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Fitzgerald KA, Shmuel-Galia L. Lnc-ing RNA to intestinal homeostasis and inflammation. Trends Immunol 2024; 45:127-137. [PMID: 38220553 DOI: 10.1016/j.it.2023.12.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2023] [Revised: 12/14/2023] [Accepted: 12/21/2023] [Indexed: 01/16/2024]
Abstract
Long noncoding RNAs (lncRNAs) play important roles in numerous biological processes, including the immune system. Initial research in this area focused on cell-based studies, but recent advances underscore the profound significance of lncRNAs at the organismal level, providing invaluable insights into their roles in inflammatory diseases. In this rapidly evolving field, lncRNAs have been described with pivotal roles in the intestinal tract where they regulate intestinal homeostasis and inflammation by influencing processes such as immune cell development, inflammatory signaling pathways, epithelial barrier function, and cellular metabolism. Understanding the regulation and function of lncRNAs in this tissue may position lncRNAs not only as potential disease biomarkers but also as promising targets for therapeutic intervention in inflammatory bowel disease and related diseases.
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Affiliation(s)
- Katherine A Fitzgerald
- Program in Innate Immunity, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA.
| | - Liraz Shmuel-Galia
- Department of Pathology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA.
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2
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Zhang D, Zhang M, Zhang L, Wang W, Hua S, Zhou C, Sun X. Long non-coding RNAs and immune cells: Unveiling the role in viral infections. Biomed Pharmacother 2024; 170:115978. [PMID: 38056234 DOI: 10.1016/j.biopha.2023.115978] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2023] [Revised: 11/26/2023] [Accepted: 11/29/2023] [Indexed: 12/08/2023] Open
Abstract
Viral infections present significant challenges to human health, underscoring the importance of understanding the immune response for effective therapeutic strategies. Immune cell activation leads to dynamic changes in gene expression. Numerous studies have demonstrated the crucial role of long noncoding RNAs (lncRNAs) in immune activation and disease processes, including viral infections. This review provides a comprehensive overview of lncRNAs expressed in immune cells, including CD8 T cells, CD4 T cells, B cells, monocytes, macrophages, dendritic cells, and granulocytes, during both acute and chronic viral infections. LncRNA-mediated gene regulation encompasses various mechanisms, including the modulation of viral replication, the establishment of latency, activation of interferon pathways and other critical signaling pathways, regulation of immune exhaustion and aging, and control of cytokine and chemokine production, as well as the modulation of interferon-stimulated genes. By highlighting specific lncRNAs in different immune cell types, this review enhances our understanding of immune responses to viral infections from a lncRNA perspective and suggests potential avenues for exploring lncRNAs as therapeutic targets against viral diseases.
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Affiliation(s)
- Dan Zhang
- Department of Immunology and Pathogen Biology, School of Basic Medical Sciences, Hangzhou Normal University, Hangzhou, China
| | - Mengna Zhang
- Department of Immunology and Pathogen Biology, School of Basic Medical Sciences, Hangzhou Normal University, Hangzhou, China
| | - Liqin Zhang
- Department of Immunology and Pathogen Biology, School of Basic Medical Sciences, Hangzhou Normal University, Hangzhou, China
| | - Weijuan Wang
- Department of Immunology and Pathogen Biology, School of Basic Medical Sciences, Hangzhou Normal University, Hangzhou, China
| | - Stéphane Hua
- Laboratory of Cellular Immunology and Biotechnology, Molecular Engineering for Health Unit CEA Saclay, 91191 Gif-sur-Yvette cedex, France
| | - Chan Zhou
- Department of Population and Quantitative Health Sciences, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA
| | - Xiaoming Sun
- Department of Immunology and Pathogen Biology, School of Basic Medical Sciences, Hangzhou Normal University, Hangzhou, China; State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou 310003, China.
