1
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Li DH, Wu L, Chen FQ, Liu XK, Mei JQ. Mechanism of Huo-Xiang-Zheng-Qi in Preventing and Treating COVID-19: A Study Based on Network Pharmacology and Molecular Docking Techniques. Nat Prod Commun 2022. [DOI: 10.1177/1934578x221102028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Objective: The Chinese herbal formula Huo-Xiang-Zheng-Qi (HXZQ) is effective in preventing and treating coronavirus disease 19 (COVID-19) infection; however, its mechanism remains unclear. This study used network pharmacology and molecular docking techniques to investigate the mechanism of action of HXZQ in preventing and treating COVID-19. Methods: The Traditional Chinese Medicine Systems Pharmacology Database and Analysis Platform (TCMSP) was used to search for the active ingredients and targets of the 10 traditional Chinese medicines (TCMs) of HXZQ prescription (HXZQP). GeneCards, Online Mendelian Inheritance in Man (OMIM), Pharmacogenomics Knowledge Base (PharmGKB), Therapeutic Target Database (TTD), and DrugBank databases were used to screen COVID-19-related genes and intersect them with the targets of HXZQP to obtain the drug efficacy targets. Cytoscape 3.8 software was used to construct the drug-active ingredient–target interaction network of HXZQP and perform protein–protein interaction (PPI) network construction and topology analysis. R software was used to perform Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis. Finally, AutoDock Vina was utilized for molecular docking of the active ingredients of TCM and drug target proteins. Results: A total of 151 active ingredients and 250 HXZQP targets were identified. Among these, 136 active ingredients and 67 targets of HXZQP were found to be involved in the prevention and treatment of COVID-19. The core proteins identified in the PPI network were MAPK1, MAPK3, MAPK8, MAPK14, STAT3, and PTGS2. Using GO and KEGG pathway enrichment analysis, HXZQP was found to primarily participate in biological processes such as defense response to a virus, cellular response to biotic stimulus, response to lipopolysaccharide, PI3K-Akt signaling pathway, Th17 cell differentiation, HIF-1 signaling pathway, and other signaling pathways closely related to COVID-19. Molecular docking results reflected that the active ingredients of HXZQP have a reliable affinity toward EGFR, MAPK1, MAPK3, MAPK8, and STAT3 proteins. Conclusion: Our study elucidated the main targets and pathways of HXZQP in the prevention and treatment of COVID-19. The study findings provide a basis for further investigation of the pharmacological effects of HXZQP.
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Affiliation(s)
- De-hui Li
- The First Affiliated Hospital of Hebei University of Chinese Medicine, Hebei Provincial Hospital of Chinese Medicine, Shi Jiazhuang, China
| | - Lei Wu
- The First Affiliated Hospital of Hebei University of Chinese Medicine, Hebei Provincial Hospital of Chinese Medicine, Shi Jiazhuang, China
| | - Fen-qiao Chen
- The First Affiliated Hospital of Hebei University of Chinese Medicine, Hebei Provincial Hospital of Chinese Medicine, Shi Jiazhuang, China
| | - Xu-kuo Liu
- Graduate School of Hebei University of Chinese Medicine, Shijiazhuang, China
| | - Jian-qiang Mei
- The First Affiliated Hospital of Hebei University of Chinese Medicine, Hebei Provincial Hospital of Chinese Medicine, Shi Jiazhuang, China
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2
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Liu X, Wen YZ, Huang ZL, Shen X, Wang JH, Luo YH, Chen WX, Lun ZR, Li HB, Qu LH, Shan H, Zheng LL. SARS-CoV-2 causes a significant stress response mediated by small RNAs in the blood of COVID-19 patients. MOLECULAR THERAPY. NUCLEIC ACIDS 2022; 27:751-762. [PMID: 35003892 PMCID: PMC8719421 DOI: 10.1016/j.omtn.2021.12.034] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Accepted: 12/29/2021] [Indexed: 12/24/2022]
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has had a serious impact on the world. In this study, small RNAs from the blood of COVID-19 patients with moderate or severe symptoms were extracted for high-throughput sequencing and analysis. Interestingly, the levels of a special group of tRNA-derived small RNAs (tsRNAs) were found to be dramatically upregulated after SARS-CoV-2 infection, particularly in coronavirus disease 2019 (COVID-19) patients with severe symptoms. In particular, the 3′CCA tsRNAs from tRNA-Gly were highly consistent with the inflammation indicator C-reactive protein (CRP). In addition, we found that the majority of significantly changed microRNAs (miRNAs) were associated with endoplasmic reticulum (ER)/unfolded protein response (UPR) sensors, which may lead to the induction of proinflammatory cytokine and immune responses. This study found that SARS-CoV-2 infection caused significant changes in the levels of stress-associated small RNAs in patient blood and their potential functions. Our research revealed that the cells of COVID-19 patients undergo tremendous stress and respond, which can be reflected or regulated by small non-coding RNA (sncRNAs), thus providing potential thought for therapeutic intervention in COVID-19 by modulating small RNA levels or activities.
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Affiliation(s)
- Xi Liu
- Department of Infectious Diseases, The Fifth Affiliated Hospital of Sun Yat-sen University, Zhuhai 519000, P. R. China
| | - Yan-Zi Wen
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory for Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, P. R. China
| | - Zi-Liang Huang
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory for Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, P. R. China
| | - Xia Shen
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory for Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, P. R. China.,Greater Bay Area Institute of Precision Medicine (Guangzhou), Fudan University, Guangzhou 511458, P. R. China.,Center for Global Health Research, Usher Institute, University of Edinburgh, Edinburgh EH8 9AG, UK
| | - Jun-Hao Wang
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory for Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, P. R. China
| | - Yi-Hai Luo
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory for Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, P. R. China
| | - Wen-Xin Chen
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory for Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, P. R. China
| | - Zhao-Rong Lun
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory for Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, P. R. China
| | - Hui-Bin Li
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory for Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, P. R. China
| | - Liang-Hu Qu
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory for Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, P. R. China
| | - Hong Shan
- Guangdong Provincial Engineering Research Center of Molecular Imaging, the Fifth Affiliated Hospital of Sun Yat-sen University, Zhuhai 519000, P. R. China.,Guangdong Provincial Key Laboratory of Biomedical Imaging, The Fifth Affiliated Hospital of Sun Yat-sen University, Zhuhai 519000, P. R. China.,Department of Interventional Medicine, The Fifth Affiliated Hospital of Sun Yat-sen University, Zhuhai 519000, P. R. China
| | - Ling-Ling Zheng
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory for Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, P. R. China
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3
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MicroRNA let-7 and viral infections: focus on mechanisms of action. Cell Mol Biol Lett 2022; 27:14. [PMID: 35164678 PMCID: PMC8853298 DOI: 10.1186/s11658-022-00317-9] [Citation(s) in RCA: 55] [Impact Index Per Article: 27.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2021] [Accepted: 01/26/2022] [Indexed: 02/06/2023] Open
Abstract
MicroRNAs (miRNAs) are fundamental post-transcriptional modulators of several critical cellular processes, a number of which are involved in host defense mechanisms. In particular, miRNA let-7 functions as an essential regulator of the function and differentiation of both innate and adaptive immune cells. Let-7 is involved in several human diseases, including cancer and viral infections. Several viral infections have found ways to dysregulate the expression of miRNAs. Extracellular vesicles (EV) are membrane-bound lipid structures released from many types of human cells that can transport proteins, lipids, mRNAs, and miRNAs, including let-7. After their release, EVs are taken up by the recipient cells and their contents released into the cytoplasm. Let-7-loaded EVs have been suggested to affect cellular pathways and biological targets in the recipient cells, and can modulate viral replication, the host antiviral response, and the action of cancer-related viruses. In the present review, we summarize the available knowledge concerning the expression of let-7 family members, functions, target genes, and mechanistic involvement in viral pathogenesis and host defense. This may provide insight into the development of new therapeutic strategies to manage viral infections.
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4
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Baluni M, Ghildiyal S, Fatima T, Tiwari R, Upadhyay S, Dhole TN, Reddy DH, Singh D. Differential expression of circulating microRNAs in serum: Potential biomarkers to track Japanese encephalitis virus infection. J Med Virol 2021; 94:531-539. [PMID: 34698413 DOI: 10.1002/jmv.27419] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Revised: 10/11/2021] [Accepted: 10/23/2021] [Indexed: 11/11/2022]
Abstract
Japanese encephalitis is one of the serious vector-borne viral encephalitis diseases found worldwide and poses a major threat to public health. Most Japanese encephalitis virus (JEV) infections are subclinical; only 1: 250 to 1:1000 infected persons develop clinical presentations. Delay in proper diagnosis of JE affects the timeliness of treatment initiation and increases the mortality rate in patients. Therefore, there is an extreme need to develop potential biomarkers, which might improve the diagnosis and can become the basis for development of new therapeutics. The microRNAs (miRNAs/or miRs) are small noncoding RNAs of 17-24 nucleotides that are known to regulate about 60% of human genes. Although miRNAs have been found to regulate various aspects of innate and adaptive immune responses, less information on circulating miRNAs in JE is known. The study of JEV infected human serum miRNAs will provide novel information for the diagnosis of JE as well as for the improvement of disease outcome. Total RNA, including miRNA, was extracted from serum followed by the complementary DNA (cDNA) synthesis by using sequence-specific primers. cDNA was amplified using target-specific TaqMan MicroRNA Assay. Real-time polymerase chain reaction data was normalized using both exogenous (cel-miR-39) and endogenous (hsa-miR-93) controls. We have found significantly altered expression of miR-155 and miR-21 in serum of JEV infected patients as compared to healthy controls, revealing their role as a a noninvasive biomarker in JE. A significant correlation between miRNAs and JE was observed that offers the basis for miRNAs to serve as a new component to develop possible therapeutic strategies for JE in near future.
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Affiliation(s)
- Manjari Baluni
- Department of Microbiology, Sanjay Gandhi Post Graduate Institute of Medical Sciences, Lucknow, Uttar Pradesh, India
| | - Sneha Ghildiyal
- Department of Microbiology, Sanjay Gandhi Post Graduate Institute of Medical Sciences, Lucknow, Uttar Pradesh, India
| | - Tanzeem Fatima
- Department of Microbiology, Sanjay Gandhi Post Graduate Institute of Medical Sciences, Lucknow, Uttar Pradesh, India
| | - Rashmi Tiwari
- Department of Microbiology, Sanjay Gandhi Post Graduate Institute of Medical Sciences, Lucknow, Uttar Pradesh, India
| | - Shivbrat Upadhyay
- Department of Biochemistry, ERA's Medical College and Hospital, Sarfarazganj, Uttar Pradesh, India
| | - Tapan N Dhole
- Department of Microbiology, Sanjay Gandhi Post Graduate Institute of Medical Sciences, Lucknow, Uttar Pradesh, India
| | - D Himanshu Reddy
- Department of Medicine, King George's Medical University, Lucknow, Uttar Pradesh, India
| | - Dharamveer Singh
- Department of Microbiology, All India Institute of Medical Sciences, Patna, Bihar, India
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5
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Non-Coding RNAs and Reactive Oxygen Species–Symmetric Players of the Pathogenesis Associated with Bacterial and Viral Infections. Symmetry (Basel) 2021. [DOI: 10.3390/sym13071307] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Infections can be triggered by a wide range of pathogens. However, there are few strains of bacteria that cause illness, but some are quite life-threatening. Likewise, viral infections are responsible for many human diseases, usually characterized by high contagiousness. Hence, as bacterial and viral infections can both cause similar symptoms, it can be difficult to determine the exact cause of a specific infection, and this limitation is critical. However, recent scientific advances have geared us up with the proper tools required for better diagnoses. Recent discoveries have confirmed the involvement of non-coding RNAs (ncRNAs) in regulating the pathogenesis of certain bacterial or viral infections. Moreover, the presence of reactive oxygen species (ROS) is also known as a common infection trait that can be used to achieve a more complete description of such pathogen-driven conditions. Thus, this opens further research opportunities, allowing scientists to explore infection-associated genetic patterns and develop better diagnosis and treatment methods. Therefore, the aim of this review is to summarize the current knowledge of the implication of ncRNAs and ROS in bacterial and viral infections, with great emphasis on their symmetry but, also, on their main differences.
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6
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Wan T, Liu X, Su Y, Zou J, Wu X, Jiang C, Cao C, Yao M, Zhou Y, Rong L, Li B, Wen L, Feng Q. Biological differentiation of traditional Chinese medicine from excessive to deficient syndromes in AIDS: Comparative microRNA microarray profiling and syndrome-specific biomarker identification. J Med Virol 2021; 93:3634-3646. [PMID: 33289096 DOI: 10.1002/jmv.26704] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2020] [Revised: 11/26/2020] [Accepted: 11/27/2020] [Indexed: 12/12/2022]
Abstract
Traditional Chinese medicine (TCM) has been widely applied as a supplementary therapy of human immunodeficiency virus infection and acquired immunodeficiency syndrome (HIV/AIDS) in China. TCM has a positive effect on improving the quality of life, prolonging life, and ameliorating the symptoms of HIV/AIDS patients. Yang deficiency of spleen and kidney (YDSK) syndrome is a typical deficient TCM syndrome in AIDS patients, and accumulation of heat-toxicity (AHT) syndrome is a common excessive syndrome in the earlier stage of AIDS. Thus, accurate diagnosis of these two syndromes can improve the targeted treatment effect, and predict the prognosis of the disease. However, the scientific basis of TCM syndromes remains lacking, greatly hindering the accuracy of diagnosis and effectiveness of treatment. In this research, microRNA (miRNA) microarray and quantitative real-time polymerase chain reaction combined with bioinformatics were used for comparative analysis between YDSK and AHT patients. Significantly differential expressed miRNAs (SDE-miRNAs) of each TCM syndrome were identified, including hsa-miR-766-3p and hsa-miR-1260a and so on, as well hsa-miR-6124, hsa-let-7g-5p and so on, for YDSK and AHT, respectively. Biological differences were found between their SDE-miRNAs based on bioinformatics analyses, for example, ErbB signaling pathway mainly linked to AHT, while focal adhesion dominated in YDSK. Syndrome-specific SDE-miRNAs were further identified as potential biomarkers, including hsa-miR-30e-5p, hsa-miR-144-5p for YDSK and hsa-let-7g-5p, hsa-miR-126-3p for AHT, respectively. All of them have laid biological and clinical bases for TCM diagnosis and treatment of AIDS syndrome at the miRNA level, offering potential diagnostic indicators of immune reconstitution.
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Affiliation(s)
- Tingjun Wan
- Chengdu University of Traditional Chinese Medicine, Chengdu, Sichuan, China
| | - Xiyang Liu
- Chengdu University of Traditional Chinese Medicine, Chengdu, Sichuan, China
| | - Yue Su
- Chengdu University of Traditional Chinese Medicine, Chengdu, Sichuan, China
| | - Jiaxi Zou
- Chengdu University of Traditional Chinese Medicine, Chengdu, Sichuan, China
| | - Xi Wu
- Guizhou University of Traditional Chinese Medicine, Guiyang, Guizhou, China
| | - Cen Jiang
- Chengdu University of Traditional Chinese Medicine, Chengdu, Sichuan, China
| | - Chunhui Cao
- Chengdu University of Traditional Chinese Medicine, Chengdu, Sichuan, China
| | - Mingyue Yao
- Chengdu University of Traditional Chinese Medicine, Chengdu, Sichuan, China
| | - Yuyu Zhou
- Chengdu University of Traditional Chinese Medicine, Chengdu, Sichuan, China
| | - Lijun Rong
- Department of Microbiology and Immunology, University of Illinois at Chicago, Chicago, Illinois, USA
| | - Baixue Li
- Chengdu University of Traditional Chinese Medicine, Chengdu, Sichuan, China
| | - Li Wen
- Chengdu University of Traditional Chinese Medicine, Chengdu, Sichuan, China
| | - Quansheng Feng
- Chengdu University of Traditional Chinese Medicine, Chengdu, Sichuan, China
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7
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Bamunuarachchi G, Pushparaj S, Liu L. Interplay between host non-coding RNAs and influenza viruses. RNA Biol 2021; 18:767-784. [PMID: 33404285 PMCID: PMC8078518 DOI: 10.1080/15476286.2021.1872170] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2020] [Revised: 12/28/2020] [Accepted: 01/01/2021] [Indexed: 01/20/2023] Open
Abstract
Influenza virus infection through seasonal epidemics and occasional pandemics has been a major public health concern for decades. Incomplete protection from vaccination and increased antiviral resistance due to frequent mutations of influenza viruses have led to a continuous need for new therapeutic options. The functional significance of host protein and influenza virus interactions has been established, but relatively less is known about the interaction of host noncoding RNAs, including microRNAs and long noncoding RNAs, with influenza viruses. In this review, we summarize host noncoding RNA profiles during influenza virus infection and the regulation of influenza virus infection by host noncoding RNAs. Influenza viral non-coding RNAs are briefly discussed. Increased understanding of the molecular regulation of influenza viral replication will be beneficial in identifying potential therapeutic targets against the influenza virus.
