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Jaglan K, Dhaka SS, Magotra A, Patil CS, Ghanghas A. Exploring MicroRNA biogenesis, applications and bioinformatics analysis in livestock: A comprehensive review. Reprod Domest Anim 2024; 59:e14529. [PMID: 38268204 DOI: 10.1111/rda.14529] [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: 08/29/2023] [Revised: 12/20/2023] [Accepted: 01/04/2024] [Indexed: 01/26/2024]
Abstract
Small non-coding RNAs called microRNAs (miRNAs) control the expression of genes post-transcriptionally. Their correlation with commercial economic traits including milk, meat and egg production, as well as their effective role in animal productivity, fertility, embryo survival and disease resistance, make them significant in livestock research. The miRNAs exhibit distinct spatial and temporal expression patterns, offering insights into their functional roles within cells and tissues. Aberrant miRNA production can disrupt vital cellular processes and genetic networks, contributing to conditions like metabolic disorders and viral diseases. These short RNA molecules are present in extracellular fluids, displaying remarkable stability against RNA degradation enzymes and extreme environmental conditions. miRNAs preservation is facilitated through packaging in lipid vesicles or complex formation with RNA-binding proteins. Numerous studies have illuminated the roles of miRNAs in diverse physiological processes, including embryonic stem cell differentiation, haematopoietic stem cell proliferation and differentiation and the coordinated development of organ systems. The integration of miRNA profiling, next-generation sequencing and bioinformatics analysis paves the way for transformative advancements in livestock research and industry. The present review underscores the applications of miRNAs in livestock, showcasing their potential to improve breeding strategies, diagnose diseases and enhance our understanding of fundamental biological processes.
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Affiliation(s)
- Komal Jaglan
- Department of Animal Genetics & Breeding, Lala Lajpat Rai University of Veterinary and Animal Sciences, Hisar, Haryana, India
| | - S S Dhaka
- Department of Animal Genetics & Breeding, Lala Lajpat Rai University of Veterinary and Animal Sciences, Hisar, Haryana, India
| | - Ankit Magotra
- Department of Animal Genetics & Breeding, Lala Lajpat Rai University of Veterinary and Animal Sciences, Hisar, Haryana, India
| | - C S Patil
- Department of Animal Genetics & Breeding, Lala Lajpat Rai University of Veterinary and Animal Sciences, Hisar, Haryana, India
| | - Amandeep Ghanghas
- Department of Livestock Production Management, Lala Lajpat Rai University of Veterinary and Animal Sciences, Hisar, Haryana, India
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Tahamtan A, Samadizadeh S, Salimi V, Natarelli L, Nakstad B. Editorial: miRNAs and inflammation: from biogenesis to therapeutic option. Front Immunol 2023; 14:1296589. [PMID: 37854607 PMCID: PMC10579885 DOI: 10.3389/fimmu.2023.1296589] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2023] [Accepted: 09/22/2023] [Indexed: 10/20/2023] Open
Affiliation(s)
- Alireza Tahamtan
- Department of Microbiology, Golestan University of Medical Sciences, Gorgan, Iran
- Infectious Diseases Research Center, Golestan University of Medical Sciences, Gorgan, Iran
| | - Saeed Samadizadeh
- Department of Microbiology, Golestan University of Medical Sciences, Gorgan, Iran
- Infectious Diseases Research Center, Golestan University of Medical Sciences, Gorgan, Iran
| | - Vahid Salimi
- Department of Virology, Tehran University of Medical Sciences, Tehran, Iran
| | - Lucia Natarelli
- Institute for Cardiovascular Prevention, Ludwig-Maximillians University, Munich, Germany
| | - Britt Nakstad
- Department of Paediatrics and Adolescent Health, University of Botswana, Gaborone, Botswana
- Division of Paediatrics and Adeolescent Medicine, Institute of Clinical Medicine, University of Oslo, Oslo, Norway
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3
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Samir M. Editorial: Host response to veterinary infectious diseases: role of coding and non-coding RNAs as biomarkers and disease modulators. Front Vet Sci 2023; 10:1275169. [PMID: 37711434 PMCID: PMC10497942 DOI: 10.3389/fvets.2023.1275169] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2023] [Accepted: 08/14/2023] [Indexed: 09/16/2023] Open
Affiliation(s)
- Mohamed Samir
- The Immunogenetics Group, The Pirbright Institute, Woking, United Kingdom