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3
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Jiang S, Hu J, Bai Y, Hao R, Liu L, Chen H. Transcriptome-wide 5-methylcytosine modification profiling of long non-coding RNAs in A549 cells infected with H1N1 influenza A virus. BMC Genomics 2023; 24:316. [PMID: 37308824 DOI: 10.1186/s12864-023-09432-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2022] [Accepted: 06/06/2023] [Indexed: 06/14/2023] Open
Abstract
BACKGROUND In recent years, accumulating evidences have revealed that influenza A virus (IAV) infections induce significant differential expression of host long noncoding RNAs (lncRNAs), some of which play important roles in the regulation of virus-host interactions and determining the virus pathogenesis. However, whether these lncRNAs bear post-translational modifications and how their differential expression is regulated remain largely unknown. In this study, the transcriptome-wide 5-methylcytosine (m5C) modification of lncRNAs in A549 cells infected with an H1N1 influenza A virus was analyzed and compared with uninfected cells by Methylated RNA immunoprecipitation sequencing (MeRIP-Seq). RESULTS Our data identified 1317 upregulated m5C peaks and 1667 downregulated peaks in the H1N1 infected group. Gene ontology (GO) and the Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses showed that the differentially modified lncRNAs were associated with protein modification, organelle localization, nuclear export and other biological processes. Furthermore, conjoint analysis of the differentially modified (DM) and differentially expressed (DE) lncRNAs identified 143 'hyper-up', 81 'hypo-up', 6 'hypo-down' and 4 'hyper-down' lncRNAs. GO and KEGG analyses revealed that these DM and DE lncRNAs were predominantly associated with pathogen recognition and disease pathogenesis pathways, indicating that m5C modifications could play an important role in the regulation of host response to IAV replication by modulating the expression and/or stability of lncRNAs. CONCLUSION This study presented the first m5C modification profile of lncRNAs in A549 cells infected with IAV and demonstrated a significant alteration of m5C modifications on host lncRNAs upon IAV infection. These data could give a reference to future researches on the roles of m5C methylation in virus infection.
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Affiliation(s)
- Shengqiang Jiang
- College of Life Sciences, Northwest A & F University, Yangling, 712100, Shanxi, P. R. China
| | - Jing Hu
- College of Life Sciences, Northwest A & F University, Yangling, 712100, Shanxi, P. R. China
| | - Yang Bai
- College of Life Sciences, Northwest A & F University, Yangling, 712100, Shanxi, P. R. China
| | - Ruiwei Hao
- College of Life Sciences, Northwest A & F University, Yangling, 712100, Shanxi, P. R. China
| | - Long Liu
- School of Basic Medical Sciences, Hubei University of Medicine, Shiyan, 442000, Hubei, P. R. China
| | - Hongying Chen
- College of Life Sciences, Northwest A & F University, Yangling, 712100, Shanxi, P. R. China.
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Wang K, Gong M, Zhao S, Lai C, Zhao L, Cheng S, Xia M, Li Y, Wang K, Sun H, Zhu P, Zhou Y, Ao Q, Deng X. A novel lncRNA DFRV plays a dual function in influenza A virus infection. Front Microbiol 2023; 14:1171423. [PMID: 37303776 PMCID: PMC10248499 DOI: 10.3389/fmicb.2023.1171423] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2023] [Accepted: 04/27/2023] [Indexed: 06/13/2023] Open
Abstract
Long noncoding RNAs (lncRNAs) have been associated with a variety of biological activities, including immune responses. However, the function of lncRNAs in antiviral innate immune responses are not fully understood. Here, we identified a novel lncRNA, termed dual function regulating influenza virus (DFRV), elevating in a dose- and time-dependent manner during influenza A virus (IAV) infection, which was dependent on the NFκB signaling pathway. Meanwhile, DFRV was spliced into two transcripts post IAV infection, in which DFRV long suppress the viral replication while DFRV short plays the opposite role. Moreover, DFRV regulates IL-1β and TNF-α via activating several pro-inflammatory signaling cascades, including NFκB, STAT3, PI3K, AKT, ERK1/2 and p38. Besides, DFRV short can inhibit DFRV long expression in a dose-dependent manner. Collectively, our studies reveal that DFRV may act as a potential dual-regulator to preserve innate immune homeostasis in IAV infection.