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Affiliation(s)
- Gayan Bamunuarachchi
- Oklahoma Center for Respiratory and Infectious Diseases, Oklahoma State University, Stillwater, Oklahoma, USA
- Lundberg-Kienlen Lung Biology and Toxicology Laboratory, Department of Physiological Sciences, Oklahoma State University, Stillwater, USA
- Department of Physiological Sciences, Oklahoma State University, Stillwater, USA
| | - Samuel Pushparaj
- Oklahoma Center for Respiratory and Infectious Diseases, Oklahoma State University, Stillwater, Oklahoma, USA
- Lundberg-Kienlen Lung Biology and Toxicology Laboratory, Department of Physiological Sciences, Oklahoma State University, Stillwater, USA
- Department of Physiological Sciences, Oklahoma State University, Stillwater, USA
| | - Lin Liu
- Oklahoma Center for Respiratory and Infectious Diseases, Oklahoma State University, Stillwater, Oklahoma, USA
- Lundberg-Kienlen Lung Biology and Toxicology Laboratory, Department of Physiological Sciences, Oklahoma State University, Stillwater, USA
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8
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Sun J, Shen F, Zhang L, Luo L, Fan Z, Hou R, Yue B, Zhang X. Changes in the MicroRNA Profile of the Giant Panda After Canine Distemper Vaccination and the Integrated Analysis of MicroRNA-Messenger RNA. DNA Cell Biol 2021; 40:595-605. [PMID: 33769863 DOI: 10.1089/dna.2020.5942] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Canine distemper (CD) is a significant threat to wild and captive giant panda populations. Captive giant pandas are inoculated with canine distemper virus (CDV) vaccination to prevent the infection with the CDV. As an important regulator, microRNA (miRNA) plays a crucial role in regulating gene expression, including in disease immunity. To understand the role of miRNA in immune response to CDV vaccination, we investigated the miRNA expression profile in five giant panda cubs after two inoculations, 21 days apart. A total of 187 conserved miRNAs and 96 novel miRNAs were identified. Among the 187 conserved miRNAs, 29 differentially expressed miRNAs were found postinoculation. The upregulation of miR-16, miR-182, miR-30b, and miR-101 indicated that the innate immune may be enhanced, whereas the upregulation of miR-142 and miR-19a are probably involved in the enhanced cellular immune response. However, the downregulated miR-155 and miR-181a might indicate the giant panda has weak ability to produce antibodies and memory B cells. Integrated analysis of miRNA-messenger RNA (mRNA) found 20 negatively regulated miRNA-mRNA pairs, where downregulated miR-204 might enhance giant panda cub innate immunity by increasing TLR6 expression, and downregulated miR-330 might activate macrophages and regulate the immune response by increasing TMEM106A expression. Our research provides key information for future development to enhance the immune response of giant pandas and potentially improve the survival of captive and wild giant panda populations threatened by CD.
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Affiliation(s)
- Jie Sun
- Key Laboratory of Bio-resources and Eco-environment, Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China
| | - Fujun Shen
- The Sichuan Key Laboratory for Conservation Biology of Endangered Wildlife, Chengdu Research Base of Giant Panda Breeding, Chengdu, China
| | - Liang Zhang
- The Sichuan Key Laboratory for Conservation Biology of Endangered Wildlife, Chengdu Research Base of Giant Panda Breeding, Chengdu, China
| | - Li Luo
- The Sichuan Key Laboratory for Conservation Biology of Endangered Wildlife, Chengdu Research Base of Giant Panda Breeding, Chengdu, China
| | - Zhenxin Fan
- Sichuan Key Laboratory of Conservation Biology on Endangered Wildlife, College of Life Sciences, Sichuan University, Chengdu, China
| | - Rong Hou
- The Sichuan Key Laboratory for Conservation Biology of Endangered Wildlife, Chengdu Research Base of Giant Panda Breeding, Chengdu, China
| | - Bisong Yue
- Sichuan Key Laboratory of Conservation Biology on Endangered Wildlife, College of Life Sciences, Sichuan University, Chengdu, China
| | - Xiuyue Zhang
- Key Laboratory of Bio-resources and Eco-environment, Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China
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9
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Lorente-Pozo S, Navarrete P, Garzón MJ, Lara-Cantón I, Beltrán-García J, Osca-Verdegal R, Mena-Mollá S, García-López E, Vento M, Pallardó FV, García-Giménez JL. DNA Methylation Analysis to Unravel Altered Genetic Pathways Underlying Early Onset and Late Onset Neonatal Sepsis. A Pilot Study. Front Immunol 2021; 12:622599. [PMID: 33659006 PMCID: PMC7917190 DOI: 10.3389/fimmu.2021.622599] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2020] [Accepted: 01/25/2021] [Indexed: 12/12/2022] Open
Abstract
Background: Neonatal sepsis is a systemic condition widely affecting preterm infants and characterized by pro-inflammatory and anti-inflammatory responses. However, its pathophysiology is not yet fully understood. Epigenetics regulates the immune system, and its alteration leads to the impaired immune response underlying sepsis. DNA methylation may contribute to sepsis-induced immunosuppression which, if persistent, will cause long-term adverse effects in neonates. Objective: To analyze the methylome of preterm infants in order to determine whether there are DNA methylation marks that may shed light on the pathophysiology of neonatal sepsis. Design: Prospective observational cohort study performed in the neonatal intensive care unit (NICU) of a tertiary care center. Patients: Eligible infants were premature ≤32 weeks admitted to the NICU with clinical suspicion of sepsis. The methylome analysis was performed in DNA from blood using Infinium Human Methylation EPIC microarrays to uncover methylation marks. Results: Methylation differential analysis revealed an alteration of methylation levels in genomic regions involved in inflammatory pathways which participate in both the innate and the adaptive immune response. Moreover, differences between early and late onset sepsis as compared to normal controls were assessed. Conclusions: DNA methylation marks can serve as a biomarker for neonatal sepsis and even contribute to differentiating between early and late onset sepsis.
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Affiliation(s)
- Sheila Lorente-Pozo
- Neonatal Research Group, Health Research Institute La Fe, Valencia, Spain.,Division of Neonatology, University and Polytechnic Hospital La Fe, Valencia, Spain
| | - Paula Navarrete
- EpiDisease S.L. (Spin-off From the CIBER-ISCIII), Parc Científic de la Universitat de València, Paterna, Spain
| | - María José Garzón
- EpiDisease S.L. (Spin-off From the CIBER-ISCIII), Parc Científic de la Universitat de València, Paterna, Spain
| | - Inmaculada Lara-Cantón
- Neonatal Research Group, Health Research Institute La Fe, Valencia, Spain.,Division of Neonatology, University and Polytechnic Hospital La Fe, Valencia, Spain
| | - Jesús Beltrán-García
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Valencia, Spain.,Department Fisiología, Facultad de Medicina y Odontología, Universidad de Valencia-INCLIVA, Valencia, Spain
| | - Rebeca Osca-Verdegal
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Valencia, Spain.,Department Fisiología, Facultad de Medicina y Odontología, Universidad de Valencia-INCLIVA, Valencia, Spain
| | - Salvador Mena-Mollá
- EpiDisease S.L. (Spin-off From the CIBER-ISCIII), Parc Científic de la Universitat de València, Paterna, Spain.,Department Fisiología, Facultad de Medicina y Odontología, Universidad de Valencia-INCLIVA, Valencia, Spain
| | - Eva García-López
- EpiDisease S.L. (Spin-off From the CIBER-ISCIII), Parc Científic de la Universitat de València, Paterna, Spain
| | - Máximo Vento
- Neonatal Research Group, Health Research Institute La Fe, Valencia, Spain.,Division of Neonatology, University and Polytechnic Hospital La Fe, Valencia, Spain
| | - Federico V Pallardó
- EpiDisease S.L. (Spin-off From the CIBER-ISCIII), Parc Científic de la Universitat de València, Paterna, Spain.,Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Valencia, Spain.,Department Fisiología, Facultad de Medicina y Odontología, Universidad de Valencia-INCLIVA, Valencia, Spain
| | - José Luis García-Giménez
- EpiDisease S.L. (Spin-off From the CIBER-ISCIII), Parc Científic de la Universitat de València, Paterna, Spain.,Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Valencia, Spain.,Department Fisiología, Facultad de Medicina y Odontología, Universidad de Valencia-INCLIVA, Valencia, Spain
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10
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Sarkar JP, Saha I, Sarkar A, Maulik U. Machine learning integrated ensemble of feature selection methods followed by survival analysis for predicting breast cancer subtype specific miRNA biomarkers. Comput Biol Med 2021; 131:104244. [PMID: 33550016 DOI: 10.1016/j.compbiomed.2021.104244] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2020] [Revised: 01/24/2021] [Accepted: 01/24/2021] [Indexed: 12/25/2022]
Abstract
Breast cancer is the second leading cancer type among females. In this regard, it is found that microRNAs play an important role by regulating the gene expressions at the post-transcriptional phase. However, identification of the most influencing miRNAs in breast cancer subtypes is a challenging task, while the recent advancement in Next Generation Sequencing techniques allows analyzing high throughput expression data of miRNAs. Thus, we have conducted this research with the help of NGS data of breast cancer in order to identify the most significant miRNA biomarkers. The selected miRNA biomarkers are highly associated with the multiple breast cancer subtypes. For this purpose, a two-phase technique, called Machine Learning Integrated Ensemble of Feature Selection Methods, followed by survival analysis, is proposed. In the first phase, we have selected the best among seven machine learning techniques based on classification accuracy using the entire set of features (in this case miRNAs). Subsequently, eight different feature selection methods are used separately in order to rank the features and validate each set of top features using the selected machine learning technique by considering a multi-class classification task of the breast cancer subtypes. In the second phase, based on the classification accuracy values, the top features from each feature selection method are considered to make an ensemble to provide further categorization of the miRNAs as 8*, 7* up to 1*. The 8* miRNAs provide the highest average classification accuracy of 86% after 10-fold cross-validation. Thereafter, 27 miRNAs are identified from the list that is confined within 8* to 4* miRNAs based on their importance in survival for breast cancer subtypes using Cox regression based survival analysis. Moreover, expression analysis, regulatory network analysis, protein-protein interaction analysis, KEGG pathway and gene ontology enrichment analysis are performed in order to validate biological significance of the proposed solution. Additionally, we have prepared a miRNA-protein-drug interaction network to identify possible drug for the selected miRNAs. Thus, our findings may be considered during a clinical trial for the treatment of breast cancer patients.
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Affiliation(s)
- Jnanendra Prasad Sarkar
- Larsen & Toubro Infotech Ltd., Pune, India; Department of Computer Science and Engineering, Jadavpur University, Kolkata, India
| | - Indrajit Saha
- Department of Computer Science and Engineering, National Institute of Technical Teachers' Training & Research, Kolkata, 700106, India.
| | - Anasua Sarkar
- Department of Computer Science and Engineering, Jadavpur University, Kolkata, India
| | - Ujjwal Maulik
- Department of Computer Science and Engineering, Jadavpur University, Kolkata, India
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11
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Yang X, Liang Y, Bamunuarachchi G, Xu Y, Vaddadi K, Pushparaj S, Xu D, Zhu Z, Blaha R, Huang C, Liu L. miR-29a is a negative regulator of influenza virus infection through targeting of the frizzled 5 receptor. Arch Virol 2020; 166:363-373. [PMID: 33206218 DOI: 10.1007/s00705-020-04877-z] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2019] [Accepted: 09/29/2020] [Indexed: 12/11/2022]
Abstract
Influenza A virus (IAV) infections result in a large number of deaths and substantial economic losses each year. MicroRNAs repress gene expression and are involved in virus-host interactions. miR-29a is known to have anti-tumor and anti-fibrotic effects. However, the role of miR-29a in IAV infection is unclear. In the present study, we investigated the effect of miR-29a on IAV infection and the mechanisms by which it functions. IAV infection was found to cause decreased miR-29a expression in lung epithelial A549 cells and mouse lungs. Overexpression of miR-29a reduced IAV mRNA and protein levels and progeny virus production in HEK293 and A549 cells. Inhibition of IAV infection by miR-29a was observed with different strains of IAV, including A/PR/8/34, A/WSN/1933, and clinical isolates A/OK/3052/09 and A/OK/309/06 H3N2. Knockout of miR-29a using CRISPR/Cas9 resulted in an increase in viral mRNA and protein levels, confirming that miR-29a suppresses IAV infection. A 3' untranslated region (3'-UTR) reporter assay showed that miR-29a had binding sites in the 3'-UTR of the Wnt-Ca2+ signaling receptor frizzled 5 gene, and overexpression of miR-29a reduced the level of the endogenous frizzled 5 protein. Wnt5a treatment of HEK293 and A549 cells enhanced IAV infection. Our results suggest that miR-29a inhibits IAV infection, probably via the frizzled 5 receptor.
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Affiliation(s)
- Xiaoyun Yang
- Oklahoma Center for Respiratory and Infectious Diseases, Oklahoma State University, Stillwater, Oklahoma, USA
- Lundberg-Kienlen Lung Biology and Toxicology Laboratory, Department of Physiological Sciences, Oklahoma State University, 264 McElroy Hall, Stillwater, OK, 74078, USA
| | - Yurong Liang
- Oklahoma Center for Respiratory and Infectious Diseases, Oklahoma State University, Stillwater, Oklahoma, USA
- Lundberg-Kienlen Lung Biology and Toxicology Laboratory, Department of Physiological Sciences, Oklahoma State University, 264 McElroy Hall, Stillwater, OK, 74078, USA
| | - Gayan Bamunuarachchi
- Oklahoma Center for Respiratory and Infectious Diseases, Oklahoma State University, Stillwater, Oklahoma, USA
- Lundberg-Kienlen Lung Biology and Toxicology Laboratory, Department of Physiological Sciences, Oklahoma State University, 264 McElroy Hall, Stillwater, OK, 74078, USA
| | - Yanzhao Xu
- Oklahoma Center for Respiratory and Infectious Diseases, Oklahoma State University, Stillwater, Oklahoma, USA
- Lundberg-Kienlen Lung Biology and Toxicology Laboratory, Department of Physiological Sciences, Oklahoma State University, 264 McElroy Hall, Stillwater, OK, 74078, USA
| | - Kishore Vaddadi
- Oklahoma Center for Respiratory and Infectious Diseases, Oklahoma State University, Stillwater, Oklahoma, USA
- Lundberg-Kienlen Lung Biology and Toxicology Laboratory, Department of Physiological Sciences, Oklahoma State University, 264 McElroy Hall, Stillwater, OK, 74078, USA
| | - Samuel Pushparaj
- Oklahoma Center for Respiratory and Infectious Diseases, Oklahoma State University, Stillwater, Oklahoma, USA
- Lundberg-Kienlen Lung Biology and Toxicology Laboratory, Department of Physiological Sciences, Oklahoma State University, 264 McElroy Hall, Stillwater, OK, 74078, USA
| | - Dao Xu
- Oklahoma Center for Respiratory and Infectious Diseases, Oklahoma State University, Stillwater, Oklahoma, USA
- Lundberg-Kienlen Lung Biology and Toxicology Laboratory, Department of Physiological Sciences, Oklahoma State University, 264 McElroy Hall, Stillwater, OK, 74078, USA
| | - Zhengyu Zhu
- Oklahoma Center for Respiratory and Infectious Diseases, Oklahoma State University, Stillwater, Oklahoma, USA
- Lundberg-Kienlen Lung Biology and Toxicology Laboratory, Department of Physiological Sciences, Oklahoma State University, 264 McElroy Hall, Stillwater, OK, 74078, USA
| | - Rachel Blaha
- Lundberg-Kienlen Lung Biology and Toxicology Laboratory, Department of Physiological Sciences, Oklahoma State University, 264 McElroy Hall, Stillwater, OK, 74078, USA
| | - Chaoqun Huang
- Oklahoma Center for Respiratory and Infectious Diseases, Oklahoma State University, Stillwater, Oklahoma, USA
- Lundberg-Kienlen Lung Biology and Toxicology Laboratory, Department of Physiological Sciences, Oklahoma State University, 264 McElroy Hall, Stillwater, OK, 74078, USA
| | - Lin Liu
- Oklahoma Center for Respiratory and Infectious Diseases, Oklahoma State University, Stillwater, Oklahoma, USA.
