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Chowdhury D, Nayeem M, Vanderven HA, Sarker S. Role of miRNA in Highly Pathogenic H5 Avian Influenza Virus Infection: An Emphasis on Cellular and Chicken Models. Viruses 2024; 16:1102. [PMID: 39066264 PMCID: PMC11281567 DOI: 10.3390/v16071102] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2024] [Revised: 07/01/2024] [Accepted: 07/06/2024] [Indexed: 07/28/2024] Open
Abstract
The avian influenza virus, particularly the H5N1 strain, poses a significant and ongoing threat to both human and animal health. Recent outbreaks have affected domestic and wild birds on a massive scale, raising concerns about the virus' spread to mammals. This review focuses on the critical role of microRNAs (miRNAs) in modulating pro-inflammatory signaling pathways during the pathogenesis of influenza A virus (IAV), with an emphasis on highly pathogenic avian influenza (HPAI) H5 viral infections. Current research indicates that miRNAs play a significant role in HPAI H5 infections, influencing various aspects of the disease process. This review aims to synthesize recent findings on the impact of different miRNAs on immune function, viral cytopathogenicity, and respiratory viral replication. Understanding these mechanisms is essential for developing new therapeutic strategies to combat avian influenza and mitigate its effects on both human and animal populations.
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Affiliation(s)
- Dibakar Chowdhury
- Laboratory of Influenza Research, College of Veterinary Medicine, Chungnam National University, Daejeon 34134, Republic of Korea;
| | - Md. Nayeem
- One Health Institute, Chattogram Veterinary and Animal Sciences University, Khulshi, Chattogram 4225, Bangladesh;
| | - Hillary A. Vanderven
- Biomedical Sciences & Molecular Biology, College of Public Health, Medical and Veterinary Sciences, James Cook University, Townsville, QLD 4811, Australia;
- Australian Institute of Tropical Health and Medicine, James Cook University, Townsville, QLD 4811, Australia
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, University of Melbourne, Parkville, VIC 3010, Australia
| | - Subir Sarker
- Biomedical Sciences & Molecular Biology, College of Public Health, Medical and Veterinary Sciences, James Cook University, Townsville, QLD 4811, Australia;
- Australian Institute of Tropical Health and Medicine, James Cook University, Townsville, QLD 4811, Australia
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2
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Kappari L, Dasireddy JR, Applegate TJ, Selvaraj RK, Shanmugasundaram R. MicroRNAs: exploring their role in farm animal disease and mycotoxin challenges. Front Vet Sci 2024; 11:1372961. [PMID: 38803799 PMCID: PMC11129562 DOI: 10.3389/fvets.2024.1372961] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2024] [Accepted: 04/04/2024] [Indexed: 05/29/2024] Open
Abstract
MicroRNAs (miRNAs) serve as key regulators in gene expression and play a crucial role in immune responses, holding a significant promise for diagnosing and managing diseases in farm animals. This review article summarizes current research on the role of miRNAs in various farm animal diseases and mycotoxicosis, highlighting their potential as biomarkers and using them for mitigation strategies. Through an extensive literature review, we focused on the impact of miRNAs in the pathogenesis of several farm animal diseases, including viral and bacterial infections and mycotoxicosis. They regulate gene expression by inducing mRNA deadenylation, decay, or translational inhibition, significantly impacting cellular processes and protein synthesis. The research revealed specific miRNAs associated with the diseases; for instance, gga-miR-M4 is crucial in Marek's disease, and gga-miR-375 tumor-suppressing function in Avian Leukosis. In swine disease such as Porcine Respiratory and Reproductive Syndrome (PRRS) and swine influenza, miRNAs like miR-155 and miR-21-3p emerged as key regulatory factors. Additionally, our review highlighted the interaction between miRNAs and mycotoxins, suggesting miRNAs can be used as a biomarker for mycotoxin exposure. For example, alterations in miRNA expression, such as the dysregulation observed in response to Aflatoxin B1 (AFB1) in chickens, may indicate potential mechanisms for toxin-induced changes in lipid metabolism leading to liver damage. Our findings highlight miRNAs potential for early disease detection and intervention in farm animal disease management, potentially reducing significant economic losses in agriculture. With only a fraction of miRNAs functionally characterized in farm animals, this review underlines more focused research on specific miRNAs altered in distinct diseases, using advanced technologies like CRISPR-Cas9 screening, single-cell sequencing, and integrated multi-omics approaches. Identifying specific miRNA targets offers a novel pathway for early disease detection and the development of mitigation strategies against mycotoxin exposure in farm animals.
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Affiliation(s)
- Laharika Kappari
- Department of Poultry Science, The University of Georgia, Athens, GA, United States
| | | | - Todd J. Applegate
- Department of Poultry Science, The University of Georgia, Athens, GA, United States
| | - Ramesh K. Selvaraj
- Department of Poultry Science, The University of Georgia, Athens, GA, United States
| | - Revathi Shanmugasundaram
- Toxicology and Mycotoxin Research Unit, U.S. National Poultry Research Center, Agricultural Research Service, U.S. Department of Agriculture, Athens, GA, United States
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Cammayo-Fletcher PLT, Flores RA, Nguyen BT, Villavicencio AGM, Lee SY, Kim WH, Min W. Promotion of Th1 and Th2 responses over Th17 in Riemerella anatipestifer stimulation in chicken splenocytes: Correlation of gga-miR-456-3p and gga-miR-16-5p with NOS2 and CCL5 expression. PLoS One 2023; 18:e0294031. [PMID: 37930983 PMCID: PMC10627459 DOI: 10.1371/journal.pone.0294031] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2023] [Accepted: 10/20/2023] [Indexed: 11/08/2023] Open
Abstract
Riemerella (R.) anatipestifer poses a significant threat to ducks, resulting in mortality rates ranging from 5-75%. This disease is highly infectious and economically consequential for domestic ducks. Although other avian species, such as chickens, also display susceptibility, the impact is comparatively less severe than in ducks. IL-17A has a pronounced correlation with R. anatipestifer infection in ducks, which is less in chickens. This study performed an in vitro transcriptome analysis using chicken splenic lymphocytes collected at 4-, 8-, and 24-hour intervals following R. anatipestifer stimulation. The primary objective was to discern the differentially expressed genes, with a specific focus on IL-17A and IL-17F expression. Moreover, an association between specific miRNAs with NOS2 and CCL5 was identified. The manifestation of riemerellosis in chickens was linked to heightened expression of Th1- and Th2-associated cells, while Th17 cells exhibited minimal involvement. This study elucidated the mechanism behind the absence of a Th17 immune response, shedding light on its role throughout disease progression. Additionally, through small RNA sequencing, we identified a connection between miRNAs, specifically miR-456-3p and miR-16-5p, and their respective target genes NOS2 and CCL5. These miRNAs are potential regulators of the inflammatory process during riemerellosis in chickens.
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Affiliation(s)
| | - Rochelle A. Flores
- College of Veterinary Medicine & Institute of Animal Medicine, Gyeongsang National University, Jinju, Korea
| | - Binh T. Nguyen
- College of Veterinary Medicine & Institute of Animal Medicine, Gyeongsang National University, Jinju, Korea
| | | | - Seung Yun Lee
- College of Veterinary Medicine & Institute of Animal Medicine, Gyeongsang National University, Jinju, Korea
| | - Woo H. Kim
- College of Veterinary Medicine & Institute of Animal Medicine, Gyeongsang National University, Jinju, Korea
| | - Wongi Min
- College of Veterinary Medicine & Institute of Animal Medicine, Gyeongsang National University, Jinju, Korea
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4
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Micro-Players of Great Significance-Host microRNA Signature in Viral Infections in Humans and Animals. Int J Mol Sci 2022; 23:ijms231810536. [PMID: 36142450 PMCID: PMC9504570 DOI: 10.3390/ijms231810536] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2022] [Revised: 09/04/2022] [Accepted: 09/08/2022] [Indexed: 11/22/2022] Open
Abstract
Over time, more and more is becoming known about micro-players of great significance. This is particularly the case for microRNAs (miRNAs; miR), which have been found to participate in the regulation of many physiological and pathological processes in both humans and animals. One such process is viral infection in humans and animals, in which the host miRNAs—alone or in conjunction with the virus—interact on two levels: viruses may regulate the host’s miRNAs to evade its immune system, while the host miRNAs can play anti- or pro-viral roles. The purpose of this comprehensive review is to present the key miRNAs involved in viral infections in humans and animals. We summarize the data in the available literature, indicating that the signature miRNAs in human viral infections mainly include 12 miRNAs (i.e., miR-155, miR-223, miR-146a, miR-122, miR-125b, miR-132, miR-34a, miR -21, miR-16, miR-181 family, let-7 family, and miR-10a), while 10 miRNAs are commonly found in animals (i.e., miR-155, miR-223, miR-146a, miR-145, miR-21, miR-15a/miR-16 cluster, miR-181 family, let-7 family, and miR-122) in this context. Knowledge of which miRNAs are involved in different viral infections and the biological functions that they play can help in understanding the pathogenesis of viral diseases, facilitating the future development of therapeutic agents for both humans and animals.
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5
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Mishra A, Asaf M, Kumar A, Kulkarni DD, Sood R, Bhatia S, Bhushan B, Raut AA. Differential miRNA expression profiling of Highly Pathogenic Avian Influenza Virus H5N1 infected chicken lungs reveals critical microRNAs, biological pathways and genes involved in the molecular pathogenesis. Virol Sin 2022; 37:465-468. [PMID: 35278696 PMCID: PMC9243614 DOI: 10.1016/j.virs.2022.03.004] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2021] [Accepted: 03/07/2022] [Indexed: 11/26/2022] Open
Abstract
Highthrouput sequencing of small RNA of H5N1 infected and mock infected chicken lungs. 297 miRNAs identified in mock-infected and 201 miRNAs identified in AIV infected chicken lungs. 36 miRNAs were upregulated and 90 were downregulated during H5N1 infection. Functional analysis and gene ontology of predicted target genes of expressed miRNAs. MAPK pathway, NF-κB, IGF and gga-let-7b might play important role during H5N1 pathogenesis.
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Affiliation(s)
- Anamika Mishra
- Pathogenomics Laboratory, ICAR-National Institute of High Security Animal Diseases, OIE referral laboratory for Avian Influenza, Bhopal 462 021, India.
| | - Muhasin Asaf
- Division of Animal Genetics, ICAR-Indian Veterinary Research Institute, Bareilly 243 122, India
| | - Amod Kumar
- Division of Animal Genetics, ICAR-Indian Veterinary Research Institute, Bareilly 243 122, India
| | - Diwakar Dattatreya Kulkarni
- ICAR-National Institute of High Security Animal Diseases, OIE referral lab for Avian Influenza, Bhopal 462 021, India
| | - Richa Sood
- ICAR-National Institute of High Security Animal Diseases, OIE referral lab for Avian Influenza, Bhopal 462 021, India
| | - Sandeep Bhatia
- ICAR-National Institute of High Security Animal Diseases, OIE referral lab for Avian Influenza, Bhopal 462 021, India
| | - Bharat Bhushan
- Division of Animal Genetics, ICAR-Indian Veterinary Research Institute, Bareilly 243 122, India
| | - Ashwin Ashok Raut
- Pathogenomics Laboratory, ICAR-National Institute of High Security Animal Diseases, OIE referral laboratory for Avian Influenza, Bhopal 462 021, India
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6
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Sun Y, Wang Y, Zhao Y, Zou M, Peng X. Exosomal miR-181a-5p reduce Mycoplasma gallisepticum (HS strain) infection in chicken by targeting PPM1B and activating the TLR2-mediated MyD88/NF-κB signaling pathway. Mol Immunol 2021; 140:144-157. [PMID: 34715577 DOI: 10.1016/j.molimm.2021.09.005] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Revised: 08/19/2021] [Accepted: 09/06/2021] [Indexed: 01/13/2023]
Abstract
Mycoplasma gallisepticum (MG) is one of the most important pathogens that causes chronic respiratory disease (CRD) in chickens. Exosomes secreted from cells have been well demonstrated to deliver miRNAs to recipient cells to modulate cellular functions. The purpose of this study is to explore the underlying functions and mechanisms of exosomal miR-181a-5p in MG-HS infection. In this study, we found that miR-181a-5p expression in vivo and in vitro was significantly up-regulated after MG-HS infection. It was also upregulated in exosomes, which were derived from MG-HS-infected type-II pneumocytes cells (CP-II). In addition, exosomes secreted by MG-HS-infected CP-II were able to transfer miR-181a-5p to recipient chicken embryo fibroblast cells (DF-1), resulting in a significant upregulation of miR-181a-5p expression in recipient DF-1 cells. We further identified that Mg2+/Mn2+-dependent protein phosphatase 1B (PPM1B) was the target gene of miR-181a-5p. Overexpression of miR-181a-5p or knockdown of PPM1B activated the nuclear factor-κB (NF-κB) signaling pathway, whereas inhibition of miR-181a-5p and overexpression of PPM1B led to the opposite results. Besides, up-regulation of miR-181a-5p significantly increased the expression of toll-like receptor 2 (TLR2), myeloid differentiation factor 88 (MyD88), tumor necrosis factors alpha (TNF-α) and interleukin-1β (IL-1β), whereas inhibition of miR-181a-5p showed a contrary result. Up-regulation of miR-181a-5p promoted cell proliferation, cell cycle progression and inhibited apoptosis to resist MG-HS infection. Moreover, overexpression of miR-181a-5p significantly negative regulated the expression of Mycoplasma gallisepticum adhesin protein (pMGA1.2) by directly inhibiting PPM1B. Thus, we concluded that exosomal miR-181a-5p from CP-II cells activated the TLR2-mediated MyD88/NF-κB signaling pathways by directly targeting PPM1B to promote the expression of pro-inflammatory cytokines for defending against MG-HS infection in recipient DF-1 cells.