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Affiliation(s)
- Keyu Wang
- Department of Clinical Laboratory, National Clinical Research Center for Geriatric Diseases, The Second Medical Center of Chinese PLA General Hospital, Beijing, China
| | - Meiliang Gong
- Department of Clinical Laboratory, National Clinical Research Center for Geriatric Diseases, The Second Medical Center of Chinese PLA General Hospital, Beijing, China
| | - Sumin Zhao
- The PLA Rocket Force Characteristic Medical Center, Beijing, China
| | - Chengcai Lai
- Department of Pharmaceutical Sciences, Beijing Institute of Radiation Medicine, Beijing, China
| | - Lingna Zhao
- Beijing Key Laboratory for Immunological Research on Chronic Diseases, School of Medicine and Institute for Immunology, Tsinghua University, Beijing, China
| | - Sijie Cheng
- Center for Disease Prevention and Control, Changde, Hunan, China
| | - Min Xia
- Department of Vascular Cell Biology, Max Plank Institute for Molecular Biomedicine, Münster, Germany
| | - Yuru Li
- Department of Clinical Laboratory, National Clinical Research Center for Geriatric Diseases, The Second Medical Center of Chinese PLA General Hospital, Beijing, China
| | - Kun Wang
- Department of Clinical Laboratory, National Clinical Research Center for Geriatric Diseases, The Second Medical Center of Chinese PLA General Hospital, Beijing, China
| | - Heqiang Sun
- Department of Clinical Laboratory, National Clinical Research Center for Geriatric Diseases, The Second Medical Center of Chinese PLA General Hospital, Beijing, China
| | - Pingjun Zhu
- Department of Respiratory and Critical Care Medicine, National Clinical Research Center for Geriatric Diseases, The Second Medical Center of Chinese PLA General Hospital, Beijing, China
| | - Yu Zhou
- Department of Clinical Laboratory, National Clinical Research Center for Geriatric Diseases, The Second Medical Center of Chinese PLA General Hospital, Beijing, China
| | - Qiangguo Ao
- Department of Nephrology, National Clinical Research Center for Geriatric Diseases, The Second Medical Center of Chinese PLA General Hospital, Beijing, China
| | - Xinli Deng
- Department of Clinical Laboratory, National Clinical Research Center for Geriatric Diseases, The Second Medical Center of Chinese PLA General Hospital, Beijing, China
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Basavappa MG, Ferretti M, Dittmar M, Stoute J, Sullivan MC, Whig K, Shen H, Liu KF, Schultz DC, Beiting DP, Lynch KW, Henao-Mejia J, Cherry S. The lncRNA ALPHA specifically targets chikungunya virus to control infection. Mol Cell 2022; 82:3729-3744.e10. [PMID: 36167073 PMCID: PMC10464526 DOI: 10.1016/j.molcel.2022.08.030] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2021] [Revised: 07/06/2022] [Accepted: 08/26/2022] [Indexed: 11/17/2022]
Abstract
Arthropod-borne viruses, including the alphavirus chikungunya virus (CHIKV), cause acute disease in millions of people and utilize potent mechanisms to antagonize and circumvent innate immune pathways including the type I interferon (IFN) pathway. In response, hosts have evolved antiviral counterdefense strategies that remain incompletely understood. Recent studies have found that long noncoding RNAs (lncRNAs) regulate classical innate immune pathways; how lncRNAs contribute to additional antiviral counterdefenses remains unclear. Using high-throughput genetic screening, we identified a cytoplasmic antiviral lncRNA that we named antiviral lncRNA prohibiting human alphaviruses (ALPHA), which is transcriptionally induced by alphaviruses and functions independently of IFN to inhibit the replication of CHIKV and its closest relative, O'nyong'nyong virus (ONNV), but not other viruses. Furthermore, we showed that ALPHA interacts with CHIKV genomic RNA and restrains viral RNA replication. Together, our findings reveal that ALPHA and potentially other lncRNAs can mediate non-canonical antiviral immune responses against specific viruses.