- Lundberg-Kienlen Lung Biology and Toxicology Laboratory, Department of Physiological Sciences, Oklahoma State University, 264 McElroy Hall, Stillwater, OK, 74078, USA.
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12
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Wang H. Anti-NMDA Receptor Encephalitis, Vaccination and Virus. Curr Pharm Des 2020; 25:4579-4588. [PMID: 31820697 DOI: 10.2174/1381612825666191210155059] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2019] [Accepted: 11/21/2019] [Indexed: 12/13/2022]
Abstract
Anti-N-methyl-d-aspartate (Anti-NMDA) receptor encephalitis is an acute autoimmune disorder. The symptoms range from psychiatric symptoms, movement disorders, cognitive impairment, and autonomic dysfunction. Previous studies revealed that vaccination might induce this disease. A few cases were reported to be related to H1N1 vaccine, tetanus/diphtheria/pertussis and polio vaccine, and Japanese encephalitis vaccine. Although vaccination is a useful strategy to prevent infectious diseases, in a low risk, it may trigger serious neurological symptoms. In addition to anti-NMDA receptor encephalitis, other neurological diseases were reported to be associated with a number of vaccines. In this paper, the anti-NMDA receptor encephalitis cases related to a number of vaccines and other neurological symptoms that might be induced by these vaccines were reviewed. In addition, anti-NMDA receptor encephalitis cases that were induced by virus infection were also reviewed.
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Affiliation(s)
- Hsiuying Wang
- Institute of Statistics, National Chiao Tung University, Hsinchu, Taiwan
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13
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miR-1975 serves as an indicator of clinical severity upon influenza infection. Eur J Clin Microbiol Infect Dis 2020; 40:141-149. [PMID: 32814996 PMCID: PMC7437959 DOI: 10.1007/s10096-020-04008-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2020] [Accepted: 08/11/2020] [Indexed: 10/29/2022]
Abstract
Emerging evidence highlights the role of non-coding small RNAs in host-influenza interaction. We have identified a Y RNA-derived small RNA, miR-1975, which is upregulated upon influenza A virus infection in A549 cells. The aim of this study is to investigate whether miR-1975 serves as an indicator of clinical severity upon influenza infection. We investigate the abundance of miR-1975 in sera from clinical patients and its correlation with hypoxemia status. We quantified its amounts in sera from influenza virus-infected patients and healthy volunteers by means of stem-loop RT-PCR. Median values of miR-1975 were significantly higher in influenza virus-infected patients, especially in hypoxemic patients. miR-1975 levels at the acute stage of the disease were highly correlated with the fraction of inspired oxygen used by the patients and total ventilator days. Receiver operator characteristic curve analysis revealed that miR-1975 levels in combination with days of fever before presenting to hospital had significant predictive value for hypoxemia and respiratory failure for patients infected with influenza virus. Our results reveal that circulating miR-1975 has great potential to serve as a biomarker for predicting prognosis in patients infected with influenza virus.
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14
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Bao S, Zheng Z, Aweya JJ, Yao D, Li S, Sun C, Hong Y, Zhang Y. microRNA-589-5p modulates the expression of hemocyanin as part of the anti-WSSV immune response in Litopenaeus vannamei. DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2020; 107:103642. [PMID: 32061940 DOI: 10.1016/j.dci.2020.103642] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/12/2020] [Revised: 02/09/2020] [Accepted: 02/10/2020] [Indexed: 06/10/2023]
Abstract
The respiratory glycoprotein, hemocyanin (HMC) has multiple immune-related functions, including antiviral activity. In this study, in silico methods were used to predict seven miRNAs targeting Litopenaeus vannamei HMC (LvHMC), out of which miR-589-5p was selected for further investigation because of its role in immune response. Transcript levels of miR-589-5p were ubiquitously distributed in all shrimp tissues examined, and significantly induced in hemocytes and hepatopancreas upon challenge with white-spot syndrome virus (WSSV) as well as by marine bacterial pathogens, which suggest that miR-589-5p is involved in shrimp immune response to pathogens. Morever, using Drosophila S2 cells stably overexpressing EGFP-LvHMC, flow cytometry and dual luciferase reporter assays, miR-589-5p was shown to significantly inhibit the in vitro expression of LvHMC. In addition, in vivo knockdown of miR-589-5p using antagomir-589-5p resulted in significant down-regulation in LvHMC expression, while overexpression of miR-589-5p using agomir-589-5p decreased the level of LvHMC expression in shrimp hemocytes and hepatopancreas. Further, the increased expression of miR-589-5p resulted in high shrimp mortality following WSSV challenge, coupled with an increase in the number of WSSV copies in hemocytes and hepatopancreas. These results suggest that miR-589-5p is involved in shrimp immune response to WSSV by negatively regulating the expression of LvHMC.
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Affiliation(s)
- Shiyuan Bao
- Institute of Marine Sciences and Guangdong Provincial Key Laboratory of Marine Biotechnology, Shantou University, Shantou, 515063, China; STU-UMT Joint Shellfish Research Laboratory, Shantou University, Shantou, 515063, China
| | - Zhihong Zheng
- Institute of Marine Sciences and Guangdong Provincial Key Laboratory of Marine Biotechnology, Shantou University, Shantou, 515063, China; STU-UMT Joint Shellfish Research Laboratory, Shantou University, Shantou, 515063, China
| | - Jude Juventus Aweya
- Institute of Marine Sciences and Guangdong Provincial Key Laboratory of Marine Biotechnology, Shantou University, Shantou, 515063, China; STU-UMT Joint Shellfish Research Laboratory, Shantou University, Shantou, 515063, China
| | - Defu Yao
- Institute of Marine Sciences and Guangdong Provincial Key Laboratory of Marine Biotechnology, Shantou University, Shantou, 515063, China; STU-UMT Joint Shellfish Research Laboratory, Shantou University, Shantou, 515063, China
| | - Shengkang Li
- Institute of Marine Sciences and Guangdong Provincial Key Laboratory of Marine Biotechnology, Shantou University, Shantou, 515063, China; STU-UMT Joint Shellfish Research Laboratory, Shantou University, Shantou, 515063, China
| | - Caihui Sun
- Guangdong Yuequn Marine Biological Research and Development Co., Ltd., Jieyang, 515200, China
| | - Yujian Hong
- Guangdong Yuequn Marine Biological Research and Development Co., Ltd., Jieyang, 515200, China
| | - Yueling Zhang
- Institute of Marine Sciences and Guangdong Provincial Key Laboratory of Marine Biotechnology, Shantou University, Shantou, 515063, China; STU-UMT Joint Shellfish Research Laboratory, Shantou University, Shantou, 515063, China.
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15
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Yoshikawa Y, Sugimoto K, Ochiai Y, Ohashi N. Intracellular proliferation of Anaplasma phagocytophilum is promoted via modulation of endoplasmic reticulum stress signaling in host cells. Microbiol Immunol 2020; 64:270-279. [PMID: 31909489 DOI: 10.1111/1348-0421.12770] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2019] [Revised: 12/17/2019] [Accepted: 01/05/2020] [Indexed: 02/06/2023]
Abstract
Anaplasma phagocytophilum, an obligate intracellular bacterium that propagates within host granulocytes, is considered to modify the host intracellular environment for pathogenesis. However, the mechanism(s) underlying such host modifications remain unclear. Here, we aimed to investigate the relation between A. phagocytophilum and endoplasmic reticulum (ER) stress in THP-1 cells. A. phagocytophilum activated the three ER stress sensors: inositol-requiring enzyme-1 (IRE1), protein kinase RNA-like endoplasmic reticulum kinase (PERK), and activating transcription factor-6 (ATF6). IRE1 activation occurred immediately after host cell invasion by A. phagocytophilum; however, the activated IRE1-induced splicing of X-box-binding protein 1 was not promoted during A. phagocytophilum infection. This suppression was sustained even after the doxycycline-mediated elimination of intracellular A. phagocytophilum. IRE1 knockdown accelerated A. phagocytophilum-induced apoptosis and decreased intracellular A. phagocytophilum. These data suggest that A. phagocytophilum utilizes IRE1 activation to promote its own intracellular proliferation. Moreover, PERK and ATF6 partially mediated A. phagocytophilum-induced apoptosis by promoting the expression of CCAAT/enhancer-binding protein homologous protein, which induces the transcription of several proapoptotic genes. Thus, A. phagocytophilum possibly manipulates the host ER stress signals to facilitate intracellular proliferation and infection of surrounding cells before/after host cell apoptosis.
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Affiliation(s)
- Yuko Yoshikawa
- Laboratory of Microbiology, Department of Food and Nutritional Sciences, Graduate School of Integrated Pharmaceutical and Nutritional Sciences, University of Shizuoka, Shizuoka, Japan.,Laboratory of Veterinary Public Health, School of Veterinary Medicine, Faculty of Veterinary Science, Nippon Veterinary and Life Science University, Tokyo, Japan
| | - Kei Sugimoto
- Laboratory of Microbiology, Department of Food and Nutritional Sciences, Graduate School of Integrated Pharmaceutical and Nutritional Sciences, University of Shizuoka, Shizuoka, Japan
| | - Yoshitsugu Ochiai
- Laboratory of Veterinary Public Health, School of Veterinary Medicine, Faculty of Veterinary Science, Nippon Veterinary and Life Science University, Tokyo, Japan
| | - Norio Ohashi
- Laboratory of Microbiology, Department of Food and Nutritional Sciences, Graduate School of Integrated Pharmaceutical and Nutritional Sciences, University of Shizuoka, Shizuoka, Japan
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16
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Samir M, Vidal RO, Abdallah F, Capece V, Seehusen F, Geffers R, Hussein A, Ali AAH, Bonn S, Pessler F. Organ-specific small non-coding RNA responses in domestic (Sudani) ducks experimentally infected with highly pathogenic avian influenza virus (H5N1). RNA Biol 2019; 17:112-124. [PMID: 31538530 DOI: 10.1080/15476286.2019.1669879] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
The duck represents an important reservoir of influenza viruses for transmission to other avian and mammalian hosts, including humans. The increased pathogenicity of the recently emerging clades of highly pathogenic avian influenza (HPAI) viruses of the H5N1 subtype in ducks features systemic viral spread and organ-to-organ variation in viral transcription and tissue damage. We previously reported that experimental infection of Sudani ducks (Cairina moschata) with an Egyptian HPAI (H5N1) virus (clade 2.2.1.2) features high viral replication and severe tissue damage in lung, but lower viral replication and only mild histological changes in brain. Little is known about the involvement of miRNA in organ-specific responses to H5N1 viruses in ducks, and involvement of the other classes of small noncoding RNA (sncRNA) has not been investigated so far. Following RNA sequencing, we have annotated the duck sncRNome and compared global expression changes of the four major sncRNA classes (miRNAs, piRNAs, snoRNAs, snRNAs) between duck lung and brain during a 120 h time course of infection with this HPAI strain. We find major organ-specific differences in miRNA, piRNA and snoRNA populations even before infection and substantial reprogramming of all sncRNA classes throughout infection, which was less pronounced in brain. Pathway prediction analysis of miRNA targets revealed enrichment of inflammation-, infection- and apoptosis-related pathways in lung, but enrichment of metabolism-related pathways (including tryptophan metabolism) in brain. Thus, organ-specific differences in sncRNA responses may contribute to differences in viral replication and organ damage in ducks infected with isolates from this emerging HPAI clade, and likely other strains.
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Affiliation(s)
- Mohamed Samir
- Department of Zoonoses, Faculty of Veterinary Medicine, Zagazig University, Zagazig, Egypt.,Research Group Biomarkers for Infectious Diseases, TWINCORE, Centre for Experimental and Clinical Infection Research, Hannover, Germany
| | - Ramon O Vidal
- Group of Computational Systems Biology, German Center for Neurodegenerative Diseases, Goettingen, Germany.,Department of Genomics, Max-Delbrück-Centrum für Molekulare Medizin (MDC), Berlin, Germany
| | - Fatma Abdallah
- Department of Virology, Faculty of Veterinary Medicine, Zagazig University, Zagazig, Egypt
| | - Vincenzo Capece
- Group of Computational Systems Biology, German Center for Neurodegenerative Diseases, Goettingen, Germany.,ID Research IT Platforms, Swiss Federal Institute of Technology (ETH), Zurich, Switzerland
| | - Frauke Seehusen
- Department of Pathology, University of Veterinary Medicine (TiHo), Hannover, Germany
| | - Robert Geffers
- Genome Analytics, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Ashraf Hussein
- Department of Avian and Rabbit Medicine, Faculty of Veterinary Medicine, Zagazig University, Zagazig, Egypt
| | - Ahmed A H Ali
- Department of Virology, Faculty of Veterinary Medicine, Zagazig University, Zagazig, Egypt
| | - Stefan Bonn
- Group of Computational Systems Biology, German Center for Neurodegenerative Diseases, Goettingen, Germany.,Institute of Medical Systems Biology, Center for Molecular Neurobiology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany.,German Center for Neurodegenerative Diseases, Tuebingen, Germany
| | - Frank Pessler
- Research Group Biomarkers for Infectious Diseases, TWINCORE, Centre for Experimental and Clinical Infection Research, Hannover, Germany.,Research Group Biomarkers for Infectious Diseases, Helmholtz Centre for Infection Research, Braunschweig, Germany.,Centre for Individualized Infection Medicine, Hannover, Germany
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17
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Exosome-delivered and Y RNA-derived small RNA suppresses influenza virus replication. J Biomed Sci 2019; 26:58. [PMID: 31416454 PMCID: PMC6694579 DOI: 10.1186/s12929-019-0553-6] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2019] [Accepted: 08/08/2019] [Indexed: 12/18/2022] Open
Abstract
Background Multiple interplays between viral and host factors are involved in influenza virus replication and pathogenesis. Several small RNAs have recently emerged as important regulators of host response to viral infections. The aim of this study was to characterize the functional role of hsa-miR-1975, a Y5 RNA-derived small RNA, in defending influenza virus and delineate the mechanisms. Methods We performed high throughput sequencing of small RNAs in influenza virus-infected cells to identify up- or down- regulated small RNA species. The expression of the most abundant RNA species (hsa-miR-1975) was validated by stem-loop reverse transcription-polymerase chain reaction (RT-PCR). Antiviral effects of hsa-miR-1975 were confirmed by Western Blot, RT-PCR and plaque assay. In vitro perturbation of hsa-miR-1975 combined with exosomes isolation was used to elucidate the role and mechanism of hsa-miR-1975 in the context of antiviral immunity. Results Small RNA sequencing revealed that hsa-miR-1975 was the most up-regulated small RNA in influenza virus-infected cells. The amount of intracellular hsa-miR-1975 increased in the late stage of the influenza virus replication cycle. The increased hsa-miR-1975 was at least partially derived from degradation of Y5RNA as a result of cellular apoptosis. Unexpectedly, hsa-miR-1975 mimics inhibited influenza virus replication while hsa-miR-1975 sponges enhanced the virus replication. Moreover, hsa-miR-1975 was secreted in exosomes and taken up by the neighboring cells to induce interferon expression. Conclusions Our findings unravel a critical role of Y-class small RNA in host’s defense against influenza virus infection and reveal its antiviral mechanism through exosome delivery. This may provide a new candidate for targeting influenza virus. Electronic supplementary material The online version of this article (10.1186/s12929-019-0553-6) contains supplementary material, which is available to authorized users.