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Affiliation(s)
- Yingfei Sun
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction, Ministry of Education, Huazhong Agricultural University, Wuhan, Hubei Province, 430070, China
| | - Yingjie Wang
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction, Ministry of Education, Huazhong Agricultural University, Wuhan, Hubei Province, 430070, China
| | - Yabo Zhao
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction, Ministry of Education, Huazhong Agricultural University, Wuhan, Hubei Province, 430070, China
| | - Mengyun Zou
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction, Ministry of Education, Huazhong Agricultural University, Wuhan, Hubei Province, 430070, China
| | - Xiuli Peng
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction, Ministry of Education, Huazhong Agricultural University, Wuhan, Hubei Province, 430070, 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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Distinct transcriptomic response to Newcastle disease virus infection during heat stress in chicken tracheal epithelial tissue. Sci Rep 2021; 11:7450. [PMID: 33811240 PMCID: PMC8018950 DOI: 10.1038/s41598-021-86795-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Accepted: 03/19/2021] [Indexed: 12/13/2022] Open
Abstract
Newcastle disease (ND) has a great impact on poultry health and welfare with its most virulent (velogenic) strain. In addition, issues exacerbated by the increase in global temperatures necessitates a greater understanding of the host immune response when facing a combination of biotic and abiotic stress factors in poultry production. Previous investigations have revealed that the host immune response is tissue-specific. The goal of this study was to identify genes and/or signaling pathways associated with immune response to NDV (Newcastle disease virus) in the trachea, an essential organ where NDV replicate after the infection, by profiling the tissue specific transcriptome response in two genetically distinct inbred chicken lines when exposed to both abiotic and biotic stressors. Fayoumis appear to be able to respond more effectively (lower viral titer, higher antibody levels, immune gene up-regulation) and earlier than Leghorns. Our results suggest NDV infection in Fayoumis appears to elicit proinflammatory processes, and pathways such as the inhibition of cell viability, cell proliferation of lymphocytes, and transactivation of RNA, more rapidly than in Leghorns. These differences in immune response converge at later timepoints which may indicate that Leghorns eventually regulate its immune response to infection. The profiling of the gene expression response in the trachea adds to our understanding of the chicken host response to NDV infection and heat stress on a whole genome level and provides potential candidate genes and signaling pathways for further investigation into the characterization of the time-specific and pathway specific responses in Fayoumis and Leghorns.
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Abstract
Viral infections lead to the death of more than a million people each year around the world, both directly and indirectly. Viruses interfere with many cell functions, particularly critical pathways for cell death, by affecting various intracellular mediators. MicroRNAs (miRNAs) are a major example of these mediators because they are involved in many (if not most) cellular mechanisms. Virus-regulated miRNAs have been implicated in three cell death pathways, namely, apoptosis, autophagy, and anoikis. Several molecules (e.g., BECN1 and B cell lymphoma 2 [BCL2] family members) are involved in both apoptosis and autophagy, while activation of anoikis leads to cell death similar to apoptosis. These mechanistic similarities suggest that common regulators, including some miRNAs (e.g., miR-21 and miR-192), are involved in different cell death pathways. Because the balance between cell proliferation and cell death is pivotal to the homeostasis of the human body, miRNAs that regulate cell death pathways have drawn much attention from researchers. miR-21 is regulated by several viruses and can affect both apoptosis and anoikis via modulating various targets, such as PDCD4, PTEN, interleukin (IL)-12, Maspin, and Fas-L. miR-34 can be downregulated by viral infection and has different effects on apoptosis, depending on the type of virus and/or host cell. The present review summarizes the existing knowledge on virus-regulated miRNAs involved in the modulation of cell death pathways. Understanding the mechanisms for virus-mediated regulation of cell death pathways could provide valuable information to improve the diagnosis and treatment of many viral diseases.
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miRNA Regulatory Functions in Farm Animal Diseases, and Biomarker Potentials for Effective Therapies. Int J Mol Sci 2021; 22:ijms22063080. [PMID: 33802936 PMCID: PMC8002598 DOI: 10.3390/ijms22063080] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2020] [Revised: 03/03/2021] [Accepted: 03/08/2021] [Indexed: 02/06/2023] Open
Abstract
MicroRNAs (miRNAs) are small endogenous RNAs that regulate gene expression post-transcriptionally by targeting either the 3′ untranslated or coding regions of genes. They have been reported to play key roles in a wide range of biological processes. The recent remarkable developments of transcriptomics technologies, especially next-generation sequencing technologies and advanced bioinformatics tools, allow more in-depth exploration of messenger RNAs (mRNAs) and non-coding RNAs (ncRNAs), including miRNAs. These technologies have offered great opportunities for a deeper exploration of miRNA involvement in farm animal diseases, as well as livestock productivity and welfare. In this review, we provide an overview of the current knowledge of miRNA roles in major farm animal diseases with a particular focus on diseases of economic importance. In addition, we discuss the steps and future perspectives of using miRNAs as biomarkers and molecular therapy for livestock disease management as well as the challenges and opportunities for understanding the regulatory mechanisms of miRNAs related to disease pathogenesis.
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11
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Hong Y, Truong AD, Lee J, Vu TH, Lee S, Song KD, Lillehoj HS, Hong YH. Exosomal miRNA profiling from H5N1 avian influenza virus-infected chickens. Vet Res 2021; 52:36. [PMID: 33658079 PMCID: PMC7931527 DOI: 10.1186/s13567-021-00892-3] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2020] [Accepted: 01/02/2021] [Indexed: 12/31/2022] Open
Abstract
Exosomes are membrane vesicles containing proteins, lipids, DNA, mRNA, and micro RNA (miRNA). Exosomal miRNA from donor cells can regulate the gene expression of recipient cells. Here, Ri chickens were divided into resistant (Mx/A; BF2/B21) and susceptible (Mx/G; BF2/B13) trait by genotyping of Mx and BF2 genes. Then, Ri chickens were infected with H5N1, a highly pathogenic avian influenza virus (HPAIV). Exosomes were purified from blood serum of resistant chickens for small RNA sequencing. Sequencing data were analysed using FastQCv0.11.7, Cutadapt 1.16, miRBase v21, non-coding RNA database, RNAcentral 10.0, and miRDeep2. Differentially expressed miRNAs were determined using statistical methods, including fold-change, exactTest using edgeR, and hierarchical clustering. Target genes were predicted using miRDB. Gene ontology analysis was performed using gProfiler. Twenty miRNAs showed significantly different expression patterns between resistant control and infected chickens. Nine miRNAs were up-regulated and 11 miRNAs were down-regulated in the infected chickens compared with that in the control chickens. In target gene analysis, various immune-related genes, such as cytokines, chemokines, and signalling molecules, were detected. In particular, mitogen-activated protein kinase (MAPK) pathway molecules were highly controlled by differentially expressed miRNAs. The result of qRT-PCR for miRNAs was identical with sequencing data and miRNA expression level was higher in resistant than susceptible chickens. This study will help to better understand the host immune response, particularly exosomal miRNA expression against HPAIV H5N1 and could help to determine biomarkers for disease resistance.
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Affiliation(s)
- Yeojin Hong
- Department of Animal Science and Technology, Chung-Ang University, Anseong, 17546, Republic of Korea
| | - Anh Duc Truong
- Department of Biochemistry and Immunology, National Institute of Veterinary Research, 86 Truong Chinh, Dong Da, Hanoi, 100000, Vietnam
| | - Jiae Lee
- Department of Animal Science and Technology, Chung-Ang University, Anseong, 17546, Republic of Korea
| | - Thi Hao Vu
- Department of Animal Science and Technology, Chung-Ang University, Anseong, 17546, Republic of Korea
| | - Sooyeon Lee
- Department of Animal Science and Technology, Chung-Ang University, Anseong, 17546, Republic of Korea
| | - Ki-Duk Song
- Department of Animal Biotechnology, College of Agricultural and Life Sciences, Jeonbuk National University, Jeonju, 54896, Republic of Korea
| | - Hyun S Lillehoj
- Animal Biosciences and Biotechnology Laboratory, Agricultural Research Services, United States Department of Agriculture, Beltsville, MD, 20705, USA
| | - Yeong Ho Hong
- Department of Animal Science and Technology, Chung-Ang University, Anseong, 17546, Republic of Korea.
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12
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Zhang S, Hong Y, Liu H, Wang Q, Xu J, Zhang Y, Zhao X, Yao Y, Zhou K, Ding X. miR-584 and miR-146 are candidate biomarkers for acute respiratory distress syndrome. Exp Ther Med 2021; 21:445. [PMID: 33747181 DOI: 10.3892/etm.2021.9873] [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: 05/10/2020] [Accepted: 10/06/2020] [Indexed: 12/11/2022] Open
Abstract
MicroRNAs (miRNAs/miRs) have important roles in inflammation and infections, which are common manifestations of acute respiratory distress syndrome (ARDS). The present study aimed to assess whether serum miRNAs are potential diagnostic biomarkers for human ARDS. For this, two sets of serum samples from healthy individuals and patients with ARDS were analysed by high-throughput sequencing to identify differentially expressed genes in ARDS. A total of 679 valid sequences were identified as differentially expressed (P<0.05). Of these, five differentially expressed miRNAs were subjected to reverse transcription-quantitative PCR validation. Finally, two miRNAs (miR-584 and miR-146a) were successfully verified. These two miRNAs were significantly downregulated in the serum of patients with ARDS. Gene Ontology annotations and Kyoto Encyclopedia of Genes and Genomes pathway analysis revealed that their target transcripts were implicated in a broad range of biological processes and various metabolic pathways, including involvement in the regulation of various inflammatory factors. The present study provided a framework for understanding the molecular mechanisms of ARDS and suggested that miR-584 and miR-146a are associated with ARDS and may be potential therapeutic targets.
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Affiliation(s)
- Siquan Zhang
- Intensive Care Unit, XiXi Hospital of Hangzhou, Hangzhou, Zhejiang 310023, P.R. China
| | - Yinuo Hong
- College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, Zhejiang 310018, P.R. China
| | - Huafeng Liu
- Intensive Care Unit, XiXi Hospital of Hangzhou, Hangzhou, Zhejiang 310023, P.R. China
| | - Qianpeng Wang
- College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, Zhejiang 310018, P.R. China
| | - Juan Xu
- College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, Zhejiang 310018, P.R. China
| | - Yujuan Zhang
- Intensive Care Unit, XiXi Hospital of Hangzhou, Hangzhou, Zhejiang 310023, P.R. China
| | - Xi Zhao
- Intensive Care Unit, XiXi Hospital of Hangzhou, Hangzhou, Zhejiang 310023, P.R. China
| | - Yan Yao
- Intensive Care Unit, XiXi Hospital of Hangzhou, Hangzhou, Zhejiang 310023, P.R. China
| | - Kexing Zhou
- Intensive Care Unit, XiXi Hospital of Hangzhou, Hangzhou, Zhejiang 310023, P.R. China
| | - Xianfeng Ding
- College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, Zhejiang 310018, P.R. China
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13
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Yu H, Xu H, Yan C, Zhu S, Lan X, Lu Y, He Q, Yin H, Zhu Q, Zhao X, Li D, Liu Y, Wang Y. gga-miR-148a-5p-Targeting PDPK1 Inhibits Proliferation and Cell Cycle Progression of Avain Leukosis Virus Subgroup J (ALV-J)-Infected Cells. Front Cell Dev Biol 2021; 8:587889. [PMID: 33384993 PMCID: PMC7769946 DOI: 10.3389/fcell.2020.587889] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2020] [Accepted: 11/17/2020] [Indexed: 11/21/2022] Open
Abstract
Avian leukosis virus subgroup J disease (ALV-J) is a contagious and immunosuppressive avian disease caused by ALV-J virus. Although miRNA participate in various biological processes of tumors, little is known about the potential role of miRNA in ALV-J. Our previous miRNA and RNA sequencing data showed that the expression of gga-miR-148a-5p was significantly different in ALV-J-infected chicken spleens compared with non-infected chickens. The aim of this study was to investigate the functional roles of gga-miR-148a-5p and identify downstream targets regulated by gga-miR-148a-5p in ALV-J-infected chickens. We found that the expression of gga-miR-148a-5p was significantly downregulated during ALV-J infection of chicken embryo fibroblasts (CEF). Dual luciferase reporter assays demonstrated that PDPK1 is a direct target gene of gga-miR-148a-5p. In vitro, overexpression of gga-miR-148a-5p significantly promoted ALV-J-infected CEF cell proliferation, included cell cycle, whereas inhibition of gga-miR-148a-5p had an opposite effect. Inhibition of PDPK1 promoted the proliferation of ALV-J-infected cells but had no effect on the activity of NF-κB. Together, these results suggested that gga-miR-148a-5p targets PDPK1 to inhibit the proliferation and cell cycle of ALV-J-infected CEF cells. Our study provides a new understanding for the tumor mechanism of ALV-J infection.