- Department of Zoonoses, Faculty of Veterinary Medicine, Zagazig University, Zagazig, Egypt
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Wu B, Yang J, Dai Y, Xiong L. Combination of the BISAP Score and miR-155 is Applied in Predicting the Severity of Acute Pancreatitis. Int J Gen Med 2022; 15:7467-7474. [PMID: 36187163 PMCID: PMC9519123 DOI: 10.2147/ijgm.s384068] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Accepted: 09/14/2022] [Indexed: 11/24/2022] Open
Abstract
Purpose To evaluate the predictive value of combination of Bedside Index for Severity in AP (BISAP) score and miR-155 for the severity of acute pancreatitis (AP). Patients and Methods A total of 1046 AP patients were divided into control group and case group according to the severity of AP [mild and moderately severe AP vs severe AP (SAP)]. Demographic data, comorbidities, clinical characteristics and laboratory data were collected. Multivariate analysis was conducted for the variables with two-sided P<0.10 in univariate analysis to identify independent associated factors for progression to SAP in AP patients. The predictive values were evaluated using receiver operating characteristic (ROC) curve, and the area under curve (AUC) was compared using Z test. Results A total of 117 (11.2%) patients were evaluated as SAP. Univariate analysis showed that there were significant differences in age, hypertension, ICU admission, hospital stay, Leukocytes, CRP, BUN, BISAP score and miR-155 between case group and control group (P<0.05), and the P value of Fibrinogen was <0.10. Multivariate analysis showed that the BISAP score, BUN, Leukocytes, age and CRP were independent risk factors for progression to SAP among AP patients after adjusting for hypertension, ICU admission, hospital stay and Fibrinogen, while miR-155 was a protective factor. The ROC curves demonstrated the AUCs of BISAP score, miR-155 and their combination were 0.842 (SE: 0.017, 95% CI: 0.809–0.874), 0.751 (SE: 0.022, 95% CI: 0.708–0.793) and 0.945 (SE: 0.007, 95% CI: 0.931–0.959), respectively. Z test showed that the AUC of combination prediction was significantly higher than that of individual predictions (0.945 vs 0.842, Z=5.602, P<0.001; 0.945 vs 0.751, Z=8.403, P<0.001). The sensitivity, specificity and negative predictive value (NPV) of combination prediction were 95.7%, 93.6% and 99.4%, respectively. Conclusion The combination of the BISAP score and miR-155 should be utilized to elevate the predictive value for the severity of AP in clinic.
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Affiliation(s)
- Bing Wu
- Department of Critical Care Medicine, Jiangjin Central Hospital, Chongqing, People’s Republic of China
| | - Jun Yang
- Department of Critical Care Medicine, Jiangjin Central Hospital, Chongqing, People’s Republic of China
| | - Yonghong Dai
- Department of Critical Care Medicine, Jiangjin Central Hospital, Chongqing, People’s Republic of China
| | - Le Xiong
- Department of Critical Care Medicine, Jiangjin Central Hospital, Chongqing, People’s Republic of China
- Correspondence: Le Xiong, Department of Critical Care Medicine, Jiangjin Central Hospital, No. 725, Jiangzhou Road, Dingshan Street, Jiangjin District, Chongqing, 402260, People’s Republic of China, Tel +86-2347521342, Email
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Chen Q, Tong M, Sun N, Yang Y, Cheng Y, Yi L, Wang G, Cao Z, Zhao Q, Cheng S. Integrated Analysis of miRNA-mRNA Expression in Mink Lung Epithelial Cells Infected With Canine Distemper Virus. Front Vet Sci 2022; 9:897740. [PMID: 35711811 PMCID: PMC9194998 DOI: 10.3389/fvets.2022.897740] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Accepted: 04/25/2022] [Indexed: 01/10/2023] Open
Abstract
Canine distemper (CD) caused by canine distemper virus (CDV) is one of the major infectious diseases in minks, bringing serious economic losses to the mink breeding industry. By an integrated analysis of microRNA (miRNA)-messenger RNA (mRNA), the present study analyzed the changes in the mink transcriptome upon CDV infection in mink lung epithelial cells (Mv. l. Lu cells) for the first time. A total of 4,734 differentially expressed mRNAs (2,691 upregulated and 2,043 downregulated) with |log2(FoldChange) |>1 and P-adj<0.05 and 181 differentially expressed miRNAs (152 upregulated and 29 downregulated) with |log2(FoldChange) |>2 and P-adj<0.05 were identified. Gene Ontology (GO) enrichment indicated that differentially expressed genes (DEGs) were associated with various biological processes and molecular function, such as response to stimulus, cell communication, signaling, cytokine activity, transmembrane signaling receptor activity and signaling receptor activity. