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Cheng Y, Liang Y, Tan X, Liu L. Host long noncoding RNAs in bacterial infections. Front Immunol 2024; 15:1419782. [PMID: 39295861 PMCID: PMC11408731 DOI: 10.3389/fimmu.2024.1419782] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2024] [Accepted: 08/15/2024] [Indexed: 09/21/2024] Open
Abstract
Bacterial infections remain a significant global health concern, necessitating a comprehensive understanding of the intricate host-pathogen interactions that play a critical role in the outcome of infectious diseases. Recent investigations have revealed that noncoding RNAs (ncRNAs) are key regulators of these complex interactions. Among them, long noncoding RNAs (lncRNAs) have gained significant attention because of their diverse regulatory roles in gene expression, cellular processes and the production of cytokines and chemokines in response to bacterial infections. The host utilizes lncRNAs as a defense mechanism to limit microbial pathogen invasion and replication. On the other hand, some host lncRNAs contribute to the establishment and maintenance of bacterial pathogen reservoirs within the host by promoting bacterial pathogen survival, replication, and dissemination. However, our understanding of host lncRNAs in the context of bacterial infections remains limited. This review focuses on the impact of host lncRNAs in shaping host-pathogen interactions, shedding light on their multifaceted functions in both host defense and bacterial survival, and paving the way for future research aimed at harnessing their regulatory potential for clinical applications.
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Affiliation(s)
- Yong Cheng
- Department of Biochemistry and Molecular Biology, Oklahoma State University, Stillwater, OK, United States
- Oklahoma Center for Respiratory and Infectious Diseases, Oklahoma State University, Stillwater, OK, United States
| | - Yurong Liang
- Oklahoma Center for Respiratory and Infectious Diseases, Oklahoma State University, Stillwater, OK, United States
- Department of Physiological Sciences, Oklahoma State University, Stillwater, OK, United States
| | - Xuejuan Tan
- Department of Biochemistry and Molecular Biology, Oklahoma State University, Stillwater, OK, United States
- Oklahoma Center for Respiratory and Infectious Diseases, Oklahoma State University, Stillwater, OK, United States
| | - Lin Liu
- Oklahoma Center for Respiratory and Infectious Diseases, Oklahoma State University, Stillwater, OK, United States
- Department of Physiological Sciences, Oklahoma State University, Stillwater, OK, United States
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Valverde A, Naqvi RA, Naqvi AR. Macrophage-enriched novel functional long noncoding RNAs LRRC75A-AS1 and GAPLINC regulate polarization and innate immune responses. Inflamm Res 2024; 73:771-792. [PMID: 38592458 DOI: 10.1007/s00011-024-01865-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2024] [Revised: 01/29/2024] [Accepted: 02/21/2024] [Indexed: 04/10/2024] Open
Abstract
INTRODUCTION Macrophages (Mφs) are functionally dynamic immune cells that bridge innate and adaptive immune responses; however, the underlying epigenetic mechanisms that control Mφ plasticity and innate immune functions are not well elucidated. OBJECTIVE To identify novel functions of macrophage-enriched lncRNAs in regulating polarization and innate immune responses. METHODS Total RNA isolated from differentiating monocyte-derived M1 and M2 Mφs was profiled for lncRNAs expression using RNAseq. Impact of LRRC75A-AS1, GAPLINC and AL139099.5 knockdown was examined on macrophage differentiation, polarization markers, phagocytosis, and antigen processing by flow cytometry and florescence microscopy. Cytokine profiles were examined by multiplex bead array and cytoskeletal signaling pathway genes were quantified by PCR-based array. Gingival biopsies were collected from periodontally healthy and diseased subjects to examine lncRNAs, M1/M2 marker expression. RESULTS Transcriptome profiling of M1 and M2 Mφs identified thousands of differentially expressed known and novel lncRNAs. We characterized three Mφ-enriched lncRNAs LRRC75A-AS1, GAPLINC and AL139099.5 in polarization and innate immunity. Knockdown of LRRC75A-AS1 and GAPLINC downregulated the Mφ differentiation markers and skewed Mφ polarization by decreasing M1 markers without a significant impact on M2 markers. LRRC75A-AS1 and GAPLINC knockdown also attenuated bacterial phagocytosis, antigen processing and inflammatory cytokine secretion in Mφs, supporting their functional role in potentiating innate immune functions. Mechanistically, LRRC75A-AS1 and GAPLINC knockdown impaired Mφ migration by downregulating the expression of multiple cytoskeletal signaling pathways suggesting their critical role in regulating Mφ migration. Finally, we showed that LRRC75A-AS1 and GAPLINC were upregulated in periodontitis and their expression correlates with higher M1 markers suggesting their role in macrophage polarization in vivo. CONCLUSION Our results show that polarized Mφs acquire a unique lncRNA repertoire and identified many previously unknown lncRNA sequences. LRRC75A-AS1 and GAPLINC, which are induced in periodontitis, regulate Mφ polarization and innate immune functions supporting their critical role in inflammation.
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Affiliation(s)
- Araceli Valverde
- Department of Periodontics, College of Dentistry, University of Illinois Chicago, Chicago, IL, 60612, USA.
- Department of Microbiology and Immunology, College of Medicine, University of Illinois Chicago, Chicago, IL, 60612, USA.
| | - Raza Ali Naqvi
- Department of Periodontics, College of Dentistry, University of Illinois Chicago, Chicago, IL, 60612, USA
- Department of Microbiology and Immunology, College of Medicine, University of Illinois Chicago, Chicago, IL, 60612, USA
| | - Afsar R Naqvi
- Department of Periodontics, College of Dentistry, University of Illinois Chicago, Chicago, IL, 60612, USA.
- Department of Microbiology and Immunology, College of Medicine, University of Illinois Chicago, Chicago, IL, 60612, USA.
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Valverde A, Naqvi RA, Naqvi AR. Non-coding RNA LINC01010 regulates macrophage polarization and innate immune functions by modulating NFκB signaling pathway. J Cell Physiol 2024; 239:e31225. [PMID: 38403999 PMCID: PMC11096022 DOI: 10.1002/jcp.31225] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2023] [Revised: 01/31/2024] [Accepted: 02/06/2024] [Indexed: 02/27/2024]
Abstract
Innate immune response is regulated by tissue resident or infiltrating immune cells such as macrophages (Mφ) that play critical role in tissue development, homeostasis, and repair of damaged tissue. However, the epigenetic mechanisms that regulate Mφ plasticity and innate immune functions are not well understood. Long non-coding RNA (lncRNA) are among the most abundant class of transcriptome but their function in myeloid cell biology is less explored. In this study, we deciphered the regulatory role of previously uncharacterized lncRNAs in Mφ polarization and innate immune responses. Two lncRNAs showed notable changes in their levels during M1 and M2 Mφ differentiation. Our findings indicate that LINC01010 expression increased and AC007032 expression decreased significantly. LINC01010 exhibit myeloid cell-specificity, while AC007032.1 is ubiquitous and expressed in both myeloid and lymphoid (T cells, B cells and NK cells) cells. Expression of these lncRNAs is dysregulated in periodontal disease (PD), a microbial biofilm-induced immune disease, and responsive to lipopolysaccharide (LPS) from different oral and non-oral bacteria. Knockdown of LINC01010 but not AC007032.1 reduced the surface expression of Mφ differentiation markers CD206 and CD68, and M1Mφ polarization markers MHCII and CD32. Furthermore, LINC01010 RNAi attenuated bacterial phagocytosis, antigen processing and cytokine secretion suggesting its key function in innate immunity. Mechanistically, LINC01010 knockdown Mφ treated with Escherichia coli LPS exhibit significantly reduced expression of multiple nuclear factor kappa B pathway genes. Together, our data highlight functional role of a PD-associated lncRNA LINC01010 in shaping macrophage differentiation, polarization, and innate immune activation.
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Affiliation(s)
- Araceli Valverde
- Department of Periodontics, College of Dentistry, University of Illinois Chicago, Chicago, Illinois, United States
| | - Raza Ali Naqvi
- Department of Periodontics, College of Dentistry, University of Illinois Chicago, Chicago, Illinois, United States
| | - Afsar R. Naqvi
- Department of Periodontics, College of Dentistry, University of Illinois Chicago, Chicago, Illinois, United States
- Department of Microbiology and Immunology, College of Medicine, University of Illinois Chicago, Chicago, Illinois, United States
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Valverde AM, Naqvi RA, Naqvi AR. Global Profiling of Differentiating Macrophages Identifies Novel Functional Long Non-coding RNAs Regulating Polarization and Innate Immune Responses. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.04.09.536159. [PMID: 37066353 PMCID: PMC10104173 DOI: 10.1101/2023.04.09.536159] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/18/2023]
Abstract
Macrophages (Mφ) are functionally dynamic immune cells that bridge innate and adaptive immune responses. However, the underlying epigenetic mechanisms that control the macrophage plasticity and innate immune functions are not well-elucidated. Here we performed transcriptome profiling of differentiating M1Mφ and M2Mφ and identified thousands of previously known and novel lncRNAs. We characterized three Mφ-enriched lncRNAs (LRRC75A-As1, GAPLINC and AL139099.5) with novel functions in Mφ differentiation, polarization and innate immunity. Knockdown of LRRC75A-As1, and GAPLINC downregulated Mφ differentiation markers CDw93 and CD68, and skewed macrophage polarization by decreasing M1 markers but had no significant impact on M2 markers. LRRC75A-As1, and GAPLINC RNAi in Mφ attenuated bacterial phagocytosis, antigen processing and inflammatory cytokine secretion supporting their functional role in potentiating innate immune functions. Mechanistically, lncRNA knockdown perturbed the expression of multiple cytoskeleton signaling thereby impairing Mφ migration suggesting their critical role in regulating macrophage polarity and motility. Together, our results show that Mφ acquire a unique repertoire of lncRNAs to shape differentiation, polarization and innate immune functions.
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Yang F, Jing F, Li Y, Kong S, Zhang S, Huo Y, Huang X, Yu S. Plasma lncRNA LOC338963 and mRNA AP3B2 are upregulated in paraneoplastic Lambert-Eaton myasthenic syndrome. Muscle Nerve 2022; 66:216-222. [PMID: 35508598 DOI: 10.1002/mus.27571] [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: 06/16/2021] [Revised: 05/01/2022] [Accepted: 05/02/2022] [Indexed: 11/10/2022]
Abstract
INTRODUCTION/AIMS Lambert-Eaton myasthenic syndrome (LEMS) is an autoimmune neuromuscular junction disorder. Long noncoding RNA (lncRNA) can regulate the expression of mRNA and is involved in the development of autoimmune diseases, but few genetic studies are available. In this study we aimed to explore the lncRNA and mRNA changes of LEMS. METHODS Plasma lncRNA and mRNA expression profiles of three LEMS patients with small cell lung cancer (SCLC) and three matched healthy controls were analyzed by microarray. Differentially expressed lncRNAs and adjacent mRNAs were jointly analyzed, and candidates were verified by quantitative real-time polymerase chain reaction (qRT-PCR). The identified genes were subsequently evaluated in 9, 8, and 4 patients with paraneoplastic LEMS, nontumor LEMS, and SCLC, respectively. Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses were performed to determine possible functions. RESULTS A total of 320 lncRNA and 168 mRNAs were differentially expressed in the three LEMS with SCLC and compared with healthy controls. Among these, lncRNA LOC338963 and its neighboring mRNA AP3B2 were upregulated jointly, which was confirmed by qRT-PCR. qRT-PCR revealed significant upregulation of the two genes in patients with paraneoplastic LEMS compared with nontumor LEMS or SCLC. GO analysis of AP3B2 identified the enrichment terms anterograde synaptic vesicle transport and establishment of synaptic vesicle localization. KEEG analysis showed that AP3B2 was enriched in lysosomal pathways. DISCUSSION LOC338963 and AP3B2 were upregulated in patients with paraneoplastic LEMS, suggesting their involvement in pathogenesis. These genes could be targets for exploring the pathomechanism of paraneoplastic LEMS.