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Affiliation(s)
- Heling Yu
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, China
| | - Hengyong Xu
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, China
| | - Chaoyang Yan
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, China
| | - Shiliang Zhu
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, China
| | - Xi Lan
- College of Animal Science and Technology, Southwest University, Chongqing, China
| | - Yuxiang Lu
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, China
| | - Qijian He
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, China
| | - Huadong Yin
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, China
| | - Qing Zhu
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, China
| | - Xiaoling Zhao
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, China
| | - Diyan Li
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, China
| | - Yiping Liu
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, China
| | - Yan Wang
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, China
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14
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Host factors involved in influenza virus infection. Emerg Top Life Sci 2020; 4:389-398. [PMID: 33210707 DOI: 10.1042/etls20200232] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2020] [Revised: 10/14/2020] [Accepted: 10/30/2020] [Indexed: 12/17/2022]
Abstract
Influenza virus causes an acute febrile respiratory disease in humans that is commonly known as 'flu'. Influenza virus has been around for centuries and is one of the most successful, and consequently most studied human viruses. This has generated tremendous amount of data and information, thus it is pertinent to summarise these for, particularly interdisciplinary readers. Viruses are acellular organisms and exist at the interface of living and non-living. Due to this unique characteristic, viruses require another organism, i.e. host to survive. Viruses multiply inside the host cell and are obligate intracellular pathogens, because their relationship with the host is almost always harmful to host. In mammalian cells, the life cycle of a virus, including influenza is divided into five main steps: attachment, entry, synthesis, assembly and release. To complete these steps, some viruses, e.g. influenza utilise all three parts - plasma membrane, cytoplasm and nucleus, of the cell; whereas others, e.g. SARS-CoV-2 utilise only plasma membrane and cytoplasm. Hence, viruses interact with numerous host factors to complete their life cycle, and these interactions are either exploitative or antagonistic in nature. The host factors involved in the life cycle of a virus could be divided in two broad categories - proviral and antiviral. This perspective has endeavoured to assimilate the information about the host factors which promote and suppress influenza virus infection. Furthermore, an insight into host factors that play a dual role during infection or contribute to influenza virus-host adaptation and disease severity has also been provided.
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15
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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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16
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Bamunuarachchi G, Yang X, Huang C, Liang Y, Guo Y, Liu L. MicroRNA-206 inhibits influenza A virus replication by targeting tankyrase 2. Cell Microbiol 2020; 23:e13281. [PMID: 33099847 DOI: 10.1111/cmi.13281] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2020] [Revised: 10/08/2020] [Accepted: 10/16/2020] [Indexed: 12/31/2022]
Abstract
Due to the frequent mutations, influenza A virus (IAV) becomes resistant to anti-viral drugs targeting influenza viral proteins. There are increasing interests in anti-viral agents that target host cellular proteins required for virus replication. Tankyrase (TNKS) has poly (ADP-ribose) polymerase activity and is a negative regulator of many host proteins. The objectives of this study are to study the role of TNKS2 in IAV infection, identify the microRNAs targeting TNKS2, and to understand the mechanisms involved. We found that TNKS2 expression was elevated in human lung epithelial cells and mouse lungs during IAV infection. Knock-down of TNKS2 by RNA interference reduced viral replication. Using a computation approach and 3'-untranslation regions (3'-UTR) reporter assay, we identified miR-206 as the microRNA that targeted TNKS2. Overexpression of miR-206 reduced viral protein levels and virus production in cell culture. The effect of miR-206 on IAV replication was strain-independent. miR-206 activated JNK/c-Jun signalling, induced type I interferon expression and enhanced Stat signalling. Finally, the delivery of an adenovirus expressing miR-206 into the lung of mice challenged with IAV increased type I interferon response, suppressed viral load in the lungs and increased survival. Our results indicate that miR-206 has anti-influenza activity by targeting TNKS2 and subsequently activating the anti-viral state.
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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, Oklahoma, USA
| | - 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, Stillwater, Oklahoma, 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, Stillwater, Oklahoma, 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, Stillwater, Oklahoma, 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, Oklahoma, USA
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17
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Li K, Chen X, Zhong J, Ye H, Zhang S, Ge D, Wang X, Wu Y. The effects of the Xijiao Dihuang decoction combined with Yinqiao powder on miRNA-mRNA profiles in mice infected with influenza a virus. BMC Complement Med Ther 2020; 20:286. [PMID: 32957919 PMCID: PMC7507722 DOI: 10.1186/s12906-020-03074-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2019] [Accepted: 09/08/2020] [Indexed: 01/12/2023] Open
Abstract
Background MicroRNAs (miRNAs) play vital roles in acute inflammatory and antiviral responses during influenza A virus (IAV) infection. The Xijiao Dihuang decoction combined with Yinqiao powder (XDY) is applied to remedy viral pneumonia in China and its therapeutic efficacy in pneumonic mice challenged with IAV was demonstrated; however, the underlying mechanisms remain elusive. Thus, this study aimed to explore the miRNA-mRNA profiles in the lungs of IAV-infected mice and investigate the therapeutic mechanisms of XDY involving miRNAs and associated pathways. Methods We detected the cellular miRNA contents in the lungs of mice treated with XDY (23 g/kg/d) for A/FM/1/47 (H1N1) (FM1) infection at 4 days postinoculation (dpi) and 7 dpi. MiRNA and mRNA high-throughput sequencing analyses, and miRNA and mRNA qRT-PCR analyses were used to detect and verify the relevant miRNAs and mRNAs. Conjoint analysis, GO enrichment analysis, and KEGG database analysis were applied to identify the miRNA-mRNA regulatory relationships. Results The quantities of differentially expressed miRNAs and mRNAs were upregulated over time. The data showed that 104 miRNAs and 3485 mRNAs were differentially expressed after challenge with FM1 on day 4, while 191 miRNAs and 6126 mRNAs were differentially expressed on day 7. The GO enrichment analysis and KEGG database data showed that the differentially expressed miRNAs and mRNAs were mainly enriched in JNK activity, MAPK phosphatase activity, and the TLR, Jak-STAT and TNF signalling pathways after treatment of FM1 infection with XDY. Generally, the expression trends of differentially expressed miRNAs and mRNAs based on the qRT-PCR results exhibited good consistency with the results of the high-throughput sequencing analysis. Conclusions MiRNAs and mRNAs were differentially expressed during FM1 infection. The therapeutic mechanisms of XDY in FM1-infected mice, might be related to regulating antiviral immunity and ameliorating excessive inflammatory responses by modulating the expression of dysregulated miRNAs and mRNAs involved in the ERK/JNK-AP-1, and IFN-β/STAT signalling pathways.
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Affiliation(s)
- Ke Li
- Department of Microbiology and Immunology, School of Life Sciences, Beijing University of Chinese Medicine, Beijing, 102400, China
| | - Xiaoming Chen
- Department of Microbiology and Immunology, School of Life Sciences, Beijing University of Chinese Medicine, Beijing, 102400, China
| | - Jing Zhong
- Department of Microbiology and Immunology, School of Life Sciences, Beijing University of Chinese Medicine, Beijing, 102400, China
| | - Hehe Ye
- Department of Microbiology and Immunology, School of Life Sciences, Beijing University of Chinese Medicine, Beijing, 102400, China
| | - Shujing Zhang
- Center of Research and Experiments, Institute of Traditional Chinese Medicine, Beijing University of Chinese Medicine, Beijing, 102400, China
| | - Dongyu Ge
- Center of Research and Experiments, Institute of Traditional Chinese Medicine, Beijing University of Chinese Medicine, Beijing, 102400, China
| | - Xudan Wang
- Department of Microbiology and Immunology, School of Life Sciences, Beijing University of Chinese Medicine, Beijing, 102400, China
| | - Ying Wu
- Clinical Medicine Research Centre, Liuzhou People's Hospital, Guangxi Medical University, Liuzhou, 545001, China.
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18
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Epigenetic Regulation by Non-Coding RNAs in the Avian Immune System. Life (Basel) 2020; 10:life10080148. [PMID: 32806547 PMCID: PMC7459779 DOI: 10.3390/life10080148] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Revised: 08/06/2020] [Accepted: 08/10/2020] [Indexed: 12/20/2022] Open
Abstract
The identified non-coding RNAs (ncRNAs) include circular RNAs, long non-coding RNAs, microRNAs, ribosomal RNAs, small interfering RNAs, small nuclear RNAs, piwi-interacting RNAs, and transfer RNAs, etc. Among them, long non-coding RNAs, circular RNAs, and microRNAs are regulatory RNAs that have different functional mechanisms and were extensively participated in various biological processes. Numerous research studies have found that circular RNAs, long non-coding RNAs, and microRNAs played their important roles in avian immune system during the infection of parasites, virus, or bacterium. Here, we specifically review and expand this knowledge with current advances of circular RNAs, long non-coding RNAs, and microRNAs in the regulation of different avian diseases and discuss their functional mechanisms in response to avian diseases.
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19
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O’Dowd K, Emam M, El Khili MR, Emad A, Ibeagha-Awemu EM, Gagnon CA, Barjesteh N. Distinct miRNA Profile of Cellular and Extracellular Vesicles Released from Chicken Tracheal Cells Following Avian Influenza Virus Infection. Vaccines (Basel) 2020; 8:vaccines8030438. [PMID: 32764349 PMCID: PMC7565416 DOI: 10.3390/vaccines8030438] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2020] [Revised: 07/25/2020] [Accepted: 07/30/2020] [Indexed: 01/08/2023] Open
Abstract
Innate responses provide the first line of defense against viral infections, including the influenza virus at mucosal surfaces. Communication and interaction between different host cells at the early stage of viral infections determine the quality and magnitude of immune responses against the invading virus. The release of membrane-encapsulated extracellular vesicles (EVs), from host cells, is defined as a refined system of cell-to-cell communication. EVs contain a diverse array of biomolecules, including microRNAs (miRNAs). We hypothesized that the activation of the tracheal cells with different stimuli impacts the cellular and EV miRNA profiles. Chicken tracheal rings were stimulated with polyI:C and LPS from Escherichia coli 026:B6 or infected with low pathogenic avian influenza virus H4N6. Subsequently, miRNAs were isolated from chicken tracheal cells or from EVs released from chicken tracheal cells. Differentially expressed (DE) miRNAs were identified in treated groups when compared to the control group. Our results demonstrated that there were 67 up-regulated miRNAs, 157 down-regulated miRNAs across all cellular and EV samples. In the next step, several genes or pathways targeted by DE miRNAs were predicted. Overall, this study presented a global miRNA expression profile in chicken tracheas in response to avian influenza viruses (AIV) and toll-like receptor (TLR) ligands. The results presented predicted the possible roles of some DE miRNAs in the induction of antiviral responses. The DE candidate miRNAs, including miR-146a, miR-146b, miR-205a, miR-205b and miR-449, can be investigated further for functional validation studies and to be used as novel prophylactic and therapeutic targets in tailoring or enhancing antiviral responses against AIV.
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Affiliation(s)
- Kelsey O’Dowd
- Research Group on Infectious Diseases in Production Animals (GREMIP), Department of Pathology and Microbiology, Faculty of Veterinary Medicine, University of Montreal, Saint-Hyacinthe, QC J2S 2M2, Canada; (K.O.); (C.A.G.)
- Swine and Poultry Infectious Diseases Research Center (CRIPA), Department of Pathology and Microbiology, Faculty of Veterinary Medicine, University of Montreal, Saint-Hyacinthe, QC J2S 2M2, Canada
- Department of Pathology and Microbiology, Faculty of Veterinary Medicine, University of Montreal, Saint-Hyacinthe, QC J2S 2M2, Canada;
| | - Mehdi Emam
- Department of Pathology and Microbiology, Faculty of Veterinary Medicine, University of Montreal, Saint-Hyacinthe, QC J2S 2M2, Canada;
- McGill University Research Centre on Complex Traits (MRCCT), Department of Human Genetics, Faculty of Medicine, McGill University, Montreal, QC H3G 0B1, Canada
| | - Mohamed Reda El Khili
- Department of Electrical and Computer Engineering, Faculty of Engineering, McGill University, Montreal, QC H3A 0E9, Canada; (M.R.E.K.); (A.E.)
| | - Amin Emad
- Department of Electrical and Computer Engineering, Faculty of Engineering, McGill University, Montreal, QC H3A 0E9, Canada; (M.R.E.K.); (A.E.)
| | - Eveline M. Ibeagha-Awemu
- Sherbrooke Research & Development Centre, Agriculture and Agri-Food Canada, Sherbrooke, QC J1M 0C8, Canada;
| | - Carl A. Gagnon
- Research Group on Infectious Diseases in Production Animals (GREMIP), Department of Pathology and Microbiology, Faculty of Veterinary Medicine, University of Montreal, Saint-Hyacinthe, QC J2S 2M2, Canada; (K.O.); (C.A.G.)
- Swine and Poultry Infectious Diseases Research Center (CRIPA), Department of Pathology and Microbiology, Faculty of Veterinary Medicine, University of Montreal, Saint-Hyacinthe, QC J2S 2M2, Canada
- Department of Pathology and Microbiology, Faculty of Veterinary Medicine, University of Montreal, Saint-Hyacinthe, QC J2S 2M2, Canada;
| | - Neda Barjesteh
- Research Group on Infectious Diseases in Production Animals (GREMIP), Department of Pathology and Microbiology, Faculty of Veterinary Medicine, University of Montreal, Saint-Hyacinthe, QC J2S 2M2, Canada; (K.O.); (C.A.G.)