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis of the combination of miRNA and mRNA was done for immune and inflammatory responses, such as Janus kinase (JAK)-signal transducer and activator (STAT) signaling pathway and nuclear factor (NF)-kappa B signaling pathway. The enrichment analysis of target mRNA of differentially expressed miRNA revealed that mir-140-5p and mir-378-12 targeted corresponding genes to regulate NF-kappa B signaling pathway. JAK-STAT signaling pathway could be modulated by mir-425-2, mir-139-4, mir-140-6, mir-145-3, mir-140-5p and mir-204-2. This study compared the influence of miRNA-mRNA expression in Mv. l. Lu cells before and after CDV infection by integrated analysis of miRNA-mRNA and analyzed the complex network interaction between virus and host cells. The results can help understand the molecular mechanism of the natural immune response induced by CDV infection in host cells.
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Affiliation(s)
- Qiang Chen
- College of Veterinary Medicine, College of Animal Science and Technology, Jilin Agricultural University, Changchun, China
- Key Laboratory of Special Animal Epidemic Disease, Ministry of Agriculture, Institute of Special Economic Animals and Plants, Chinese Academy of Agricultural Sciences, Changchun, China
- College of Landscape Architecture, Changchun University, Changchun, China
| | - Mingwei Tong
- School of Basic Medical Sciences, Shanxi Medical University, Taiyuan, China
| | - Na Sun
- College of Animal Science and Technology, Jilin Agricultural Science and Technology University, Jilin City, China
| | - Yong Yang
- School of Basic Medical Sciences, Shanxi Medical University, Taiyuan, China
| | - Yuening Cheng
- Key Laboratory of Special Animal Epidemic Disease, Ministry of Agriculture, Institute of Special Economic Animals and Plants, Chinese Academy of Agricultural Sciences, Changchun, China
| | - Li Yi
- Key Laboratory of Special Animal Epidemic Disease, Ministry of Agriculture, Institute of Special Economic Animals and Plants, Chinese Academy of Agricultural Sciences, Changchun, China
| | - Gaili Wang
- Jilin Academy of Animal Husbandry and Veterinary Medicine, Changchun, China
| | - Zhigang Cao
- Key Laboratory of Special Animal Epidemic Disease, Ministry of Agriculture, Institute of Special Economic Animals and Plants, Chinese Academy of Agricultural Sciences, Changchun, China
| | - Quan Zhao
- College of Veterinary Medicine, College of Animal Science and Technology, Jilin Agricultural University, Changchun, China
- *Correspondence: Quan Zhao
| | - Shipeng Cheng
- Key Laboratory of Special Animal Epidemic Disease, Ministry of Agriculture, Institute of Special Economic Animals and Plants, Chinese Academy of Agricultural Sciences, Changchun, China
- Shipeng Cheng
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Abstract
Severe acute respiratory syndrome coronavirus (SARS-CoV) and the closely related SARS-CoV-2 are emergent highly pathogenic human respiratory viruses causing acute lethal disease associated with lung damage and dysregulated inflammatory responses. SARS-CoV envelope protein (E) is a virulence factor involved in the activation of various inflammatory pathways. Here, we study the contribution of host miRNAs to the virulence mediated by E protein. Small RNAseq analysis of infected mouse lungs identified miRNA-223 as a potential regulator of pulmonary inflammation, since it was significantly increased in SARS-CoV-WT virulent infection compared to the attenuated SARS-CoV-ΔE infection. In vivo inhibition of miRNA-223-3p increased mRNA levels of pro-inflammatory cytokines and NLRP3 inflammasome, suggesting that during lung infection, miRNA-223 might contribute to restrict an excessive inflammatory response. Interestingly, miRNA-223-3p inhibition also increased the levels of the CFTR transporter, which is involved in edema resolution and was significantly downregulated in the lungs of mice infected with the virulent SARS-CoV-WT virus. At the histopathological level, a decrease in the pulmonary edema was observed when miR-223-3p was inhibited, suggesting that miRNA-223-3p was involved in the regulation of the SARS-CoV-induced inflammatory pathology. These results indicate that miRNA-223 participates in the regulation of E protein-mediated inflammatory response during SARS-CoV infection by targeting different host mRNAs involved in the pulmonary inflammation, and identify miRNA-223 as a potential therapeutic target in SARS-CoV infection.