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18
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Jumeaux C, Kim E, Howes PD, Kim H, Chandrawati R, Stevens MM. Detection of microRNA biomarkers via inhibition of DNA-mediated liposome fusion. NANOSCALE ADVANCES 2019; 1:532-536. [PMID: 36132259 PMCID: PMC9473185 DOI: 10.1039/c8na00331a] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/08/2018] [Accepted: 11/14/2018] [Indexed: 06/01/2023]
Abstract
We report the specific and sensitive detection of microRNA using an inverse DNA-mediated liposome fusion assay. This assay is homogeneous, and does not require washing, separation, or enzyme-associated amplification steps. By fine-tuning the surface functionalisation of the liposomes, liposome concentration, and assay temperature, we demonstrated a sub-nanomolar limit of detection for the target.
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Affiliation(s)
- Coline Jumeaux
- Department of Materials, Department of Bioengineering, Institute of Biomedical Engineering, Imperial College London London SW7 2AZ UK
| | - Eunjung Kim
- Department of Materials, Department of Bioengineering, Institute of Biomedical Engineering, Imperial College London London SW7 2AZ UK
| | - Philip D Howes
- Department of Materials, Department of Bioengineering, Institute of Biomedical Engineering, Imperial College London London SW7 2AZ UK
| | - Hyemin Kim
- Department of Materials, Department of Bioengineering, Institute of Biomedical Engineering, Imperial College London London SW7 2AZ UK
| | - Rona Chandrawati
- Department of Materials, Department of Bioengineering, Institute of Biomedical Engineering, Imperial College London London SW7 2AZ UK
| | - Molly M Stevens
- Department of Materials, Department of Bioengineering, Institute of Biomedical Engineering, Imperial College London London SW7 2AZ UK
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19
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Poore GD, Ko ER, Valente A, Henao R, Sumner K, Hong C, Burke TW, Nichols M, McClain MT, Huang ES, Ginsburg GS, Woods CW, Tsalik EL. A miRNA Host Response Signature Accurately Discriminates Acute Respiratory Infection Etiologies. Front Microbiol 2018; 9:2957. [PMID: 30619110 PMCID: PMC6298190 DOI: 10.3389/fmicb.2018.02957] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2018] [Accepted: 11/16/2018] [Indexed: 12/22/2022] Open
Abstract
Background: Acute respiratory infections (ARIs) are the leading indication for antibacterial prescriptions despite a viral etiology in the majority of cases. The lack of available diagnostics to discriminate viral and bacterial etiologies contributes to this discordance. Recent efforts have focused on the host response as a source for novel diagnostic targets although none have explored the ability of host-derived microRNAs (miRNA) to discriminate between these etiologies. Methods: In this study, we compared host-derived miRNAs and mRNAs from human H3N2 influenza challenge subjects to those from patients with Streptococcus pneumoniae pneumonia. Sparse logistic regression models were used to generate miRNA signatures diagnostic of ARI etiologies. Generalized linear modeling of mRNAs to identify differentially expressed (DE) genes allowed analysis of potential miRNA:mRNA relationships. High likelihood miRNA:mRNA interactions were examined using binding target prediction and negative correlation to further explore potential changes in pathway regulation in response to infection. Results: The resultant miRNA signatures were highly accurate in discriminating ARI etiologies. Mean accuracy was 100% [88.8-100; 95% Confidence Interval (CI)] in discriminating the healthy state from S. pneumoniae pneumonia and 91.3% (72.0-98.9; 95% CI) in discriminating S. pneumoniae pneumonia from influenza infection. Subsequent differential mRNA gene expression analysis revealed alterations in regulatory networks consistent with known biology including immune cell activation and host response to viral infection. Negative correlation network analysis of miRNA:mRNA interactions revealed connections to pathways with known immunobiology such as interferon regulation and MAP kinase signaling. Conclusion: We have developed novel human host-response miRNA signatures for bacterial and viral ARI etiologies. miRNA host response signatures reveal accurate discrimination between S. pneumoniae pneumonia and influenza etiologies for ARI and integrated analyses of the host-pathogen interface are consistent with expected biology. These results highlight the differential miRNA host response to bacterial and viral etiologies of ARI, offering new opportunities to distinguish these entities.
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Affiliation(s)
- Gregory D. Poore
- Department of Biomedical Engineering, Duke University, Durham, NC, United States
- Center for Applied Genomics and Precision Medicine, Duke University School of Medicine, Durham, NC, United States
| | - Emily R. Ko
- Center for Applied Genomics and Precision Medicine, Duke University School of Medicine, Durham, NC, United States
- Department of Hospital Medicine, Duke Regional Hospital, Durham, NC, United States
| | - Ashlee Valente
- Center for Applied Genomics and Precision Medicine, Duke University School of Medicine, Durham, NC, United States
| | - Ricardo Henao
- Center for Applied Genomics and Precision Medicine, Duke University School of Medicine, Durham, NC, United States
| | - Kelsey Sumner
- Center for Applied Genomics and Precision Medicine, Duke University School of Medicine, Durham, NC, United States
| | - Christopher Hong
- Center for Applied Genomics and Precision Medicine, Duke University School of Medicine, Durham, NC, United States
| | - Thomas W. Burke
- Center for Applied Genomics and Precision Medicine, Duke University School of Medicine, Durham, NC, United States
| | - Marshall Nichols
- Center for Applied Genomics and Precision Medicine, Duke University School of Medicine, Durham, NC, United States
| | - Micah T. McClain
- Center for Applied Genomics and Precision Medicine, Duke University School of Medicine, Durham, NC, United States
- Division of Infectious Diseases, Duke University School of Medicine, Durham, NC, United States
- Medicine Service, Durham VA Medical Center, Durham, NC, United States
| | - Erich S. Huang
- Department of Biostatistics and Bioinformatics, Duke University School of Medicine, Durham, NC, United States
- Duke Clinical and Translational Science Institute, Durham, NC, United States
| | - Geoffrey S. Ginsburg
- Department of Biomedical Engineering, Duke University, Durham, NC, United States
- Center for Applied Genomics and Precision Medicine, Duke University School of Medicine, Durham, NC, United States
| | - Christopher W. Woods
- Center for Applied Genomics and Precision Medicine, Duke University School of Medicine, Durham, NC, United States
- Division of Infectious Diseases, Duke University School of Medicine, Durham, NC, United States
- Medicine Service, Durham VA Medical Center, Durham, NC, United States
| | - Ephraim L. Tsalik
- Center for Applied Genomics and Precision Medicine, Duke University School of Medicine, Durham, NC, United States
- Division of Infectious Diseases, Duke University School of Medicine, Durham, NC, United States
- Emergency Medicine Service, Durham VA Health Care System, Durham, NC, United States
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20
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Starbæk SMR, Brogaard L, Dawson HD, Smith AD, Heegaard PMH, Larsen LE, Jungersen G, Skovgaard K. Animal Models for Influenza A Virus Infection Incorporating the Involvement of Innate Host Defenses: Enhanced Translational Value of the Porcine Model. ILAR J 2018; 59:323-337. [DOI: 10.1093/ilar/ily009] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2017] [Revised: 06/19/2018] [Indexed: 12/20/2022] Open
Abstract
Abstract
Influenza is a viral respiratory disease having a major impact on public health. Influenza A virus (IAV) usually causes mild transitory disease in humans. However, in specific groups of individuals such as severely obese, the elderly, and individuals with underlying inflammatory conditions, IAV can cause severe illness or death. In this review, relevant small and large animal models for human IAV infection, including the pig, ferret, and mouse, are discussed. The focus is on the pig as a large animal model for human IAV infection as well as on the associated innate immune response. Pigs are natural hosts for the same IAV subtypes as humans, they develop clinical disease mirroring human symptoms, they have similar lung anatomy, and their respiratory physiology and immune responses to IAV infection are remarkably similar to what is observed in humans. The pig model shows high face and target validity for human IAV infection, making it suitable for modeling many aspects of influenza, including increased risk of severe disease and impaired vaccine response due to underlying pathologies such as low-grade inflammation. Comparative analysis of proteins involved in viral pattern recognition, interferon responses, and regulation of interferon-stimulated genes reveals a significantly higher degree of similarity between pig, ferret, and human compared with mice. It is concluded that the pig is a promising animal model displaying substantial human translational value with the ability to provide essential insights into IAV infection, pathogenesis, and immunity.
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Affiliation(s)
- Sofie M R Starbæk
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Louise Brogaard
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Harry D Dawson
- Beltsville Human Nutrition Research Center, Agricultural Research Service, United States Department of Agriculture, Beltsville, Maryland
| | - Allen D Smith
- Beltsville Human Nutrition Research Center, Agricultural Research Service, United States Department of Agriculture, Beltsville, Maryland
| | - Peter M H Heegaard
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Lars E Larsen
- National Veterinary Institute, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Gregers Jungersen
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Kerstin Skovgaard
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Kongens Lyngby, Denmark
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21
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Wang Y, Howes PD, Kim E, Spicer CD, Thomas MR, Lin Y, Crowder SW, Pence IJ, Stevens MM. Duplex-Specific Nuclease-Amplified Detection of MicroRNA Using Compact Quantum Dot-DNA Conjugates. ACS APPLIED MATERIALS & INTERFACES 2018; 10:28290-28300. [PMID: 30113161 PMCID: PMC6141140 DOI: 10.1021/acsami.8b07250] [Citation(s) in RCA: 45] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/03/2018] [Accepted: 07/31/2018] [Indexed: 05/18/2023]
Abstract
Advances in nanotechnology have provided new opportunities for the design of next-generation nucleic acid biosensors and diagnostics. Indeed, combining advances in functional nanoparticles, DNA nanotechnology, and nuclease-enzyme-based amplification can give rise to new assays with advantageous properties. In this work, we developed a microRNA (miRNA) assay using bright fluorescent quantum dots (QDs), simple DNA probes, and the enzyme duplex-specific nuclease. We employed an isothermal target-recycling mechanism, where a single miRNA target triggers the cleavage of many DNA signal probes. The incorporation of DNA-functionalized QDs enabled a quantitative fluorescent readout, mediated by Förster resonance energy transfer (FRET)-based interaction with the DNA signal probes. Our approach splits the reaction in two, performing the enzyme-mediated amplification and QD-based detection steps separately such that each reaction could be optimized for performance of the active components. Target recycling gave ca. 3 orders of magnitude amplification, yielding highly sensitive detection with a limit of 42 fM (or 1.2 amol) of miR-148, with excellent selectivity versus mismatched sequences and other miRNAs. Furthermore, we used an alternative target (miR-21) and FRET pair for direct and absolute quantification of miR-21 in RNA extracts from human cancer and normal cell lines.
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22
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Salazar C, Marshall SH. Involvement of selected cellular miRNAs in the in vitro and in vivo infection of infectious salmon anemia virus (ISAV). Microb Pathog 2018; 123:353-360. [PMID: 30041004 DOI: 10.1016/j.micpath.2018.07.023] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2018] [Revised: 07/19/2018] [Accepted: 07/20/2018] [Indexed: 12/16/2022]
Abstract
Infectious salmon anemia virus (ISAV) is the causative agent of infectious salmon anemia (ISA), a relatively novel disease primarily affecting farmed salmon species, primarily in Salmo salar specimens, causing severe outbreaks in most producer countries. Although ISAV has been extensively studied at the molecular level, not much is known about the host/cell interaction at the small RNA level. MicroRNAs (miRNAs) are small, non-coding RNA that regulate mRNA expression at the post-transcriptional level. In recent years, the putative role of these molecules in host-pathogen interactions has drawn particular attention because of their pivotal involvement as regulatory elements in a number of eukaryotic organisms. Given the importance of the salmon industry in Chile, a deep understanding of the interaction between ISAV and its hosts is of importance. In the present work, we studied the kinetic expression of selected miRNAs during ISAV infection, both in vitro and in vivo. Based on initial experimental data derived from a small RNA-Seq analysis, a group of miRNAs that were differentially expressed in infected cells were selected for analysis. As a result, two miRNAs, miR-462a-5p and miR-125 b-5p, showed increased and decreased expression, respectively, during ISAV infection.
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Affiliation(s)
- Carolina Salazar
- Laboratorio de Genética e Inmunología Molecular, Instituto de Biología, Facultad de Ciencias, Pontificia Universidad Católica de Valparaíso, Valparaíso, Chile
| | - Sergio H Marshall
- Laboratorio de Genética e Inmunología Molecular, Instituto de Biología, Facultad de Ciencias, Pontificia Universidad Católica de Valparaíso, Valparaíso, Chile.
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23
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Nguyen TH, Liu X, Su ZZ, Hsu ACY, Foster PS, Yang M. Potential Role of MicroRNAs in the Regulation of Antiviral Responses to Influenza Infection. Front Immunol 2018; 9:1541. [PMID: 30022983 PMCID: PMC6039551 DOI: 10.3389/fimmu.2018.01541] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2018] [Accepted: 06/21/2018] [Indexed: 12/21/2022] Open
Abstract
Influenza is a major health burden worldwide and is caused by influenza viruses that are enveloped and negative stranded RNA viruses. Little progress has been achieved in targeted intervention, either at a population level or at an individual level (to treat the cause), due to the toxicity of drugs and ineffective vaccines against influenza viruses. MicroRNAs (miRNAs) are small non-coding RNAs that play critical roles in gene expression, cell differentiation, and tissue development and have been shown to silence viral replication in a sequence-specific manner. Investigation of these small endogenous nucleotides may lead to new therapeutics against influenza virus infection. Here, we describe our current understanding of the role of miRNAs in host defense response against influenza virus, as well as their potential and limitation as new therapeutic approaches.
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Affiliation(s)
- Thi Hiep Nguyen
- Priority Research Centre for Healthy Lungs, The University of Newcastle, Callaghan, NSW, Australia.,Faculty of Health and Medicine, School of Biomedical Sciences and Pharmacy, The University of Newcastle, Callaghan, NSW, Australia
| | - Xiaoming Liu
- Priority Research Centre for Healthy Lungs, The University of Newcastle, Callaghan, NSW, Australia.,Faculty of Health and Medicine, School of Biomedical Sciences and Pharmacy, The University of Newcastle, Callaghan, NSW, Australia
| | - Zhen Zhong Su
- Department of Respiratory Medicine, The Second Hospital, Jilin University, ChangChun, China
| | - Alan Chen-Yu Hsu
- Priority Research Centre for Healthy Lungs, The University of Newcastle, Callaghan, NSW, Australia.,Faculty of Health and Medicine, School of Medicine and Public Health, The University of Newcastle, Callaghan, NSW, Australia
| | - Paul S Foster
- Priority Research Centre for Healthy Lungs, The University of Newcastle, Callaghan, NSW, Australia.,Faculty of Health and Medicine, School of Biomedical Sciences and Pharmacy, The University of Newcastle, Callaghan, NSW, Australia
| | - Ming Yang
- Priority Research Centre for Healthy Lungs, The University of Newcastle, Callaghan, NSW, Australia.,Faculty of Health and Medicine, School of Biomedical Sciences and Pharmacy, The University of Newcastle, Callaghan, NSW, Australia
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24
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Keshavarz M, Dianat-Moghadam H, Sofiani VH, Karimzadeh M, Zargar M, Moghoofei M, Biglari H, Ghorbani S, Nahand JS, Mirzaei H. miRNA-based strategy for modulation of influenza A virus infection. Epigenomics 2018; 10:829-844. [DOI: 10.2217/epi-2017-0170] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
Influenza A virus is known worldwide as a threat associated with human and livestock diseases. Hence, identification of physiological and molecular aspects of influenza A could contribute to better design of therapeutic approaches for reducing adverse effects associated with disease caused by this virus. miRNAs are epigenetic regulators playing important roles in many pathological processes that help in progression of influenza A. Besides miRNAs, exosomes have ememrged as other effective players in influenza A pathogenesis. Exosomes exert their effects via targeting their cargos (e.g., DNAs, mRNA, miRNAs and proteins) to recipient cells. Here, we summarized various roles of miRNAs and exosomes in influenza A pathogenesis. Moreover, we highlighted therapeutic applications of miRNAs and exosomes in influenza.