- Swine and Poultry Infectious Diseases Research Center (CRIPA), Department of Pathology and Microbiology, Faculty of Veterinary Medicine, University of Montreal, Saint-Hyacinthe, QC J2S 2M2, Canada
- Department of Pathology and Microbiology, Faculty of Veterinary Medicine, University of Montreal, Saint-Hyacinthe, QC J2S 2M2, Canada;
- Correspondence: ; Tel.: +1-450-773-8521 (ext. 33191)
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Gga-miR-3525 Targets PDLIM3 through the MAPK Signaling Pathway to Regulate the Proliferation and Differentiation of Skeletal Muscle Satellite Cells. Int J Mol Sci 2020; 21:ijms21155573. [PMID: 32759823 PMCID: PMC7432556 DOI: 10.3390/ijms21155573] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2020] [Revised: 07/24/2020] [Accepted: 07/31/2020] [Indexed: 01/02/2023] Open
Abstract
MicroRNAs (miRNAs) are evolutionarily conserved, small noncoding RNAs that post-transcriptionally regulate expression of their target genes. Emerging evidence demonstrates that miRNAs are important regulators in the development of skeletal muscle satellite cells (SMSCs). Our previous research showed that gga-miR-3525 is differentially expressed in breast muscle of broilers (high growth rate) and layers (low growth rate). In this study, we report a new role for gga-miR-3525 as a myogenic miRNA that regulates skeletal muscle development in chickens. Exogenous increases in the expression of gga-miR-3525 significantly inhibited proliferation and differentiation of SMSCs, whereas the opposite effects were observed in gga-miR-3525 knockdown SMSCs. We confirmed that PDLIM3 (PDZ and LIM domain 3) is a target gene of gga-miR-3525 that can promote proliferation and differentiation of SMSCs. We found that PDLIM3 overexpression elevated the abundance of phosphorylated (p-)p38 protein but that the gga-miR-3525 mimic and p38-MAPK inhibitor (SB203580) weakened the activation of p-p38. Furthermore, treatment with SB203580 reduced the promoting effect of PDLIM3 on SMSC proliferation and differentiation. Overall, our results indicate that gga-miR-3525 regulates the proliferation and differentiation of SMSCs by targeting PDLIM3 via the p38/MAPK signaling pathway in chickens.
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21
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Duan X, Wang L, Sun G, Yan W, Yang Y. Understanding the cross-talk between host and virus in poultry from the perspectives of microRNA. Poult Sci 2020; 99:1838-1846. [PMID: 32241464 PMCID: PMC7587795 DOI: 10.1016/j.psj.2019.11.053] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2019] [Revised: 11/18/2019] [Accepted: 11/18/2019] [Indexed: 01/05/2023] Open
Abstract
In poultry, viral infections (e.g., Marek's disease virus, avian leukosis virus, influenza A virus, and so on) can cause devastating mortality and economic losses. Because viruses are solely dependent on host cells to propagate, they alter the host intracellular microenvironment. Thus, understanding the virus-host interaction is important for antiviral immunity and drug development in the poultry industry. MicroRNAs are crucial posttranscriptional regulators of gene expression in a wide spectrum of biological processes, including viral infection. Recently, microRNAs have been identified as key players in virus-host interactions. In this review, we will discuss the intricacies involved in the virus-host cross-talk mediated by host and viral microRNAs in poultry (i.e., chicken and ducks), as well as recent trends and challenges in this field. These findings may provide some insights into the rapidly developing area of research regarding viral pathogenesis and antiviral immunity in poultry production.
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Affiliation(s)
- Xiujun Duan
- Department of Animal Science and Technology, Jiangsu Agri-animal Husbandry Vocational College, Taizhou 225300, China; National Gene Bank of Waterfowl Resources, Taizhou 225300, China
| | - Lihua Wang
- Department of Animal Science and Technology, Jiangsu Agri-animal Husbandry Vocational College, Taizhou 225300, China
| | - Guobo Sun
- Department of Animal Science and Technology, Jiangsu Agri-animal Husbandry Vocational College, Taizhou 225300, China; National Gene Bank of Waterfowl Resources, Taizhou 225300, China
| | - Wenying Yan
- School of Biology and Basic Medical Sciences, Medical College of Soochow University, Suzhou 215123, China.
| | - Yang Yang
- School of Computer Science and Technology, Soochow University, Suzhou 215123, China.
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22
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Kemp V, Laconi A, Cocciolo G, Berends AJ, Breit TM, Verheije MH. miRNA repertoire and host immune factor regulation upon avian coronavirus infection in eggs. Arch Virol 2020; 165:835-843. [PMID: 32025807 PMCID: PMC7086581 DOI: 10.1007/s00705-020-04527-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2019] [Accepted: 09/20/2019] [Indexed: 02/08/2023]
Abstract
Avian infectious bronchitis virus (IBV) is a coronavirus with great economic impact on the poultry industry, causing an acute and highly contagious disease in chickens that primarily affects the respiratory and reproductive systems. The cellular regulation of IBV pathogenesis and the host immune responses involved remain to be fully elucidated. MicroRNAs (miRNAs) have emerged as a class of crucial regulators of numerous cellular processes, including responses to viral infections. Here, we employed a high-throughput sequencing approach to analyze the miRNA composition of the spleen and the lungs of chicken embryos upon IBV infection. Compared to healthy chicken embryos, 13 and six miRNAs were upregulated in the spleen and the lungs, respectively, all predicted to influence viral transcription, cytokine production, and lymphocyte functioning. Subsequent downregulation of NFATC3, NFAT5, SPPL3, and TGFB2 genes in particular was observed only in the spleen, demonstrating the biological functionality of the miRNAs in this lymphoid organ. This is the first study that describes the modulation of miRNAs and the related host immune factors by IBV in chicken embryos. Our data provide novel insight into complex virus-host interactions and specifically highlight components that could affect the host's immune response to IBV infection.
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Affiliation(s)
- Vera Kemp
- Faculty of Veterinary Medicine, Department Biomolecular Health Sciences, Division Pathology, Utrecht University, Utrecht, The Netherlands
| | - Andrea Laconi
- Faculty of Veterinary Medicine, Department Biomolecular Health Sciences, Division Pathology, Utrecht University, Utrecht, The Netherlands.,Department of Comparative Biomedicine and Food Science, University of Padua, Legnaro, Italy
| | - Giulio Cocciolo
- Department of Veterinary Medicine, University of Bari, Valenzano, Italy
| | - Alinda J Berends
- Faculty of Veterinary Medicine, Department Biomolecular Health Sciences, Division Pathology, Utrecht University, Utrecht, The Netherlands
| | - Timo M Breit
- RNA Biology and Applied Bioinformatics Research Group, Swammerdam Institute for Life Sciences, Faculty of Science, University of Amsterdam, Amsterdam, The Netherlands
| | - M Hélène Verheije
- Faculty of Veterinary Medicine, Department Biomolecular Health Sciences, Division Pathology, Utrecht University, Utrecht, The Netherlands.
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23
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Abstract
MicroRNAs (miRNAs) are small, non-coding RNA molecules that inhibit protein translation from target mRNAs. Accumulating evidence suggests that miRNAs can regulate a broad range of biological pathways, including cell differentiation, apoptosis, and carcinogenesis. With the development of miRNAs, the investigation of miRNA functions has emerged as a hot research field. Due to the intensive farming in recent decades, chickens are easily influenced by various pathogen transmissions, and this has resulted in large economic losses. Recent reports have shown that miRNAs can play critical roles in the regulation of chicken diseases. Therefore, the aim of this review is to briefly discuss the current knowledge regarding the effects of miRNAs on chickens suffering from common viral diseases, mycoplasmosis, necrotic enteritis, and ovarian tumors. Additionally, the detailed targets of miRNAs and their possible functions are also summarized. This review intends to highlight the key role of miRNAs in regard to chickens and presents the possibility of improving chicken disease resistance through the regulation of miRNAs.
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Yang Y, Qin X, Meng X, Zhu X, Zhang X, Li Y, Zhang Z. MicroRNA Expression Profile in Peripheral Blood Lymphocytes of Sheep Vaccinated with Nigeria 75/1 Peste Des Petits Ruminants Virus. Viruses 2019; 11:v11111025. [PMID: 31694166 PMCID: PMC6893480 DOI: 10.3390/v11111025] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2019] [Revised: 10/25/2019] [Accepted: 10/31/2019] [Indexed: 12/15/2022] Open
Abstract
Peste des petits ruminants (PPR) is one of the highly contagious transboundary viral diseases of small ruminants. Host microRNA (miRNA) expression patterns may change in response to virus infection, and it mainly works as a post-transcriptional moderator in gene expression and affects viral pathogenesis and replication. In this study, the change of miRNA expression profile in peripheral blood lymphocyte (PBMC) from sheep inoculated with PPR vaccine virus in vivo as well as primary sheep testicular (ST) cells inoculated with PPR vaccine virus in vitro were determined via deep sequencing technology. In PBMC cells, 373 and 115 differentially expressed miRNAs (DEmiRNAs) were identified 3 days and 5 days post inoculated (dpi), respectively. While, 575 DEmiRNAs were identified when comparing miRNA profiles on 5 dpi with 3 dpi. Some of the DEmiRNAs were found to change significantly via time-course during PPR vaccine virus inoculated. Similarly, in ST cells, 136 DEmiRNAs were identified at 3 dpi in comparison with mock-inoculation. A total of 12 DEmiRNAs were validated by real-time quantitative PCR (RT-qPCR). The oar-miR-150, oar-miR-370-3p and oar-miR-411b-3p were found common differentially expressed in both PPR vaccine virus-inoculated PBMC cells and ST cells. Targets prediction and functional analysis of the DEmiRNAs uncovered mainly gathering in antigen processing and presentation pathways, protein processing in endoplasmic reticulum pathways and cell adhesion molecules pathways. Our study supplies information about the DEmiRNAs in PPR vaccine virus-inoculated PBMC cells and ST cells, and provides clues for further understanding the function of miRNAs in PPR vaccine virus replication.
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Affiliation(s)
| | | | | | | | | | - Yanmin Li
- Correspondence: ; Tel.: +86-0931-8374622
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25
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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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26
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Peroxisome proliferator-activated receptor gamma (PPARγ), a key regulatory gene of lipid metabolism in chicken. WORLD POULTRY SCI J 2019. [DOI: 10.1017/s0043933916000684] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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27
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Functional genomics in chicken (Gallus gallus) - status and implications in poultry. WORLD POULTRY SCI J 2019. [DOI: 10.1017/s004393391400004x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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28
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Genetic lines respond uniquely within the chicken thymic transcriptome to acute heat stress and low dose lipopolysaccharide. Sci Rep 2019; 9:13649. [PMID: 31541148 PMCID: PMC6754502 DOI: 10.1038/s41598-019-50051-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2019] [Accepted: 08/31/2019] [Indexed: 12/16/2022] Open
Abstract
Exposure to high temperatures is known to impair immune functions and disease resistance of poultry. Characterizing changes in the transcriptome can help identify mechanisms by which immune tissues, such as the thymus, respond to heat stress. In this study, 22-day-old chickens from two genetic lines (a relatively resistant Fayoumi line and a more susceptible broiler line) were exposed to acute heat stress (35 °C) and/or immune simulation with lipopolysaccharide (LPS; 100 µg/kg). Transcriptome responses in the thymus were identified by RNA-sequencing (RNA-seq). Expression of most genes was unaffected by heat and/or LPS in the Fayoumi line, whereas these treatments had more impact in the broiler line. Comparisons between the broiler and Fayoumi transcriptomes identified a large number of significant genes both at homeostasis and in response to treatment. Functional analyses predicted that gene expression changes impact immune responses, apoptosis, cell activation, migration, and adhesion. In broilers, acute heat stress changed thymic expression responses to LPS and could impact thymocyte survival and trafficking, and thereby contribute to the negative effects of high temperatures on immune responses. Identification of these genes and pathways provides a foundation for testing targets to improve disease resistance in heat-stressed chickens.
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29
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Lin J, Wang Z, Wang J, Yang Q. Microarray analysis of infectious bronchitis virus infection of chicken primary dendritic cells. BMC Genomics 2019; 20:557. [PMID: 31286855 PMCID: PMC6615177 DOI: 10.1186/s12864-019-5940-6] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2018] [Accepted: 06/26/2019] [Indexed: 02/07/2023] Open
Abstract
Background Avian infectious bronchitis virus (IBV) is a major respiratory disease-causing agent in birds that leads to significant losses. Dendritic cells (DCs) are specialised cells responsible for sampling antigens and presenting them to T cells, which also play an essential role in recognising and neutralising viruses. Recent studies have suggested that non-coding RNAs may regulate the functional program of DCs. Expression of host non-coding RNAs changes markedly during infectious bronchitis virus infection, but their role in regulating host immune function has not been explored. Here, microarrays of mRNAs, miRNAs, and lncRNAs were globally performed to analyse how avian DCs respond to IBV. Results First, we found that IBV stimulation did not enhance the maturation ability of avian DCs. Interestingly, inactivated IBV was better able than IBV to induce DC maturation and activate lymphocytes. We identified 1093 up-regulated and 845 down-regulated mRNAs in IBV-infected avian DCs. Gene Ontology analysis suggested that cellular macromolecule and protein location (GO-BP) and transcription factor binding (GO-MF) were abundant in IBV-stimulated avian DCs. Meanwhile, pathway analysis indicated that the oxidative phosphorylation and leukocyte transendothelial migration signalling pathways might be activated in the IBV group. Moreover, alteration of microRNAs (miRNAs) and long non-coding RNAs (lncRNAs) was detected in IBV-stimulated avian DCs. In total, 19 significantly altered (7 up and 12 down) miRNAs and 101 (75 up and 26 down) lncRNAs were identified in the IBV-treated group. Further analysis showed that the actin cytoskeleton and MAPK signal pathway were related to the target genes of IBV-stimulated miRNAs. Finally, our study identified 2 TF-microRNA and 53 TF–microRNA–mRNA interactions involving 1 TF, 2 miRNAs, and 53 mRNAs in IBV-stimulated avian DCs. Conclusions Our research suggests a new mechanism to explain why IBV actively blocks innate responses needed for inducing immune gene expression and also provides insight into the pathogenic mechanisms of avian IBV. Electronic supplementary material The online version of this article (10.1186/s12864-019-5940-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Jian Lin
- College of Life Sciences, Nanjing Agricultural University, Wei gang 1, Nanjing, Jiangsu, 210095, People's Republic of China.,College of Veterinary medicine, Nanjing Agricultural University, Wei gang 1, Nanjing, Jiangsu, 210095, People's Republic of China
| | - Zhisheng Wang
- National Veterinary Product Engineering Research Center, Jiangsu Academy of Agricultural Sciences, Nanjing, China
| | - Jialu Wang
- College of Veterinary medicine, Nanjing Agricultural University, Wei gang 1, Nanjing, Jiangsu, 210095, People's Republic of China
| | - Qian Yang
- College of Life Sciences, Nanjing Agricultural University, Wei gang 1, Nanjing, Jiangsu, 210095, People's Republic of China. .,College of Veterinary medicine, Nanjing Agricultural University, Wei gang 1, Nanjing, Jiangsu, 210095, People's Republic of China.