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Reed KM, Mendoza KM, Abrahante JE, Velleman SG, Strasburg GM. Data Mining Identifies Differentially Expressed Circular RNAs in Skeletal Muscle of Thermally Challenged Turkey Poults. Front Physiol 2021; 12:732208. [PMID: 34512399 PMCID: PMC8424120 DOI: 10.3389/fphys.2021.732208] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2021] [Accepted: 08/06/2021] [Indexed: 11/30/2022] Open
Abstract
Precise regulation of gene expression is critical for normal muscle growth and development. Changes in gene expression patterns caused by external stressors such as temperature can have dramatic effects including altered cellular structure and function. Understanding the cellular mechanisms that underlie muscle growth and development and how these are altered by external stressors are crucial in maintaining and improving meat quality. This study investigated circular RNAs (circRNAs) as an emerging aspect of gene regulation. We used data mining to identify circRNAs and characterize their expression profiles within RNAseq data collected from thermally challenged turkey poults of the RBC2 and F-lines. From sequences of 28 paired-end libraries, 8924 unique circRNAs were predicted of which 1629 were common to all treatment groups. Expression analysis identified significant differentially expressed circRNAs (DECs) in comparisons between thermal treatments (41 DECs) and between genetic lines (117 DECs). No intersection was observed between the DECs and differentially expressed gene transcripts indicating that the DECs are not simply the result of expression changes in the parental genes. Comparative analyses based on the chicken microRNA (miRNA) database suggest potential interactions between turkey circRNAs and miRNAs. Additional studies are needed to reveal the functional significance of the predicted circRNAs and their role in muscle development in response to thermal challenge. The DECs identified in this study provide an important framework for future investigation.
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Affiliation(s)
- Kent M Reed
- Department of Veterinary and Biomedical Sciences, College of Veterinary Medicine, University of Minnesota, Saint Paul, MN, United States
| | - Kristelle M Mendoza
- Department of Veterinary and Biomedical Sciences, College of Veterinary Medicine, University of Minnesota, Saint Paul, MN, United States
| | - Juan E Abrahante
- University of Minnesota Informatics Institute, University of Minnesota, Minneapolis, MN, United States
| | - Sandra G Velleman
- Department of Animal Sciences, The Ohio State University, Ohio Agricultural Research and Development Center, Wooster, OH, United States
| | - Gale M Strasburg
- Department of Food Science and Human Nutrition, Michigan State University, East Lansing, MI, United States
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Zhang K, Zhang Y, Chen C, Yuan Y, Jiang X, Yuan X, Wang Y. miR-139-5p mediates the palmitate-induced inhibition of insulin secretion by targeting neuronal pentraxin 1 in INS-1 cells. Acta Biochim Biophys Sin (Shanghai) 2021; 53:1017-1026. [PMID: 34142698 DOI: 10.1093/abbs/gmab082] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2020] [Indexed: 11/13/2022] Open
Abstract
High fatty acid reduces insulin secretion in pancreatic β-cells and miR-139-5p is increased in diabetic pancreatic tissues and induces islet β-cell apoptosis. However, to date, there is no study exploring whether or not miR-139-5p is involved in high fatty acid-induced insulin secretion. In the present study, INS-1 cells were exposed to different concentrations (0.1, 0.2, and 0.4 mM) of palmitate for different time periods (12, 24, and 48 h). The expression levels of miR-139-5p and neuronal pentraxin 1 (NPTX1) were evaluated by real-time PCR and western blot analysis. The regulation of NPTX1 by miR-139-5p was examined by luciferase assay. Cell transfection was conducted using Lipo8000 or Lipofectamine RNAiMAX. Potassium or glucose-stimulated insulin secretion levels were used to verify the function of miR-139-5p or NPTX1 in insulin secretion. Insulin secretion levels were detected by radioimmunoassay. We found that miR-139-5p was increased in INS-1 cells stimulated with palmitate. In addition, miR-139-5p was also elevated in islets of high-fat diet-fed mice and db/db mice compared to those in islets of normal diet-fed mice and wild-type mice. Knockdown of miR-139-5p could reverse high fatty acid-induced insulin secretion defects in INS-1 cells. Furthermore, we demonstrated that NPTX1 is a target of miR-139-5p. miR-139-5p mediated palmitate-induced insulin secretion defects by targeting NPTX1. Moreover, palmitate treatment declined the expression of NPTX1 and the NPTX1 expression was also decreased in islets of high-fat diet-fed mice and db/db mice. Impaired NPTX1 expression is involved in fatty acid-induced insulin secretion defects. Collectively, our results illustrate that the induction of β-cell insulin secretion defects by fatty acids is mediated, at least in part, by miR-139-5p via downregulation of NPTX1 expression.
