- Department of Molecular Biology and Microbiology, Case Western Reserve University, Cleveland, OH 44106
| | - Alan D Levine
- Department of Pathology, Case Western Reserve University, Cleveland, OH 44106; .,Department of Molecular Biology and Microbiology, Case Western Reserve University, Cleveland, OH 44106.,Department of Pharmacology, Case Western Reserve University, Cleveland, OH 44106.,Department of Medicine, Case Western Reserve University, Cleveland, OH 44106.,Department of Pediatrics, Case Western Reserve University, Cleveland, OH 44106; and.,Case Comprehensive Cancer Center, Case Western Reserve University, Cleveland, OH 44106
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7
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Interferon Response in Hepatitis C Virus-Infected Hepatocytes: Issues to Consider in the Era of Direct-Acting Antivirals. Int J Mol Sci 2020; 21:ijms21072583. [PMID: 32276399 PMCID: PMC7177520 DOI: 10.3390/ijms21072583] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2020] [Revised: 04/04/2020] [Accepted: 04/07/2020] [Indexed: 12/16/2022] Open
Abstract
When interferons (IFNs) bind to their receptors, they upregulate numerous IFN-stimulated genes (ISGs) with antiviral and immune regulatory activities. Hepatitis C virus (HCV) is a single-stranded, positive-sense RNA virus that affects over 71 million people in the global population. Hepatocytes infected with HCV produce types I and III IFNs. These endogenous IFNs upregulate a set of ISGs that negatively impact the outcome of pegylated IFN-α and ribavirin treatments, which were previously used to treat HCV. In addition, the IFNL4 genotype was the primary polymorphism responsible for a suboptimal treatment response to pegylated IFN-α and ribavirin. However, recently developed direct-acting antivirals have demonstrated a high rate of sustained virological response without pegylated IFN-α. Herein, we review recent studies on types I and III IFN responses to in HCV-infected hepatocytes. In particular, we focused on open issues related to IFN responses in the direct-acting antiviral era.
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8
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Unfried JP, Fortes P. LncRNAs in HCV Infection and HCV-Related Liver Disease. Int J Mol Sci 2020; 21:ijms21062255. [PMID: 32214045 PMCID: PMC7139329 DOI: 10.3390/ijms21062255] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2020] [Revised: 03/19/2020] [Accepted: 03/20/2020] [Indexed: 12/14/2022] Open
Abstract
Long non-coding RNAs (lncRNAs) are transcripts with poor coding capacity that may interact with proteins, DNA, or other RNAs to perform structural and regulatory functions. The lncRNA transcriptome changes significantly in most diseases, including cancer and viral infections. In this review, we summarize the functional implications of lncRNA-deregulation after infection with hepatitis C virus (HCV). HCV leads to chronic infection in many patients that may progress to liver cirrhosis and hepatocellular carcinoma (HCC). Most lncRNAs deregulated in infected cells that have been described function to potentiate or block the antiviral response and, therefore, they have a great impact on HCV viral replication. In addition, several lncRNAs upregulated by the infection contribute to viral release. Finally, many lncRNAs have been described as deregulated in HCV-related HCC that function to enhance cell survival, proliferation, and tumor progression by different mechanisms. Interestingly, some HCV-related HCC lncRNAs can be detected in bodily fluids, and there is great hope that they could be used as biomarkers to predict cancer initiation, progression, tumor burden, response to treatment, resistance to therapy, or tumor recurrence. Finally, there is high confidence that lncRNAs could also be used to improve the suboptimal long-term outcomes of current HCC treatment options.