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Affiliation(s)
- Mohsen Keshavarz
- Department of Virology, Faculty of Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Hassan Dianat-Moghadam
- Department of Medical Biotechnology, Faculty of Advanced Medicine Sciences, Tabriz University of Medical Science, Tabriz, Iran
| | | | - Mohammad Karimzadeh
- Department of Virology, Faculty of Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Mohsen Zargar
- Department of Microbiology, Faculty of Science, Qom Branch, Islamic Azad University, Qom, Iran
| | - Mohsen Moghoofei
- Department of Microbiology, Faculty of Medicine, Kermanshah University of Medical Sciences, Kermanshah, Iran
| | - Hamed Biglari
- Department of Environmental Health Engineering, School of Public Health, Gonabad University of Medical Sciences, Gonabad, Iran
| | - Saied Ghorbani
- Department of Virology, Faculty of Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Javid Sadri Nahand
- Department of Virology, Faculty of Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Hamed Mirzaei
- Department of Biomaterials, Tissue Engineering & Nanotechnology, School of Advanced Technologies in Medicine, Isfahan University of Medical Sciences, Isfahan, Iran
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25
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Zhang S, Li J, Li J, Yang Y, Kang X, Li Y, Wu X, Zhu Q, Zhou Y, Hu Y. Up-regulation of microRNA-203 in influenza A virus infection inhibits viral replication by targeting DR1. Sci Rep 2018; 8:6797. [PMID: 29717211 PMCID: PMC5931597 DOI: 10.1038/s41598-018-25073-9] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2017] [Accepted: 04/13/2018] [Indexed: 12/11/2022] Open
Abstract
MicroRNAs (miRNAs) are small noncoding RNA molecules that play important roles in various biological processes. Much evidence shows that miRNAs are closely associated with numerous virus infections; however, involvement of cellular miRNAs in influenza A virus (IAV) infection is unclear. Here, we found that expression of miR-203 was up-regulated markedly via two different mechanisms during IAV infection. First, we examined the effects of type I interferon induced by IAV on direct activation of miR-203 expression. Next, we showed that DNA demethylation within the miR-203 promoter region in A549 cells induced its up-regulation, and that expression of DNA methyltransferase 1 was down-regulated following H5N1 virus infection. Ectopic expression of miR-203 in turn inhibited H5N1 virus replication by targeting down-regulator of transcription 1 (DR1), which was identified as a novel target of miR-203. Silencing DR1 in miR-203 knockout cells using a specific siRNA inhibited replication of the H5N1 virus, an effect similar to that of miR-203. In summary, the data show that host cell expression of miR-203 is up-regulated upon IAV infection, which increases antiviral responses by suppressing a novel target gene, DR1. Thus, we have identified a novel mechanism underlying the relationship between miR-203 and IAV infection.
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Affiliation(s)
- Sen Zhang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, 100071, People's Republic of China
| | - Jing Li
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, 100071, People's Republic of China
| | - Junfeng Li
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, 100071, People's Republic of China
| | - Yinhui Yang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, 100071, People's Republic of China
| | - Xiaoping Kang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, 100071, People's Republic of China
| | - Yuchang Li
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, 100071, People's Republic of China
| | - Xiaoyan Wu
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, 100071, People's Republic of China
| | - Qingyu Zhu
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, 100071, People's Republic of China
| | - Yusen Zhou
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, 100071, People's Republic of China.
| | - Yi Hu
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, 100071, People's Republic of China.
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26
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Jumeaux C, Wahlsten O, Block S, Kim E, Chandrawati R, Howes PD, Höök F, Stevens MM. MicroRNA Detection by DNA-Mediated Liposome Fusion. Chembiochem 2018; 19:434-438. [PMID: 29333674 PMCID: PMC5861668 DOI: 10.1002/cbic.201700592] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2017] [Indexed: 12/17/2022]
Abstract
Membrane fusion is a process of fundamental importance in biological systems that involves highly selective recognition mechanisms for the trafficking of molecular and ionic cargos. Mimicking natural membrane fusion mechanisms for the purpose of biosensor development holds great potential for amplified detection because relatively few highly discriminating targets lead to fusion and an accompanied engagement of a large payload of signal-generating molecules. In this work, sequence-specific DNA-mediated liposome fusion is used for the highly selective detection of microRNA. The detection of miR-29a, a known flu biomarker, is demonstrated down to 18 nm within 30 min with high specificity by using a standard laboratory microplate reader. Furthermore, one order of magnitude improvement in the limit of detection is demonstrated by using a novel imaging technique combined with an intensity fluctuation analysis, which is coined two-color fluorescence correlation microscopy.
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Affiliation(s)
- Coline Jumeaux
- Department of MaterialsDepartment of Bioengineering, and Institute of Biomedical EngineeringImperial College LondonExhibition RoadLondonSW7 2AZUK
| | - Olov Wahlsten
- Department of PhysicsChalmers University of Technology41296GöteborgSweden
| | - Stephan Block
- Department of PhysicsChalmers University of Technology41296GöteborgSweden
- Present address: Department of Chemistry and BiochemistryFreie Universität Berlin14195BerlinGermany
| | - Eunjung Kim
- Department of MaterialsDepartment of Bioengineering, and Institute of Biomedical EngineeringImperial College LondonExhibition RoadLondonSW7 2AZUK
| | - Rona Chandrawati
- Department of MaterialsDepartment of Bioengineering, and Institute of Biomedical EngineeringImperial College LondonExhibition RoadLondonSW7 2AZUK
- Present address: School of Chemical and Biomolecular EngineeringThe University of SydneySydneyNSW2006Australia
| | - Philip D. Howes
- Department of MaterialsDepartment of Bioengineering, and Institute of Biomedical EngineeringImperial College LondonExhibition RoadLondonSW7 2AZUK
| | - Fredrik Höök
- Department of PhysicsChalmers University of Technology41296GöteborgSweden
| | - Molly M. Stevens
- Department of MaterialsDepartment of Bioengineering, and Institute of Biomedical EngineeringImperial College LondonExhibition RoadLondonSW7 2AZUK
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27
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Chen BB, Li ZH, Gao S. Circulating miR-146a/b correlates with inflammatory cytokines in COPD and could predict the risk of acute exacerbation COPD. Medicine (Baltimore) 2018; 97:e9820. [PMID: 29443743 PMCID: PMC5839872 DOI: 10.1097/md.0000000000009820] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
The aim of this study was to investigate the predicting value of miR-146a/b for acute exacerbation chronic obstructive pulmonary disease (AECOPD) and COPD, and to explore their associations with inflammatory cytokines in AECOPD and stable COPD patients.One hundred six AECOPD, 122 stable COPD patients, and 110 health volunteers with age and sex matched to total COPD patients (AECOPD and stable COPD) were enrolled. Blood samples were collected from all participants. Relative expression of miR-146a/b was determined by real-time polymerase chain reaction. Tumor necrosis factor-α (TNF-α), interleukin-1β (IL-1β), interleukin-6 (IL-6), interleukin-8 (IL-8), leukotriene B4 (LTB-4) expression in serum from AECOPD and stable COPD patients were assessed using commercial ELISA kit.Serum levels of miR-146a and miR-146b were down regulated in AECOPD patients compared with stable COPD patients and HCs. miR-146a and miR-146b are of good values for predicting the risk of AECOPD in HCs with AUC of 0.702 and 0.715. Additionally, miR-146a and miR-146b could distinguish AECOPD from stable COPD patients with AUC of 0.670 and 0.643. In AECOPD patients, levels of miR-146a in AECOPD patients were negatively associated with TNF-α, IL-6, IL-8, and LTE-4 expression. In stable COPD patients, miR-146a expressions were negatively correlated with TNF-α, IL-1β, IL-6, IL-8, and LTE-4 levels. And, the expressions of miR-146b in AECOPD patients were negatively associated with IL-1β and LTB-4 expression. While in stable COPD patients, miR-146b expressions were only negatively correlated with TNF-α level.In conclusion, miR-146a and miR-146b were negatively correlated with inflammatory cytokines, and could be promising biomarkers for predicting the risk of AECOPD in stable COPD patients and healthy individuals.
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28
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Zhou P, Tu L, Lin X, Hao X, Zheng Q, Zeng W, Zhang X, Zheng Y, Wang L, Li S. cfa-miR-143 Promotes Apoptosis via the p53 Pathway in Canine Influenza Virus H3N2-Infected Cells. Viruses 2017; 9:v9120360. [PMID: 29186842 PMCID: PMC5744135 DOI: 10.3390/v9120360] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2017] [Revised: 11/16/2017] [Accepted: 11/21/2017] [Indexed: 12/25/2022] Open
Abstract
MicroRNAs regulate multiple aspects of the host response to viral infection. This study verified that the expression of cfa-miR-143 was upregulated in vivo and in vitro by canine influenza virus (CIV) H3N2 infection. To understand the role of cfa-miR-143 in CIV-infected cells, the target gene of cfa-miR-143 was identified and assessed for correlations with proteins involved in the apoptosis pathway. A dual luciferase reporter assay showed that cfa-miR-143 targets insulin-like growth factor binding protein 5 (Igfbp5). Furthermore, a miRNA agomir and antagomir of cfa-miR-143 caused the downregulation and upregulation of Igfbp5, respectively, in CIV-infected madin-darby canine kidney (MDCK) cells. This study demonstrated that cfa-miR-143 stimulated p53 and caspase3 activation and induced apoptosis via the p53 pathway in CIV H3N2-infected cells. In conclusion, CIV H3N2 induced the upregulation of cfa-miR-143, which contributes to apoptosis via indirectly activating the p53-caspase3 pathway.
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Affiliation(s)
- Pei Zhou
- College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China.
- Guangdong Provincial Key Laboratory of Prevention and Control for Severe Clinical Animal Diseases, Guangzhou 510642, China.
- Guangdong Provincial Pet Engineering Technology Research Center, Guangzhou 510642, China.
| | - Liqing Tu
- College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China.
- Guangdong Provincial Key Laboratory of Prevention and Control for Severe Clinical Animal Diseases, Guangzhou 510642, China.
- Guangdong Provincial Pet Engineering Technology Research Center, Guangzhou 510642, China.
| | - Xi Lin
- College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China.
- Guangdong Provincial Key Laboratory of Prevention and Control for Severe Clinical Animal Diseases, Guangzhou 510642, China.
- Guangdong Provincial Pet Engineering Technology Research Center, Guangzhou 510642, China.
| | - Xiangqi Hao
- College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China.
- Guangdong Provincial Key Laboratory of Prevention and Control for Severe Clinical Animal Diseases, Guangzhou 510642, China.
- Guangdong Provincial Pet Engineering Technology Research Center, Guangzhou 510642, China.
| | - Qingxu Zheng
- College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China.
- Guangdong Provincial Key Laboratory of Prevention and Control for Severe Clinical Animal Diseases, Guangzhou 510642, China.
- Guangdong Provincial Pet Engineering Technology Research Center, Guangzhou 510642, China.
| | - Weijie Zeng
- College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China.
- Guangdong Provincial Key Laboratory of Prevention and Control for Severe Clinical Animal Diseases, Guangzhou 510642, China.
- Guangdong Provincial Pet Engineering Technology Research Center, Guangzhou 510642, China.
| | - Xin Zhang
- College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China.
- Guangdong Provincial Key Laboratory of Prevention and Control for Severe Clinical Animal Diseases, Guangzhou 510642, China.
- Guangdong Provincial Pet Engineering Technology Research Center, Guangzhou 510642, China.
| | - Yun Zheng
- College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China.
- Guangdong Provincial Key Laboratory of Prevention and Control for Severe Clinical Animal Diseases, Guangzhou 510642, China.
- Guangdong Provincial Pet Engineering Technology Research Center, Guangzhou 510642, China.
| | - Lifang Wang
- College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China.
- Guangdong Provincial Key Laboratory of Prevention and Control for Severe Clinical Animal Diseases, Guangzhou 510642, China.
- Guangdong Provincial Pet Engineering Technology Research Center, Guangzhou 510642, China.
| | - Shoujun Li
- College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China.
- Guangdong Provincial Key Laboratory of Prevention and Control for Severe Clinical Animal Diseases, Guangzhou 510642, China.
- Guangdong Provincial Pet Engineering Technology Research Center, Guangzhou 510642, China.
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29
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Andreassen R, Woldemariam NT, Egeland IØ, Agafonov O, Sindre H, Høyheim B. Identification of differentially expressed Atlantic salmon miRNAs responding to salmonid alphavirus (SAV) infection. BMC Genomics 2017; 18:349. [PMID: 28472924 PMCID: PMC5418855 DOI: 10.1186/s12864-017-3741-3] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2016] [Accepted: 04/27/2017] [Indexed: 02/07/2023] Open
Abstract
Background MicroRNAs (miRNAs) control multiple biological processes including the innate immune responses by negative post-transcriptional regulation of gene expression. As there were no studies on the role(s) of miRNAs in viral diseases in Atlantic salmon, we aimed to identify miRNAs responding to salmonid alphavirus (SAV) infection. Their expression were studied at different time points post infection with SAV isolates associated with different mortalities. Furthermore, the genome sequences of the identified miRNAs were analysed to reveal putative cis-regulatory elements, and, finally, their putative target genes were predicted. Results Twenty differentially expressed miRNAs (DE miRNAs) were identified. The expression of the majority of these increased post infection with maximum levels reached after the viral load were stabilized or decreasing. On the other hand, some miRNAs (e.g. the miRNA-21 family) showed decreased expression at the early time points post infection. There were significant differences in the temporal expression of individual miRNA associated with different SAV isolates. Target gene prediction in SAV responsive immune network genes showed that seventeen of the DE miRNAs could target 24 genes (e.g. IRF3, IRF7). Applying the Atlantic salmon transcriptome as input 28 more immune network genes were revealed as putative targets (e.g. IRF5, IRF4). The majority of the predicted target genes promote inflammatory response. The upstream sequences of the miRNA genes revealed a high density of cis-regulatory sequences known as binding sites for immune network transcription factors (TFs). A high expression in the late phase could therefore be due to increased transcription promoted by immune response activated TFs. Based on the in silico target predictions, we discuss their putative roles as early promotors or late inhibitors of inflammation. We propose that the differences in expressions associated with different SAV isolates could contribute to their differences in mortality rates. Conclusions This study represents the first steps in exploring miRNAs important in viral-host interaction in Atlantic salmon. We identified several miRNAs responding to SAV infection. Some likely to prohibit harmful inflammation while other may promote an early immune response. Their predicted functions need to be validated and further studied in functional assays to fully understand their roles in immune homeostasis. Electronic supplementary material The online version of this article (doi:10.1186/s12864-017-3741-3) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Rune Andreassen
- Department of Pharmacy and Biomedical and Laboratory Sciences, Faculty of Health Sciences, Oslo and Akershus University College of Applied Sciences, Pilestredet 50, N-0130, Oslo, Norway.
| | - Nardos Tesfaye Woldemariam
- Department of Pharmacy and Biomedical and Laboratory Sciences, Faculty of Health Sciences, Oslo and Akershus University College of Applied Sciences, Pilestredet 50, N-0130, Oslo, Norway
| | - Ine Østråt Egeland
- Department of Pharmacy and Biomedical and Laboratory Sciences, Faculty of Health Sciences, Oslo and Akershus University College of Applied Sciences, Pilestredet 50, N-0130, Oslo, Norway
| | - Oleg Agafonov
- Bioinformatics Core Facility, Department of Core Facilities, Institute of Cancer Research, Radium hospital, part of Oslo University Hospital, Oslo, Norway
| | - Hilde Sindre
- Norwegian Veterinary Institute, PB 750 Sentrum, N-106, Oslo, Norway
| | - Bjørn Høyheim
- Department of Basic Sciences and Aquatic Medicine, School of Veterinary Medicine, Norwegian University of Life Sciences, Ullevålsveien 72, 0454, Oslo, Norway
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30
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Preusse M, Schughart K, Pessler F. Host Genetic Background Strongly Affects Pulmonary microRNA Expression before and during Influenza A Virus Infection. Front Immunol 2017; 8:246. [PMID: 28377766 PMCID: PMC5359533 DOI: 10.3389/fimmu.2017.00246] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2016] [Accepted: 02/20/2017] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND Expression of host microRNAs (miRNAs) changes markedly during influenza A virus (IAV) infection of natural and adaptive hosts, but their role in genetically determined host susceptibility to IAV infection has not been explored. We, therefore, compared pulmonary miRNA expression during IAV infection in two inbred mouse strains with differential susceptibility to IAV infection. RESULTS miRNA expression profiles were determined in lungs of the more susceptible strain DBA/2J and the less susceptible strain C57BL/6J within 120 h post infection (hpi) with IAV (H1N1) PR8. Even the miRNomes of uninfected lungs differed substantially between the two strains. After a period of relative quiescence, major miRNome reprogramming was detected in both strains by 48 hpi and increased through 120 hpi. Distinct groups of miRNAs regulated by IAV infection could be defined: (1) miRNAs (n = 39) whose expression correlated with hemagglutinin (HA) mRNA expression and represented the general response to IAV infection independent of host genetic background; (2) miRNAs (n = 20) whose expression correlated with HA mRNA expression but differed between the two strains; and (3) remarkably, miR-147-3p, miR-208b-3p, miR-3096a-5p, miR-3069b-3p, and the miR-467 family, whose abundance even in uninfected lungs differentiated nearly perfectly (area under the ROC curve > 0.99) between the two strains throughout the time course, suggesting a particularly strong association with the differential susceptibility of the two mouse strains. Expression of subsets of miRNAs correlated significantly with peripheral blood granulocyte and monocyte numbers, particularly in DBA/2J mice; miR-223-3p, miR-142-3p, and miR-20b-5p correlated most positively with these cell types in both mouse strains. Higher abundance of antiapoptotic (e.g., miR-467 family) and lower abundance of proapoptotic miRNAs (e.g., miR-34 family) and those regulating the PI3K-Akt pathway (e.g., miR-31-5p) were associated with the more susceptible DBA/2J strain. CONCLUSION Substantial differences in pulmonary miRNA expression between the two differentially susceptible mouse strains were evident even before infection, but evolved further throughout infection and could in part be attributed to differences in peripheral blood leukocyte populations. Thus, pulmonary miRNA expression both before and during IAV infection is in part determined genetically and contributes to susceptibility to IAV infection in this murine host, and likely in humans.