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Affiliation(s)
- Kai Zhang
- Department of Endocrinology, Zhongda Hospital, Institute of Diabetes, Medical School, Southeast University, Nanjing 210009, China
| | - Yijian Zhang
- Department of Biochemistry and Molecular Biology, Nanjing Medical University, Nanjing 210009, China
| | - Cheng Chen
- Department of Endocrinology, Zhongda Hospital, Institute of Diabetes, Medical School, Southeast University, Nanjing 210009, China
| | - Yuexing Yuan
- Department of Endocrinology, Zhongda Hospital, Institute of Diabetes, Medical School, Southeast University, Nanjing 210009, China
| | - Xiaotian Jiang
- Department of Biochemistry and Molecular Biology, Nanjing Medical University, Nanjing 210009, China
| | - Xiangjiang Yuan
- Department of Biochemistry and Molecular Biology, Nanjing Medical University, Nanjing 210009, China
| | - Yao Wang
- Department of Endocrinology, Zhongda Hospital, Institute of Diabetes, Medical School, Southeast University, Nanjing 210009, China
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Abstract
The COVID-19 coronavirus is a new strain of coronavirus that had not been previously detected in humans. As its severe pathogenicity is concerned, it is important to study it thoroughly to aid in the discovery of a cure. In this study, the microRNAs (miRNAs) of COVID-19 were annotated to provide a powerful tool for the study of this novel coronavirus. We obtained 16 novel coronavirus genome sequences and the mature sequences of all viruses in the microRNA database (miRbase), and then used the miRNA mature sequences of the virus to perform the Basic Local Alignment Search Tool (BLAST) analysis in the coronavirus genome, extending the matched regions of approximately 20 bp to two segments by 200 bp. Six sequences were obtained after deleting redundant sequences. Then, the hairpin structures of the mature miRNAs were determined using RNAfold. The mature sequence on one hairpin arm was selected into a total of 4 sequences, and finally the relevant miRNA precursor prediction tools were used to verify whether the selected sequences are miRNA precursor sequences of the novel coronavirus. The miRNAs of the novel coronavirus were annotated by our newly developed method, which will lay the foundation for further study of this virus.
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Heydarzadeh S, Ranjbar M, Karimi F, Seif F, Alivand MR. Overview of host miRNA properties and their association with epigenetics, long non-coding RNAs, and Xeno-infectious factors. Cell Biosci 2021; 11:43. [PMID: 33632341 PMCID: PMC7905430 DOI: 10.1186/s13578-021-00552-1] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Accepted: 02/06/2021] [Indexed: 12/19/2022] Open
Abstract
MicroRNA-derived structures play impressive roles in various biological processes. So dysregulation of miRNAs can lead to different human diseases. Recent studies have extended our comprehension of the control of miRNA function and features. Here, we overview some remarkable miRNA properties that have potential implications for the miRNA functions, including different variants of a miRNA called isomiRs, miRNA arm selection/arm switching, and the effect of these factors on miRNA target selection. Besides, we review some aspects of miRNA interactions such as the interaction between epigenetics and miRNA (different miRNAs and their related processing enzymes are epigenetically regulated by multiple DNA methylation enzymes. moreover, DNA methylation could be controlled by diverse mechanisms related to miRNAs), direct and indirect crosstalk between miRNA and lnc (Long Non-Coding) RNAs as a further approach to conduct intercellular regulation called "competing endogenous RNA" (ceRNA) that is involved in the pathogenesis of different diseases, and the interaction of miRNA activities and some Xeno-infectious (virus/bacteria/parasite) factors, which result in modulation of the pathogenesis of infections. This review provides some related studies to a better understanding of miRNA involvement mechanisms and overcoming the complexity of related diseases that may be applicable and useful to prognostic, diagnostic, therapeutic purposes and personalized medicine in the future.