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30
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Yakovlev AF. The Role of miRNA in Differentiation, Cell Proliferation, and Pathogenesis of Poultry Diseases. Russ J Dev Biol 2019. [DOI: 10.1134/s1062360419030081] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
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31
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Al-Shaer AE, Flentke GR, Berres ME, Garic A, Smith SM. Exon level machine learning analyses elucidate novel candidate miRNA targets in an avian model of fetal alcohol spectrum disorder. PLoS Comput Biol 2019; 15:e1006937. [PMID: 30973878 PMCID: PMC6478348 DOI: 10.1371/journal.pcbi.1006937] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2018] [Revised: 04/23/2019] [Accepted: 03/11/2019] [Indexed: 12/20/2022] Open
Abstract
Gestational alcohol exposure causes fetal alcohol spectrum disorder (FASD) and is a prominent cause of neurodevelopmental disability. Whole transcriptome sequencing (RNA-Seq) offer insights into mechanisms underlying FASD, but gene-level analysis provides limited information regarding complex transcriptional processes such as alternative splicing and non-coding RNAs. Moreover, traditional analytical approaches that use multiple hypothesis testing with a false discovery rate adjustment prioritize genes based on an adjusted p-value, which is not always biologically relevant. We address these limitations with a novel approach and implemented an unsupervised machine learning model, which we applied to an exon-level analysis to reduce data complexity to the most likely functionally relevant exons, without loss of novel information. This was performed on an RNA-Seq paired-end dataset derived from alcohol-exposed neural fold-stage chick crania, wherein alcohol causes facial deficits recapitulating those of FASD. A principal component analysis along with k-means clustering was utilized to extract exons that deviated from baseline expression. This identified 6857 differentially expressed exons representing 1251 geneIDs; 391 of these genes were identified in a prior gene-level analysis of this dataset. It also identified exons encoding 23 microRNAs (miRNAs) having significantly differential expression profiles in response to alcohol. We developed an RDAVID pipeline to identify KEGG pathways represented by these exons, and separately identified predicted KEGG pathways targeted by these miRNAs. Several of these (ribosome biogenesis, oxidative phosphorylation) were identified in our prior gene-level analysis. Other pathways are crucial to facial morphogenesis and represent both novel (focal adhesion, FoxO signaling, insulin signaling) and known (Wnt signaling) alcohol targets. Importantly, there was substantial overlap between the exomes themselves and the predicted miRNA targets, suggesting these miRNAs contribute to the gene-level expression changes. Our novel application of unsupervised machine learning in conjunction with statistical analyses facilitated the discovery of signaling pathways and miRNAs that inform mechanisms underlying FASD.
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Affiliation(s)
- Abrar E. Al-Shaer
- Nutrition Research Institute, Department of Nutrition, University of North Carolina at Chapel Hill, Kannapolis, North Carolina, United States of America
| | - George R. Flentke
- Nutrition Research Institute, Department of Nutrition, University of North Carolina at Chapel Hill, Kannapolis, North Carolina, United States of America
| | - Mark E. Berres
- Department of Nutritional Sciences, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Ana Garic
- Department of Nutritional Sciences, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Susan M. Smith
- Nutrition Research Institute, Department of Nutrition, University of North Carolina at Chapel Hill, Kannapolis, North Carolina, United States of America
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32
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Upregulated gga-miR-16-5p Inhibits the Proliferation Cycle and Promotes the Apoptosis of MG-Infected DF-1 Cells by Repressing PIK3R1-Mediated the PI3K/Akt/NF-κB Pathway to Exert Anti-Inflammatory Effect. Int J Mol Sci 2019; 20:ijms20051036. [PMID: 30818821 PMCID: PMC6429190 DOI: 10.3390/ijms20051036] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2019] [Revised: 02/21/2019] [Accepted: 02/25/2019] [Indexed: 12/11/2022] Open
Abstract
Mycoplasma gallisepticum (MG) mainly infects chickens to initiate chronic respiratory disease (CRD). microRNAs (miRNAs) play vital roles according to previously reported studies. Our previous study showed that gga-miR-16-5p, in MG-infected lungs of chicken embryo, was upregulated by Illumina sequencing. The study aimed to reveal what role gga-miR-16-5p plays in CRD progression. gga-miR-16-5p was upregulated in MG-infected fibroblast cells (DF-1). Phosphoinositide-3-kinase regulatory subunit 1 (PIK3R1) was demonstrated as the target gene of gga-miR-16-5p. Furthermore, PIK3R1 expression was lower in MG-infected groups than it in noninfected controls measured by qPCR. Additionally, overexpressed gga-miR-16-5p could downregulate PIK3R1 and phosphorylated serine/threonine kinase (p-Akt) to express protein, whereas there is an opposite effect on inhibition. Overexpressed gga-miR-16-5p resulted in decreased activity of tumor necrosis factor alpha (TNF-α) and the nuclear factor-kappaB (NF-κB) by qPCR. Furthermore, overexpressed gga-miR-16-5p restricted cell multiplication, cycle progression, and increased apoptosis of MG-infected DF-1 cells, whereas inhibited gga-miR-16-5p led to the opposite effect. Collectively, upregulated gga-miR-16-5p could decrease multiplication, cycle progression, and increase apoptosis of MG-infected DF-1 cells, at least partly through directly targeting PIK3R1 and inhibiting PI3K/Akt/NF-κB pathway to exert an anti-inflammatory effect. Our results will provide more experimental evidence to bring pathogenesis of MG infection to light.
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33
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Khanduri A, Sahu AR, Wani SA, Khan RIN, Pandey A, Saxena S, Malla WA, Mondal P, Rajak KK, Muthuchelvan D, Mishra B, Sahoo AP, Singh YP, Singh RK, Gandham RK, Mishra BP. Dysregulated miRNAome and Proteome of PPRV Infected Goat PBMCs Reveal a Coordinated Immune Response. Front Immunol 2018; 9:2631. [PMID: 30524425 PMCID: PMC6262310 DOI: 10.3389/fimmu.2018.02631] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2018] [Accepted: 10/25/2018] [Indexed: 12/11/2022] Open
Abstract
In this study, the miRNAome and proteome of virulent Peste des petits ruminants virus (PPRV) infected goat peripheral blood mononuclear cells (PBMCs) were analyzed. The identified differentially expressed miRNAs (DEmiRNAs) were found to govern genes that modulate immune response based on the proteome data. The top 10 significantly enriched immune response processes were found to be governed by 98 genes. The top 10 DEmiRNAs governing these 98 genes were identified based on the number of genes governed by them. Out of these 10 DEmiRNAs, 7 were upregulated, and 3 were downregulated. These include miR-664, miR-2311, miR-2897, miR-484, miR-2440, miR-3533, miR-574, miR-210, miR-21-5p, and miR-30. miR-664 and miR-484 with proviral and antiviral activities, respectively, were upregulated in PPRV infected PBMCs. miR-210 that inhibits apoptosis was downregulated. miR-21-5p that decreases the sensitivity of cells to the antiviral activity of IFNs and miR-30b that inhibits antigen processing and presentation by primary macrophages were downregulated, indicative of a strong host response to PPRV infection. miR-21-5p was found to be inhibited on IPA upstream regulatory analysis of RNA-sequencing data. This miRNA that was also highly downregulated and was found to govern 16 immune response genes in the proteome data was selected for functional validation vis-a-vis TGFBR2 (TGF-beta receptor type-2). TGFBR2 that regulates cell differentiation and is involved in several immune response pathways was found to be governed by most of the identified immune modulating DEmiRNAs. The decreased luciferase activity in Dual Luciferase Reporter Assay indicated specific binding of miR-21-5p and miR-484 to their target thus establishing specific binding of the miRNAs to their targets.This is the first report on the miRNAome and proteome of virulent PPRV infected goat PBMCs.
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Affiliation(s)
- Alok Khanduri
- Division of Veterinary Biotechnology, ICAR-Indian Veterinary Research Institute (IVRI), Bareilly, India
| | - Amit Ranjan Sahu
- Division of Veterinary Biotechnology, ICAR-Indian Veterinary Research Institute (IVRI), Bareilly, India.,DBT-National Institute of Animal Biotechnology, Hyderabad, India
| | - Sajad Ahmad Wani
- Division of Veterinary Biotechnology, ICAR-Indian Veterinary Research Institute (IVRI), Bareilly, India.,The Ohio State University, Columbus, Ohio, OH, United States
| | - Raja Ishaq Nabi Khan
- Division of Veterinary Biotechnology, ICAR-Indian Veterinary Research Institute (IVRI), Bareilly, India
| | - Aruna Pandey
- Division of Veterinary Biotechnology, ICAR-Indian Veterinary Research Institute (IVRI), Bareilly, India
| | - Shikha Saxena
- Division of Veterinary Biotechnology, ICAR-Indian Veterinary Research Institute (IVRI), Bareilly, India
| | - Waseem Akram Malla
- Division of Veterinary Biotechnology, ICAR-Indian Veterinary Research Institute (IVRI), Bareilly, India
| | - Piyali Mondal
- Division of Veterinary Biotechnology, ICAR-Indian Veterinary Research Institute (IVRI), Bareilly, India
| | - Kaushal Kishor Rajak
- Division of Biological Products, ICAR-Indian Veterinary Research Institute (IVRI), Bareilly, India
| | - D Muthuchelvan
- Division of Virology, ICAR-Indian Veterinary Research Institute (IVRI), Mukteswar, India
| | - Bina Mishra
- Division of Biological Products, ICAR-Indian Veterinary Research Institute (IVRI), Bareilly, India
| | - Aditya P Sahoo
- ICAR- Directorate of Foot and Mouth Disease, Mukteswar, India
| | - Yash Pal Singh
- ARIS Cell, ICAR-Indian Veterinary Research Institute (IVRI), Bareilly, India
| | - Raj Kumar Singh
- Division of Veterinary Biotechnology, ICAR-Indian Veterinary Research Institute (IVRI), Bareilly, India
| | - Ravi Kumar Gandham
- Division of Veterinary Biotechnology, ICAR-Indian Veterinary Research Institute (IVRI), Bareilly, India.,DBT-National Institute of Animal Biotechnology, Hyderabad, India
| | - Bishnu Prasad Mishra
- Division of Veterinary Biotechnology, ICAR-Indian Veterinary Research Institute (IVRI), Bareilly, India
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Ouyang W, Qian J, Pan QX, Wang JY, Xia XX, Wang XL, Zhu YM, Wang YS. gga-miR-142-5p attenuates IRF7 signaling and promotes replication of IBDV by directly targeting the chMDA5's 3' untranslated region. Vet Microbiol 2018; 221:74-80. [PMID: 29981711 DOI: 10.1016/j.vetmic.2018.05.018] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2018] [Revised: 05/21/2018] [Accepted: 05/29/2018] [Indexed: 01/12/2023]
Abstract
Chicken melanoma differentiation-associated gene 5 (chMDA5) is a key pattern recognition receptor (PRR) that recognizes RNA viral infections and initiates an antiviral innate immune response in chickens. MicroRNAs (miRNAs) are involved in the regulation of chMDA5 to sense RNA virus infection, but how it exerts antiviral activity against infectious bursal disease virus (IBDV) infection and regulates chMDA5 in chicken cells is unclear. Thus, we measured the expression of chMDA5 in IBDV-infected DT40 cells and found it significantly increased. Overexpression of chMDA5 activated the IFN-β and Mx promoters via IRF7-dependent pathways and inhibited replication of IBDV in DT40 cells. The opposite effect occurred after chMDA5 knockdown using siRNA. Also, gga-miR-142-5p regulated chMDA5 according to bioinformatic analysis and data from a dual-luciferase reporter system. Overexpression of gga-miR-142-5p reduced the expression of the chMDA5 protein, promoting IBDV replication, and decreased the activity of the IFN-β and Mx promoters via an IRF7-dependent pathway; however, it had no effect on the NF-κB-dependent pathway in DT40 cells. Thus, gga-miR-142-5p is a negative regulator of chMDA5 and promotes IBDV replication in DT40 cells through an IRF7-dependent pathway.