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Affiliation(s)
- Matthias Preusse
- Institute for Experimental Infection Research, TWINCORE Center for Experimental and Clinical Infection Research, Hannover, Germany; Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Klaus Schughart
- Department of Infection Genetics, Helmholtz Centre for Infection Research, Braunschweig, Germany; University of Veterinary Medicine Hannover, Hannover, Germany; Department of Microbiology, Immunology and Biochemistry, University of Tennessee Health Science Centre, Memphis, TN, USA
| | - Frank Pessler
- Institute for Experimental Infection Research, TWINCORE Center for Experimental and Clinical Infection Research, Hannover, Germany; Helmholtz Centre for Infection Research, Braunschweig, Germany; Centre for Individualised Infection Medicine, Hannover, Germany
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31
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Deng Y, Yan Y, Tan KS, Liu J, Chow VT, Tao ZZ, Wang DY. MicroRNA-146a induction during influenza H3N2 virus infection targets and regulates TRAF6 levels in human nasal epithelial cells (hNECs). Exp Cell Res 2017; 352:184-192. [PMID: 28131813 DOI: 10.1016/j.yexcr.2017.01.011] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2016] [Revised: 01/13/2017] [Accepted: 01/21/2017] [Indexed: 12/25/2022]
Abstract
We have previously shown that human nasal epithelial cells (hNECs) are highly permissive cells for respiratory viruses including influenza A virus (IAV) and respiratory syncytial virus. Recent studies have indicated that microRNAs (miRNAs) are involved in virus-host relationship, and this led us to investigate its essential roles in the in vitro hNECs model derived from multiple donors. By comparing the differential expression of miRNAs upon IAV infection among animal and cell line studies, candidates were selected with focus on the initial immune response. After infection of influenza H3N2 virus, hNECs showed constant increase virus titer at 24-72h post-infection (hpi); accompanied with a significantly elevated level of miR-146a-5p at 72 hpi. The exponential elevation of progeny virus titer correlated with a key influenza sensing Toll-like receptor (TLR)7 pathway. TLR7 downstream gene transcripts, myeloid differentiation primary response gene 88 (MyD88), interferon regulator factor 7 (IRF7), and interferon-β (IFN-β) were significantly upregulated at 48 and 72 hpi, while interleukin-1 receptor-associated kinase 1 (IRAK1) and TNF receptor associated factor-6 (TRAF6) were unchanged. Interestingly, when miR-146a was overexpressed with miRNA mimics prior to H3N2 infection, further decreased transcripts of TRAF6, but not IRAK1, were detected. By using the in vitro hNEC model, we demonstrated that H3N2-induced miR-146a specifically targets and regulates TRAF6 expression; but not IRAK expression in the nasal epithelium. We also found that unlike the cell model studies that lead to our studies, when ran across a heterogeneous model of different individual, miRNA signals were highly varied and the expression of most miRNAs, including miR-146a-5p, was more subdued compared to homogenous cell line model, highlighting a need for a more thorough analysis of miRNA signals and targets in a model more mimicking a clinical influenza infection.
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Affiliation(s)
- Yuqin Deng
- Department of Otolaryngology, Renmin Hospital of Wuhan University, Wuhan 430060, Hubei Province, PR China; Department of Otolaryngology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Yan Yan
- Department of Otolaryngology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Kai Sen Tan
- Department of Otolaryngology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Jing Liu
- Department of Otolaryngology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Vincent T Chow
- Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Ze-Zhang Tao
- Department of Otolaryngology, Renmin Hospital of Wuhan University, Wuhan 430060, Hubei Province, PR China.
| | - De-Yun Wang
- Department of Otolaryngology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore.
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Wang H. Anti-NMDA Receptor Encephalitis and Vaccination. Int J Mol Sci 2017; 18:ijms18010193. [PMID: 28106787 PMCID: PMC5297824 DOI: 10.3390/ijms18010193] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2016] [Revised: 01/10/2017] [Accepted: 01/13/2017] [Indexed: 12/12/2022] Open
Abstract
Anti-N-methyl-d-aspartate (Anti-NMDA) receptor encephalitis is an acute autoimmune neurological disorder. The cause of this disease is often unknown, and previous studies revealed that it might be caused by a virus, vaccine or tumor. It occurs more often in females than in males. Several cases were reported to be related to vaccination such as the H1N1 vaccine and tetanus/diphtheria/pertussis and polio vaccines. In this study, we reported an anti-NMDA receptor encephalitis case that may be caused by Japanese encephalitis vaccination. To investigate the association between anti-NMDA receptor encephalitis and vaccination, we analyzed the phylogenetic relationship of the microRNAs, which significantly regulate these vaccine viruses or bacteria, and the phylogenetic relationship of these viruses and bacteria. This reveals that anti-NMDA receptor encephalitis may be caused by Japanese encephalitis vaccination, as well as H1N1 vaccination or tetanus/diphtheria/pertussis and polio vaccinations, from the phylogenetic viewpoint.
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Affiliation(s)
- Hsiuying Wang
- Institute of Statistics, National Chiao Tung University, Hsinchu 30010, Taiwan.
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Involvement of Host Non-Coding RNAs in the Pathogenesis of the Influenza Virus. Int J Mol Sci 2016; 18:ijms18010039. [PMID: 28035991 PMCID: PMC5297674 DOI: 10.3390/ijms18010039] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2016] [Revised: 12/11/2016] [Accepted: 12/19/2016] [Indexed: 12/19/2022] Open
Abstract
Non-coding RNAs (ncRNAs) are a new type of regulators that play important roles in various cellular processes, including cell growth, differentiation, survival, and apoptosis. ncRNAs, including small non-coding RNAs (e.g., microRNAs, small interfering RNAs) and long non-coding RNAs (lncRNAs), are pervasively transcribed in human and mammalian cells. Recently, it has been recognized that these ncRNAs are critically implicated in the virus-host interaction as key regulators of transcription or post-transcription during viral infection. Influenza A virus (IAV) is still a major threat to human health. Hundreds of ncRNAs are differentially expressed in response to infection with IAV, such as infection by pandemic H1N1 and highly pathogenic avian strains. There is increasing evidence demonstrating functional involvement of these regulatory microRNAs, vault RNAs (vtRNAs) and lncRNAs in pathogenesis of influenza virus, including a variety of host immune responses. For example, it has been shown that ncRNAs regulate activation of pattern recognition receptor (PRR)-associated signaling and transcription factors (nuclear factor κ-light-chain-enhancer of activated B cells, NF-κB), as well as production of interferons (IFNs) and cytokines, and expression of critical IFN-stimulated genes (ISGs). The vital functions of IAV-regulated ncRNAs either to against defend viral invasion or to promote progeny viron production are summarized in this review. In addition, we also highlight the potentials of ncRNAs as therapeutic targets and diagnostic biomarkers.
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Tahamtan A, Inchley CS, Marzban M, Tavakoli‐Yaraki M, Teymoori‐Rad M, Nakstad B, Salimi V. The role of microRNAs in respiratory viral infection: friend or foe? Rev Med Virol 2016; 26:389-407. [PMID: 27373545 PMCID: PMC7169129 DOI: 10.1002/rmv.1894] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2016] [Revised: 06/06/2016] [Accepted: 06/08/2016] [Indexed: 12/20/2022]
Abstract
MicroRNAs (miRNAs) have emerged as a class of regulatory RNAs in host-pathogen interactions. Aberrant miRNA expression seems to play a central role in the pathology of several respiratory viruses, promoting development and progression of infection. miRNAs may thus serve as therapeutic and prognostic factors for respiratory viral infectious disease caused by a variety of agents. We present a comprehensive review of recent findings related to the role of miRNAs in different respiratory viral infections and discuss possible therapeutic opportunities aiming to attenuate the burden of viral infections. Our review supports the emerging concept that cellular and viral-encoded miRNAs might be broadly implicated in human respiratory viral infections, with either positive or negative effects on virus life cycle. Copyright © 2016 John Wiley & Sons, Ltd.
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Affiliation(s)
- Alireza Tahamtan
- Department of Virology, School of Public HealthTehran University of Medical SciencesTehranIran
| | - Christopher S. Inchley
- Department of Pediatric and Adolescent MedicineAkershus University HospitalLørenskogNorway
| | - Mona Marzban
- Department of Virology, School of Public HealthTehran University of Medical SciencesTehranIran
| | | | - Majid Teymoori‐Rad
- Department of Virology, School of Public HealthTehran University of Medical SciencesTehranIran
| | - Britt Nakstad
- Department of Pediatric and Adolescent MedicineAkershus University HospitalLørenskogNorway
- Institute of Clinical MedicineUniversity of OsloOsloNorway
| | - Vahid Salimi
- Department of Virology, School of Public HealthTehran University of Medical SciencesTehranIran
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Samir M, Vaas LAI, Pessler F. MicroRNAs in the Host Response to Viral Infections of Veterinary Importance. Front Vet Sci 2016; 3:86. [PMID: 27800484 PMCID: PMC5065965 DOI: 10.3389/fvets.2016.00086] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2016] [Accepted: 09/12/2016] [Indexed: 12/13/2022] Open
Abstract
The discovery of small regulatory non-coding RNAs has been an exciting advance in the field of genomics. MicroRNAs (miRNAs) are endogenous RNA molecules, approximately 22 nucleotides in length, that regulate gene expression, mostly at the posttranscriptional level. MiRNA profiling technologies have made it possible to identify and quantify novel miRNAs and to study their regulation and potential roles in disease pathogenesis. Although miRNAs have been extensively investigated in viral infections of humans, their implications in viral diseases affecting animals of veterinary importance are much less understood. The number of annotated miRNAs in different animal species is growing continuously, and novel roles in regulating host–pathogen interactions are being discovered, for instance, miRNA-mediated augmentation of viral transcription and replication. In this review, we present an overview of synthesis and function of miRNAs and an update on the current state of research on host-encoded miRNAs in the genesis of viral infectious diseases in their natural animal host as well as in selected in vivo and in vitro laboratory models.
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Affiliation(s)
- Mohamed Samir
- TWINCORE, Center for Experimental and Clinical Infection Research, Hannover, Germany; Department of Zoonoses, Faculty of Veterinary Medicine, Zagazig University, Zagazig, Egypt
| | - Lea A I Vaas
- TWINCORE, Center for Experimental and Clinical Infection Research , Hannover , Germany
| | - Frank Pessler
- TWINCORE, Center for Experimental and Clinical Infection Research, Hannover, Germany; Helmholtz Center for Infection Research, Braunschweig, Germany
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Down-regulation of MicroRNA-31 in CD4+ T Cells Contributes to Immunosuppression in Human Sepsis by Promoting TH2 Skewing. Anesthesiology 2016; 124:908-22. [PMID: 26978146 DOI: 10.1097/aln.0000000000001031] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
BACKGROUND Immunosuppression has been recognized as a major cause of sepsis-related mortality. Currently, there is much interest in identifying central hubs controlling septic immunoparalysis. In this context, in this study, the authors investigate the role of microRNA-31 (miR-31) as a regulator of T cell functions. METHODS Primary human T cells were separated from healthy volunteers (n = 16) and from sepsis patients by magnetic beads (n = 23). Expression of mRNA/microRNA (miRNA) was determined by real-time polymerase chain reaction. Gene silencing was performed by small interfering RNA transfection, and miRNA-binding sites were validated by reporter gene assays. Effects of miR-31 or anti-miR-31 transfection were analyzed by real-time polymerase chain reaction, Western blotting, and flow cytometry. RESULTS Overexpression of miR-31 in stimulated CD4 T cells promoted a proinflammatory phenotype with increased levels of interferon-γ (1.63 ± 0.43; P = 0.001; means ± SD) and reduced expression of interleukin (IL)-2 (0.66 ± 0.19; P = 0.005) and IL-4 (0.80 ± 0.2; P = 0.0001). In contrast, transfection of anti-miR-31 directed cells toward a TH2 phenotype. Effects on IL-2 and IL-4 were mediated by targeting of nuclear factor-kappa B-inducing kinase and factor-inhibiting hypoxia-inducible factor-1α. Interferon-γ, however, was influenced via control of signaling lymphocytic activation molecule (SLAM)-associated protein, an essential adaptor molecule of immunomodulatory SLAM receptor signaling, which was identified as a novel target gene of miR-31. In sepsis patients, an epigenetically driven down-regulation of miR-31 was found (0.44 ± 0.25; P = 0.0001), associated with increased nuclear factor-kappa B-inducing kinase, factor-inhibiting hypoxia-inducible factor-1α, SLAM-associated protein expression, and a cytokine shift toward TH2. CONCLUSIONS In this study, the authors provide novel evidence of miR-31 as an emerging key posttranscriptional regulator of sepsis-associated immunosuppression. The study results contribute to a further understanding of septic immunoparalysis and provide new perspectives on miRNA-based diagnostic approaches.
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Shu L, Li C, Zhang X. The role of shrimp miR-965 in virus infection. FISH & SHELLFISH IMMUNOLOGY 2016; 54:427-434. [PMID: 27134077 DOI: 10.1016/j.fsi.2016.04.129] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2015] [Revised: 04/25/2016] [Accepted: 04/27/2016] [Indexed: 06/05/2023]
Abstract
RNAi, mediated by microRNAs (miRNAs), has attracted increasing attention for its important role in cross-talk between host and virus. However, the role of host miRNA in the virus infection in vivo has not been intensively investigated. In this study, the effects of a shrimp miRNA (miR-965) on the white spot syndrome virus (WSSV) infection were characterized. The results indicated that the expression of miR-965 was significantly upregulated in shrimp in response to the WSSV challenge, suggesting its involvement in the virus infection. The miR-965 silencing led to significant increases of WSSV copies and virus-infected shrimp mortality, while the miR-965 overexpression resulted in the decreased WSSV copies and virus-infected shrimp mortality, indicating that miR-965 played a negative role in the WSSV infection. The further data revealed that miR-965 inhibited the virus infection by targeting the viral wsv240 gene, an important gene required for the WSSV infection in shrimp. The results demonstrated that miR-965 could promote the shrimp phagocytosis against virus infection by targeting the shrimp ATG5 (autophagy related 5) gene. Therefore, our findings presented novel evidence to better understand the anfractuous host-virus interactions in vivo.