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Affiliation(s)
- Fei Yang
- Department of Neurology, the First Medical Centre, Chinese PLA General Hospital, Beijing, China
| | - Feng Jing
- Department of Neurology, the First Medical Centre, Chinese PLA General Hospital, Beijing, China
| | - Yang Li
- Department of Neurology, the First Medical Centre, Chinese PLA General Hospital, Beijing, China
| | - Shanshan Kong
- Department of Neurology, the First Medical Centre, Chinese PLA General Hospital, Beijing, China
| | - Shimin Zhang
- Department of Neurology, the First Medical Centre, Chinese PLA General Hospital, Beijing, China
| | - Yunyun Huo
- Department of Neurology, the First Medical Centre, Chinese PLA General Hospital, Beijing, China
| | - Xusheng Huang
- Department of Neurology, the First Medical Centre, Chinese PLA General Hospital, Beijing, China
| | - Shengyuan Yu
- Department of Neurology, the First Medical Centre, Chinese PLA General Hospital, Beijing, China
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A Novel Regulatory Player in the Innate Immune System: Long Non-Coding RNAs. Int J Mol Sci 2021; 22:ijms22179535. [PMID: 34502451 PMCID: PMC8430513 DOI: 10.3390/ijms22179535] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2021] [Revised: 08/30/2021] [Accepted: 08/31/2021] [Indexed: 12/12/2022] Open
Abstract
Long non-coding RNAs (lncRNAs) represent crucial transcriptional and post-transcriptional gene regulators during antimicrobial responses in the host innate immune system. Studies have shown that lncRNAs are expressed in a highly tissue- and cell-specific- manner and are involved in the differentiation and function of innate immune cells, as well as inflammatory and antiviral processes, through versatile molecular mechanisms. These lncRNAs function via the interactions with DNA, RNA, or protein in either cis or trans pattern, relying on their specific sequences or their transcriptions and processing. The dysregulation of lncRNA function is associated with various human non-infectious diseases, such as inflammatory bowel disease, cardiovascular diseases, and diabetes mellitus. Here, we provide an overview of the regulation and mechanisms of lncRNA function in the development and differentiation of innate immune cells, and during the activation or repression of innate immune responses. These elucidations might be beneficial for the development of therapeutic strategies targeting inflammatory and innate immune-mediated diseases.
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Nociti V, Santoro M. What do we know about the role of lncRNAs in multiple sclerosis? Neural Regen Res 2021; 16:1715-1722. [PMID: 33510060 PMCID: PMC8328773 DOI: 10.4103/1673-5374.306061] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2020] [Revised: 08/21/2020] [Accepted: 11/11/2020] [Indexed: 12/24/2022] Open
Abstract
Multiple sclerosis is a chronic, inflammatory and degenerative disease of the central nervous system of unknown aetiology although well-defined evidence supports an autoimmune pathogenesis. So far, the exact mechanisms leading to autoimmune diseases are still only partially understood. We know that genetic, epigenetic, molecular, and cellular factors resulting in pathogenic inflammatory responses are certainly involved. Long non-coding RNAs (lncRNAs) are non-protein coding transcripts longer than 200 nucleotides that play an important role in both innate and acquired immunity, so there is great interest in lncRNAs involved in autoimmune diseases. The research on multiple sclerosis has been enriched with many studies on the molecular role of lncRNAs in the pathogenesis of the disease and their potential application as diagnostic and prognostic biomarkers. In particular, many multiple sclerosis fields of research are based on the identification of lncRNAs as possible biomarkers able to predict the onset of the disease, its activity degree, its progression phase and the response to disease-modifying drugs. Last but not least, studies on lncRNAs can provide a new molecular target for new therapies, missing, so far, a cure for multiple sclerosis. While our knowledge on the role of lncRNA in multiple sclerosis has recently improved, further studies are required to better understand the specific role of lncRNAs in this neurological disease. In this review, we present the most recent studies on molecular characterization of lncRNAs in multiple sclerosis disorder discussing their clinical relevance as biomarkers for diagnosis and treatments.
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Affiliation(s)
- Viviana Nociti
- Institute of Neurology, Fondazione Policlinico Universitario 'A. Gemelli' IRCCS, Università Cattolica del Sacro Cuore, Rome, Italy
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Ghafouri-Fard S, Abak A, Shoorei H, Talebi SF, Mohaqiq M, Sarabi P, Taheri M, Mokhtari M. Interaction between non-coding RNAs and Toll-like receptors. Biomed Pharmacother 2021; 140:111784. [PMID: 34087695 DOI: 10.1016/j.biopha.2021.111784] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2021] [Revised: 05/24/2021] [Accepted: 05/25/2021] [Indexed: 12/11/2022] Open
Abstract
Toll-like receptors (TLRs) are a large group of pattern recognition receptors which are involved in the regulation of innate immune responses. Based on the interplay between TLRs and adapter molecules, two distinctive signaling cascades, namely the MyD88-dependent and TRIF-dependent pathways have been recognized. TLRs are involved in the development of a wide variety of diseases including cancer and autoimmune disorders. A large body of evidence has shown interaction between two classes of non-coding RNAs, namely microRNAs (miRNAs) and long noncoding RNAs (lncRNAs). These interactions have prominent roles in the pathogenesis of several disorders including infectious disorders, autoimmune conditions and neoplastic disorders. This review aims at description of the interaction between these non-coding RNAs and TLRs.
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Affiliation(s)
- Soudeh Ghafouri-Fard
- Department of Medical Genetics, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Atefe Abak
- Phytochemistry Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Hamed Shoorei
- Department of Anatomical Sciences, Faculty of Medicine, Birjand University of Medical Sciences, Birjand, Iran
| | | | - Mahdi Mohaqiq
- School of Advancement, Centennial College, Ashtonbee Campus, Toronto, ON, Canada
| | - Parisa Sarabi
- Deputy for Research & Technology, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Mohammad Taheri
- Urology and Nephrology Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
| | - Majid Mokhtari
- Skull Base Research Center, Loghman Hakim Hospital, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
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Huang G, Garikipati VNS, Zhou Y, Benedict C, Houser SR, Koch WJ, Kishore R. Identification and Comparison of Hyperglycemia-Induced Extracellular Vesicle Transcriptome in Different Mouse Stem Cells. Cells 2020; 9:cells9092098. [PMID: 32942572 PMCID: PMC7564160 DOI: 10.3390/cells9092098] [Citation(s) in RCA: 5] [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: 08/11/2020] [Revised: 09/04/2020] [Accepted: 09/11/2020] [Indexed: 12/19/2022] Open
Abstract
Extracellular vesicles (EVs) derived from stem /progenitor cells harbor immense potential to promote cardiomyocyte survival and neovascularization, and to mitigate ischemic injury. However, EVs’ parental stem/progenitor cells showed modest benefits in clinical trials, suggesting autologous stem cell/EV quality might have been altered by stimuli associated with the co-morbidities such as hyperglycemia associated with diabetes. Hyperglycemia is a characteristic of diabetes and a major driving factor in cardiovascular disease. The functional role of stem/progenitor cell-derived EVs and the molecular signature of their secreted EV cargo under hyperglycemic conditions remain elusive. Therefore, we hypothesized that hyperglycemic stress causes transcriptome changes in stem/progenitor cell-derived EVs that may compromise their reparative function. In this study, we performed an unbiased analysis of EV transcriptome signatures from 3 different stem/progenitor cell types by RNA sequencing. The analysis revealed differential expression of a variety of RNA species in EVs. Specifically, we identified 241 common-dysregulated mRNAs, 21 ncRNAs, and 16 miRNAs in three stem cell-derived EVs. Gene Ontology revealed that potential function of common mRNAs mostly involved in metabolism and transcriptional regulation. This study provides potential candidates for preventing the adverse effects of hyperglycemia-induced stem/progenitor cell-derived EV dysfunction, and reference data for future biological studies and application of stem/progenitor cell-derived EVs.
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Affiliation(s)
- Grace Huang
- Center for Translational Medicine, Lewis Katz School of Medicine, Temple University, Philadelphia, PA 19140, USA; (G.H.); (C.B.); (W.J.K.)
| | - Venkata Naga Srikanth Garikipati
- Department of Emergency Medicine, Dorothy M Davis Heart and Lung Research Institute, Wexner Medical School, The Ohio State University, Columbus, OH 43210, USA;
| | - Yan Zhou
- Biostatistics and Bioinformatics Facility, Fox-Chase Cancer Center, Temple Health, Philadelphia, PA 19140, USA;
| | - Cynthia Benedict
- Center for Translational Medicine, Lewis Katz School of Medicine, Temple University, Philadelphia, PA 19140, USA; (G.H.); (C.B.); (W.J.K.)
| | - Steven R. Houser
- Cardiovascular Research Center, Lewis Katz School of Medicine, Temple University, Philadelphia, PA 19140, USA;
| | - Walter J. Koch
- Center for Translational Medicine, Lewis Katz School of Medicine, Temple University, Philadelphia, PA 19140, USA; (G.H.); (C.B.); (W.J.K.)
- Department of Pharmacology, Lewis Katz School of Medicine, Temple University, Philadelphia, PA 19140, USA
| | - Raj Kishore
- Center for Translational Medicine, Lewis Katz School of Medicine, Temple University, Philadelphia, PA 19140, USA; (G.H.); (C.B.); (W.J.K.)
- Department of Pharmacology, Lewis Katz School of Medicine, Temple University, Philadelphia, PA 19140, USA
- Correspondence: ; Tel.: +1-215-707-2523
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Ye M, Xie M, Zhu J, Wang C, Zhou R, Li X. LPS-Inducible lncRNA TMC3-AS1 Negatively Regulates the Expression of IL-10. Front Immunol 2020; 11:1418. [PMID: 32774335 PMCID: PMC7387720 DOI: 10.3389/fimmu.2020.01418] [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: 03/13/2020] [Accepted: 06/02/2020] [Indexed: 12/29/2022] Open
Abstract
Long non-coding RNAs are essential regulators of the inflammatory response, especially for transcriptional regulation of inflammatory genes. It has been reported that the expression of transmembrane channel-like 3 (TMC3)–AS1 is increased following lipopolysaccharide stimulation. However, the potential function of TMC3-AS1 in immunity is largely unknown. Herein, we report a specific role for TMC3-AS1 in the regulation of inflammatory gene expression. TMC3-AS1 negatively regulates the expression of interleukin 10 (IL-10) in macrophage and intestinal epithelial cell lines. Mechanistically, TMC3-AS1 may interact with p65 in the nucleus, preventing p65 from binding to the κB consensus site within IL-10 promoter. These findings suggest that TMC3-AS1 may function as an important regulator in the innate immune response.
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Affiliation(s)
- Mengling Ye
- Hubei Province Key Laboratory of Allergy and Immunology, Wuhan University School of Basic Medical Sciences, Wuhan University, Wuhan, China
| | - Minghong Xie
- Institute of Materials Research and Engineering, The Second Affiliated Hospital of Fujian Medical University, Quanzhou, China
| | - Jie Zhu
- Hubei Province Key Laboratory of Allergy and Immunology, Wuhan University School of Basic Medical Sciences, Wuhan University, Wuhan, China
| | - Chen Wang
- Hubei Province Key Laboratory of Allergy and Immunology, Wuhan University School of Basic Medical Sciences, Wuhan University, Wuhan, China
| | - Rui Zhou
- Hubei Province Key Laboratory of Allergy and Immunology, Wuhan University School of Basic Medical Sciences, Wuhan University, Wuhan, China
| | - Xiaoqing Li
- Center for Stem Cell Research and Application, Union Hospital, Tongji Medical School, Huazhong University of Science and Technology, Wuhan, China
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Identification of Differentially Expressed lncRNAs in a CpG ODN-Activated Macrophage. J Immunol Res 2020; 2020:1407654. [PMID: 32626785 PMCID: PMC7306844 DOI: 10.1155/2020/1407654] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2019] [Revised: 10/31/2019] [Accepted: 12/10/2019] [Indexed: 12/20/2022] Open
Abstract
A macrophage is an important component of innate immunity which can be activated by infection. A series of inflammatory cytokines are produced and released to eliminate pathogens. CpG DNA is an immune stimulator recognized by TLR9, subsequently inducing inflammatory responses in macrophages. Long noncoding RNA (lncRNA) is a novel class of noncoding RNA, whose length is more than 200 nt, but without protein-coding capacity. lncRNAs are involved in many physiological and pathological processes, including inflammatory responses. In our study, a lncRNA microarray assay was performed to identify differentially expressed lncRNAs and mRNAs in RAW264.7 cells at different time points following CpG ODN stimulation. The results revealed that expression levels of 734 lncRNAs and 734 mRNAs were altered at all time points. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) biological pathway analyses were performed to predict the functions of dysregulated genes. Coexpression networks of lncRNA-mRNA were constructed based on the correlation analysis between differentially expressed lncRNAs and 10 selected upregulated mRNAs, which have been reported to be involved in CpG DNA-induced inflammatory responses. In addition, we selected 8 dysregulated lncRNAs for further validation by quantitative real-time PCR. The present study provided a systematic perspective on the potential functions of lncRNAs in CpG ODN-induced macrophage activation.