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Affiliation(s)
| | - P. Fortes
- Correspondence: ; Tel.: +34-948194700
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9
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Gan J, Huang L, Qu Y, Luo R, Cai Q, Zhao F, Mu D. Expression and functional analysis of lncRNAs in the hippocampus of immature rats with status epilepticus. J Cell Mol Med 2019; 24:149-159. [PMID: 31738000 PMCID: PMC6933385 DOI: 10.1111/jcmm.14676] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2019] [Revised: 07/27/2019] [Accepted: 08/28/2019] [Indexed: 01/01/2023] Open
Abstract
Long non-coding RNAs (lncRNAs) have been implicated in the regulation of gene expression at various levels. However, to date, the expression profile of lncRNAs in status epilepticus (SE) was unclear. In our study, the expression profile of lncRNAs was investigated by high-throughput sequencing based on a lithium/pilocarpine-induced SE model in immature rats. Furthermore, weighted correlation network analysis (WGCNA), gene ontology (GO) analysis and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis were performed to construct co-expression networks and establish functions of the identified hub lncRNAs in SE. The functional role of a hub lncRNA (NONRATT010788.2) in SE was investigated in an in vitro model. Our results indicated that 7082 lncRNAs (3522 up-regulated and 3560 down-regulated), which are involved in cell proliferation, inflammatory responses, angiogenesis and autophagy, were dysregulated in the hippocampus of immature rats with SE. Additionally, WGCNA identified 667 up-regulated hub lncRNAs in turquoise module that were involved in apoptosis, inflammatory responses and angiogenesis via regulation of HIF-1, p53 and chemokine signalling pathways and via inflammatory mediator regulation of TRP channels. Knockdown of an identified hub lncRNA (NONRATT010788.2) inhibited neuronal apoptosis in vitro. Taken together, our study is the first to demonstrate the expression profile and potential function of lncRNAs in the hippocampus of immature rats with SE. The defined hub lncRNAs may participate in the pathogenesis of SE via lncRNA-miRNA-mRNA network.
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Affiliation(s)
- Jing Gan
- Department of Pediatrics, West China Second University Hospital, Sichuan University, Chengdu, China.,Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University) Ministry of Education, Sichuan University, Chengdu, China
| | - Lingyi Huang
- West China College of Stomatology, Sichuan University, Chengdu, China
| | - Yi Qu
- Department of Pediatrics, West China Second University Hospital, Sichuan University, Chengdu, China.,Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University) Ministry of Education, Sichuan University, Chengdu, China
| | - Rong Luo
- Department of Pediatrics, West China Second University Hospital, Sichuan University, Chengdu, China.,Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University) Ministry of Education, Sichuan University, Chengdu, China
| | - Qianyun Cai
- Department of Pediatrics, West China Second University Hospital, Sichuan University, Chengdu, China.,Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University) Ministry of Education, Sichuan University, Chengdu, China
| | - Fengyan Zhao
- Department of Pediatrics, West China Second University Hospital, Sichuan University, Chengdu, China.,Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University) Ministry of Education, Sichuan University, Chengdu, China
| | - Dezhi Mu
- Department of Pediatrics, West China Second University Hospital, Sichuan University, Chengdu, China.,Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University) Ministry of Education, Sichuan University, Chengdu, China
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10
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Hu P, Wilhelm J, Gerresheim GK, Shalamova LA, Niepmann M. Lnc-ITM2C-1 and GPR55 Are Proviral Host Factors for Hepatitis C Virus. Viruses 2019; 11:v11060549. [PMID: 31200545 PMCID: PMC6631246 DOI: 10.3390/v11060549] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2019] [Revised: 06/01/2019] [Accepted: 06/12/2019] [Indexed: 02/07/2023] Open
Abstract
Multiple host factors are known to play important roles in hepatitis C virus (HCV) replication, in immune responses induced by HCV infection, or in processes that facilitate virus escape from immune clearance, while yet only few studies examined the contribution of long non-coding RNAs (lncRNAs/lncRs). Using microarrays, we identified lncRNAs with altered expression levels in HCV replicating Huh-7.5 hepatoma cells. Of these, lncR 8(Lnc-ITM2C-1/LOC151484) was confirmed by quantitative real-time PCR (qRT-PCR) to be upregulated early after HCV infection. After suppressing the expression of lncR 8, HCV RNA and protein were downregulated, confirming a positive correlation between lncR 8 expression and HCV replication. lncR 8 knockdown in Huh-7.5 cells reduced expression of the neighboring gene G protein-coupled receptor 55 (GPR55) mRNA level at early times, and leads to increased levels of several Interferon stimulated genes (ISGs) including ISG15, Mx1 and IFITM1. Importantly, the effect of lncR 8 on ISGs and GPR55 precedes its effect on HCV replication. Furthermore, knockdown of GPR55 mRNA induces ISG expression, providing a possible link between lncR 8 and ISGs. We conclude that HCV induces lncR 8 expression, while lncR 8 indirectly favors HCV replication by stimulating expression of its neighboring gene GPR55, which in turn downregulates expression of ISGs. The latter fact is also consistent with an anti-inflammatory role of GPR55. These events may contribute to the failure to eliminate ongoing HCV infection.