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Affiliation(s)
- Le Shu
- College of Life Sciences, Zhejiang University, Hangzhou 310058, People's Republic of China
| | - Changrun Li
- Institute of Health Sciences, Anhui University, People's Republic of China.
| | - Xiaobo Zhang
- College of Life Sciences, Zhejiang University, Hangzhou 310058, People's Republic of China.
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38
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Basile K, Dwyer DE, Kok J. Fat and flu: fact or fiction? Future Virol 2016. [DOI: 10.2217/fvl-2016-0014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Novel risk factors for severe influenza infection were described during the early phases of the influenza pandemic of 2009. Worldwide, the rate of severe influenza in the obese and morbidly obese population was disproportionate to that of the general population. This risk factor has now been recognized presumably due to the increasing prevalence of obesity. The cause behind this trend may extend beyond the known deleterious effects of obesity on respiratory physiology, as emerging evidence in animal models demonstrate A(H1N1)pdm09 itself confers worse outcomes compared with seasonal influenza subtypes. Currently, uncertainty remains regarding the optimal antiviral regimen and vaccination strategies in obese individuals. Therefore, further studies on the effects of obesity on influenza infection need to be prioritized.
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Affiliation(s)
- Kerri Basile
- Centre for Infectious Diseases & Microbiology Laboratory Services, Institute of Clinical Pathology & Medical Research, Westmead Hospital, University of Sydney, Westmead, New South Wales, Australia
- Marie Bashir Institute for Infectious Diseases & Biosecurity, Westmead Hospital, University of Sydney, Westmead, New South Wales, Australia
- Centre for Research Excellence in Critical Infections, Westmead Hospital, University of Sydney, Westmead, New South Wales, Australia
| | - Dominic E Dwyer
- Centre for Infectious Diseases & Microbiology Laboratory Services, Institute of Clinical Pathology & Medical Research, Westmead Hospital, University of Sydney, Westmead, New South Wales, Australia
- Marie Bashir Institute for Infectious Diseases & Biosecurity, Westmead Hospital, University of Sydney, Westmead, New South Wales, Australia
- Centre for Research Excellence in Critical Infections, Westmead Hospital, University of Sydney, Westmead, New South Wales, Australia
| | - Jen Kok
- Centre for Infectious Diseases & Microbiology Laboratory Services, Institute of Clinical Pathology & Medical Research, Westmead Hospital, University of Sydney, Westmead, New South Wales, Australia
- Marie Bashir Institute for Infectious Diseases & Biosecurity, Westmead Hospital, University of Sydney, Westmead, New South Wales, Australia
- Centre for Research Excellence in Critical Infections, Westmead Hospital, University of Sydney, Westmead, New South Wales, Australia
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Rivera A, Barr T, Rais M, Engelmann F, Messaoudi I. microRNAs Regulate Host Immune Response and Pathogenesis During Influenza Infection in Rhesus Macaques. Viral Immunol 2016; 29:212-27. [PMID: 27008411 DOI: 10.1089/vim.2015.0074] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
microRNAs (miRNAs) are small noncoding RNAs that are key regulators of biological processes, including the immune response to viral infections. Differential expression levels of cellular miRNAs and their predicted targets have been described in the lungs of H1N1-infected BALB/c mice, the lungs of H5N1 influenza-infected cynomolgus macaques, and in peripheral blood mononuclear cells (PBMCs) of critically ill patients infected with 2009 pandemic H1N1. However, a longitudinal analysis of changes in the expression of miRNAs and their targets during influenza infection and how they relate to viral replication and host response has yet to be carried out. In the present study, we conducted a comprehensive analysis of innate and adaptive immune responses as well as the expression of several miRNAs and their validated targets in both peripheral blood and bronchoalveolar lavage (BAL) collected from rhesus macaques over the course of infection with the 2009 H1N1 virus A/Mexico/4108/2009 (MEX4108). We describe a distinct set of differentially expressed miRNAs in BAL and PBMCs, which regulate the expression of genes involved in inflammation, immune response, and regulation of cell cycle and apoptosis.
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Affiliation(s)
- Andrea Rivera
- 1 Division of Biomedical Sciences, University of California , Riverside, Riverside, California
| | - Tasha Barr
- 1 Division of Biomedical Sciences, University of California , Riverside, Riverside, California
| | - Maham Rais
- 1 Division of Biomedical Sciences, University of California , Riverside, Riverside, California
| | - Flora Engelmann
- 1 Division of Biomedical Sciences, University of California , Riverside, Riverside, California
| | - Ilhem Messaoudi
- 1 Division of Biomedical Sciences, University of California , Riverside, Riverside, California.,2 Oregon Primate Research Center , Beaverton, Oregon
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The Effect of Oseltamivir on the Disease Progression of Lethal Influenza A Virus Infection: Plasma Cytokine and miRNA Responses in a Mouse Model. DISEASE MARKERS 2016; 2016:9296457. [PMID: 27110056 PMCID: PMC4824134 DOI: 10.1155/2016/9296457] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/22/2016] [Accepted: 02/11/2016] [Indexed: 12/25/2022]
Abstract
Lethal influenza A virus infection leads to acute lung injury and possibly lethal complications. There has been a continuous effort to identify the possible predictors of disease severity. Unlike earlier studies, where biomarkers were analyzed on certain time points or days after infection, in this study biomarkers were evaluated over the entire course of infection. Circulating proinflammatory cytokines and/or miRNAs that track with the onset and progression of lethal A/Puerto Rico/8/34 (PR8) influenza A virus infection and their response to oseltamivir treatment were investigated up to 10 days after infection. Changes in plasma cytokines (IL-1β, IL-10, IL-12p70, IL-6, KC, TNF-α, and IFN-γ) and several candidate miRNAs were profiled. Among the cytokines analyzed, IL-6 and KC/GRO cytokines appeared to correlate with peak viral titer. Over the selected 48 miRNAs profiled, certain miRNAs were up- or downregulated in a manner that was dependent on the oseltamivir treatment and disease severity. Our findings suggest that IL-6 and KC/GRO cytokines can be a potential disease severity biomarker and/or marker for the progression/remission of infection. Further studies to explore other cytokines, miRNAs, and lung injury proteins in serum with different subtypes of influenza A viruses with varying disease severity may provide new insight into other unique biomarkers.
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41
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Brogaard L, Heegaard PMH, Larsen LE, Mortensen S, Schlegel M, Dürrwald R, Skovgaard K. Late regulation of immune genes and microRNAs in circulating leukocytes in a pig model of influenza A (H1N2) infection. Sci Rep 2016; 6:21812. [PMID: 26893019 PMCID: PMC4759598 DOI: 10.1038/srep21812] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2015] [Accepted: 02/01/2016] [Indexed: 01/18/2023] Open
Abstract
MicroRNAs (miRNAs) are a class of short regulatory RNA molecules which are implicated in modulating gene expression. Levels of circulating, cell-associated miRNAs in response to influenza A virus (IAV) infection has received limited attention so far. To further understand the temporal dynamics and biological implications of miRNA regulation in circulating leukocytes, we collected blood samples before and after (1, 3, and 14 days) IAV challenge of pigs. Differential expression of miRNAs and innate immune factor mRNA transcripts was analysed using RT-qPCR. A total of 20 miRNAs were regulated after IAV challenge, with the highest number of regulated miRNAs seen on day 14 after infection at which time the infection was cleared. Targets of the regulated miRNAs included genes involved in apoptosis and cell cycle regulation. Significant regulation of both miRNAs and mRNA transcripts at 14 days after challenge points to a protracted effect of IAV infection, potentially affecting the host’s ability to respond to secondary infections. In conclusion, experimental IAV infection of pigs demonstrated the dynamic nature of miRNA and mRNA regulation in circulating leukocytes during and after infection, and revealed the need for further investigation of the potential immunosuppressing effect of miRNA and innate immune signaling after IAV infection.
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Affiliation(s)
- Louise Brogaard
- Section for Immunology and Vaccinology, National Veterinary Institute, Technical University of Denmark, 1870 Frederiksberg C, Denmark
| | - Peter M H Heegaard
- Section for Immunology and Vaccinology, National Veterinary Institute, Technical University of Denmark, 1870 Frederiksberg C, Denmark
| | - Lars E Larsen
- Section for Virology, National Veterinary Institute, Technical University of Denmark, 1870 Frederiksberg C, Denmark
| | - Shila Mortensen
- Section for Immunology and Vaccinology, National Veterinary Institute, Technical University of Denmark, 1870 Frederiksberg C, Denmark
| | | | | | - Kerstin Skovgaard
- Section for Immunology and Vaccinology, National Veterinary Institute, Technical University of Denmark, 1870 Frederiksberg C, Denmark
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Peng F, He J, Loo JFC, Yao J, Shi L, Liu C, Zhao C, Xie W, Shao Y, Kong SK, Gu D. Identification of microRNAs in Throat Swab as the Biomarkers for Diagnosis of Influenza. Int J Med Sci 2016; 13:77-84. [PMID: 26917988 PMCID: PMC4747873 DOI: 10.7150/ijms.13301] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/21/2015] [Accepted: 12/15/2015] [Indexed: 12/11/2022] Open
Abstract
BACKGROUND Influenza is a serious worldwide disease that captures global attention in the past few years after outbreaks. The recent discoveries of microRNA (miRNA) and its unique expression profile in influenza patients have offered a new method for early influenza diagnosis. The aim of this study was to examine the utility of miRNAs for the diagnosis of influenza. METHODS Thirteen selected miRNAs were investigated with the hosts' throat swabs (25 H1N1, 20 H3N2, 20 influenza B and 21 healthy controls) by real-time quantitative polymerase chain reaction (RT-qPCR) using U6 snRNA as endogenous control for normalization, and receiver operating characteristic (ROC) curve/Area under curve (AUC) for analysis. RESULTS miR-29a-3p, miR-30c-5p, miR-34c-3p and miR-181a-5p are useful biomarkers for influenza A detection; and miR-30c-5p, miR-34b-5p, miR-205-5p and miR-449b-5p for influenza B detection. Also, use of both miR-30c-5p and miR-34c-3p (AUC=0.879); and miR-30c-5p and miR-449b-5p (AUC=0.901) are better than using one miRNA to confirm influenza A and influenza B infection, respectively. CONCLUSIONS Given its simplicity, non-invasiveness and specificity, we found that the throat swab-derived miRNAs miR-29a-3p, miR-30c-5p, miR-34b-5p, miR-34c-3p, miR-181a-5p, miR-205-5p and miR-449b-5p are a useful tool for influenza diagnosis on influenza A and B.
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Affiliation(s)
- Fang Peng
- 1. Department of Health Inspection and Quarantine, School of Public Health, Sun Yat-sen University, Guangzhou, China; 2. Shenzhen Entry-exit Inspection and Quarantine Bureau, Shenzhen, China
| | - Jianan He
- 2. Shenzhen Entry-exit Inspection and Quarantine Bureau, Shenzhen, China
| | - Jacky Fong Chuen Loo
- 3. Biochemistry Programme, School of Life Sciences, The Chinese University of Hong Kong, Hong Kong, China
| | - Jingyu Yao
- 4. Guangdong Medical University, Zhanjiang, China
| | - Lei Shi
- 2. Shenzhen Entry-exit Inspection and Quarantine Bureau, Shenzhen, China
| | - Chunxiao Liu
- 2. Shenzhen Entry-exit Inspection and Quarantine Bureau, Shenzhen, China
| | - Chunzhong Zhao
- 2. Shenzhen Entry-exit Inspection and Quarantine Bureau, Shenzhen, China
| | - Weidong Xie
- 5. Shenzhen Key Lab of Health Science and Technology, Division of Life Sciences & Health, Graduate School at Shenzhen, Tsinghua University, Shenzhen, China
| | - Yonghong Shao
- 6. College of Optoelectronics Engineering, Key Laboratory of Optoelectronic Devices and Systems, Ministry of Education and Guangdong Province, Shenzhen Key Laboratory of Sensor Technology, Shenzhen University, Shenzhen, China
| | - Siu Kai Kong
- 3. Biochemistry Programme, School of Life Sciences, The Chinese University of Hong Kong, Hong Kong, China
| | - Dayong Gu
- 1. Department of Health Inspection and Quarantine, School of Public Health, Sun Yat-sen University, Guangzhou, China; 2. Shenzhen Entry-exit Inspection and Quarantine Bureau, Shenzhen, China
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Makkoch J, Poomipak W, Saengchoowong S, Khongnomnan K, Praianantathavorn K, Jinato T, Poovorawan Y, Payungporn S. Human microRNAs profiling in response to influenza A viruses (subtypes pH1N1, H3N2, and H5N1). Exp Biol Med (Maywood) 2015; 241:409-20. [PMID: 26518627 DOI: 10.1177/1535370215611764] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2015] [Accepted: 09/21/2015] [Indexed: 01/12/2023] Open
Abstract
MicroRNAs (miRNAs) play an important role in regulation of gene silencing and are involved in many cellular processes including inhibition of infected viral replication. This study investigated cellular miRNA expression profiles operating in response to influenza virus in early stage of infection which might be useful for understanding and control of viral infection. A549 cells were infected with different subtypes of influenza virus (pH1N1, H3N2 and H5N1). After 24 h post-infection, miRNAs were extracted and then used for DNA library construction. All DNA libraries with different indexes were pooled together with equal concentration, followed by high-throughput sequencing based on MiSeq platform. The miRNAs were identified and counted from sequencing data by using MiSeq reporter software. The miRNAs expressions were classified into up and downregulated miRNAs compared to those found in non-infected cells. Mostly, each subtype of influenza A virus triggered the upregulated responses in miRNA expression profiles. Hsa-miR-101, hsa-miR-193b, hsa-miR-23b, and hsa-miR-30e* were upregulated when infected with all three subtypes of influenza A virus. Target prediction results showed that virus infection can trigger genes in cellular process, metabolic process, developmental process and biological regulation. This study provided some insights into the cellular miRNA profiling in response to various subtypes of influenza A viruses in circulation and which have caused outbreaks in human population. The regulated miRNAs might be involved in virus-host interaction or host defense mechanism, which should be investigated for effective antiviral therapeutic interventions.
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Affiliation(s)
- Jarika Makkoch
- Department of Biochemistry, Faculty of Medicine, Chulalongkorn University, Bangkok 10330 Thailand
| | - Witthaya Poomipak
- Research affairs, Faculty of Medicine, Chulalongkorn University, Bangkok 10330 Thailand
| | - Suthat Saengchoowong
- Joint Chulalongkorn University - University of Liverpool PhD Programme in Biomedical Sciences and Biotechnology, Bangkok 10330, Thailand
| | - Kritsada Khongnomnan
- Department of Biochemistry, Faculty of Medicine, Chulalongkorn University, Bangkok 10330 Thailand
| | | | - Thananya Jinato
- Systems Biology Center, Research Affairs, Faculty of Medicine, Chulalongkorn University, Bangkok, 10330 Thailand
| | - Yong Poovorawan
- Center of Excellence in Clinical Virology, Faculty of Medicine, Chulalongkorn University, Bangkok 10330, Thailand
| | - Sunchai Payungporn
- Department of Biochemistry, Faculty of Medicine, Chulalongkorn University, Bangkok 10330 Thailand Systems Biology Center, Research Affairs, Faculty of Medicine, Chulalongkorn University, Bangkok, 10330 Thailand
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44
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Zhao L, Zhu J, Zhou H, Zhao Z, Zou Z, Liu X, Lin X, Zhang X, Deng X, Wang R, Chen H, Jin M. Identification of cellular microRNA-136 as a dual regulator of RIG-I-mediated innate immunity that antagonizes H5N1 IAV replication in A549 cells. Sci Rep 2015; 5:14991. [PMID: 26450567 PMCID: PMC4598873 DOI: 10.1038/srep14991] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2015] [Accepted: 09/11/2015] [Indexed: 12/26/2022] Open
Abstract
H5N1 influenza A virus (IAV) causes severe respiratory diseases and high mortality rates in animals and humans. MicroRNAs are being increasingly studied to evaluate their potential as therapeutic entities to combat viral infection. However, mechanistic studies delineating the roles of microRNAs in regulating host-H5N1 virus interactions remain scarce. Here, we performed microRNA microarray analysis using A549 human lung epithelial cells infected with a highly pathogenic avian influenza virus. The microRNA expression profile of infected cells identified a small number of microRNAs being dysregulated upon H5N1 influenza A virus infection. Of the differentially expressed microRNAs, miR-136 was up-regulated 5-fold and exhibited potent antiviral activity in vitro against H5N1 influenza A virus, as well as vesicular stomatitis virus. On the one hand, 3'-untranslated region (UTR) reporter analysis revealed a miR-136 binding site in the 3' UTR of IL-6. However, on the other hand, we subsequently determined that miR-136 meanwhile acts as an immune agonist of retinoic acid-inducible gene 1 (RIG-I), thereby causing IL-6 and IFN-β accumulation in A549 cells. Overall, this study implicates the dual role of miRNA-136 in the regulation of host antiviral innate immunity and suggests an important role for the microRNA-activated pathway in viral infection via pattern recognition receptors.