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12
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Denzer L, Schroten H, Schwerk C. From Gene to Protein-How Bacterial Virulence Factors Manipulate Host Gene Expression During Infection. Int J Mol Sci 2020; 21:ijms21103730. [PMID: 32466312 PMCID: PMC7279228 DOI: 10.3390/ijms21103730] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Revised: 05/19/2020] [Accepted: 05/20/2020] [Indexed: 02/06/2023] Open
Abstract
Bacteria evolved many strategies to survive and persist within host cells. Secretion of bacterial effectors enables bacteria not only to enter the host cell but also to manipulate host gene expression to circumvent clearance by the host immune response. Some effectors were also shown to evade the nucleus to manipulate epigenetic processes as well as transcription and mRNA procession and are therefore classified as nucleomodulins. Others were shown to interfere downstream with gene expression at the level of mRNA stability, favoring either mRNA stabilization or mRNA degradation, translation or protein stability, including mechanisms of protein activation and degradation. Finally, manipulation of innate immune signaling and nutrient supply creates a replicative niche that enables bacterial intracellular persistence and survival. In this review, we want to highlight the divergent strategies applied by intracellular bacteria to evade host immune responses through subversion of host gene expression via bacterial effectors. Since these virulence proteins mimic host cell enzymes or own novel enzymatic functions, characterizing their properties could help to understand the complex interactions between host and pathogen during infections. Additionally, these insights could propose potential targets for medical therapy.
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Zhu M, Cai Y, Zhao W, He C, Yang Y, Gao Q, Su S. Long non-coding RNAs are associated with Seneca Valley virus infection. Vet Microbiol 2020; 246:108728. [PMID: 32605750 DOI: 10.1016/j.vetmic.2020.108728] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2020] [Revised: 05/11/2020] [Accepted: 05/17/2020] [Indexed: 11/29/2022]
Abstract
Sporadic outbreaks of Seneca Valley virus (SVV) have been detected in recent years causing huge economic losses to the pig industry. SVV infection can lead to redness and fever of the mouth, nose or hoof wall, ulcerative injury and inflammation in pigs. Although long non-coding RNAs (lncRNAs) have been shown to play an important role in antiviral and inflammatory regulation, how lncRNAs regulate and induce SVV infection inflammation remains unclear. Here, we found the differential expression of 1332 lncRNAs and 3299 mRNAs in SVV-infected ST cells using RNA-seq. Functional annotation analysis revealed that regulated transcripts are mainly involved in signaling pathways related to host immunity and inflammatory responses. We identified lnc-MSTRG.18940.1 as an important immune regulator in SVV infection. Lnc-MSTRG.18940.1 silencing specifically inhibited SVV replication and the production of inflammatory factors TNF-α, IL-1, IL-6, and IL-8. Our findings aid to a better understanding of host responses to SVV infection and provide new directions for understanding the potential association between lncRNAs and SVV pathogenesis.
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Affiliation(s)
- 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
| | - 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
| | - Wen Zhao
- 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
| | - Chengxi He
- 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
| | - Yichen Yang
- 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
| | - Qi Gao
- 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.
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14
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Liu J, Liu Y, Zhang L, Chen Y, Du H, Wen Z, Wang T, Chen D. Down-regulation of circDMNT3B is conducive to intestinal mucosal permeability dysfunction of rats with sepsis via sponging miR-20b-5p. J Cell Mol Med 2020; 24:6731-6740. [PMID: 32383354 PMCID: PMC7299677 DOI: 10.1111/jcmm.15324] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2020] [Revised: 03/23/2020] [Accepted: 04/01/2020] [Indexed: 12/13/2022] Open
Abstract
Sepsis is a life‐threatening syndrome with a high risk of mortality, which is caused by the dysregulated host response to infection. We examined significant roles of circDMNT3B and miR‐20b‐5p in the intestinal mucosal permeability dysfunction of rats with sepsis. SD rats were randomly divided into 6 groups (n = 10/group): sham group, sepsis group, si‐negative control group, circDNMT3B‐si1 group, circDNMT3B‐si2 group and circDNMT3B‐si1 + anti‐miR‐20b‐5p group. The level of malondialdehyde (MDA) content, superoxide dismutase (SOD) activity, interleukin (IL)‐6 and IL‐10 levels were measured through ELISA assay kits. Cell survival rate and cell apoptosis were evaluated by Cell‐Counting Kit‐8 Assay and flow cytometry, respectively. Luciferase reporter assays were used to investigate interactions between miR‐20b‐5p circDMNT3B in HEK‐293T cells. Silencing circDNMT3B can significantly increase the level of d‐lactic acid, FD‐40, MDA, diamine oxidase, IL‐10 and IL‐6, compared with sepsis group, while the SOD activity was lower. Silencing circDNMT3B leads to oxidative damage and influence inflammatory factors level in intestinal tissue. CircDNMT3B was identified as a target gene of miR‐20b‐5p. Silencing circDNMT3B decreased cell survival and induced apoptosis in Caco2 cells treated with LPS, which was reversed by anti‐miR‐20b‐5p. MiR‐20b‐5p inhibitor remarkably down‐regulated mentioned‐above levels, in addition to up‐regulate SOD activity, which may relieve the damage of intestinal mucosal permeability caused by silencing circDNMT3B in sepsis rats. Down‐regulation of circDMNT3B was conducive to the dysfunction of intestinal mucosal permeability via sponging miR‐20b‐5p in sepsis rats, which may provide the novel strategy for sepsis treatment in the future.
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Affiliation(s)
- Jiao Liu
- Department of Critical Care Medicine, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China.,Department of Critical Care Medicine, Ruijin Hospital North, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yongan Liu
- Department of Critical Care Medicine, Ruijin Hospital North, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Lidi Zhang
- Department of Critical Care Medicine, Ruijin Hospital North, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yizhu Chen
- Department of Critical Care Medicine, Ruijin Hospital North, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Hangxiang Du
- Department of Critical Care Medicine, Ruijin Hospital North, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Zhenliang Wen
- Department of Critical Care Medicine, Ruijin Hospital North, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Tao Wang
- Department of Critical Care Medicine, Ruijin Hospital North, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Dechang Chen
- Department of Critical Care Medicine, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China.,Department of Critical Care Medicine, Ruijin Hospital North, Shanghai Jiao Tong University School of Medicine, Shanghai, China
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15
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Involvement of lncRNAs and Macrophages: Potential Regulatory Link to Angiogenesis. J Immunol Res 2020; 2020:1704631. [PMID: 32190702 PMCID: PMC7066414 DOI: 10.1155/2020/1704631] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2019] [Revised: 01/29/2020] [Accepted: 02/04/2020] [Indexed: 12/12/2022] Open
Abstract
Macrophages are involved in angiogenesis, an essential process for organ growth and tissue repair, and could contribute to the pathogenesis of angiogenesis-related diseases such as malignant tumors and diabetic retinopathy. Recently, long noncoding RNAs (lncRNAs) have been proved to be important in cell differentiation, organismal development, and various diseases of pathological angiogenesis. Moreover, it has been indicated that numerous lncRNAs exhibit different functions in macrophage infiltration and polarization and regulate the secretion of inflammatory cytokines released by macrophages. Therefore, the focus of macrophage-related lncRNAs could be considered to be a potential method in therapeutic targeting angiogenesis-related diseases. This review mainly summarizes the roles played by lncRNAs which associated with macrophages in angiogenesis. The possible mechanisms of the regulatory link between lncRNAs and macrophages in various angiogenesis-related diseases were also discussed.
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16
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Li X, Zhang Y, Pei W, Zhang M, Yang H, Zhong M, Kong X, Xu Y, Zhu X, Chen T, Ye J, Lv K. LncRNA Dnmt3aos regulates Dnmt3a expression leading to aberrant DNA methylation in macrophage polarization. FASEB J 2020; 34:5077-5091. [PMID: 32052888 DOI: 10.1096/fj.201902379r] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2019] [Revised: 01/07/2020] [Accepted: 01/27/2020] [Indexed: 01/18/2023]
Abstract
Long non-coding RNAs (lncRNAs) play key roles in various biological processes. However, the roles of lncRNAs in macrophage polarization remain largely unexplored. In this study, thousands of lncRNAs were identified that are differentially expressed in distinct polarized bone marrow-derived macrophages. Among them, Dnmt3aos (DNA methyltransferase 3A, opposite strand), as a known lncRNA, locates on the antisense strand of Dnmt3a. Functional experiments further confirmed that Dnmt3aos were highly expressed in M(IL-4) macrophages and participated in the regulation of Dnmt3a expression, and played a key role in macrophage polarization. The DNA methylation profiles between the Dnmt3aos knockdown group and the control group in M(IL-4) macrophages were determined by MeDIP-seq technique for the first time, and the Dnmt3aos-Dnmt3a axis-mediated DNA methylation modification-regulated macrophage polarization- related gene IFN-γ was identified. Our study will help to enrich our knowledge of the mechanism of macrophage polarization.
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Affiliation(s)
- Xueqin Li
- Key Laboratory of Non-coding RNA Transformation Research of Anhui Higher Education Institutes, Wannan Medical College, Wuhu, PR China.,Central Laboratory of Yijishan Hospital, Wannan Medical College, Wuhu, PR China
| | - Yingying Zhang
- Key Laboratory of Non-coding RNA Transformation Research of Anhui Higher Education Institutes, Wannan Medical College, Wuhu, PR China.,Laboratory Medicine of Yijishan Hospital, Wannan Medical College, Wuhu, PR China
| | - Weiya Pei
- Key Laboratory of Non-coding RNA Transformation Research of Anhui Higher Education Institutes, Wannan Medical College, Wuhu, PR China.,Central Laboratory of Yijishan Hospital, Wannan Medical College, Wuhu, PR China
| | - Mengying Zhang
- Key Laboratory of Non-coding RNA Transformation Research of Anhui Higher Education Institutes, Wannan Medical College, Wuhu, PR China.,Central Laboratory of Yijishan Hospital, Wannan Medical College, Wuhu, PR China
| | - Hui Yang
- Key Laboratory of Non-coding RNA Transformation Research of Anhui Higher Education Institutes, Wannan Medical College, Wuhu, PR China.,Central Laboratory of Yijishan Hospital, Wannan Medical College, Wuhu, PR China
| | - Min Zhong
- Key Laboratory of Non-coding RNA Transformation Research of Anhui Higher Education Institutes, Wannan Medical College, Wuhu, PR China.,Central Laboratory of Yijishan Hospital, Wannan Medical College, Wuhu, PR China
| | - Xiang Kong
- Key Laboratory of Non-coding RNA Transformation Research of Anhui Higher Education Institutes, Wannan Medical College, Wuhu, PR China.,Central Laboratory of Yijishan Hospital, Wannan Medical College, Wuhu, PR China
| | - Yang Xu
- Key Laboratory of Non-coding RNA Transformation Research of Anhui Higher Education Institutes, Wannan Medical College, Wuhu, PR China.,Central Laboratory of Yijishan Hospital, Wannan Medical College, Wuhu, PR China
| | - Xiaolong Zhu
- Key Laboratory of Non-coding RNA Transformation Research of Anhui Higher Education Institutes, Wannan Medical College, Wuhu, PR China.,Central Laboratory of Yijishan Hospital, Wannan Medical College, Wuhu, PR China
| | - Tianbing Chen
- Key Laboratory of Non-coding RNA Transformation Research of Anhui Higher Education Institutes, Wannan Medical College, Wuhu, PR China.,Central Laboratory of Yijishan Hospital, Wannan Medical College, Wuhu, PR China
| | - Jingjing Ye
- Key Laboratory of Non-coding RNA Transformation Research of Anhui Higher Education Institutes, Wannan Medical College, Wuhu, PR China.,Central Laboratory of Yijishan Hospital, Wannan Medical College, Wuhu, PR China
| | - Kun Lv
- Key Laboratory of Non-coding RNA Transformation Research of Anhui Higher Education Institutes, Wannan Medical College, Wuhu, PR China.,Central Laboratory of Yijishan Hospital, Wannan Medical College, Wuhu, PR China
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17
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Ma Z, Zhang J, Xu X, Qu Y, Dong H, Dang J, Huo Z, Xu G. LncRNA expression profile during autophagy and Malat1 function in macrophages. PLoS One 2019; 14:e0221104. [PMID: 31425535 PMCID: PMC6699732 DOI: 10.1371/journal.pone.0221104] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2019] [Accepted: 07/30/2019] [Indexed: 01/05/2023] Open
Abstract
Long noncoding RNAs (lncRNAs) are a class of functional non-coding transcripts that are longer than 200 nt and regulate gene expression via diverse mechanisms in eukaryotes. In fact, they have emerged as critical epigenetic and transcriptional regulators of autophagy in mammals in response to various stressors. Autophagy not only plays a crucial role in maintaining cellular homeostasis, but it is also essential to immunity, targets intracellular pathogens for degradation, modulates inflammation, and participates in adaptive immune responses. However, the expression profile of lncRNA and its role in regulating autophagy in macrophages have been poorly defined. Here, we used transcriptomic and bioinformatics to analysis LncRNA expression profile during autophagy and functional studies to evaluate the function of the metastasis-associated lung adenocarcinoma transcript-1 (Malat1) lncRNA in macrophages. A total of 1112 putative lncRNAs (240 novel lncRNAs) were identified, including 831 large intergenic, 129 intronic, and 152 anti-sense lncRNA, of which 59 differentially expressed transcripts exhibited a greater than 1.5-fold change under different conditions. The interaction of Malat1 lncRNA with microRNA (mir)-23-3p and lysosomal-associated membrane protein 1 (Lamp1) was found, Malat1 releases inhibition of Lamp1 expression in macrophages through competitive adsorption of mir-23-3p. The results of this study provide a better understanding of lncRNA function in macrophages and a basis for further investigation into the roles and mechanisms of ncRNA in immunology, particularly the functions of Malat1 and mir-23-3p in the pathogenesis of macrophages.