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Affiliation(s)
- Megha G Basavappa
- Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Institute for Immunology, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Max Ferretti
- Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Mark Dittmar
- Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Institute for Immunology, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Julian Stoute
- Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Megan C Sullivan
- Department of Pathobiology, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Kanupriya Whig
- Institute for Immunology, University of Pennsylvania, Philadelphia, PA 19104, USA; Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, PA 19104, USA; High-Throughput Screening Core, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Hui Shen
- Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Kathy Fange Liu
- Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - David C Schultz
- Institute for Immunology, University of Pennsylvania, Philadelphia, PA 19104, USA; Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, PA 19104, USA; High-Throughput Screening Core, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Daniel P Beiting
- Department of Pathobiology, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Kristen W Lynch
- Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Jorge Henao-Mejia
- Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Institute for Immunology, University of Pennsylvania, Philadelphia, PA 19104, USA; Division of Protective Immunity, Department of Pathology and Laboratory Medicine, Children's Hospital of Pennsylvania, University of Pennsylvania, Philadelphia, PA 19104, USA.
| | - Sara Cherry
- Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Institute for Immunology, University of Pennsylvania, Philadelphia, PA 19104, USA; Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, PA 19104, USA; High-Throughput Screening Core, University of Pennsylvania, Philadelphia, PA 19104, USA.
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Chen W, Li J, Li J, Zhang J, Zhang J. Roles of Non-Coding RNAs in Virus-Host Interaction About Pathogenesis of Hand-Foot-Mouth Disease. Curr Microbiol 2022; 79:247. [PMID: 35834056 PMCID: PMC9281230 DOI: 10.1007/s00284-022-02928-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Accepted: 06/06/2022] [Indexed: 11/28/2022]
Abstract
Noncoding RNAs (ncRNAs) represent the largest and main transcriptome products and play various roles in the biological activity of cells and pathological processes. Accumulating evidence shows that microRNA (miRNA), long non-coding RNA (lncRNA), and circular RNA (circRNA) are important ncRNAs that play vital regulatory roles during viral infection. Hand-foot-mouth disease (HFMD) virus causes hand-foot-mouth disease, and is also associated with various serious complications and high mortality. However, there is currently no effective treatment. In this review, we focus on advances in the understanding of the modulatory role of ncRNAs during HFMD virus infection. Specifically, we discuss the generation, classification, and regulatory mechanisms of miRNA, lncRNA, and circRNA in the interaction between virus and host, with a particular focus on their influence with viral replication and infection. Analysis of these underlying mechanisms can help provide a foundation for the development of ncRNA-based antiviral therapies.
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Affiliation(s)
- Wei Chen
- Medical School, Kunming University of Science and Technology, Chenggong District, No. 727, Southern Jingming Road, Kunming, Yunnan Province, 650500, People's Republic of China.
| | - Jinwei Li
- Medical School, Kunming University of Science and Technology, Chenggong District, No. 727, Southern Jingming Road, Kunming, Yunnan Province, 650500, People's Republic of China
| | - Jing Li
- Medical School, Kunming University of Science and Technology, Chenggong District, No. 727, Southern Jingming Road, Kunming, Yunnan Province, 650500, People's Republic of China
| | - Jiayu Zhang
- Medical School, Kunming University of Science and Technology, Chenggong District, No. 727, Southern Jingming Road, Kunming, Yunnan Province, 650500, People's Republic of China
| | - Jihong Zhang
- Medical School, Kunming University of Science and Technology, Chenggong District, No. 727, Southern Jingming Road, Kunming, Yunnan Province, 650500, People's Republic of China.