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Affiliation(s)
- Wei Ouyang
- Institute of Veterinary Medicine, Jiangsu Academy of Agricultural Sciences/Key Laboratory of Veterinary Biological Engineering and Technology, Ministry of Agriculture, Nanjing 210014, China; Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou 225009, China
| | - Jing Qian
- Institute of Veterinary Medicine, Jiangsu Academy of Agricultural Sciences/Key Laboratory of Veterinary Biological Engineering and Technology, Ministry of Agriculture, Nanjing 210014, China
| | - Qun-Xing Pan
- Institute of Veterinary Medicine, Jiangsu Academy of Agricultural Sciences/Key Laboratory of Veterinary Biological Engineering and Technology, Ministry of Agriculture, Nanjing 210014, China
| | - Jing-Yu Wang
- Institute of Veterinary Medicine, Jiangsu Academy of Agricultural Sciences/Key Laboratory of Veterinary Biological Engineering and Technology, Ministry of Agriculture, Nanjing 210014, China
| | - Xing-Xia Xia
- Institute of Veterinary Medicine, Jiangsu Academy of Agricultural Sciences/Key Laboratory of Veterinary Biological Engineering and Technology, Ministry of Agriculture, Nanjing 210014, China
| | - Xiao-Li Wang
- Institute of Veterinary Medicine, Jiangsu Academy of Agricultural Sciences/Key Laboratory of Veterinary Biological Engineering and Technology, Ministry of Agriculture, Nanjing 210014, China
| | - Yu-Mei Zhu
- Institute of Veterinary Medicine, Jiangsu Academy of Agricultural Sciences/Key Laboratory of Veterinary Biological Engineering and Technology, Ministry of Agriculture, Nanjing 210014, China
| | - Yong-Shan Wang
- Institute of Veterinary Medicine, Jiangsu Academy of Agricultural Sciences/Key Laboratory of Veterinary Biological Engineering and Technology, Ministry of Agriculture, Nanjing 210014, China.
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35
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Zheng Y, Fu X, Wang L, Zhang W, Zhou P, Zhang X, Zeng W, Chen J, Cao Z, Jia K, Li S. Comparative analysis of MicroRNA expression in dog lungs infected with the H3N2 and H5N1 canine influenza viruses. Microb Pathog 2018; 121:252-261. [PMID: 29772263 DOI: 10.1016/j.micpath.2018.05.015] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2018] [Revised: 05/10/2018] [Accepted: 05/11/2018] [Indexed: 11/16/2022]
Abstract
MicroRNAs, a class of noncoding RNAs 18 to 23 nucleotides (nt) in length, play critical roles in a wide variety of biological processes. The objective of this study was to examine differences in microRNA expression profiles derived from the lungs of beagle dogs infected with the avian-origin H3N2 canine influenza virus (CIV) or the highly pathogenic avian influenza (HPAI) H5N1 virus (canine-origin isolation strain). After dogs were infected with H3N2 or H5N1, microRNA expression in the lungs was assessed using a deep-sequencing approach. To identify the roles of microRNAs in viral pathogenicity and the host immune response, microRNA target genes were predicted, and their functions were analyzed using bioinformatics software. A total of 229 microRNAs were upregulated in the H5N1 infection group compared with those in the H3N2 infection group, and 166 microRNAs were downregulated. MicroRNA target genes in the H5N1 group were more significantly involved in metabolic pathways, such as glycerolipid metabolism and glycerophospholipid metabolism, than those in the H3N2 group. The inhibition of metabolic pathways may lead to appetite loss, weight loss and weakened immunity. Moreover, miR-485, miR-144, miR-133b, miR-4859-5p, miR-6902-3p, miR-7638, miR-1307-3p and miR-1346 were significantly altered microRNAs that potentially led to the inhibition of innate immune pathways and the heightened pathogenicity of H5N1 compared with that of H3N2 in dogs. This study deepens our understanding of the complex relationships among microRNAs, the influenza virus-mediated immune response and immune injury in dogs.
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Affiliation(s)
- Yun Zheng
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, Guangdong Province 510642, People's Republic of China; Guangdong Provincial Key Laboratory of Prevention and Control for Severe Clinical Animal Diseases, Guangzhou, Guangdong Province 510642, People's Republic of China; Guangdong Provincial Pet Engineering Technology Research Center, Guangzhou, Guangdong Province 510642, People's Republic of China
| | - Xinliang Fu
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, Guangdong Province 510642, People's Republic of China; Guangdong Provincial Key Laboratory of Prevention and Control for Severe Clinical Animal Diseases, Guangzhou, Guangdong Province 510642, People's Republic of China
| | - Lifang Wang
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, Guangdong Province 510642, People's Republic of China; Guangdong Provincial Key Laboratory of Prevention and Control for Severe Clinical Animal Diseases, Guangzhou, Guangdong Province 510642, People's Republic of China; Guangdong Provincial Pet Engineering Technology Research Center, Guangzhou, Guangdong Province 510642, People's Republic of China
| | - Wenyan Zhang
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, Guangdong Province 510642, People's Republic of China
| | - Pei Zhou
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, Guangdong Province 510642, People's Republic of China; Guangdong Provincial Key Laboratory of Prevention and Control for Severe Clinical Animal Diseases, Guangzhou, Guangdong Province 510642, People's Republic of China; Guangdong Provincial Pet Engineering Technology Research Center, Guangzhou, Guangdong Province 510642, People's Republic of China
| | - Xin Zhang
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, Guangdong Province 510642, People's Republic of China; Guangdong Provincial Key Laboratory of Prevention and Control for Severe Clinical Animal Diseases, Guangzhou, Guangdong Province 510642, People's Republic of China; Guangdong Provincial Pet Engineering Technology Research Center, Guangzhou, Guangdong Province 510642, People's Republic of China
| | - Weijie Zeng
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, Guangdong Province 510642, People's Republic of China; Guangdong Provincial Key Laboratory of Prevention and Control for Severe Clinical Animal Diseases, Guangzhou, Guangdong Province 510642, People's Republic of China; Guangdong Provincial Pet Engineering Technology Research Center, Guangzhou, Guangdong Province 510642, People's Republic of China
| | - Jidang Chen
- School of Life Science and Engineering, Foshan University, Guangzhou, People's Republic of China
| | - Zongxi Cao
- Hainan Academy of Agricultural Science, Hainan, People's Republic of China
| | - Kun Jia
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, Guangdong Province 510642, People's Republic of China; Guangdong Provincial Key Laboratory of Prevention and Control for Severe Clinical Animal Diseases, Guangzhou, Guangdong Province 510642, People's Republic of China; Guangdong Provincial Pet Engineering Technology Research Center, Guangzhou, Guangdong Province 510642, People's Republic of China.
| | - Shoujun Li
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, Guangdong Province 510642, People's Republic of China; Guangdong Provincial Key Laboratory of Prevention and Control for Severe Clinical Animal Diseases, Guangzhou, Guangdong Province 510642, People's Republic of China; Guangdong Provincial Pet Engineering Technology Research Center, Guangzhou, Guangdong Province 510642, People's Republic of China.
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Deist MS, Lamont SJ. What Makes the Harderian Gland Transcriptome Different From Other Chicken Immune Tissues? A Gene Expression Comparative Analysis. Front Physiol 2018; 9:492. [PMID: 29867543 PMCID: PMC5952037 DOI: 10.3389/fphys.2018.00492] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2018] [Accepted: 04/17/2018] [Indexed: 11/13/2022] Open
Abstract
The Harderian gland is a sparsely characterized immune tissue known to play an important role in local immunity. The function of the Harderian gland, however, is not clearly defined. Measuring the expression of all genes using RNA-seq enables the identification of genes, pathways, or networks of interest. Our relative RNA-seq expression analysis compared the chicken Harderian gland transcriptome to other important primary and secondary immune tissues including the bursa of Fabricius, thymus, and spleen of non-challenged birds. A total of 2,386 transcripts were identified as highly expressed in the Harderian gland. Gene set enrichment showed the importance of G-protein coupled receptor signaling and several immune pathways. Among the genes highly expressed in the Harderian gland were 48 miRNAs, a category of genetic elements involved in regulation of gene expression. Several identified miRNAs have immune related functions. This analysis gives insight to the unique immune processes inherent in the Harderian gland.
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Affiliation(s)
- Melissa S Deist
- Department of Animal Science, Iowa State University, Ames, IA, United States
| | - Susan J Lamont
- Department of Animal Science, Iowa State University, Ames, IA, United States
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Zhang N, Bao YJ, Tong AHY, Zuyderduyn S, Bader GD, Malik Peiris JS, Lok S, Lee SMY. Whole transcriptome analysis reveals differential gene expression profile reflecting macrophage polarization in response to influenza A H5N1 virus infection. BMC Med Genomics 2018; 11:20. [PMID: 29475453 PMCID: PMC6389164 DOI: 10.1186/s12920-018-0335-0] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2017] [Accepted: 01/25/2018] [Indexed: 11/10/2022] Open
Abstract
Background Avian influenza A H5N1 virus can cause lethal disease in humans. The virus can trigger severe pneumonia and lead to acute respiratory distress syndrome. Data from clinical, in vitro and in vivo suggest that virus-induced cytokine dysregulation could be a contributory factor to the pathogenesis of human H5N1 disease. However, the precise mechanism of H5N1 infection eliciting the unique host response are still not well understood. Methods To obtain a better understanding of the molecular events at the earliest time points, we used RNA-Seq to quantify and compare the host mRNA and miRNA transcriptomes induced by the highly pathogenic influenza A H5N1 (A/Vietnam/3212/04) or low virulent H1N1 (A/Hong Kong/54/98) viruses in human monocyte-derived macrophages at 1-, 3-, and 6-h post infection. Results Our data reveals that two macrophage populations corresponding to M1 (classically activated) and M2 (alternatively activated) macrophage subtypes respond distinctly to H5N1 virus infection when compared to H1N1 virus or mock infection, a distinction that could not be made from previous microarray studies. When this confounding variable is considered in our statistical model, a clear set of dysregulated genes and pathways emerges specifically in H5N1 virus-infected macrophages at 6-h post infection, whilst was not found with H1N1 virus infection. Furthermore, altered expression of genes in these pathways, which have been previously implicated in viral host response, occurs specifically in the M1 subtype. We observe a significant up-regulation of genes in the RIG-I-like receptor signaling pathway. In particular, interferons, and interferon-stimulated genes are broadly affected. The negative regulators of interferon signaling, the suppressors of cytokine signaling, SOCS-1 and SOCS-3, were found to be markedly up-regulated in the initial round of H5N1 virus replication. Elevated levels of these suppressors could lead to the eventual suppression of cellular antiviral genes, contributing to pathophysiology of H5N1 virus infection. Conclusions Our study provides important mechanistic insights into the understanding of H5N1 viral pathogenesis and the multi-faceted host immune responses. The dysregulated genes could be potential candidates as therapeutic targets for treating H5N1 disease. Electronic supplementary material The online version of this article (10.1186/s12920-018-0335-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Na Zhang
- Centre for Genomic Sciences, The University of Hong Kong, Hong Kong, China
| | - Yun-Juan Bao
- Centre for Genomic Sciences, The University of Hong Kong, Hong Kong, China.,W.M. Keck Center for Transgene Research, University of Notre Dame, Notre Dame, IN, USA
| | - Amy Hin-Yan Tong
- Centre for Genomic Sciences, The University of Hong Kong, Hong Kong, China.,The Donnelly Centre, University of Toronto, Toronto, ON, Canada
| | | | - Gary D Bader
- The Donnelly Centre, University of Toronto, Toronto, ON, Canada
| | - J S Malik Peiris
- HKU-Pasteur Research Pole and Centre of Influenza Research, School of Public Health, The University of Hong Kong, Hong Kong, China
| | - Si Lok
- Centre for Genomic Sciences, The University of Hong Kong, Hong Kong, China. .,The Centre for Applied Genomics (TCAG), The Hospital for Sick Children, Toronto, ON, Canada.
| | - Suki Man-Yan Lee
- HKU-Pasteur Research Pole and Centre of Influenza Research, School of Public Health, The University of Hong Kong, Hong Kong, China.
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Cui L, Markou A, Stratton CW, Lianidou E. Diagnosis and Assessment of Microbial Infections with Host and Microbial MicroRNA Profiles. ADVANCED TECHNIQUES IN DIAGNOSTIC MICROBIOLOGY 2018. [PMCID: PMC7119978 DOI: 10.1007/978-3-319-95111-9_23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
MicroRNAs (miRNAs) encoded by viral genome or host have been found participating in host-microbe interactions. Differential expression profiles of miRNAs were shown linking to specific disease pathologies which indicated its potency as diagnostic/prognostic biomarkers of infectious disease. This was emphasized by the discovery of circulating miRNAs which were found to be remarkably stable in mammalian biofluids. Standardized methods of miRNA quantification including RNA isolation should be established before they will be ready for use in clinical practice.
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Resistant and susceptible chicken lines show distinctive responses to Newcastle disease virus infection in the lung transcriptome. BMC Genomics 2017; 18:989. [PMID: 29281979 PMCID: PMC5745900 DOI: 10.1186/s12864-017-4380-4] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2017] [Accepted: 12/11/2017] [Indexed: 01/28/2023] Open
Abstract
Background Newcastle disease virus (NDV) is a threat to poultry production worldwide. A better understanding of mechanisms of resistance and susceptibility to this virus will improve measures for NDV prevention and control. Males and females from resistant Fayoumi and susceptible Leghorn lines were either challenged with a lentogenic strain of the virus or given a mock infection at 3 weeks of age. The lung transcriptomes generated by RNA-seq were studied using contrasts across the challenged and nonchallenged birds, the two lines, and three time points post-infection, and by using Weighted Gene Co-expression Network Analysis (WGNCA). Results Genetic line and sex had a large impact on the lung transcriptome. When contrasting the challenged and nonchallenged birds, few differentially expressed genes (DEG) were identified within each line at 2, 6, and 10 days post infection (dpi), except for the more resistant Fayoumi line at 10 dpi, for which several pathways were activated and inhibited at this time. The interaction of challenge and line at 10 dpi significantly impacted 131 genes (False Discovery Rate (FDR) <0.05), one of which was PPIB. Many DEG were identified between the Fayoumi and Leghorns. The number of DEG between the two lines in the challenged birds decreased over time, but increased over time in the nonchallenged birds. The nonchallenged Fayoumis at 10 dpi showed enrichment of immune type cells when compared to 2 dpi, suggesting important immune related development at this age. These changes between 10 and 2 dpi were not identified in the challenged Fayoumis. The energy allocated to host defense may have interrupted normal lung development. WGCNA identified important modules and driver genes within those modules that were associated with traits of interest, several of which had no known associated function. Conclusions The lines’ unique response to NDV offers insights into the potential means of their resistance and susceptibility. The lung transcriptome shows a unique response to lentogenic NDV compared to a previous study on the trachea of the same birds. It is important to analyze multiple tissues in order to best understand the chicken’s overall response to NDV challenge and improve strategies to combat this devastating disease. Electronic supplementary material The online version of this article (10.1186/s12864-017-4380-4) contains supplementary material, which is available to authorized users.