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MESH Headings
- 3' Untranslated Regions/genetics
- 3' Untranslated Regions/immunology
- Animals
- Blotting, Western
- Cell Line, Tumor
- DEAD Box Protein 58
- DEAD-box RNA Helicases/genetics
- DEAD-box RNA Helicases/immunology
- Dogs
- Gene Expression Profiling/methods
- Gene Expression Regulation, Neoplastic/immunology
- HEK293 Cells
- Host-Pathogen Interactions/genetics
- Host-Pathogen Interactions/immunology
- Humans
- Immunity, Innate/genetics
- Immunity, Innate/immunology
- Influenza A Virus, H5N1 Subtype/genetics
- Influenza A Virus, H5N1 Subtype/immunology
- Influenza A Virus, H5N1 Subtype/physiology
- Interleukin-6/genetics
- Interleukin-6/immunology
- Interleukin-6/metabolism
- Lung Neoplasms/genetics
- Lung Neoplasms/immunology
- Lung Neoplasms/virology
- Madin Darby Canine Kidney Cells
- MicroRNAs/genetics
- MicroRNAs/immunology
- Microscopy, Confocal
- Oligonucleotide Array Sequence Analysis
- Receptors, Immunologic
- Reverse Transcriptase Polymerase Chain Reaction
- Virus Replication/genetics
- Virus Replication/immunology
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Affiliation(s)
- Lianzhong Zhao
- State Key Laboratory of Agriculture Microbiology, Huazhong Agricultural University, Wuhan 430070, Hubei Province, P. R. China
- Laboratory of Animal Virology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, Hubei Province, P. R. China
| | - Jiping Zhu
- State Key Laboratory of Agriculture Microbiology, Huazhong Agricultural University, Wuhan 430070, Hubei Province, P. R. China
- Laboratory of Animal Virology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, Hubei Province, P. R. China
| | - Hongbo Zhou
- State Key Laboratory of Agriculture Microbiology, Huazhong Agricultural University, Wuhan 430070, Hubei Province, P. R. China
- Laboratory of Animal Virology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, Hubei Province, P. R. China
| | - Zongzheng Zhao
- State Key Laboratory of Agriculture Microbiology, Huazhong Agricultural University, Wuhan 430070, Hubei Province, P. R. China
- Laboratory of Animal Virology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, Hubei Province, P. R. China
| | - Zhong Zou
- State Key Laboratory of Agriculture Microbiology, Huazhong Agricultural University, Wuhan 430070, Hubei Province, P. R. China
- Laboratory of Animal Virology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, Hubei Province, P. R. China
| | - Xiaokun Liu
- State Key Laboratory of Agriculture Microbiology, Huazhong Agricultural University, Wuhan 430070, Hubei Province, P. R. China
- Laboratory of Animal Virology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, Hubei Province, P. R. China
| | - Xian Lin
- State Key Laboratory of Agriculture Microbiology, Huazhong Agricultural University, Wuhan 430070, Hubei Province, P. R. China
- Laboratory of Animal Virology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, Hubei Province, P. R. China
| | - Xue Zhang
- State Key Laboratory of Agriculture Microbiology, Huazhong Agricultural University, Wuhan 430070, Hubei Province, P. R. China
- Laboratory of Animal Virology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, Hubei Province, P. R. China
| | - Xuexia Deng
- State Key Laboratory of Agriculture Microbiology, Huazhong Agricultural University, Wuhan 430070, Hubei Province, P. R. China
- Laboratory of Animal Virology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, Hubei Province, P. R. China
| | - Ruifang Wang
- State Key Laboratory of Agriculture Microbiology, Huazhong Agricultural University, Wuhan 430070, Hubei Province, P. R. China
- Laboratory of Animal Virology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, Hubei Province, P. R. China
| | - Huanchun Chen
- State Key Laboratory of Agriculture Microbiology, Huazhong Agricultural University, Wuhan 430070, Hubei Province, P. R. China
- Laboratory of Animal Virology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, Hubei Province, P. R. China
| | - Meilin Jin
- State Key Laboratory of Agriculture Microbiology, Huazhong Agricultural University, Wuhan 430070, Hubei Province, P. R. China
- Laboratory of Animal Virology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, Hubei Province, P. R. China
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45
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Ko ER, Yang WE, McClain MT, Woods CW, Ginsburg GS, Tsalik EL. What was old is new again: using the host response to diagnose infectious disease. Expert Rev Mol Diagn 2015; 15:1143-58. [PMID: 26145249 DOI: 10.1586/14737159.2015.1059278] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
A century of advances in infectious disease diagnosis and treatment changed the face of medicine. However, challenges continue to develop including multi-drug resistance, globalization that increases pandemic risks and high mortality from severe infections. These challenges can be mitigated through improved diagnostics, focusing on both pathogen discovery and the host response. Here, we review how 'omics' technologies improve sepsis diagnosis, early pathogen identification and personalize therapy. Such host response diagnostics are possible due to the confluence of advanced laboratory techniques (e.g., transcriptomics, metabolomics, proteomics) along with advanced mathematical modeling such as machine learning techniques. The road ahead is promising, but obstacles remain before the impact of such advanced diagnostic modalities is felt at the bedside.
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Affiliation(s)
- Emily R Ko
- a 1 Department of Medicine Center for Applied Genomics & Precision Medicine, Duke University, Durham, NC 27708, USA
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46
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Morán J, Ramírez-Martínez G, Jiménez-Alvarez L, Cruz A, Pérez-Patrigeon S, Hidalgo A, Orozco L, Martínez A, Padilla-Noriega L, Avila-Moreno F, Cabello C, Granados J, Ortíz-Quintero B, Ramírez-Venegas A, Ruíz-Palacios GM, Zlotnik A, Merino E, Zúñiga J. Circulating levels of miR-150 are associated with poorer outcomes of A/H1N1 infection. Exp Mol Pathol 2015; 99:253-61. [PMID: 26148929 DOI: 10.1016/j.yexmp.2015.07.001] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2015] [Accepted: 07/02/2015] [Indexed: 01/13/2023]
Abstract
BACKGROUND Overproduction of pro-inflammatory cytokines and chemokines is frequently associated with severe clinical manifestations in patients infected with influenza A/H1N1 virus. Micro-RNAs (miRNAs) are highly conserved small non-coding RNA molecules that post-transcriptionally regulate gene expression and are potential biomarkers and therapeutic targets in different inflammatory conditions. METHODS We studied the circulating and miRNA profiles in critically ill A/H1N1 patients, A/H1N1 patients with milder disease, asymptomatic housemates and healthy controls. Cytokine, chemokine and growth factors that were potential targets of differentially expressed miRNAs were assessed. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment and interactome analysis of these miRNAs were also performed. RESULTS Critically ill patients exhibited a significant over-expression of circulating miR-150 (p<0.005) when compared to patients with milder disease. miR-29c, miR-145 and miR-22 were differentially expressed in patients with severe A/H1N1 disease whereas miR-210, miR-126 and miR-222 were downregulated in individuals exposed to the A/H1N1 virus. Significant correlations (p<0.05) between circulating levels of miR-150 with IL-1ra, IL-2, IL-6, CXCL8, IFN-γ, CXCL10 and G-CSF were detected, particularly in critically ill patients. CONCLUSION The up-regulation of miR-150 is associated with poorer outcomes of A/H1N1 infection. The differential expression of miRNAs related with immune processes in severe A/H1N1 disease supports the potential role of these miRNAs as biomarkers of disease progression.
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Affiliation(s)
- Juan Morán
- Instituto Nacional de Enfermedades Respiratorias Ismael Cosío Villegas, Mexico City, Mexico
| | | | - Luis Jiménez-Alvarez
- Instituto Nacional de Enfermedades Respiratorias Ismael Cosío Villegas, Mexico City, Mexico
| | - Alfredo Cruz
- Instituto Nacional de Enfermedades Respiratorias Ismael Cosío Villegas, Mexico City, Mexico
| | - Santiago Pérez-Patrigeon
- Department of Infectious Diseases, Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, Mexico
| | - Alfredo Hidalgo
- Instituto Nacional de Medicina Genómica, Mexico City, Mexico
| | - Lorena Orozco
- Instituto Nacional de Medicina Genómica, Mexico City, Mexico
| | | | - Luis Padilla-Noriega
- Department of Microbiology and Parasitology, Facultad de Medicina, Posgrado en Ciencias Biológicas, Universidad Nacional Autónoma de México, Mexico
| | - Federico Avila-Moreno
- FES-Iztacala, Unidad de Biomedicina, UBIMED, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Carlos Cabello
- Instituto Nacional de Enfermedades Respiratorias Ismael Cosío Villegas, Mexico City, Mexico
| | - Julio Granados
- Department of Transplantation, Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, Mexico City, Mexico
| | - Blanca Ortíz-Quintero
- Instituto Nacional de Enfermedades Respiratorias Ismael Cosío Villegas, Mexico City, Mexico
| | | | - Guillermo M Ruíz-Palacios
- Department of Infectious Diseases, Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, Mexico
| | - Albert Zlotnik
- Department of Biophysics and Physiology, University of California Irvine, CA, USA
| | - Enrique Merino
- Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca City, Mexico
| | - Joaquín Zúñiga
- Instituto Nacional de Enfermedades Respiratorias Ismael Cosío Villegas, Mexico City, Mexico.
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47
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Inchley CS, Sonerud T, Fjærli HO, Nakstad B. Nasal mucosal microRNA expression in children with respiratory syncytial virus infection. BMC Infect Dis 2015; 15:150. [PMID: 25884957 PMCID: PMC4387708 DOI: 10.1186/s12879-015-0878-z] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2014] [Accepted: 03/10/2015] [Indexed: 01/22/2023] Open
Abstract
Background Respiratory syncytial virus (RSV) infection is a common cause of pediatric hospitalization. microRNA, key regulators of the immune system, have not previously been investigated in respiratory specimens during viral infection. We investigated microRNA expression in the nasal mucosa of 42 RSV-positive infants, also comparing microRNA expression between disease severity subgroups. Methods Nasal mucosa cytology specimens were collected from RSV-positive infants and healthy controls. 32 microRNA were selected by microarray for qPCR verification in 19 control, 16 mild, 7 moderate and 19 severe disease samples. Results Compared to healthy controls, RSV-positive infants downregulated miR-34b, miR-34c, miR-125b, miR-29c, mir125a, miR-429 and miR-27b and upregulated miR-155, miR-31, miR-203a, miR-16 and let-7d. On disease subgroups analysis, miR-125a and miR-429 were downregulated in mild disease (p = 0.03 and 0.02, respectively), but not in severe disease (p = 0.3 and 0.3). Conclusion microRNA expression in nasal epithelium cytology brushings of RSV-positive infants shows a distinct profile of immune-associated miRNA. miR-125a has important functions within NF-κB signaling and macrophage function. The lack of downregulation of miR-125a and miR-429 in severe disease may help explain differences in disease manifestations on infection with RSV.
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Affiliation(s)
- Christopher S Inchley
- Department of Pediatric and Adolescent Medicine, Akershus University Hospital, 1478, Lørenskog, Norway. .,Institute of Clinical Medicine, University of Oslo, 0316, Oslo, Norway.
| | - Tonje Sonerud
- Department of Pediatric and Adolescent Medicine, Akershus University Hospital, 1478, Lørenskog, Norway. .,Department of Clinical Molecular Biology and Laboratory Sciences (EpiGen), Akershus University Hospital, 1478, Lørenskog, Norway.
| | - Hans O Fjærli
- Department of Pediatric and Adolescent Medicine, Akershus University Hospital, 1478, Lørenskog, Norway.
| | - Britt Nakstad
- Department of Pediatric and Adolescent Medicine, Akershus University Hospital, 1478, Lørenskog, Norway. .,Institute of Clinical Medicine, University of Oslo, 0316, Oslo, Norway.
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48
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Godard P, van Eyll J. Pathway analysis from lists of microRNAs: common pitfalls and alternative strategy. Nucleic Acids Res 2015; 43:3490-7. [PMID: 25800743 PMCID: PMC4402548 DOI: 10.1093/nar/gkv249] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2014] [Accepted: 03/10/2015] [Indexed: 11/17/2022] Open
Abstract
MicroRNAs (miRNAs) are involved in the regulation of gene expression at a post-transcriptional level. As such, monitoring miRNA expression has been increasingly used to assess their role in regulatory mechanisms of biological processes. In large scale studies, once miRNAs of interest have been identified, the target genes they regulate are often inferred using algorithms or databases. A pathway analysis is then often performed in order to generate hypotheses about the relevant biological functions controlled by the miRNA signature. Here we show that the method widely used in scientific literature to identify these pathways is biased and leads to inaccurate results. In addition to describing the bias and its origin we present an alternative strategy to identify potential biological functions specifically impacted by a miRNA signature. More generally, our study exemplifies the crucial need of relevant negative controls when developing, and using, bioinformatics methods.
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Affiliation(s)
- Patrice Godard
- IP & Science, Thomson Reuters, 5901 Priestly Drive, #200, Carlsbad, CA 92008, USA
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49
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Zhu H, Xin X. Common Dysregulation of Ribosomal Genes Present in Infants with Acute Respiratory Infection of Respiratory Syncytial Virus, Rhinovirus, and Influenza A. PEDIATRIC ALLERGY, IMMUNOLOGY, AND PULMONOLOGY 2015. [DOI: 10.1089/ped.2014.0400] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Huilan Zhu
- Department of Pediatrics, First People's Hospital of Ji'nan City, Jinan, China
| | - Xinxin Xin
- Department of Orthopedics, 2nd Affiliated Hospital of Harbin Medical University, Harbin, China
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50
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Integrative analysis of differentially expressed microRNAs of pulmonary alveolar macrophages from piglets during H1N1 swine influenza A virus infection. Sci Rep 2015; 5:8167. [PMID: 25639204 PMCID: PMC5389138 DOI: 10.1038/srep08167] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2014] [Accepted: 01/08/2015] [Indexed: 12/15/2022] Open
Abstract
H1N1 swine influenza A virus (H1N1 SwIV) is one key subtype of influenza viruses with pandemic potential. MicroRNAs (miRNAs) are endogenous small RNA molecules that regulate gene expression. MiRNAs relevant with H1N1 SwIV have rarely been reported. To understand the biological functions of miRNAs during H1N1 SwIV infection, this study profiled differentially expressed (DE) miRNAs in pulmonary alveolar macrophages from piglets during the H1N1 SwIV infection using a deep sequencing approach, which was validated by quantitative real-time PCR. Compared to control group, 70 and 16 DE miRNAs were respectively identified on post-infection day (PID) 4 and PID 7. 56 DE miRNAs were identified between PID 4 and PID 7. Our results suggest that most host miRNAs are down-regulated to defend the H1N1 SwIV infection during the acute phase of swine influenza whereas their expression levels gradually return to normal during the recovery phase to avoid the occurrence of too severe porcine lung damage. In addition, targets of DE miRNAs were also obtained, for which bioinformatics analyses were performed. Our results would be useful for investigating the functions and regulatory mechanisms of miRNAs in human influenza because pig serves as an excellent animal model to study the pathogenesis of human influenza.
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