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Affiliation(s)
- Zhanbing Ma
- Ningxia Key Laboratory of Clinical and Pathogenic Microbiology, General Hospital of Ningxia Medical University, Yinchuan, China
- Department of Medical Genetic and Cell Biology, College of Basic Medicine, Ningxia Medical University, Yinchuan, China
- Key Laboratory of Fertility Preservation and Maintenance (Ningxia Medical University), Ministry of Education, Yinchuan, China
| | - Jing Zhang
- Department of Medical Genetic and Cell Biology, College of Basic Medicine, Ningxia Medical University, Yinchuan, China
- Key Laboratory of Fertility Preservation and Maintenance (Ningxia Medical University), Ministry of Education, Yinchuan, China
| | - Xiangrong Xu
- Department of Medical Laboratory, College of Clinical Medicine, Ningxia Medical University, Yinchuan, China
| | - Yuliang Qu
- Department of Medical Laboratory, College of Clinical Medicine, Ningxia Medical University, Yinchuan, China
| | - Hui Dong
- Key Laboratory of Fertility Preservation and Maintenance (Ningxia Medical University), Ministry of Education, Yinchuan, China
| | - Jie Dang
- Department of Medical Genetic and Cell Biology, College of Basic Medicine, Ningxia Medical University, Yinchuan, China
- Key Laboratory of Fertility Preservation and Maintenance (Ningxia Medical University), Ministry of Education, Yinchuan, China
| | - Zhenghao Huo
- Department of Medical Genetic and Cell Biology, College of Basic Medicine, Ningxia Medical University, Yinchuan, China
- Key Laboratory of Fertility Preservation and Maintenance (Ningxia Medical University), Ministry of Education, Yinchuan, China
| | - Guangxian Xu
- Ningxia Key Laboratory of Clinical and Pathogenic Microbiology, General Hospital of Ningxia Medical University, Yinchuan, China
- Department of Medical Laboratory, College of Clinical Medicine, Ningxia Medical University, Yinchuan, China
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18
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Xie Y, Wang M, Tian J, Li X, Yang M, Zhang K, Tan S, Luo L, Luo C, Peng L, Tang A. Long non-coding RNA expressed in macrophage co-varies with the inflammatory phenotype during macrophage development and polarization. J Cell Mol Med 2019; 23:6530-6542. [PMID: 31419045 PMCID: PMC6787567 DOI: 10.1111/jcmm.14557] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2019] [Revised: 06/19/2019] [Accepted: 07/02/2019] [Indexed: 12/13/2022] Open
Abstract
Advances in microarray, RNA‐seq and omics techniques, thousands of long non‐coding RNAs (lncRNAs) with unknown functions have been discovered. LncRNAs have presented a diverse perspective on gene regulation in diverse biological processes, especially in human immune response. Macrophages participate in the whole phase of immune inflammatory response. They are able to shape their phenotype and arouse extensive functional activation after receiving physiological and pathological stimuli. Emerging studies indicated that lncRNAs participated in the gene regulatory network during complex biological processes of macrophage, including macrophage‐induced inflammatory responses. Here, we reviewed the existing knowledges of lncRNAs in the processes of macrophage development and polarization, and their roles in several different inflammatory diseases. Specifically, we focused on how lncRNAs function in macrophage, which might help to discover some potential therapeutic targets and diagnostic biomarkers.
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Affiliation(s)
- Yixin Xie
- Department of Laboratory Medicine, The Second Xiangya Hospital, Central South University, Changsha, Hunan, China.,Department of Urological Organ Transplantation, Center of Organ Transplantation, The Second Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Min Wang
- Department of Laboratory Medicine, The Second Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Jingjing Tian
- Department of Laboratory Medicine, The Second Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Xianping Li
- Department of Laboratory Medicine, The Second Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Min Yang
- Department of Laboratory Medicine, The Second Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Kan Zhang
- Department of Laboratory Medicine, The Second Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Shan Tan
- Department of Laboratory Medicine, The Second Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Lingli Luo
- Department of Laboratory Medicine, The Second Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Can Luo
- Department of Laboratory Medicine, The Second Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Longkai Peng
- Department of Urological Organ Transplantation, Center of Organ Transplantation, The Second Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Aiguo Tang
- Department of Laboratory Medicine, The Second Xiangya Hospital, Central South University, Changsha, Hunan, China
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19
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Abstract
Aim: Long noncoding RNAs (lncRNAs) have been reported to influence multiple gene regulatory processes. Technological advances in RNA-seq platforms allow detection of low-abundance RNA species such as lncRNAs. This study examined the relationship between expression of lncRNAs and their putative partner mRNAs. Methods: We analyzed total RNA-seq data from mouse macrophages under various inflammatory and intervention conditions. Results: The macrophage expression of lncRNAs is strongly regulated by an inflammatory stimulus. Moreover, the expression of a majority of lncRNAs was correlated or anti-correlated with the partner mRNA(s), across the different treatment conditions. This relationship was maintained even in cells from a distinct genotype. Conclusion: These results suggest a previously unappreciated tight coupling of lncRNA and mRNA expression during macrophage responses to various microenvironmental perturbations.
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Affiliation(s)
- Alicja Pacholewska
- Laboratory of Molecular Biology & Immunology, National Institute on Aging, National Institutes of Health, 251 Bayview Boulevard, Baltimore, MD 21224, USA
| | - Myong-Hee Sung
- Laboratory of Molecular Biology & Immunology, National Institute on Aging, National Institutes of Health, 251 Bayview Boulevard, Baltimore, MD 21224, USA
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20
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Zhang Q, Li X, Su X, Zhang H, Wang H, Yin S, Pei X, Yang A, Zuo Z. HNCDB: An Integrated Gene and Drug Database for Head and Neck Cancer. Front Oncol 2019; 9:371. [PMID: 31139565 PMCID: PMC6527845 DOI: 10.3389/fonc.2019.00371] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2019] [Accepted: 04/23/2019] [Indexed: 12/21/2022] Open
Abstract
Head and neck cancer (HNC) is the sixth most common cancer worldwide. Over the last decade, an enormous amount of well-annotated gene and drug data has accumulated for HNC. However, a comprehensive repository is not yet available. Here, we constructed the Head and Neck Cancer Database (HNCDB: http://hncdb.cancerbio.info) using text mining followed by manual curation of the literature to collect reliable information on the HNC-related genes and drugs. The high-throughput gene expression data for HNC were also integrated into HNCDB. HNCDB includes the following three separate but closely related components: “HNC GENE,” “Connectivity Map,” and “ANALYSIS.” The “HNC GENE” component contains comprehensive information for the 1,173 HNC-related genes manually curated from 2,564 publications. The “Connectivity Map” includes information on the potential connections between the 176 drugs manually curated from 2,032 publications and the 1,173 HNC-related genes. The “ANALYSIS” component allows users to conduct correlation, differential expression, and survival analyses in the 2,403 samples from 78 HNC gene expression datasets. Taken together, we believe that HNCDB will be of significant benefit for the HNC community and promote further advances for precision medicine research on HNC.
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Affiliation(s)
- Qingbin Zhang
- Key Laboratory of Oral Medicine, Guangzhou Institute of Oral Disease, Stomatology Hospital of Guangzhou Medical University, Guangzhou, China
| | - Xingyang Li
- Key Laboratory of Oral Medicine, Guangzhou Institute of Oral Disease, Stomatology Hospital of Guangzhou Medical University, Guangzhou, China
| | - Xuan Su
- State Key Laboratory of Oncology in South China, Sun Yat-sen University Cancer Center, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University, Guangzhou, China
| | - Hongwan Zhang
- State Key Laboratory of Oncology in South China, Sun Yat-sen University Cancer Center, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University, Guangzhou, China
| | - Hanbing Wang
- State Key Laboratory of Oncology in South China, Sun Yat-sen University Cancer Center, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University, Guangzhou, China
| | - Sanjun Yin
- Department of Cancer Biology, Health Time Gene Institute, Shenzhen, China
| | - Xiaoqing Pei
- State Key Laboratory of Oncology in South China, Sun Yat-sen University Cancer Center, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University, Guangzhou, China
| | - Ankui Yang
- State Key Laboratory of Oncology in South China, Sun Yat-sen University Cancer Center, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University, Guangzhou, China
| | - Zhixiang Zuo
- State Key Laboratory of Oncology in South China, Sun Yat-sen University Cancer Center, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University, Guangzhou, China
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21
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Zheng Y, Xu Q, Liu M, Hu H, Xie Y, Zuo Z, Ren J. lnCAR: A Comprehensive Resource for lncRNAs from Cancer Arrays. Cancer Res 2019; 79:2076-2083. [PMID: 30786995 DOI: 10.1158/0008-5472.can-18-2169] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2018] [Revised: 11/05/2018] [Accepted: 02/15/2019] [Indexed: 11/16/2022]
Abstract
Long noncoding RNAs (lncRNA) have emerged as promising biomarkers in cancer diagnosis, treatment, and prognosis. Recent studies suggest that a large number of coding gene expression microarray probes could be reannotated as lncRNAs. Microarray, once the most cutting-edge high-throughput gene expression technology, has been used for thousands of cancer studies and has brought invaluable resources for studying the functions of lncRNA in cancer development. However, a comprehensive lncRNA resource based on microarray data is still lacking. Here, we present lnCAR (lncRNAs from cancer arrays), a comprehensive open resource for providing expression profiles and prognostic landscape of lncRNAs derived from reannotation of public microarray data. Currently, lnCAR contains 52,300 samples for differential expression analysis and 12,883 samples for survival analysis from 10 cancer types. lnCAR allows users to interactively explore any annotated or novel lncRNAs. We believe lnCAR will serve as a valuable resource for the community focused on lncRNA research in cancer. SIGNIFICANCE: lnCAR, a new interactive tool of reannotated public cancer-related microarray data, provides expression profiles and prognostic landscapes of lncRNAs across thousands of samples and multiple cancer types.