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40
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Yang X, Gao W, Liu H, Li J, Chen D, Yuan F, Zhang Z, Wang H. MicroRNA transcriptome analysis in chicken kidneys in response to differing virulent infectious bronchitis virus infections. Arch Virol 2017; 162:3397-3405. [PMID: 28779232 DOI: 10.1007/s00705-017-3502-2] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2017] [Accepted: 06/19/2017] [Indexed: 10/19/2022]
Abstract
Infectious bronchitis virus (IBV) can cause a highly contagious and acute respiratory disease in poultry. MicroRNAs (miRNAs) have emerged as a class of crucial regulators for gene expression and are involved in the regulation of virus defence and immunological processes. To understand miRNA regulation in chickens in response to IBV infection, high-throughput sequencing was performed to compare the small RNA libraries from the kidneys of chicken infected with SCK2, SCDY2 and LDT3-A. By comparing these data to healthy chickens, a total of 58 differentially expressed (DE) miRNAs were identified. The DE miRNAs were further classified into five miRNA expression patterns (up or down regulation compared to control). Using Gene Ontology (GO) enrichment prediction, the DE miRNAs were shown to be mostly associated with metabolic processes, catalytic activities, gene expression, binding activities and immune responses. Seven highly expressed miRNAs (gga-miR-30d, gga-miR-1454, gga-miR-7b, gga-miR-215-5p, gga-miR-1a-3p, gga-miR-3538 and gga-miR-2954) were selected for miRNA-mRNA conjoint analysis. Furthermore, the miRNAs inversely correlated with the corresponding target gene mRNAs. These seven miRNAs were considered to play an important role in IBV-host interactions and the differing virulence of IBV strains. This is the first demonstration that infection with different virulent IBVs elicits different expression of miRNAs in chicken kidneys; this expression also seems to be associated with the virulence of IBV. These results are significant for the study of immune responses to infection with different virulent IBVs mediated by miRNAs as well as the interaction between the chicken host and IBV.
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Affiliation(s)
- Xin Yang
- School of Life Science, Sichuan University, Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, Chengdu, 610065, Sichuan, China
| | - Wenqian Gao
- School of Life Science, Sichuan University, Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, Chengdu, 610065, Sichuan, China
| | - Hui Liu
- School of Life Science, Sichuan University, Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, Chengdu, 610065, Sichuan, China
| | - Jianan Li
- School of Life Science, Sichuan University, Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, Chengdu, 610065, Sichuan, China
| | - Danyu Chen
- School of Life Science, Sichuan University, Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, Chengdu, 610065, Sichuan, China
| | - Feng Yuan
- School of Life Science, Sichuan University, Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, Chengdu, 610065, Sichuan, China
| | - Zhikun Zhang
- School of Life Science, Sichuan University, Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, Chengdu, 610065, Sichuan, China
| | - Hongning Wang
- School of Life Science, Sichuan University, Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, Chengdu, 610065, Sichuan, China.
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Gga-miR-219b targeting BCL11B suppresses proliferation, migration and invasion of Marek's disease tumor cell MSB1. Sci Rep 2017; 7:4247. [PMID: 28652615 PMCID: PMC5484716 DOI: 10.1038/s41598-017-04434-w] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2016] [Accepted: 05/16/2017] [Indexed: 12/19/2022] Open
Abstract
Marek’s disease (MD), caused by Marek’s disease virus (MDV), is a lymphotropic neoplastic disease. Previous miRNAome analysis showed gga-miR-219b was significantly downregulated in MDV-induced lymphoma, and one of its potential target genes, B-cell chronic lymphocytic /lymphoma 11B (BCL11B) was predicted. In this study, we further investigated the function of gga-miR-219b, and the gain/loss of function assay showed gga-miR-219b inhibited cell migration and reduced cell proliferation by promoting apoptosis not by cell cycle arrest. Gga-miR-219b also suppressed expression of two cell invasion-related genes MMP2 and MMP9. The results indicated suppressive effect of gga-miR-219b on MD tumorigenesis. The gene BCL11B was verified as a direct target gene of gga-miR-219b. RNA interference was performed to block BCL11B. As expected, the effects triggered by BCL11B downregulation were in accordance with that triggered by gga-miR-219b overexpression, suggesting that BCL11B was a stimulative regulator of MD transformation. Moreover, both gga-miR-219b and BCL11B influenced the expression of Meq gene, the most important oncogene in MDV. Additionally, gene expression level of anti-apoptotic genes BCL2 and BCL2L1 was downregulated and pro-apoptotic gene TNFSF10 was upregulated in MSB1 cells with gga-miR-219b overexpression or BCL11B knockdown, which suggested gga-miR-219b promoted cell apoptosis via regulating gene expression in the apoptosis pathways.
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Pandey A, Sahu AR, Wani SA, Saxena S, Kanchan S, Sah V, Rajak KK, Khanduri A, Sahoo AP, Tiwari AK, Mishra B, Muthuchelvan D, Mishra BP, Singh RK, Gandham RK. Modulation of Host miRNAs Transcriptome in Lung and Spleen of Peste des Petits Ruminants Virus Infected Sheep and Goats. Front Microbiol 2017; 8:1146. [PMID: 28694795 PMCID: PMC5483481 DOI: 10.3389/fmicb.2017.01146] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2017] [Accepted: 06/06/2017] [Indexed: 12/16/2022] Open
Abstract
Peste des petits ruminants (PPR) is one of the highly contagious viral disease, characterized by fever, sore mouth, conjunctivitis, gastroenteritis, and pneumonia, primarily affecting sheep and goats. Reports suggested variable host response in goats and sheep and this host response vis-a-vis the expression of microRNAs (miRNAs) has not been investigated. Here, miRNAs were sequenced and proteomics data were generated to identify the role of differentially expressed miRNA (DEmiRNA) in PPR virus (PPRV) infected lung and spleen tissues of sheep and goats. In lungs, 67 and 37 DEmiRNAs have been identified in goats and sheep, respectively. Similarly, in spleen, 50 and 56 DEmiRNAs were identified in goats and sheep, respectively. A total of 20 and 11 miRNAs were found to be common differentially expressed in both the species in PPRV infected spleen and lung, respectively. Six DEmiRNAs—miR-21-3p, miR-1246, miR-27a-5p, miR-760-3p, miR-320a, and miR-363 were selected based on their role in viral infections, apoptosis, and fold change. The target prediction analysis of these six selected DEmiRNAs from the proteome data generated, revealed involvement of more number of genes in lung and spleen of goats than in sheep. On gene ontology analysis of host target genes these DEmiRNAs were found to regulate several immune response signaling pathways. It was observed that the pathways viz. T cell receptor signaling, Rap1 signaling, Toll-like receptor signaling, and B cell receptor signaling governed by DEmiRNAs were more perturbed in goats than in sheep. The data suggests that PPRV-induced miR-21-3p, miR-320a, and miR-363 might act cooperatively to enhance viral pathogenesis in the lung and spleen of sheep by downregulating several immune response genes. The study gives an important insight into the molecular pathogenesis of PPR by identifying that the PPRV—Izatnagar/94 isolate elicits a strong host response in goats than in sheep.
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Affiliation(s)
- Aruna Pandey
- Computational Biology and Genomics Facility Lab, Division of Veterinary Biotechnology, Indian Council of Agricultural Research-Indian Veterinary Research Institute, BareillyIndia
| | - Amit R Sahu
- Computational Biology and Genomics Facility Lab, Division of Veterinary Biotechnology, Indian Council of Agricultural Research-Indian Veterinary Research Institute, BareillyIndia
| | - Sajad A Wani
- Computational Biology and Genomics Facility Lab, Division of Veterinary Biotechnology, Indian Council of Agricultural Research-Indian Veterinary Research Institute, BareillyIndia
| | - Shikha Saxena
- Computational Biology and Genomics Facility Lab, Division of Veterinary Biotechnology, Indian Council of Agricultural Research-Indian Veterinary Research Institute, BareillyIndia
| | - Sonam Kanchan
- Computational Biology and Genomics Facility Lab, Division of Veterinary Biotechnology, Indian Council of Agricultural Research-Indian Veterinary Research Institute, BareillyIndia
| | - Vaishali Sah
- Computational Biology and Genomics Facility Lab, Division of Veterinary Biotechnology, Indian Council of Agricultural Research-Indian Veterinary Research Institute, BareillyIndia
| | - Kaushal K Rajak
- Division of Biological Products, Indian Council of Agricultural Research-Indian Veterinary Research Institute, BareillyIndia
| | - Alok Khanduri
- Computational Biology and Genomics Facility Lab, Division of Veterinary Biotechnology, Indian Council of Agricultural Research-Indian Veterinary Research Institute, BareillyIndia
| | - Aditya P Sahoo
- Computational Biology and Genomics Facility Lab, Division of Veterinary Biotechnology, Indian Council of Agricultural Research-Indian Veterinary Research Institute, BareillyIndia
| | - Ashok K Tiwari
- Division of Biological Standardization, Indian Council of Agricultural Research-Indian Veterinary Research Institute, BareillyIndia
| | - Bina Mishra
- Division of Biological Products, Indian Council of Agricultural Research-Indian Veterinary Research Institute, BareillyIndia
| | - D Muthuchelvan
- Division of Virology, Indian Council of Agricultural Research-Indian Veterinary Research Institute, NainitalIndia
| | - Bishnu P Mishra
- Computational Biology and Genomics Facility Lab, Division of Veterinary Biotechnology, Indian Council of Agricultural Research-Indian Veterinary Research Institute, BareillyIndia
| | - Raj K Singh
- Computational Biology and Genomics Facility Lab, Division of Veterinary Biotechnology, Indian Council of Agricultural Research-Indian Veterinary Research Institute, BareillyIndia
| | - Ravi K Gandham
- Computational Biology and Genomics Facility Lab, Division of Veterinary Biotechnology, Indian Council of Agricultural Research-Indian Veterinary Research Institute, BareillyIndia
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Zhao Y, Wang Z, Hou Y, Zhang K, Peng X. gga-miR-99a targets SMARCA5 to regulate Mycoplasma gallisepticum (HS strain) infection by depressing cell proliferation in chicken. Gene 2017; 627:239-247. [PMID: 28652181 DOI: 10.1016/j.gene.2017.06.039] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2017] [Revised: 06/16/2017] [Accepted: 06/20/2017] [Indexed: 10/19/2022]
Abstract
Mycoplasma gallisepticum (MG), one of the primary etiological agents of poultry chronic respiratory disease, has caused significant economic losses worldwide, and increasing evidence has recently indicated that miRNAs are involved in its microbial pathogenesis. gga-miR-99a, a member of the miR-99 family, plays an essential role in a variety of diseases. Through miRNA Solexa sequencing, we previously found that gga-miR-99a is significantly down-regulated in the lungs of MG-infected chicken embryos. In this study, we further verified that the expression of gga-miR-99 was significantly down-regulated in both MG-infected lungs and a chicken embryonic fibroblast cell line (DF-1) by qPCR. Moreover, we predicted and validated SMARCA5 as its target gene through a luciferase reporter assay, qPCR, and western blot analysis. The over-expression of gga-miR-99a significantly depressed SMARCA5 expression, whereas a gga-miR-99a inhibitor enhanced the expression of SMARCA5. Inversely, SMARCA5 was significantly up-regulated and gga-miR-99a was obviously down-regulated in MG-HS-infected chicken embryonic lungs and DF-1 cells. At 72h post-transfection, the over-expression of gga-miR-99a significantly repressed the proliferation of DF-1 cells by inhibiting the transition from the G1 phase to the S and G2 phases. This study reveals that gga-miR-99a plays a key role in MG infection through the regulation of SMARCA5 expression and provides new insights regarding the mechanisms of MG pathogenesis.
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Affiliation(s)
- Yabo Zhao
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction (Huazhong Agricultural University), Ministry of Education, College of Animal Science and Technology & College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China
| | - Zaiwei Wang
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction (Huazhong Agricultural University), Ministry of Education, College of Animal Science and Technology & College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China
| | - Yue Hou
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction (Huazhong Agricultural University), Ministry of Education, College of Animal Science and Technology & College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China
| | - Kang Zhang
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction (Huazhong Agricultural University), Ministry of Education, College of Animal Science and Technology & College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China
| | - Xiuli Peng
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction (Huazhong Agricultural University), Ministry of Education, College of Animal Science and Technology & College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China.