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Affiliation(s)
- Samaneh Heydarzadeh
- Department of Medical Genetics, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Maryam Ranjbar
- Immunology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Farokh Karimi
- Department of Biotechnology, Faculty of Science, University of Maragheh, Maragheh, Iran
| | - Farhad Seif
- Department of Immunology and Allergy, Academic Center for Education, Culture, and Research (ACECR), Tehran, Iran
- Neuroscience Research Center, Iran University of Medical Sciences, Tehran, Iran
| | - Mohammad Reza Alivand
- Department of Medical Genetics, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran.
- Immunology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran.
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Miretti S, Lecchi C, Ceciliani F, Baratta M. MicroRNAs as Biomarkers for Animal Health and Welfare in Livestock. Front Vet Sci 2020; 7:578193. [PMID: 33392281 PMCID: PMC7775535 DOI: 10.3389/fvets.2020.578193] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Accepted: 10/30/2020] [Indexed: 12/11/2022] Open
Abstract
MicroRNAs (miRNAs) are small and highly conserved non-coding RNA molecules that orchestrate a wide range of biological processes through the post-transcriptional regulation of gene expression. An intriguing aspect in identifying these molecules as biomarkers is derived from their role in cell-to-cell communication, their active secretion from cells into the extracellular environment, their high stability in body fluids, and their ease of collection. All these features confer on miRNAs the potential to become a non-invasive tool to score animal welfare. There is growing interest in the importance of miRNAs as biomarkers for assessing the welfare of livestock during metabolic, environmental, and management stress, particularly in ruminants, pigs, and poultry. This review provides an overview of the current knowledge regarding the potential use of tissue and/or circulating miRNAs as biomarkers for the assessment of the health and welfare status in these livestock species.
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Affiliation(s)
- Silvia Miretti
- Department of Veterinary Sciences, University of Torino, Grugliasco, Italy
| | - Cristina Lecchi
- Department of Veterinary Medicine, Università degli Studi di Milano, Milan, Italy
| | - Fabrizio Ceciliani
- Department of Veterinary Medicine, Università degli Studi di Milano, Milan, Italy
| | - Mario Baratta
- Department of Veterinary Sciences, University of Torino, Grugliasco, Italy
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Casas E, Ma H, Lippolis JD. Expression of Viral microRNAs in Serum and White Blood Cells of Cows Exposed to Bovine Leukemia Virus. Front Vet Sci 2020; 7:536390. [PMID: 33195511 PMCID: PMC7536277 DOI: 10.3389/fvets.2020.536390] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2020] [Accepted: 08/17/2020] [Indexed: 12/16/2022] Open
Abstract
Bovine leukemia virus (BLV) affects the health and productivity of cattle. The virus causes abnormal immune function and immunosuppression. MicroRNAs (miRNAs) are involved in gene expression, having been associated with stress and immune response, tumor growth, and viral infection. The objective of this study was to determine the expression of circulating miRNAs produced by BLV in animals exposed to the virus. Sera from 14 animals were collected to establish IgG reactivity to BLV by ELISA, where seven animals were seropositive and seven were seronegative for BLV exposure. White blood cells (WBC) from each animal were also collected and miRNAs were identified by sequencing from sera and WBC. The seropositive group had higher counts of BLV miRNAs when compared to seronegative group in sera and WBC. Blv-miR-1-3p, blv-miR-B2-5p, blv-miR-B4-3p, and blv-miR-B5-5p were statistically significant (P < 0.00001) in serum with an average of 7 log2 fold difference between seropositive and seronegative groups. Blv-miR-B1-3p, blv-miR-B1-5p, blv-miR-B3, blv-miR-B4-3p, blv-miR-B4-5p, blv-miR-B5-5p were statistically significant (P < 1.08e−9) in WBC with an average of 7 log2 fold difference between the seropositive and the seronegative groups. Blv-miR-B2-3p and blv-miR-B2-5p were also statistically significant in WBC (P < 2.79e-17), with an average of 27 log2 fold difference between the seropositive and the seronegative groups. There were 18 genes identified as being potential targets for blv-miR-B1-5p, and 3 genes for blv-miR-B4-5p. Gene ontology analysis indicated that the target genes are mainly involved in the response to stress and in the immune system process. Several of the identified genes have been associated with leukemia development in humans and cattle. Differential expression of genes targeted by BLV miRNAs should be evaluated to determine their effect in BLV replication.