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7
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Teng P, Yang H, Li J, Yang F, Chen W. Analysis of the long noncoding RNA profiles of RD and SH-SY5Y cells infected with coxsackievirus B5, using RNA sequencing. Arch Virol 2021; 167:367-376. [PMID: 34839420 DOI: 10.1007/s00705-021-05313-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2021] [Accepted: 10/12/2021] [Indexed: 01/10/2023]
Abstract
Hand, foot, and mouth disease caused by coxsackievirus B5 (CV-B5) is a considerable threat to infant health, especially with regard to neurological damage. Long noncoding RNAs (lncRNAs) are known to play pivotal roles in virus-host interactions. However, the roles of lncRNAs in CV-B5-host interactions have not yet been elucidated. In the current study, we used RNA sequencing to determine the expression profiles of lncRNAs in CV-B5-infected human rhabdomyosarcoma (RD) and SH-SY5Y cells. Our results showed that, of the differentially expressed lncRNAs, 508 were upregulated and 760 were downregulated in RD cells. Of these, 46.2% were long noncoding intergenic RNAs (lincRNAs), 28.6% were antisense lncRNAs, 24.1% were sense overlapping lncRNAs, and 1.0% were sense intronic lncRNAs. Moreover, 792 lncRNAs were upregulated and 811 lncRNAs were downregulated in SH-SY5Y cells, 48.6% of which were lincRNAs, 34.7% were antisense lncRNAs, 16.0% were sense overlapping lncRNAs, and 0.8% were sense intronic lncRNAs. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis showed that lncRNAs that were differentially expressed in CV-B5-infected RD cells were associated with disease, and those differentially expressed in SH-SY5Y cells were involved in signaling pathways. RT-qPCR analysis of seven lncRNAs supported these results. Moreover, our study revealed that lncRNA-IL12A inhibits viral replication. We conclude that lncRNAs constitute potential novel molecular targets for the prevention and treatment of CV-B5 infection and also may serve to distinguish neurogenic diseases caused by CV-B5 infection.
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Affiliation(s)
- Peiying Teng
- Medical School, Kunming University of Science and Technology, No. 727, Southern Jingming Road, Chenggong District, Kunming, 650500, Yunnan, People's Republic of China
| | - Heng Yang
- College of Agriculture and Life Sciences, Kunming University, Kunming, Yunnan, People's Republic of China
| | - Jing Li
- Medical School, Kunming University of Science and Technology, No. 727, Southern Jingming Road, Chenggong District, Kunming, 650500, Yunnan, People's Republic of China
| | - Fan Yang
- Medical School, Kunming University of Science and Technology, No. 727, Southern Jingming Road, Chenggong District, Kunming, 650500, Yunnan, People's Republic of China
| | - Wei Chen
- Medical School, Kunming University of Science and Technology, No. 727, Southern Jingming Road, Chenggong District, Kunming, 650500, Yunnan, People's Republic of China.
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8
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Xu R, Yu SS, Yao RR, Tang RC, Liang JW, Pang X, Zhang J. Interferon-Inducible LINC02605 Promotes Antiviral Innate Responses by Strengthening IRF3 Nuclear Translocation. Front Immunol 2021; 12:755512. [PMID: 34804040 PMCID: PMC8602795 DOI: 10.3389/fimmu.2021.755512] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Accepted: 10/11/2021] [Indexed: 11/26/2022] Open
Abstract
Non-coding RNAs represent a class of important regulators in immune response. Previously, LINC02605 was identified as a candidate regulator in innate immune response by lncRNA microarray assays. In this study, we systematically analyzed the functions and the acting mechanisms of LINC02605 in antiviral innate immune response. LINC02605 was up-regulated by RNA virus, DNA virus, and type I IFNs in NF-κB and Jak-stat dependent manner. Overexpression of LINC02605 promotes RNA virus-induced type I interferon production and inhibited viral replication. Consistently, knockdown of LINC02605 resulted in reduced antiviral immune response and increased viral replication. Mechanistically, LINC02605 released the inhibition of hsa-miR-107 on the expression of phosphatase and tensin homolog (PTEN). By microRNA mimics and inhibitors, hsa-miR-107 was demonstrated to not only inhibit PTEN’s expression but also negatively regulate the antiviral immune response. Knockdown of LINC02605 led to the reduction of PTEN expression both in mRNA and protein levels. Overexpression of LINC02605 had an opposite impact. Moreover, LINC02605 attenuated the serine 97 phosphorylation level of interferon regulatory factor 3 (IRF3) by promoting PTEN expression. Nucleoplasmic fragmentation assay showed that knocking down LINC02605 inhibited the nuclear translocation of IRF3, rendering the host cells more susceptible to viral invasion, while overexpression showed opposite effects. Therefore, LINC02605 is an induced lncRNA by viral infection and plays a positive feedback in antiviral immune response through modulating the nuclear translocation of IRF3.