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Affiliation(s)
- Yueyuan Zheng
- State Key Laboratory of Oncology in South China, Cancer Center, Collaborative Innovation Center for Cancer Medicine, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Qingxian Xu
- State Key Laboratory of Oncology in South China, Cancer Center, Collaborative Innovation Center for Cancer Medicine, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Mengni Liu
- State Key Laboratory of Oncology in South China, Cancer Center, Collaborative Innovation Center for Cancer Medicine, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Huanjing Hu
- State Key Laboratory of Oncology in South China, Cancer Center, Collaborative Innovation Center for Cancer Medicine, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Yubin Xie
- State Key Laboratory of Oncology in South China, Cancer Center, Collaborative Innovation Center for Cancer Medicine, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Zhixiang Zuo
- State Key Laboratory of Oncology in South China, Cancer Center, Collaborative Innovation Center for Cancer Medicine, School of Life Sciences, Sun Yat-sen University, Guangzhou, China.
| | - Jian Ren
- State Key Laboratory of Oncology in South China, Cancer Center, Collaborative Innovation Center for Cancer Medicine, School of Life Sciences, Sun Yat-sen University, Guangzhou, China.
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22
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Chowdhury IH, Narra HP, Sahni A, Khanipov K, Fofanov Y, Sahni SK. Enhancer Associated Long Non-coding RNA Transcription and Gene Regulation in Experimental Models of Rickettsial Infection. Front Immunol 2019; 9:3014. [PMID: 30687302 PMCID: PMC6333757 DOI: 10.3389/fimmu.2018.03014] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2018] [Accepted: 12/05/2018] [Indexed: 12/20/2022] Open
Abstract
Recent discovery that much of the mammalian genome does not encode protein-coding genes (PCGs) has brought widespread attention to long noncoding RNAs (lncRNAs) as a novel layer of biological regulation. Enhancer lnc (elnc) RNAs from the enhancer regions of the genome carry the capacity to regulate PCGs in cis or in trans. Spotted fever rickettsioses represent the consequence of host infection with Gram-negative, obligate intracellular bacteria in the Genus Rickettsia. Despite being implicated in the pathways of infection and inflammation, the roles of lncRNAs in host response to Rickettsia species have remained a mystery. We have profiled the expression of host lncRNAs during infection of susceptible mice with R. conorii as a model closely mimicking the pathogenesis of human spotted fever rickettsioses. RNA sequencing on the lungs of infected hosts yielded reads mapping to 74,964 non-coding RNAs, 206 and 277 of which were determined to be significantly up- and down-regulated, respectively, in comparison to uninfected controls. Following removal of short non-coding RNAs and ambiguous transcripts, remaining transcripts underwent in-depth analysis of mouse lung epigenetic signatures H3K4Me1 and H3K4Me3, active transcript markers (POLR2A, p300, CTCF), and DNaseI hypersensitivity sites to identify two potentially active and highly up-regulated elncRNAs NONMMUT013718 and NONMMUT024103. Using Hi-3C sequencing resource, we further determined that genomic loci of NONMMUT013718 and NONMMUT024103 might interact with and regulate the expression of nearby PCGs, namely Id2 (inhibitor of DNA binding 2) and Apol10b (apolipoprotein 10b), respectively. Heterologous reporter assays confirmed the activity of elncRNAs as the inducers of their predicted PCGs. In the lungs of infected mice, expression of both elncRNAs and their targets was significantly higher than mock-infected controls. Induced expression of NONMMUT013718/Id2 in murine macrophages and NONMMUT024103/Apol10b in endothelial cells was also clearly evident during R. conorii infection in vitro. Finally, shRNA mediated knock-down of NONMMUT013718 and NONMMUT024103 elncRNAs resulted in reduced expression of endogenous Id2 and Apl10b, demonstrating the regulatory roles of these elncRNAs on their target PCGs. Our results provide very first experimental evidence suggesting altered expression of pulmonary lncRNAs and elncRNA-mediated regulation of PCGs involved in immunity and during host interactions with pathogenic rickettsiae.
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Affiliation(s)
- Imran H Chowdhury
- Department of Pathology, University of Texas Medical Branch, Galveston, TX, United States
| | - Hema P Narra
- Department of Pathology, University of Texas Medical Branch, Galveston, TX, United States
| | - Abha Sahni
- Department of Pathology, University of Texas Medical Branch, Galveston, TX, United States.,Institute for Human Infections and Immunity, University of Texas Medical Branch, University Boulevard, Galveston, TX, United States
| | - Kamil Khanipov
- Department of Pharmacology, University of Texas Medical Branch, University Boulevard, Galveston, TX, United States
| | - Yuriy Fofanov
- Department of Pharmacology, University of Texas Medical Branch, University Boulevard, Galveston, TX, United States
| | - Sanjeev K Sahni
- Department of Pathology, University of Texas Medical Branch, Galveston, TX, United States.,Institute for Human Infections and Immunity, University of Texas Medical Branch, University Boulevard, Galveston, TX, United States
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23
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Palma A, Jarrah AS, Tieri P, Cesareni G, Castiglione F. Gene Regulatory Network Modeling of Macrophage Differentiation Corroborates the Continuum Hypothesis of Polarization States. Front Physiol 2018; 9:1659. [PMID: 30546316 PMCID: PMC6278720 DOI: 10.3389/fphys.2018.01659] [Citation(s) in RCA: 76] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2018] [Accepted: 11/02/2018] [Indexed: 01/22/2023] Open
Abstract
Macrophages derived from monocyte precursors undergo specific polarization processes which are influenced by the local tissue environment: classically activated (M1) macrophages, with a pro-inflammatory activity and a role of effector cells in Th1 cellular immune responses, and alternatively activated (M2) macrophages, with anti-inflammatory functions and involved in immunosuppression and tissue repair. At least three different subsets of M2 macrophages, namely, M2a, M2b, and M2c, are characterized in the literature based on their eliciting signals. The activation and polarization of macrophages is achieved through many, often intertwined, signaling pathways. To describe the logical relationships among the genes involved in macrophage polarization, we used a computational modeling methodology, namely, logical (Boolean) modeling of gene regulation. We integrated experimental data and knowledge available in the literature to construct a logical network model for the gene regulation driving macrophage polarization to the M1, M2a, M2b, and M2c phenotypes. Using the software GINsim and BoolNet, we analyzed the network dynamics under different conditions and perturbations to understand how they affect cell polarization. Dynamic simulations of the network model, enacting the most relevant biological conditions, showed coherence with the observed behavior of in vivo macrophages. The model could correctly reproduce the polarization toward the four main phenotypes as well as to several hybrid phenotypes, which are known to be experimentally associated to physiological and pathological conditions. We surmise that shifts among different phenotypes in the model mimic the hypothetical continuum of macrophage polarization, with M1 and M2 being the extremes of an uninterrupted sequence of states. Furthermore, model simulations suggest that anti-inflammatory macrophages are resilient to shift back to the pro-inflammatory phenotype.
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Affiliation(s)
- Alessandro Palma
- Department of Biology, University of Rome Tor Vergata, Rome, Italy
| | - Abdul Salam Jarrah
- Department of Mathematics and Statistics, American University of Sharjah, Sharjah, United Arab Emirates
| | - Paolo Tieri
- Institute for Applied Computing, National Research Council of Italy, Rome, Italy.,Data Science Program, Sapienza University of Rome, Rome, Italy
| | - Gianni Cesareni
- Department of Biology, University of Rome Tor Vergata, Rome, Italy.,Fondazione Santa Lucia Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS), Rome, Italy
| | - Filippo Castiglione
- Institute for Applied Computing, National Research Council of Italy, Rome, Italy
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24
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Xu F, Jin L, Jin Y, Nie Z, Zheng H. Long noncoding RNAs in autoimmune diseases. J Biomed Mater Res A 2018; 107:468-475. [PMID: 30478988 DOI: 10.1002/jbm.a.36562] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2018] [Revised: 08/06/2018] [Accepted: 10/04/2018] [Indexed: 12/17/2022]
Abstract
With the completion of the human genome project and further development of high-throughput genomic technologies, interest in long noncoding RNAs (lncRNAs), which are defined as non-protein-coding RNAs at least 200 nucleotides in length, has strongly increased, and lncRNAs have become a major research direction. Increasing evidence demonstrates that lncRNAs are closely related to human growth and development and to disease occurrence via various mechanisms. lncRNAs also play crucial roles in the differentiation and activation of immune cells, and their relationships with human autoimmune diseases have received increasing attention. The development of biotechnology has led to the gradual discovery of many potential lncRNA functions. In this review, we discuss various lncRNAs that have been implicated in different human autoimmune diseases, focusing on their clinical applications as potential biomarkers and therapeutic targets in the pathologies of diverse human autoimmune diseases. © 2018 Wiley Periodicals, Inc. J Biomed Mater Res Part A: 107A: 468-475, 2019.
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Affiliation(s)
- Fei Xu
- Department of Microbiology and Immunology, Shanghai University of Medicine & Health Sciences, Shanghai, 201318, China
| | - Lei Jin
- Department of Inspection and Quarantine, Shanghai University of Medicine & Health Sciences, Shanghai, 201318, China
| | - Yueling Jin
- Department of Inspection and Quarantine, Shanghai University of Medicine & Health Sciences, Shanghai, 201318, China
| | - Zhiyan Nie
- Department of Microbiology and Immunology, Shanghai University of Medicine & Health Sciences, Shanghai, 201318, China
| | - Hong Zheng
- Department of Microbiology and Immunology, Shanghai University of Medicine & Health Sciences, Shanghai, 201318, China
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25
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Vergadi E, Vaporidi K, Tsatsanis C. Regulation of Endotoxin Tolerance and Compensatory Anti-inflammatory Response Syndrome by Non-coding RNAs. Front Immunol 2018; 9:2705. [PMID: 30515175 PMCID: PMC6255943 DOI: 10.3389/fimmu.2018.02705] [Citation(s) in RCA: 79] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2018] [Accepted: 11/01/2018] [Indexed: 12/17/2022] Open
Abstract
The onset and the termination of innate immune response must be tightly regulated to maintain homeostasis and prevent excessive inflammation, which can be detrimental to the organism, particularly in the context of sepsis. Endotoxin tolerance and compensatory anti-inflammatory response syndrome (CARS) describe a state of hypo-responsiveness characterized by reduced capacity of myeloid cells to respond to inflammatory stimuli, particularly those initiated by bacterial lipopolysaccharide (LPS). To achieve endotoxin tolerance, extensive reprogramming otherwise termed as “innate immune training”, is required that leads to both modifications of the intracellular components of TLR signaling and also to alterations in extracellular soluble mediators. Non-coding RNAs (ncRNAs) have been recognized as critical regulators of TLR signaling. Specifically, several microRNAs (miR-146, miR-125b, miR-98, miR-579, miR-132, let-7e and others) are induced upon TLR activation and reciprocally promote endotoxin tolerance and/or cross tolerance. Many other miRNAs have been also shown to negatively regulate TLR signaling. The long non-coding (lnc)RNAs (Mirt2, THRIL, MALAT1, lincRNA-21 and others) are also altered upon TLR activation and negatively regulate TLR signaling. Furthermore, the promotion or termination of myeloid cell tolerance is not only regulated by intracellular mediators but is also affected by other TLR-independent soluble signals that often achieve their effect via modulation of intracellular ncRNAs. In this article, we review recent evidence on the role of different ncRNAs in the context of innate immune cell tolerance and trained immunity, and evaluate their impact on immune system homeostasis.
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Affiliation(s)
- Eleni Vergadi
- Department of Paediatrics, Medical School, University of Crete, Heraklion, Greece.,Department of Clinical Chemistry, Medical School, University of Crete, Heraklion, Greece
| | - Katerina Vaporidi
- Department of Intensive Care Medicine, Medical School, University of Crete, Heraklion, Greece
| | - Christos Tsatsanis
- Department of Clinical Chemistry, Medical School, University of Crete, Heraklion, Greece
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26
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Yuan F, Lu L, Zhang Y, Wang S, Cai YD. Data mining of the cancer-related lncRNAs GO terms and KEGG pathways by using mRMR method. Math Biosci 2018; 304:1-8. [PMID: 30086268 DOI: 10.1016/j.mbs.2018.08.001] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2018] [Revised: 06/15/2018] [Accepted: 08/01/2018] [Indexed: 02/07/2023]
Abstract
LncRNAs plays an important role in the regulation of gene expression. Identification of cancer-related lncRNAs GO terms and KEGG pathways is great helpful for revealing cancer-related functional biological processes. Therefore, in this study, we proposed a computational method to identify novel cancer-related lncRNAs GO terms and KEGG pathways. By using existing lncRNA database and Max-relevance Min-redundancy (mRMR) method, GO terms and KEGG pathways were evaluated based on their importance on distinguishing cancer-related and non-cancer-related lncRNAs. Finally, GO terms and KEGG pathways with high importance were presented and analyzed. Our literature reviewing showed that the top 10 ranked GO terms and pathways were really related to interpretable tumorigenesis according to recent publications.