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Affiliation(s)
- Pan Hu
- Institute of Biochemistry, Medical Faculty, Justus-Liebig-University, Friedrichstrasse 24, 35392 Giessen, Germany.
| | - Jochen Wilhelm
- Universities of Giessen and Marburg Lung Center (UGMLC), German Center for Lung Research (DZL), 35392 Giessen, Germany.
| | - Gesche K Gerresheim
- Institute of Biochemistry, Medical Faculty, Justus-Liebig-University, Friedrichstrasse 24, 35392 Giessen, Germany.
| | - Lyudmila A Shalamova
- Institute of Biochemistry, Medical Faculty, Justus-Liebig-University, Friedrichstrasse 24, 35392 Giessen, Germany.
| | - Michael Niepmann
- Institute of Biochemistry, Medical Faculty, Justus-Liebig-University, Friedrichstrasse 24, 35392 Giessen, Germany.
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11
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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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12
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Liu X, Duan X, Holmes JA, Li W, Lee SH, Tu Z, Zhu C, Salloum S, Lidofsky A, Schaefer EA, Cai D, Li S, Wang H, Huang Y, Zhao Y, Yu ML, Xu Z, Chen L, Hong J, Lin W, Chung RT. A Long Noncoding RNA Regulates Hepatitis C Virus Infection Through Interferon Alpha-Inducible Protein 6. Hepatology 2019; 69:1004-1019. [PMID: 30199576 PMCID: PMC6393205 DOI: 10.1002/hep.30266] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/22/2018] [Accepted: 09/05/2018] [Indexed: 12/13/2022]
Abstract
Long noncoding RNAs (lncRNAs) play a critical role in the regulation of many important cellular processes. However, the mechanisms by which lncRNAs regulate viral infection and host immune responses are not well understood. We sought to explore lncRNA regulation of hepatitis C virus (HCV) infection and interferon response. We performed RNA sequencing (RNAseq) in Huh7.5.1 cells with or without interferon alpha (IFNα) treatment. Clustered regularly interspaced short palindromic repeats/Cas9 guide RNA (gRNA) was used to knock out selected genes. The promoter clones were constructed, and the activity of related interferon-stimulated genes (ISGs) were detected by the secrete-pair dual luminescence assay. We constructed the full-length and four deletion mutants of an interferon-induced lncRNA RP11-288L9.4 (lncRNA-IFI6) based on predicted secondary structure. Selected gene mRNAs and their proteins, together with HCV infection, in Huh7.5.1 cells and primary human hepatocytes (PHHs) were monitored by quantitative real-time PCR (qRT-PCR) and western blot. We obtained 7,901 lncRNAs from RNAseq. A total of 1,062 host-encoded lncRNAs were significantly differentially regulated by IFNα treatment. We found that lncRNA-IFI6 gRNA significantly inhibited HCV infection compared with negative gRNA control. The expression of the antiviral ISG IFI6 was significantly increased following lncRNA-IFI6 gRNA editing compared with negative gRNA control in Japanese fulminant hepatitis 1 (JFH1)-infected Huh7.5.1 cells and PHHs. We observed that lncRNA-IFI6 regulation of HCV was independent of Janus kinase-signal transducer and activator of transcription (JAK-STAT) signaling. lncRNA-IFI6 negatively regulated IFI6 promoter function through histone modification. Overexpression of the truncated spatial domain or full-length lncRNA-IFI6 inhibited IFI6 expression and increased HCV replication. Conclusion: A lncRNA, lncRNA-IFI6, regulates antiviral innate immunity in the JFH1 HCV infection model. lncRNA-IFI6 regulates HCV infection independently of the JAK-STAT pathway. lncRNA-IFI6 exerts its regulatory function via promoter activation and histone modification of IFI6 through its spatial domain.