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Affiliation(s)
- Rui Xu
- Department of Immunology, School of Basic Medical Sciences, NHC 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, NHC 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, NHC Key Laboratory of Medical Immunology, Ministry of Health (Peking University), Peking University Health Science Center, Beijing, China
| | - Rong-Chun Tang
- Department of Immunology, School of Basic Medical Sciences, NHC Key Laboratory of Medical Immunology, Ministry of Health (Peking University), Peking University Health Science Center, Beijing, China
| | - Jia-Wei Liang
- Department of Immunology, School of Basic Medical Sciences, NHC Key Laboratory of Medical Immunology, Ministry of Health (Peking University), Peking University Health Science Center, Beijing, China
| | - Xuewen Pang
- Department of Immunology, School of Basic Medical Sciences, NHC 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, NHC Key Laboratory of Medical Immunology, Ministry of Health (Peking University), Peking University Health Science Center, Beijing, China
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Gao F, He S, Jin A. MiRNAs and lncRNAs in NK cell biology and NK/T-cell lymphoma. Genes Dis 2021; 8:590-602. [PMID: 34291131 PMCID: PMC8278539 DOI: 10.1016/j.gendis.2020.08.006] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2020] [Revised: 08/07/2020] [Accepted: 08/19/2020] [Indexed: 12/15/2022] Open
Abstract
The important role of lncRNAs and miRNAs in directing immune responses has become increasingly clear. Recent evidence conforms that miRNAs and lncRNAs are involved in NK cell biology and diseases through RNA-protein, RNA-RNA, or RNA-DNA interactions. In this view, we summarize the contribution of miRNAs and lncRNAs to NK cell lineage development, activation and function, highlight the biological significance of functional miRNAs or lncRNAs in NKTL and discuss the potential of these miRNAs and lncRNAs as innovative biomarkers/targets for NKTL early diagnosis, target treatment and prognostic evaluations.