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Affiliation(s)
- Fei Yuan
- Department of Science & Technology, Binzhou Medical University Hospital, Binzhou 256603, Shandong, China.
| | - Lin Lu
- Department of Radiology, Columbia University Medical Center, New York 10032, USA.
| | - YuHang Zhang
- Institute of Health Sciences, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China.
| | - ShaoPeng Wang
- School of Life Sciences, Shanghai University, Shanghai 200444, China.
| | - Yu-Dong Cai
- School of Life Sciences, Shanghai University, Shanghai 200444, China.
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27
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Imamura K, Takaya A, Ishida YI, Fukuoka Y, Taya T, Nakaki R, Kakeda M, Imamachi N, Sato A, Yamada T, Onoguchi-Mizutani R, Akizuki G, Tanu T, Tao K, Miyao S, Suzuki Y, Nagahama M, Yamamoto T, Jensen TH, Akimitsu N. Diminished nuclear RNA decay upon Salmonella infection upregulates antibacterial noncoding RNAs. EMBO J 2018; 37:embj.201797723. [PMID: 29880601 DOI: 10.15252/embj.201797723] [Citation(s) in RCA: 51] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2017] [Revised: 04/16/2018] [Accepted: 04/18/2018] [Indexed: 11/09/2022] Open
Abstract
Cytoplasmic mRNA degradation controls gene expression to help eliminate pathogens during infection. However, it has remained unclear whether such regulation also extends to nuclear RNA decay. Here, we show that 145 unstable nuclear RNAs, including enhancer RNAs (eRNAs) and long noncoding RNAs (lncRNAs) such as NEAT1v2, are stabilized upon Salmonella infection in HeLa cells. In uninfected cells, the RNA exosome, aided by the Nuclear EXosome Targeting (NEXT) complex, degrades these labile transcripts. Upon infection, the levels of the exosome/NEXT components, RRP6 and MTR4, dramatically decrease, resulting in transcript stabilization. Depletion of lncRNAs, NEAT1v2, or eRNA07573 in HeLa cells triggers increased susceptibility to Salmonella infection concomitant with the deregulated expression of a distinct class of immunity-related genes, indicating that the accumulation of unstable nuclear RNAs contributes to antibacterial defense. Our results highlight a fundamental role for regulated degradation of nuclear RNA in the response to pathogenic infection.
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Affiliation(s)
- Katsutoshi Imamura
- Department of Microbiology and Molecular Genetics, Graduate School of Pharmaceutical Sciences, Chiba University, Chiba, Japan.,Department of Molecular Biology and Genetics, Aarhus University, Aarhus C, Denmark
| | - Akiko Takaya
- Department of Microbiology and Molecular Genetics, Graduate School of Pharmaceutical Sciences, Chiba University, Chiba, Japan
| | - Yo-Ichi Ishida
- Laboratory of Molecular and Cellular Biochemistry, Meiji Pharmaceutical University, Tokyo, Japan
| | | | | | | | - Miho Kakeda
- Isotope Science Center, The University of Tokyo, Tokyo, Japan
| | - Naoto Imamachi
- Isotope Science Center, The University of Tokyo, Tokyo, Japan
| | - Aiko Sato
- Isotope Science Center, The University of Tokyo, Tokyo, Japan
| | - Toshimichi Yamada
- Laboratory of Molecular and Cellular Biochemistry, Meiji Pharmaceutical University, Tokyo, Japan.,Isotope Science Center, The University of Tokyo, Tokyo, Japan
| | | | - Gen Akizuki
- Isotope Science Center, The University of Tokyo, Tokyo, Japan
| | - Tanzina Tanu
- Isotope Science Center, The University of Tokyo, Tokyo, Japan
| | - Kazuyuki Tao
- Isotope Science Center, The University of Tokyo, Tokyo, Japan
| | - Sotaro Miyao
- Laboratory of Molecular and Cellular Biochemistry, Meiji Pharmaceutical University, Tokyo, Japan
| | - Yutaka Suzuki
- Department of Medical Genome Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Chiba, Japan
| | - Masami Nagahama
- Laboratory of Molecular and Cellular Biochemistry, Meiji Pharmaceutical University, Tokyo, Japan
| | - Tomoko Yamamoto
- Medical Mycology Research Center, Chiba University, Chiba, Japan
| | - Torben Heick Jensen
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus C, Denmark
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28
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daSilva LF, Beckedorff FC, Ayupe AC, Amaral MS, Mesel V, Videira A, Reis EM, Setubal JC, Verjovski-Almeida S. Chromatin Landscape Distinguishes the Genomic Loci of Hundreds of Androgen-Receptor-Associated LincRNAs From the Loci of Non-associated LincRNAs. Front Genet 2018; 9:132. [PMID: 29875794 PMCID: PMC5985396 DOI: 10.3389/fgene.2018.00132] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2018] [Accepted: 04/03/2018] [Indexed: 11/30/2022] Open
Abstract
Cell signaling events triggered by androgen hormone in prostate cells is dependent on activation of the androgen receptor (AR) transcription factor. Androgen hormone binding to AR promotes its displacement from the cytoplasm to the nucleus and AR binding to DNA motifs, thus inducing activatory and inhibitory transcriptional programs through a complex regulatory mechanism not yet fully understood. In this work, we performed RNA-seq deep-sequencing of LNCaP prostate cancer cells and found over 7000 expressed long intergenic non-coding RNAs (lincRNAs), of which ∼4000 are novel lincRNAs, and 258 lincRNAs have their expression activated by androgen. Immunoprecipitation of AR, followed by large-scale sequencing of co-immunoprecipitated RNAs (RIP-Seq) has identified in the LNCaP cell line a total of 619 lincRNAs that were significantly enriched (FDR < 10%, DESeq2) in the anti-Androgen Receptor (antiAR) fraction in relation to the control fraction (non-specific IgG), and we named them Androgen-Receptor-Associated lincRNAs (ARA-lincRNAs). A genome-wide analysis showed that protein-coding gene neighbors to ARA-lincRNAs had a significantly higher androgen-induced change in expression than protein-coding genes neighboring lincRNAs not associated to AR. To find relevant epigenetic signatures enriched at the ARA-lincRNAs’ transcription start sites (TSSs) we used a machine learning approach and identified that the ARA-lincRNA genomic loci in LNCaP cells are significantly enriched with epigenetic marks that are characteristic of in cis enhancer RNA regulators, and that the H3K27ac mark of active enhancers is conspicuously enriched at the TSS of ARA-lincRNAs adjacent to androgen-activated protein-coding genes. In addition, LNCaP topologically associating domains (TADs) that comprise chromatin regions with ARA-lincRNAs exhibit transcription factor contents, epigenetic marks and gene transcriptional activities that are significantly different from TADs not containing ARA-lincRNAs. This work highlights the possible involvement of hundreds of lincRNAs working in synergy with the AR on the genome-wide androgen-induced gene regulatory program in prostate cells.
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Affiliation(s)
- Lucas F daSilva
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, Brazil.,Laboratório de Expressão Gênica em Eucariotos, Instituto Butantan, São Paulo, Brazil
| | - Felipe C Beckedorff
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, Brazil.,Laboratório de Expressão Gênica em Eucariotos, Instituto Butantan, São Paulo, Brazil
| | - Ana C Ayupe
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, Brazil
| | - Murilo S Amaral
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, Brazil.,Laboratório de Expressão Gênica em Eucariotos, Instituto Butantan, São Paulo, Brazil
| | - Vinícius Mesel
- Laboratório de Expressão Gênica em Eucariotos, Instituto Butantan, São Paulo, Brazil
| | - Alexandre Videira
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, Brazil.,Laboratório de Expressão Gênica em Eucariotos, Instituto Butantan, São Paulo, Brazil
| | - Eduardo M Reis
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, Brazil
| | - João C Setubal
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, Brazil.,Biocomplexity Institute of Virginia Tech, Blacksburg, VA, United States
| | - Sergio Verjovski-Almeida
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, Brazil.,Laboratório de Expressão Gênica em Eucariotos, Instituto Butantan, São Paulo, Brazil
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29
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Zhang Q, Chen L, Cui S, Li Y, Zhao Q, Cao W, Lai S, Yin S, Zuo Z, Ren J. Expression and regulation of long noncoding RNAs during the osteogenic differentiation of periodontal ligament stem cells in the inflammatory microenvironment. Sci Rep 2017; 7:13991. [PMID: 29070806 PMCID: PMC5656573 DOI: 10.1038/s41598-017-14451-4] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2017] [Accepted: 10/11/2017] [Indexed: 01/09/2023] Open
Abstract
Although long noncoding RNAs (lncRNAs) have been emerging as critical regulators in various tissues and biological processes, little is known about their expression and regulation during the osteogenic differentiation of periodontal ligament stem cells (PDLSCs) in inflammatory microenvironment. In this study, we have identified 63 lncRNAs that are not annotated in previous database. These novel lncRNAs were not randomly located in the genome but preferentially located near protein-coding genes related to particular functions and diseases, such as stem cell maintenance and differentiation, development disorders and inflammatory diseases. Moreover, we have identified 650 differentially expressed lncRNAs among different subsets of PDLSCs. Pathway enrichment analysis for neighboring protein-coding genes of these differentially expressed lncRNAs revealed stem cell differentiation related functions. Many of these differentially expressed lncRNAs function as competing endogenous RNAs that regulate protein-coding transcripts through competing shared miRNAs.
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Affiliation(s)
- Qingbin Zhang
- Key Laboratory of Oral Medicine, Guangzhou Institute of Oral Disease, Stomatology Hospital of Guangzhou Medical University, Guangzhou, 510140, China
| | - Li Chen
- Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University, Guangzhou, 510060, China.,State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, China
| | - Shiman Cui
- Key Laboratory of Oral Medicine, Guangzhou Institute of Oral Disease, Stomatology Hospital of Guangzhou Medical University, Guangzhou, 510140, China
| | - Yan Li
- Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University, Guangzhou, 510060, China.,State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, China
| | - Qi Zhao
- Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University, Guangzhou, 510060, China
| | - Wei Cao
- Key Laboratory of Oral Medicine, Guangzhou Institute of Oral Disease, Stomatology Hospital of Guangzhou Medical University, Guangzhou, 510140, China
| | - Shixiang Lai
- Key Laboratory of Oral Medicine, Guangzhou Institute of Oral Disease, Stomatology Hospital of Guangzhou Medical University, Guangzhou, 510140, China
| | - Sanjun Yin
- Health Time Gene Institute, Shenzhen, 518000, China
| | - Zhixiang Zuo
- Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University, Guangzhou, 510060, China.
| | - Jian Ren
- Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University, Guangzhou, 510060, China. .,State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, China.
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30
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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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31
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Fu Y, Gao K, Tao E, Li R, Yi Z. Aberrantly Expressed Long Non‐Coding RNAs In CD8
+
T Cells Response to Active Tuberculosis. J Cell Biochem 2017; 118:4275-4284. [DOI: 10.1002/jcb.26078] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2016] [Accepted: 04/18/2017] [Indexed: 12/29/2022]
Affiliation(s)
- Yurong Fu
- Department of Medical Microbiology of Clinical Medicine CollegeWeifang Medical UniversityShandong Weifang261053China
- School infirmary of Weifang Medical UniversityShandong Weifang261053China
| | - Kunshan Gao
- Department of Laboratory MedicineKey Laboratory of Clinical Laboratory Diagnostics in Universities of ShandongWeifang Medical UniversityShandong Weifang261053China
| | - Enxue Tao
- School infirmary of Weifang Medical UniversityShandong Weifang261053China
| | - Ruifang Li
- Department of Medical Microbiology of Clinical Medicine CollegeWeifang Medical UniversityShandong Weifang261053China
| | - Zhengjun Yi
- Department of Laboratory MedicineKey Laboratory of Clinical Laboratory Diagnostics in Universities of ShandongWeifang Medical UniversityShandong Weifang261053China
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32
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Duval M, Cossart P, Lebreton A. Mammalian microRNAs and long noncoding RNAs in the host-bacterial pathogen crosstalk. Semin Cell Dev Biol 2017; 65:11-19. [PMID: 27381344 PMCID: PMC7089780 DOI: 10.1016/j.semcdb.2016.06.016] [Citation(s) in RCA: 53] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2016] [Revised: 05/30/2016] [Accepted: 06/01/2016] [Indexed: 12/20/2022]
Abstract
Gene expression regulation is a critical question in host-pathogen interactions, and RNAs act as key players in this process. In this review, we focus on the mammalian RNA response to bacterial infection, with a special interest on microRNAs and long non-coding RNAs. We discuss the role of cellular miRNAs in immunity, the implication of circulating miRNAs as well as the influence of the microbiome on the miRNA response. We also review how pathogens counteract the host miRNA expression. Interestingly, bacterial non-coding RNAs regulate host gene expression and conversely eukaryotic miRNAs may regulate bacterial gene expression. Overall, the characterization of RNA regulatory networks represents an emerging theme in the field of host pathogen interactions.