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Affiliation(s)
- Xiao Liu
- Southwest University, College of Animal Science and technology, 400715 Chongqing, China,Liver Center and Gastrointestinal Division, Department of Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA,Animal Biotechnology Center, College of Veterinary Medicine, Sichuan Agricultural University, 610052 Chengdu, China
| | - Xiaoqiong Duan
- Institute of Blood Transfusion, Chinese Academy of Medical Sciences and Peking Union Medical College, 610052 Chengdu, China,Liver Center and Gastrointestinal Division, Department of Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA
| | - Jacinta A. Holmes
- Liver Center and Gastrointestinal Division, Department of Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA
| | - Wenting Li
- Liver Center and Gastrointestinal Division, Department of Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA,Department of Infectious Disease, Anhui Provincial Hospital, Anhui Medical University, Hefei, China
| | - Sae Hwan Lee
- Liver Center and Gastrointestinal Division, Department of Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA,Soonchunhyang University College of Medicine, Cheonan Hospital, 330721 Dongnamgu Cheonan, Republic of Korea
| | - Zeng Tu
- Liver Center and Gastrointestinal Division, Department of Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA,Department of microbiology, College of Basic Medical Science, Chongqing Medical University, 400715 Chongqing, China
| | - Chuanlong Zhu
- Liver Center and Gastrointestinal Division, Department of Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA,Department of Infectious Disease, the First Affiliated Hospital of Nanjing Medical University, Nanjing 210029, China
| | - Shadi Salloum
- Liver Center and Gastrointestinal Division, Department of Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA
| | - Anna Lidofsky
- Liver Center and Gastrointestinal Division, Department of Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA
| | - Esperance A. Schaefer
- Liver Center and Gastrointestinal Division, Department of Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA
| | - Dachuan Cai
- Liver Center and Gastrointestinal Division, Department of Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA,Department of Infectious Disease, Chongqing Medical University, 400715 Chongqing, China
| | - Shilin Li
- Institute of Blood Transfusion, Chinese Academy of Medical Sciences and Peking Union Medical College, 610052 Chengdu, China
| | - Haoju Wang
- Southwest University, College of Animal Science and technology, 400715 Chongqing, China
| | - Yongfu Huang
- Southwest University, College of Animal Science and technology, 400715 Chongqing, China
| | - Yongju Zhao
- Southwest University, College of Animal Science and technology, 400715 Chongqing, China
| | - Ming-Lung Yu
- Liver Center and Gastrointestinal Division, Department of Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA,Division of Hepatobiliary, Department of Internal Medicine and Hepatitis Center, Kaohsiung Medical University Hospital, Kaohsiung, Kaohsiung Medical University, Taiwan
| | - Zhiwen Xu
- Animal Biotechnology Center, College of Veterinary Medicine, Sichuan Agricultural University, 610052 Chengdu, China
| | - Limin Chen
- Institute of Blood Transfusion, Chinese Academy of Medical Sciences and Peking Union Medical College, 610052 Chengdu, China
| | - Jian Hong
- Liver Center and Gastrointestinal Division, Department of Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA
| | - Wenyu Lin
- Institute of Blood Transfusion, Chinese Academy of Medical Sciences and Peking Union Medical College, 610052 Chengdu, China,Liver Center and Gastrointestinal Division, Department of Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA,Corresponding authors Correspondence address: Gastrointestinal Unit, Warren 1007, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA; Tel.: +1 617 726 2061; fax: +1 617 643 0446. , or
| | - Raymond T. Chung
- Liver Center and Gastrointestinal Division, Department of Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA,Corresponding authors Correspondence address: Gastrointestinal Unit, Warren 1007, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA; Tel.: +1 617 726 2061; fax: +1 617 643 0446. , or
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