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Affiliation(s)
- FengXia Gao
- Department of Immunology, Chongqing Medical University, Chongqing, 400010, PR China
- Chongqing Key Laboratory of Tumor Immunology and Tumor Immunotherapy, Chongqing Medical University, No.1, Medical School Road, Yuzhong District, Chongqing, 400010, PR China
| | - SiRong He
- Department of Immunology, Chongqing Medical University, Chongqing, 400010, PR China
- Chongqing Key Laboratory of Tumor Immunology and Tumor Immunotherapy, Chongqing Medical University, No.1, Medical School Road, Yuzhong District, Chongqing, 400010, PR China
| | - AiShun Jin
- Department of Immunology, Chongqing Medical University, Chongqing, 400010, PR China
- Chongqing Key Laboratory of Tumor Immunology and Tumor Immunotherapy, Chongqing Medical University, No.1, Medical School Road, Yuzhong District, Chongqing, 400010, PR China
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10
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A Biological Insight into the Susceptibility to Influenza Infection in Junior Rats by Comprehensive Analysis of lncRNA Profiles. BIOMED RESEARCH INTERNATIONAL 2021; 2021:8112783. [PMID: 34447853 PMCID: PMC8384544 DOI: 10.1155/2021/8112783] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/12/2021] [Revised: 07/29/2021] [Accepted: 08/07/2021] [Indexed: 11/23/2022]
Abstract
Long noncoding RNAs (lncRNAs) have been reported to participate in regulating many biological processes, including immune response to influenza A virus (IAV). However, the association between lncRNA expression profiles and influenza infection susceptibility has not been well elucidated. Here, we analyzed the expression profiles of lncRNAs, miRNAs, and mRNAs among IAV-infected adult rat (IAR), normal adult rat (AR), IAV-infected junior rat (IJR), and normal junior rat (JR) by RNA sequencing. Compared with differently expressed lncRNAs (DElncRNAs) between AR and IAR, 24 specific DElncRNAs were found between IJR and JR. Then, based on the fold changes and P value, the top 5 DElncRNAs, including 3 upregulated and 2 downregulated lncRNAs, were chosen to establish a ceRNA network for further disclosing their regulatory mechanisms. To visualize the differentially expressed genes in the ceRNA network, GO and KEGG pathway analysis was performed to further explore their roles in influenza infection of junior rats. The results showed that the downregulated DElncRNA-target genes were mostly enriched in the IL-17 signaling pathway. It indicated that the downregulated lncRNAs conferred the susceptibility of junior rats to IAV via mediating the IL-17 signaling pathway.
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11
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Ning X, Sun L. Identification and characterization of immune-related lncRNAs and lncRNA-miRNA-mRNA networks of Paralichthys olivaceus involved in Vibrio anguillarum infection. BMC Genomics 2021; 22:447. [PMID: 34130627 PMCID: PMC8204505 DOI: 10.1186/s12864-021-07780-2] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2020] [Accepted: 06/07/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Long non-coding RNAs (lncRNAs) structurally resemble mRNAs and exert crucial effects on host immune defense against pathogen infection. Japanese flounder (Paralichthys olivaceus) is an economically important marine fish susceptible to Vibrio anguillarum infection. To date, study on lncRNAs in flounder is scarce. RESULTS Here, we reported the first systematic identification and characterization of flounder lncRNAs induced by V. anguillarum infection at different time points. A total of 2,368 lncRNAs were identified, 414 of which were differentially expressed lncRNAs (DElncRNAs) that responded significantly to V. anguillarum infection. For these DElncRNAs, 3,990 target genes (named DETGs) and 42 target miRNAs (named DETmiRs) were identified based on integrated analyses of lncRNA-mRNA and lncRNA-miRNA expressions, respectively. The DETGs were enriched in a cohort of functional pathways associated with immunity. In addition to modulating mRNAs, 36 DElncRNAs were also found to act as competitive endogenous RNAs (ceRNAs) that regulate 37 DETGs through 16 DETmiRs. The DETmiRs, DElncRNAs, and DETGs formed ceRNA regulatory networks consisting of 114 interacting DElncRNAs-DETmiRs-DETGs trinities spanning 10 immune pathways. CONCLUSIONS This study provides a comprehensive picture of lncRNAs involved in V. anguillarum infection. The identified lncRNAs and ceRNA networks add new insights into the anti-bacterial immunity of flounder.
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Affiliation(s)
- Xianhui Ning
- CAS Key Laboratory of Experimental Marine Biology, Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, 7 Nanhai Road, 266071, Qingdao, China.,College of Marine Science and Engineering, Nanjing Normal University, 210023, Nanjing, Jiangsu, China.,Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China.,Co-Innovation Center for Marine Bio-Industry Technology of Jiangsu Province, 222005, Lianyungang, Jiangsu, China
| | - Li Sun
- CAS Key Laboratory of Experimental Marine Biology, Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, 7 Nanhai Road, 266071, Qingdao, China. .,Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China.