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Affiliation(s)
- Mélodie Duval
- Institut Pasteur, Unité des Interactions Bactéries-Cellules, 75015 Paris, France; Inserm, U604, 75015 Paris, France; INRA, USC2020, 75015 Paris, France
| | - Pascale Cossart
- Institut Pasteur, Unité des Interactions Bactéries-Cellules, 75015 Paris, France; Inserm, U604, 75015 Paris, France; INRA, USC2020, 75015 Paris, France.
| | - Alice Lebreton
- École Normale Supérieure, PSL Research University, CNRS, Inserm, Institut de Biologie de l'École Normale Supérieure (IBENS), Équipe Infection et Devenir de l'ARN, 75005 Paris, France; INRA, IBENS, 75005 Paris, France.
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33
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Mumtaz PT, Bhat SA, Ahmad SM, Dar MA, Ahmed R, Urwat U, Ayaz A, Shrivastava D, Shah RA, Ganai NA. LncRNAs and immunity: watchdogs for host pathogen interactions. Biol Proced Online 2017; 19:3. [PMID: 28465674 PMCID: PMC5406993 DOI: 10.1186/s12575-017-0052-7] [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: 09/01/2016] [Accepted: 04/06/2017] [Indexed: 01/23/2023] Open
Abstract
Immune responses combat various infectious agents by inducing inflammatory responses, antimicrobial pathways and adaptive immunity. The polygenic responses to these external stimuli are temporally and coordinately regulated. Specific lncRNAs are induced to modulate innate and adaptive immune responses which can function through various target interactions like RNA-DNA, RNA-RNA, and RNA-protein interaction and hence affect the immunogenic regulation at various stages of gene expression. LncRNA are found to be present in various immune cells like monocytes, macrophages, dendritic cells, neutrophils, T cells and B cells. They have been shown to be involved in many biological processes, including the regulation of the expression of genes, the dosage compensation and genomics imprinting, but the knowledge how lncRNAs are regulated and how they alter cell differentiation/function is still obscure. Further dysregulation of lncRNA has been seen in many diseases, but as yet very less research has been carried out to understand the role of lncRNAs in regulation during host-pathogens interactions. In this review, we summarize the functional developments and mechanism of action of lncRNAs, in immunity and defense of host against pathogens.
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Affiliation(s)
- Peerzada Tajamul Mumtaz
- Division of Biotechnology, Faculty of Veterinary Sciences and Animal Husbandry, SKUAST-K, Shuhama, Srinagar, Jammu and Kashmir India
- School of Life Sciences Jaipur National University, Jaipur, Rajasthan India
| | - Shakil Ahmad Bhat
- Division of Biotechnology, Faculty of Veterinary Sciences and Animal Husbandry, SKUAST-K, Shuhama, Srinagar, Jammu and Kashmir India
| | - Syed Mudasir Ahmad
- Division of Biotechnology, Faculty of Veterinary Sciences and Animal Husbandry, SKUAST-K, Shuhama, Srinagar, Jammu and Kashmir India
| | - Mashooq Ahmad Dar
- Division of Biotechnology, Faculty of Veterinary Sciences and Animal Husbandry, SKUAST-K, Shuhama, Srinagar, Jammu and Kashmir India
| | - Raashid Ahmed
- Division of Biotechnology, Faculty of Veterinary Sciences and Animal Husbandry, SKUAST-K, Shuhama, Srinagar, Jammu and Kashmir India
| | - Uneeb Urwat
- Division of Biotechnology, Faculty of Veterinary Sciences and Animal Husbandry, SKUAST-K, Shuhama, Srinagar, Jammu and Kashmir India
| | - Aadil Ayaz
- Division of Animal Breeding and Genetics, Faculty of Veterinary Sciences and Animal Husbandry, SKUAST-K, Shuhama, Srinagar, Jammu and Kashmir India
| | - Divya Shrivastava
- School of Life Sciences Jaipur National University, Jaipur, Rajasthan India
| | - Riaz Ahmad Shah
- Division of Biotechnology, Faculty of Veterinary Sciences and Animal Husbandry, SKUAST-K, Shuhama, Srinagar, Jammu and Kashmir India
| | - Nazir Ahmad Ganai
- Division of Animal Breeding and Genetics, Faculty of Veterinary Sciences and Animal Husbandry, SKUAST-K, Shuhama, Srinagar, Jammu and Kashmir India
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Higher-Order Chromatin Regulation of Inflammatory Gene Expression. Mediators Inflamm 2017; 2017:7848591. [PMID: 28490839 PMCID: PMC5401750 DOI: 10.1155/2017/7848591] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2016] [Accepted: 03/21/2017] [Indexed: 12/14/2022] Open
Abstract
Whether it is caused by viruses and bacteria infection, or low-grade chronic inflammation of atherosclerosis and cellular senescence, the transcription factor (TF) NF-κB plays a central role in the inducible expression of inflammatory genes. Accumulated evidence has indicated that the chromatin environment is the main determinant of TF binding in gene expression regulation, including the stimulus-responsive NF-κB. Dynamic changes in intra- and interchromosomes are the key regulatory mechanisms promoting the binding of TFs. When an inflammatory process is triggered, NF-κB binds to enhancers or superenhancers, triggering the transcription of enhancer RNA (eRNA), driving the chromatin of the NF-κB-binding gene locus to construct transcriptional factories, and forming intra- or interchromosomal contacts. These processes reveal a mechanism in which intrachromosomal contacts appear to be cis-control enhancer-promoter communications, whereas interchromosomal regulatory elements construct trans-form relationships with genes on other chromosomes. This article will review emerging evidence on the genome organization hierarchy underlying the inflammatory response.
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Zur Bruegge J, Einspanier R, Sharbati S. A Long Journey Ahead: Long Non-coding RNAs in Bacterial Infections. Front Cell Infect Microbiol 2017; 7:95. [PMID: 28401065 PMCID: PMC5368183 DOI: 10.3389/fcimb.2017.00095] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2017] [Accepted: 03/13/2017] [Indexed: 12/24/2022] Open
Abstract
Bacterial pathogens have coevolved with their hosts and acquired strategies to circumvent defense mechanisms of host cells. It was shown that bacteria interfere with the expression of mammalian microRNAs to modify immune signaling, autophagy, or the apoptotic machinery. Recently, a new class of regulatory RNAs, long non-coding RNAs (lncRNAs), was reported to have a pivotal role in the regulation of eukaryotic gene expression. A growing body of literature reports on specific involvement of lncRNAs in the host cell response toward bacterial infections. This mini review summarizes recent data that focuses on lncRNA function in host cells during bacterial infection and provides a perspective where future research in this regard may be going.
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Affiliation(s)
- Jennifer Zur Bruegge
- Department of Veterinary Medicine, Institute of Veterinary Biochemistry, Freie Universität Berlin Berlin, Germany
| | - Ralf Einspanier
- Department of Veterinary Medicine, Institute of Veterinary Biochemistry, Freie Universität Berlin Berlin, Germany
| | - Soroush Sharbati
- Department of Veterinary Medicine, Institute of Veterinary Biochemistry, Freie Universität Berlin Berlin, Germany
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Ho J, Chan H, Wong SH, Wang MHT, Yu J, Xiao Z, Liu X, Choi G, Leung CCH, Wong WT, Li Z, Gin T, Chan MTV, Wu WKK. The involvement of regulatory non-coding RNAs in sepsis: a systematic review. CRITICAL CARE : THE OFFICIAL JOURNAL OF THE CRITICAL CARE FORUM 2016; 20:383. [PMID: 27890015 PMCID: PMC5125038 DOI: 10.1186/s13054-016-1555-3] [Citation(s) in RCA: 61] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/26/2016] [Accepted: 10/31/2016] [Indexed: 12/13/2022]
Abstract
Background Sepsis coincides with altered gene expression in different tissues. Accumulating evidence has suggested that microRNAs, long non-coding RNAs, and circular RNAs are important molecules involved in the crosstalk with various pathways pertinent to innate immunity, mitochondrial functions, and apoptosis. Methods We searched articles indexed in PubMed (MEDLINE), EMBASE and Europe PubMed Central databases using the Medical Subject Heading (MeSH) or Title/Abstract words (“microRNA”, “long non-coding RNA”, “circular RNA”, “sepsis” and/or “septic shock”) from inception to Sep 2016. Studies investigating the role of host-derived microRNA, long non-coding RNA, and circular RNA in the pathogenesis of and as biomarkers or therapeutics in sepsis were included. Data were extracted in terms of the role of non-coding RNAs in pathogenesis, and their applicability for use as biomarkers or therapeutics in sepsis. Two independent researchers assessed the quality of studies using a modified guideline from the Systematic Review Center for Laboratory animal Experimentation (SYRCLE), a tool based on the Cochrane Collaboration Risk of Bias tool. Results Observational studies revealed dysregulation of non-coding RNAs in septic patients. Experimental studies confirmed their crosstalk with JNK/NF-κB and other cellular pathways pertinent to innate immunity, mitochondrial function, and apoptosis. Of the included studies, the SYRCLE scores ranged from 3 to 7 (average score of 4.55). This suggests a moderate risk of bias. Of the 10 articles investigating non-coding RNAs as biomarkers, none of them included a validation cohort. Selective reporting of sensitivity, specificity, and receiver operating curve was common. Conclusions Although non-coding RNAs appear to be good candidates as biomarkers and therapeutics for sepsis, their differential expression across tissues complicated the process. Further investigation on organ-specific delivery of these regulatory molecules may be useful. Electronic supplementary material The online version of this article (doi:10.1186/s13054-016-1555-3) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Jeffery Ho
- Department of Anesthesia and Intensive Care, The Chinese University of Hong Kong, Shatin, Hong Kong, Hong Kong, Special Administrative Region of China
| | - Hung Chan
- Department of Anesthesia and Intensive Care, The Chinese University of Hong Kong, Shatin, Hong Kong, Hong Kong, Special Administrative Region of China
| | - Sunny H Wong
- State Key Laboratory of Digestive Disease, LKS Institute of Health Sciences, The Chinese University of Hong Kong, Hong Kong, Hong Kong, Special Administrative Region of China. .,Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Shatin, Hong Kong, Hong Kong, Special Administrative Region of China.
| | - Maggie H T Wang
- The Jockey Club School of Public Health and Primary Care, The Chinese University of Hong Kong, Hong Kong, Hong Kong, Special Administrative Region of China
| | - Jun Yu
- State Key Laboratory of Digestive Disease, LKS Institute of Health Sciences, The Chinese University of Hong Kong, Hong Kong, Hong Kong, Special Administrative Region of China.,Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Shatin, Hong Kong, Hong Kong, Special Administrative Region of China
| | - Zhangang Xiao
- Laboratory of Molecular Pharmacology, Department of Pharmacology, School of Pharmacy, Southwest Medical University, Luzhou, 646000, Sichuan, People's Republic of China
| | - Xiaodong Liu
- Department of Anesthesia and Intensive Care, The Chinese University of Hong Kong, Shatin, Hong Kong, Hong Kong, Special Administrative Region of China
| | - Gordon Choi
- Department of Anesthesia and Intensive Care, The Chinese University of Hong Kong, Shatin, Hong Kong, Hong Kong, Special Administrative Region of China
| | - Czarina C H Leung
- Department of Anesthesia and Intensive Care, The Chinese University of Hong Kong, Shatin, Hong Kong, Hong Kong, Special Administrative Region of China
| | - Wai T Wong
- Department of Anesthesia and Intensive Care, The Chinese University of Hong Kong, Shatin, Hong Kong, Hong Kong, Special Administrative Region of China
| | - Zheng Li
- Department of Orthopedics Surgery Peking Union Medical College Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, People's Republic of China
| | - Tony Gin
- Department of Anesthesia and Intensive Care, The Chinese University of Hong Kong, Shatin, Hong Kong, Hong Kong, Special Administrative Region of China
| | - Matthew T V Chan
- Department of Anesthesia and Intensive Care, The Chinese University of Hong Kong, Shatin, Hong Kong, Hong Kong, Special Administrative Region of China.
| | - William K K Wu
- Department of Anesthesia and Intensive Care, The Chinese University of Hong Kong, Shatin, Hong Kong, Hong Kong, Special Administrative Region of China. .,State Key Laboratory of Digestive Disease, LKS Institute of Health Sciences, The Chinese University of Hong Kong, Hong Kong, Hong Kong, Special Administrative Region of China.