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Chen Q, Tong C, Ma S, Zhou L, Zhao L, Zhao X. Involvement of MicroRNAs in Probiotics-Induced Reduction of the Cecal Inflammation by Salmonella Typhimurium. Front Immunol 2017; 8:704. [PMID: 28659929 PMCID: PMC5468434 DOI: 10.3389/fimmu.2017.00704] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2017] [Accepted: 05/31/2017] [Indexed: 12/20/2022] Open
Abstract
The microRNAs (miRNAs) have been shown to play important roles in the development of the immune system and in regulation of host inflammation responses. Probiotics can effectively alleviate the inflammation caused by Salmonella in chickens. However, whether and how miRNAs are involved in modulation of the inflammation response in the gut of chickens have not been reported. In this study, the impact of a probiotics, Lactobacillus plantarum Z01 (LPZ01), was investigated on the cecal miRNAs and cytokine secretions in Salmonella Typhimurium (S. Typhimurium)-infected chickens at the age of 3 days. Newly hatched chicks were assigned to four groups (1): NC (basal diet) (2): S (basal diet + S. Typhimurium challenged) (3): SP (basal diet + S. Typhimurium challenged + LPZ01) (4): P (basal diet + LPZ01). In comparison with the S group, chicks in the SP group reduced the number of S. Typhimurium and had lower levels of interferon-γ and lipopolysaccharide-induced tumor necrosis factor alpha factor (LITAF) in ceca post challenge. Expression of 14 miRNAs was significantly affected by the presence of S. Typhimurium and/or lactobacillus. Five differential expression miRNAs (gga-miR-215-5p, gga-miR-3525, gga-miR-193a-5p, gga-miR-122-5p, and gga-miR-375) were randomly selected for confirmation by the RT-PCR. Predicted target genes of differentially expressed miRNAs were enriched in regulation of cAMP-dependent protein kinase activity, stress-activated MAPK cascade, immune system development and regulation of immune system process as well as in immune related pathways such as MAPK and Wnt signaling pathways. The relationship between changes of miRNAs and changes of cytokines was explored. Finally, 119 novel miRNAs were identified in 36 libraries totally. Identification of novel miRNAs significantly expanded the repertoire of chicken miRNAs and provided the basis for understanding the function of miRNAs in the host. Our results suggest that the probiotics reduce the inflammation of the S. Typhimurium infection in neonatal broiler chicks, at least partially, through regulation of miRNAs expression.
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Affiliation(s)
- Qiaoling Chen
- College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Chao Tong
- College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Shaoyang Ma
- College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Luoxiong Zhou
- College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Lili Zhao
- College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Xin Zhao
- College of Animal Science and Technology, Northwest A&F University, Yangling, China.,Department of Animal Science, McGill University, Montreal, QC, Canada
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Chen W, Yi L, Feng S, Zhao L, Li J, Zhou M, Liang R, Gu N, Wu Z, Tu J, Lin L. Characterization of microRNAs in orange-spotted grouper (Epinephelus coioides) fin cells upon red-spotted grouper nervous necrosis virus infection. FISH & SHELLFISH IMMUNOLOGY 2017; 63:228-236. [PMID: 28232192 DOI: 10.1016/j.fsi.2017.02.031] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/25/2016] [Revised: 02/17/2017] [Accepted: 02/18/2017] [Indexed: 06/06/2023]
Abstract
Nervous necrosis virus (NNV), one of the most prevalent fish pathogens, has caused fatal disease of viral nervous necrosis (VNN) in many marine and freshwater fishes, and resulted in heavy economic losses in aquaculture industry worldwide. However, the molecular mechanisms underlying the pathogenicity of NNV remain elusive. In this study, the expression profiles of microRNA (miRNA) were investigated in grouper fin (GF-1) cells infected with red-spotted grouper nervous necrosis virus (RGNNV) via deep sequencing technique. The results showed that a total of 220 miRNAs were identified by aligning the small RNA sequences with the miRNA database of zebrafish, and 18 novel miRNAs were predicted using miRDeep2 software. Compared with the non-infected groups, 51 and 16 differentially expressed miRNAs (DE-miRNAs) were identified in the samples infected with RGNNV at 3 and 24 h, respectively. Six DE-miRNAs were randomly selected to validate their expressions using quantitative reverse transcription polymerase chain reaction (qRT-PCR), the results showed that their expression profiles were consistent with those obtained by deep sequencing. The target genes of the DE-miRNAs covered a wide range of functions, such as regulation of transcription, oxidation-reduction process, proteolysis, regulation of apoptotic process, and immune response. In addition, the effects of four DE-miRNAs including miR-1, miR-30b, miR-150, and miR-184 on RGNNV replication were evaluated, and the results showed that over-expression of each of the four miRNAs promoted the replication of RGNNV. These data provide insight into the molecular mechanism of RGNNV infection, and will benefit for the development of effective strategies to control RGNNV infection.
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Affiliation(s)
- Wenjie Chen
- College of Animal Sciences and Technology, Zhongkai University of Agriculture and Engineering, Guangzhou, Guangdong, 510225, China; Department of Aquatic Animal Medicine, College of Fisheries, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
| | - Lizhu Yi
- Department of Aquatic Animal Medicine, College of Fisheries, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
| | - Shuangshuang Feng
- Department of Aquatic Animal Medicine, College of Fisheries, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
| | - Lijuan Zhao
- College of Animal Sciences and Technology, Zhongkai University of Agriculture and Engineering, Guangzhou, Guangdong, 510225, China; Department of Aquatic Animal Medicine, College of Fisheries, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
| | - Jun Li
- College of Animal Sciences and Technology, Zhongkai University of Agriculture and Engineering, Guangzhou, Guangdong, 510225, China; School of Biological Sciences, Lake Superior State University, Sault Ste. Marie, MI 49783, USA
| | - Meng Zhou
- College of Animal Sciences and Technology, Zhongkai University of Agriculture and Engineering, Guangzhou, Guangdong, 510225, China
| | - Rishen Liang
- College of Animal Sciences and Technology, Zhongkai University of Agriculture and Engineering, Guangzhou, Guangdong, 510225, China
| | - Na Gu
- College of Animal Sciences and Technology, Zhongkai University of Agriculture and Engineering, Guangzhou, Guangdong, 510225, China
| | - Zaohe Wu
- College of Animal Sciences and Technology, Zhongkai University of Agriculture and Engineering, Guangzhou, Guangdong, 510225, China
| | - Jiagang Tu
- Department of Aquatic Animal Medicine, College of Fisheries, Huazhong Agricultural University, Wuhan, Hubei, 430070, China.
| | - Li Lin
- College of Animal Sciences and Technology, Zhongkai University of Agriculture and Engineering, Guangzhou, Guangdong, 510225, China; Department of Aquatic Animal Medicine, College of Fisheries, Huazhong Agricultural University, Wuhan, Hubei, 430070, China.
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Wu N, Zhu Q, Chen B, Gao J, Xu Z, Li D. High-throughput sequencing of pituitary and hypothalamic microRNA transcriptome associated with high rate of egg production. BMC Genomics 2017; 18:255. [PMID: 28335741 PMCID: PMC5364632 DOI: 10.1186/s12864-017-3644-3] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2016] [Accepted: 03/18/2017] [Indexed: 01/21/2023] Open
Abstract
Background MicroRNAs exist widely in viruses, plants and animals. As endogenous small non-coding RNAs, miRNAs regulate a variety of biological processes. Tissue miRNA expression studies have discovered numerous functions for miRNAs in various tissues of chicken, but the regulation of miRNAs in chicken pituitary and hypothalamic development related to high and low egg-laying performance has remained unclear. Results In this study, using high-throughput sequencing technology, we sequenced two tissues (pituitary and hypothalamus) in 3 high- and 3 low-rate egg production Luhua chickens at the age of 300 days. By comparing low- and high-rate egg production chickens, 46 known miRNAs and 27 novel miRNAs were identified as differentially expressed (P < 0.05). Six differentially expressed known miRNAs, which are expressed in both tissues, were used in RT-qPCR validation and SNP detection. Among them, seven SNPs in two miRNA precursors (gga-miR-1684a and gga-miR-1434) were found that might enhance or reduce the production of the mature miRNAs. In addition, 124 and 30 reciprocally expressed miRNA-target pairs were identified by RNA-seq in pituitary and hypothalamic tissues, respectively and randomly selected candidate miRNA and miRNA-target pairs were validated by RT-qPCR in Jiuyuan black fowl. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway annotation illustrated that a large number of egg laying-related pathways were enriched in the high-rate egg production chickens, including ovarian steroidogenesis and steroid hormone biosynthesis. Conclusions These differentially expressed miRNAs and their predicted target genes, especially identified reciprocally expressed miRNA-target pairs, advance the study of miRNA function and egg production associated miRNA identification. The analysis of the miRNA-related SNPs and their effects provided insights into the effects of SNPs on miRNA biogenesis and function. The data generated in this study will further our understanding of miRNA regulation mechanisms in the chicken egg-laying process. Electronic supplementary material The online version of this article (doi:10.1186/s12864-017-3644-3) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Nan Wu
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, People's Republic of China, 610000
| | - Qing Zhu
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, People's Republic of China, 610000
| | - Binlong Chen
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, People's Republic of China, 610000
| | - Jian Gao
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, People's Republic of China, 610000
| | - Zhongxian Xu
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, People's Republic of China, 610000
| | - Diyan Li
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, People's Republic of China, 610000.
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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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Mishra A, Vijayakumar P, Raut AA. Emerging avian influenza infections: Current understanding of innate immune response and molecular pathogenesis. Int Rev Immunol 2017; 36:89-107. [PMID: 28272907 DOI: 10.1080/08830185.2017.1291640] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The highly pathogenic avian influenza viruses (HPAIVs) cause severe disease in gallinaceous poultry species, domestic ducks, various aquatic and terrestrial wild bird species as well as humans. The outcome of the disease is determined by complex interactions of multiple components of the host, the virus, and the environment. While the host-innate immune response plays an important role for clearance of infection, excessive inflammatory immune response (cytokine storm) may contribute to morbidity and mortality of the host. Therefore, innate immunity response in avian influenza infection has two distinct roles. However, the viral pathogenic mechanism varies widely in different avian species, which are not completely understood. In this review, we summarized the current understanding and gaps in host-pathogen interaction of avian influenza infection in birds. In first part of this article, we summarized influenza viral pathogenesis of gallinaceous and non-gallinaceous avian species. Then we discussed innate immune response against influenza infection, cytokine storm, differential host immune responses against different pathotypes, and response in different avian species. Finally, we reviewed the systems biology approach to study host-pathogen interaction in avian species for better characterization of molecular pathogenesis of the disease. Wild aquatic birds act as natural reservoir of AIVs. Better understanding of host-pathogen interaction in natural reservoir is fundamental to understand the properties of AIV infection and development of improved vaccine and therapeutic strategies against influenza.
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Affiliation(s)
- Anamika Mishra
- a Pathogenomics Laboratory , OIE Reference Laboratory for Avian Influenza, ICAR-National Institute of High Security Animal Diseases , Bhopal , Madhya Pradesh , India
| | - Periyasamy Vijayakumar
- a Pathogenomics Laboratory , OIE Reference Laboratory for Avian Influenza, ICAR-National Institute of High Security Animal Diseases , Bhopal , Madhya Pradesh , India
| | - Ashwin Ashok Raut
- a Pathogenomics Laboratory , OIE Reference Laboratory for Avian Influenza, ICAR-National Institute of High Security Animal Diseases , Bhopal , Madhya Pradesh , India
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Wu G, Qi Y, Liu X, Yang N, Xu G, Liu L, Li X. Cecal MicroRNAome response to Salmonella enterica serovar Enteritidis infection in White Leghorn Layer. BMC Genomics 2017; 18:77. [PMID: 28086873 PMCID: PMC5237128 DOI: 10.1186/s12864-016-3413-8] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2016] [Accepted: 12/12/2016] [Indexed: 01/27/2023] Open
Abstract
Background Salmonella enterica serovar Enteritidis (SE) is a food-borne pathogen and of great threat to human health through consuming the contaminated poultry products. MicroRNAs (miRNAs) play an important role in different biological activities and have been shown to regulate the innate immunity in the bacterial infection. The objective of this study is to identify miRNAs associated with SE infection in laying chicken cecum. Results Average number of reads of three libraries constructed from infected and non-infected chickens was 12,476,156 and 10,866,976, respectively. There were 598 miRNAs including 194 potential novel miRNAs identified in which 37 miRNAs were significantly differentially expressed between infected and non-infected chickens. In total, 2897 unique target genes regulated by differentially expressed miRNAs were predicted, in which, 841 genes were uniquely regulated by up-regulated miRNAs (G1), 636 genes were uniquely regulated by down-regulated miRNAs (G2), and 1420 were co-regulated by both up and down- regulated miRNAs (G3). There were 118, 73 and 178 GO (Gene ontology) BP (Biological process) terms significantly enriched in G1, G2 and G3 groups, respectively. More immune-related GO BP terms than metabolism-related terms were found in G1. Expression of 12 immune-related genes of four differentially expressed miRNAs was detected through qRT-PCR. The regulatory direction of gga-miR-1416-5p, gga-miR-1662, and gga-miR-34a-5p were opposite with the target genes of TLR21, BCL10, TLR1LA, NOTCH2 and THBS1, respectively. Conclusion The miRNAs contribute to the response to SE infection at the onset of egg laying through regulating the homeostasis between metabolism and immunity. The gga-miR-125b-5p, gga-miR-34a-5p, gga-miR-1416-5p and gga-miR-1662 could play an important role in SE infection through regulating their target genes. The finding herein will pave the foundation for the studies of microRNA regulation in SE infection in laying hens. Electronic supplementary material The online version of this article (doi:10.1186/s12864-016-3413-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Guixian Wu
- College of Animal Science and Technology, Shandong Agricultural University, Tai'an, Shandong, 271018, China
| | - Yukai Qi
- College of Animal Science and Technology, Shandong Agricultural University, Tai'an, Shandong, 271018, China
| | - Xiaoyi Liu
- College of Animal Science and Technology, Shandong Agricultural University, Tai'an, Shandong, 271018, China
| | - Ning Yang
- College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Guiyun Xu
- College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Liying Liu
- College of Life Science, Shandong Agricultural University, Tai'an, Shandong, 271018, China.
| | - Xianyao Li
- College of Animal Science and Technology, Shandong Agricultural University, Tai'an, Shandong, 271018, China. .,Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, Tai'an, Shandong, 271018, China.
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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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