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Vierbuchen T, Fitzgerald KA. Long non-coding RNAs in antiviral immunity. Semin Cell Dev Biol 2021; 111:126-134. [DOI: 10.1016/j.semcdb.2020.06.009] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2020] [Revised: 06/07/2020] [Accepted: 06/12/2020] [Indexed: 12/15/2022]
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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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Suzuki A, Guerrini MM, Yamamoto K. Functional genomics of autoimmune diseases. Ann Rheum Dis 2021; 80:689-697. [PMID: 33408079 DOI: 10.1136/annrheumdis-2019-216794] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Accepted: 12/06/2020] [Indexed: 12/22/2022]
Abstract
For more than a decade, genome-wide association studies have been applied to autoimmune diseases and have expanded our understanding on the pathogeneses. Genetic risk factors associated with diseases and traits are essentially causative. However, elucidation of the biological mechanism of disease from genetic factors is challenging. In fact, it is difficult to identify the causal variant among multiple variants located on the same haplotype or linkage disequilibrium block and thus the responsible biological genes remain elusive. Recently, multiple studies have revealed that the majority of risk variants locate in the non-coding region of the genome and they are the most likely to regulate gene expression such as quantitative trait loci. Enhancer, promoter and long non-coding RNA appear to be the main target mechanisms of the risk variants. In this review, we discuss functional genetics to challenge these puzzles.
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Affiliation(s)
- Akari Suzuki
- Laboratory for Autoimmune Diseases, RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa, Japan
| | - Matteo Maurizio Guerrini
- Laboratory for Autoimmune Diseases, RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa, Japan
| | - Kazuhiko Yamamoto
- Laboratory for Autoimmune Diseases, RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa, Japan
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Vos LD, Dietrich J, Strieth S, Bootz F, Dietrich D, Franzen A. PD-1, CTLA4, PD-L1 and PD-L2 DNA methylation in papillary thyroid carcinoma. Immunotherapy 2020; 12:903-920. [DOI: 10.2217/imt-2020-0037] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Aim: We investigated DNA methylation patterns of immune checkpoint genes PD-1, PD-L1, PD-L2, CTLA4 and an adjacent long noncoding RNA in papillary thyroid carcinoma (PTC). Materials & methods: DNA methylation and mRNA expression were examined in PTCs. DNA methylation was correlated with mRNA expression, BRAF and RAS mutational status, and immune cell infiltration. Results: Inverse correlations between DNA methylation and mRNA expression were observed. Immune checkpoint expression correlated positively, and DNA methylation negatively, with immune cell infiltration. Higher DNA methylation levels accompanied by lower immune checkpoint expression were observed in RAS-mutated tumors. Conclusion: We suggest epigenetic regulation of immune checkpoints in PTC. Methylation was associated with BRAF and RAS mutation status. DNA methylation might be a promising biomarker candidate in the context of immunotherapies in PTC.
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Affiliation(s)
- Luka de Vos
- Department of Otorhinolaryngology, Head & Neck Surgery, University Hospital Bonn, 53127 Bonn, Germany
- Department of Dermatology & Allergy, University Hospital Bonn, 53127 Bonn, Germany
| | - Jörn Dietrich
- Department of Otorhinolaryngology, Head & Neck Surgery, University Hospital Bonn, 53127 Bonn, Germany
| | - Sebastian Strieth
- Department of Otorhinolaryngology, Head & Neck Surgery, University Hospital Bonn, 53127 Bonn, Germany
| | - Friedrich Bootz
- Department of Otorhinolaryngology, Head & Neck Surgery, University Hospital Bonn, 53127 Bonn, Germany
| | - Dimo Dietrich
- Department of Otorhinolaryngology, Head & Neck Surgery, University Hospital Bonn, 53127 Bonn, Germany
| | - Alina Franzen
- Department of Otorhinolaryngology, Head & Neck Surgery, University Hospital Bonn, 53127 Bonn, Germany
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