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Singh KK, Matkar PN, Muhammad S, Quan A, Gupta V, Teoh H, Al-Omran M, Verma S. Investigation of novel LPS-induced differentially expressed long non-coding RNAs in endothelial cells. Mol Cell Biochem 2016; 421:157-68. [PMID: 27565812 DOI: 10.1007/s11010-016-2797-8] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2016] [Accepted: 08/10/2016] [Indexed: 12/11/2022]
Abstract
The molecular mechanisms responsible for sepsis-induced endothelial dysfunction leading to an elevated risk of cardiovascular diseases remain undefined. Endotoxic or septic shock is a potentially lethal complication of systemic infection by Gram-negative bacteria. Lipopolysaccharide (LPS) is a critical glycolipid component of the outer wall of Gram-negative bacteria, and many of the sepsis-associated cellular signals by Gram-negative bacteria are attributed to LPS. Given that LPS has an established role in the pathophysiology of sepsis and long non-coding RNAs (lncRNAs) have been reported to critically regulate vascular homeostasis, a systematic transcriptional survey was conducted to evaluate the impact of LPS stimulation on human endothelial lncRNAs and protein-coding transcripts (mRNAs). LncRNAs and mRNAs from LPS-treated (100 ng/mL; 24 h) human umbilical vein endothelial cells (HUVECs) were profiled with the Arraystar Human lncRNA Expression Microarray V3.0. Of the 30,584 lncRNAs screened, 871 were significantly upregulated and 1068 significantly downregulated (p < 0.05) in response to LPS. In the same HUVEC samples, 733 of the 26,106 mRNAs screened were upregulated and 536 were downregulated. Among the differentially expressed lncRNAs, AL132709.5 was the most upregulated (~70 fold) and CTC-459I6.1 the most downregulated (~28 fold). Bioinformatics analyses indicated that the differentially expressed upregulated mRNAs are primarily enriched in cytokine-cytokine receptor interaction, infectious diseases, TNF signaling pathway, FoxO signaling pathway, and pathways in cancer. This is the first lncRNA and mRNA transcriptome profile of LPS-mediated changes in human endothelial cells. These observations may reveal novel endothelial targets of LPS that may be involved in the vascular pathology of sepsis.
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Affiliation(s)
- Krishna K Singh
- Division of Cardiac Surgery, Keenan Research Centre for Biomedical Science, St. Michael's Hospital, 8th Floor, Bond Wing, 30 Bond Street, Toronto, ON, M5B 1W8, Canada. .,Division of Vascular Surgery, Keenan Research Centre for Biomedical Science, St. Michael's Hospital, 8th Floor, Bond Wing, 30 Bond Street, Toronto, ON, M5B 1W8, Canada. .,Department of Surgery, University of Toronto, Toronto, ON, Canada. .,Institute of Medical Science, University of Toronto, Toronto, ON, Canada.
| | - Pratiek N Matkar
- Division of Cardiology, Keenan Research Centre for Biomedical Science, St. Michael's Hospital, Toronto, ON, Canada.,Institute of Medical Science, University of Toronto, Toronto, ON, Canada
| | - Shoaib Muhammad
- Division of Cardiac Surgery, Keenan Research Centre for Biomedical Science, St. Michael's Hospital, 8th Floor, Bond Wing, 30 Bond Street, Toronto, ON, M5B 1W8, Canada
| | - Adrian Quan
- Division of Cardiac Surgery, Keenan Research Centre for Biomedical Science, St. Michael's Hospital, 8th Floor, Bond Wing, 30 Bond Street, Toronto, ON, M5B 1W8, Canada
| | - Vijay Gupta
- Division of Cardiac Surgery, Keenan Research Centre for Biomedical Science, St. Michael's Hospital, 8th Floor, Bond Wing, 30 Bond Street, Toronto, ON, M5B 1W8, Canada
| | - Hwee Teoh
- Division of Cardiac Surgery, Keenan Research Centre for Biomedical Science, St. Michael's Hospital, 8th Floor, Bond Wing, 30 Bond Street, Toronto, ON, M5B 1W8, Canada.,Division of Endocrinology and Metabolism, Keenan Research Centre for Biomedical Science, St. Michael's Hospital, Toronto, ON, Canada
| | - Mohammed Al-Omran
- Division of Vascular Surgery, Keenan Research Centre for Biomedical Science, St. Michael's Hospital, 8th Floor, Bond Wing, 30 Bond Street, Toronto, ON, M5B 1W8, Canada.,Department of Surgery, University of Toronto, Toronto, ON, Canada.,Institute of Medical Science, University of Toronto, Toronto, ON, Canada.,King Saud University-Li Ka Shing Collaborative Research Program, Department of Surgery, King Saud University, Riyadh, Kingdom of Saudi Arabia
| | - Subodh Verma
- Division of Cardiac Surgery, Keenan Research Centre for Biomedical Science, St. Michael's Hospital, 8th Floor, Bond Wing, 30 Bond Street, Toronto, ON, M5B 1W8, Canada. .,Department of Surgery, University of Toronto, Toronto, ON, Canada. .,Institute of Medical Science, University of Toronto, Toronto, ON, Canada.
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Murphy MB, Medvedev AE. Long noncoding RNAs as regulators of Toll-like receptor signaling and innate immunity. J Leukoc Biol 2016; 99:839-50. [PMID: 26965636 PMCID: PMC6608019 DOI: 10.1189/jlb.2ru1215-575r] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2015] [Revised: 02/18/2016] [Accepted: 02/23/2016] [Indexed: 12/30/2022] Open
Abstract
Sensing of microbial pathogens and endogenous "alarmins" by macrophages and dendritic cells is reliant on pattern recognition receptors, including membrane-associated TLRs, cytosolic nucleotide-binding and oligomerization domain leucine-rich repeat-containing receptors, retinoic acid-inducible gene I-like receptors, and absent in melanoma 2-like receptors. Engagement of TLRs elicits signaling pathways that activate inflammatory genes whose expression is regulated by chromatin-modifying complexes and transcription factors. Long noncoding RNAs have emerged as new regulators of inflammatory mediators in the immune system. They are expressed in macrophages, dendritic cells, neutrophils, NK cells, and T- and B-lymphocytes and are involved in immune cell differentiation and activation. Long noncoding RNAs act via repression or activation of transcription factors, modulation of stability of mRNA and microRNA, regulation of ribosome entry and translation of mRNAs, and controlling components of the epigenetic machinery. In this review, we focus on recent advances in deciphering the mechanisms by which long noncoding RNAs regulate TLR-driven responses in macrophages and dendritic cells and discuss the involvement of long noncoding RNAs in endotoxin tolerance, autoimmune, and inflammatory diseases. The dissection of the role of long noncoding RNAs will improve our understanding of the mechanisms of regulation of inflammation and may provide new targets for therapeutic intervention.
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Affiliation(s)
- Michael B Murphy
- Department of Immunology, University of Connecticut Health Center, Farmington, Connecticut, USA
| | - Andrei E Medvedev
- Department of Immunology, University of Connecticut Health Center, Farmington, Connecticut, USA
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Messemaker TC, Huizinga TW, Kurreeman F. Immunogenetics of rheumatoid arthritis: Understanding functional implications. J Autoimmun 2015. [DOI: 10.1016/j.jaut.2015.07.007] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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40
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Zhang Y, Cao X. Long noncoding RNAs in innate immunity. Cell Mol Immunol 2015; 13:138-47. [PMID: 26277893 PMCID: PMC4786632 DOI: 10.1038/cmi.2015.68] [Citation(s) in RCA: 124] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2015] [Accepted: 06/13/2015] [Indexed: 12/15/2022] Open
Abstract
Long noncoding RNAs (lncRNAs) have been shown to play important roles in immune cell development and immune responses through different mechanisms, such as dosage compensation, imprinting, enhancer function, and transcriptional regulation. Although the functions of most lncRNAs are unclear, some lncRNAs have been found to control transcriptional or post-transcriptional regulation of the innate and adaptive immune responses via new methods of protein–protein interactions or pairing with DNA and RNA. Interestingly, increasing evidence has elucidated the importance of lncRNAs in the interaction between hosts and pathogens. In this review, an overview of the lncRNAs modes of action, as well as the important and diversified roles of lncRNAs in immunity, are provided, and an emerging paradigm of lncRNAs in regulating innate immune responses is highlighted.
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Wu GC, Pan HF, Leng RX, Wang DG, Li XP, Li XM, Ye DQ. Emerging role of long noncoding RNAs in autoimmune diseases. Autoimmun Rev 2015; 14:798-805. [PMID: 25989481 DOI: 10.1016/j.autrev.2015.05.004] [Citation(s) in RCA: 201] [Impact Index Per Article: 22.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2015] [Accepted: 05/07/2015] [Indexed: 12/17/2022]
Abstract
Long noncoding RNA (lncRNA), with size larger than 200 nucleotides, is a new class of noncoding RNA. Emerging evidence has revealed that lncRNAs play a key role in the regulation of immunological functions and autoimmunity. Herein, we review the recent findings of lncRNA regulation in immune functions and in the development of autoimmunity and autoimmune disease. In addition, we focus on the involvement of lncRNA regulation in innate and adaptive immune responses, immune cell development, and differential expression of lncRNAs in autoimmune diseases, including systemic lupus erythematosus (SLE), rheumatoid arthritis (RA), type 1 diabetes mellitus (T1DM), multiple sclerosis (MS), autoimmune thyroid disease (AITD), psoriasis, polymyositis/dermatomyositis (PM/DM) and Crohn's disease (CD).
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Affiliation(s)
- Guo-Cui Wu
- Department of Epidemiology and Biostatistics, School of Public Health, Anhui Medical University, 81 Meishan Road, Hefei, 230032, Anhui, China; Anhui Provincial Laboratory of Population Health and Major Disease Screening and Diagnosis, Anhui Medical University, 81 Meishan Road, Hefei, 230032, Anhui, China
| | - Hai-Feng Pan
- Department of Epidemiology and Biostatistics, School of Public Health, Anhui Medical University, 81 Meishan Road, Hefei, 230032, Anhui, China; Anhui Provincial Laboratory of Population Health and Major Disease Screening and Diagnosis, Anhui Medical University, 81 Meishan Road, Hefei, 230032, Anhui, China
| | - Rui-Xue Leng
- Department of Epidemiology and Biostatistics, School of Public Health, Anhui Medical University, 81 Meishan Road, Hefei, 230032, Anhui, China; Anhui Provincial Laboratory of Population Health and Major Disease Screening and Diagnosis, Anhui Medical University, 81 Meishan Road, Hefei, 230032, Anhui, China
| | - De-Guang Wang
- Department of Nephrology, The Second Affiliated Hospital of Anhui Medical University, 678 Furong Road, Hefei, 230601, Anhui, China
| | - Xiang-Pei Li
- Department of Rheumatology and Immunology, Anhui Provincial Hospital, Affiliated to Anhui Medical University, 17 Lujiang Road, Hefei 230001, Anhui, China
| | - Xiao-Mei Li
- Department of Rheumatology and Immunology, Anhui Provincial Hospital, Affiliated to Anhui Medical University, 17 Lujiang Road, Hefei 230001, Anhui, China
| | - Dong-Qing Ye
- Department of Epidemiology and Biostatistics, School of Public Health, Anhui Medical University, 81 Meishan Road, Hefei, 230032, Anhui, China; Anhui Provincial Laboratory of Population Health and Major Disease Screening and Diagnosis, Anhui Medical University, 81 Meishan Road, Hefei, 230032, Anhui, China
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