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Affiliation(s)
- Eduardo Casas
- National Animal Disease Center, Agricultural Research Service (ARS), United States Department of Agriculture (USDA), Ames, IA, United States
| | - Hao Ma
- National Animal Disease Center, Agricultural Research Service (ARS), United States Department of Agriculture (USDA), Ames, IA, United States
| | - John D Lippolis
- National Animal Disease Center, Agricultural Research Service (ARS), United States Department of Agriculture (USDA), Ames, IA, United States
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From the Argonauts Mythological Sailors to the Argonautes RNA-Silencing Navigators: Their Emerging Roles in Human-Cell Pathologies. Int J Mol Sci 2020; 21:ijms21114007. [PMID: 32503341 PMCID: PMC7312461 DOI: 10.3390/ijms21114007] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2020] [Revised: 06/01/2020] [Accepted: 06/01/2020] [Indexed: 12/27/2022] Open
Abstract
Regulation of gene expression has emerged as a fundamental element of transcript homeostasis. Key effectors in this process are the Argonautes (AGOs), highly specialized RNA-binding proteins (RBPs) that form complexes, such as the RNA-Induced Silencing Complex (RISC). AGOs dictate post-transcriptional gene-silencing by directly loading small RNAs and repressing their mRNA targets through small RNA-sequence complementarity. The four human highly-conserved family-members (AGO1, AGO2, AGO3, and AGO4) demonstrate multi-faceted and versatile roles in transcriptome’s stability, plasticity, and functionality. The post-translational modifications of AGOs in critical amino acid residues, the nucleotide polymorphisms and mutations, and the deregulation of expression and interactions are tightly associated with aberrant activities, which are observed in a wide spectrum of pathologies. Through constantly accumulating information, the AGOs’ fundamental engagement in multiple human diseases has recently emerged. The present review examines new insights into AGO-driven pathology and AGO-deregulation patterns in a variety of diseases such as in viral infections and propagations, autoimmune diseases, cancers, metabolic deficiencies, neuronal disorders, and human infertility. Altogether, AGO seems to be a crucial contributor to pathogenesis and its targeting may serve as a novel and powerful therapeutic tool for the successful management of diverse human diseases in the clinic.
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14
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Wu F, Lu F, Fan X, Chao J, Liu C, Pan Q, Sun H, Zhang X. Immune-related miRNA-mRNA regulation network in the livers of DHAV-3-infected ducklings. BMC Genomics 2020; 21:123. [PMID: 32019511 PMCID: PMC7001231 DOI: 10.1186/s12864-020-6539-7] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2019] [Accepted: 01/27/2020] [Indexed: 12/20/2022] Open
Abstract
Background Duck hepatitis A virus type 3 (DHAV-3) is one of the most harmful pathogens in the duck industry. However, the molecular mechanism underlying DHAV-3 infection in ducklings remains poorly understood. To study the genetic regulatory network for miRNA-mRNA and the signaling pathways involved in DHAV-3 infection in ducklings, we conducted global miRNA and mRNA expression profiling of duckling liver tissues infected with lethal DHAV-3 by high-throughput sequencing. Results We found 156 differentially expressed miRNAs (DEMs) and 7717 differentially expressed genes (DEGs) in livers of mock-infected and DHAV-3-infected duckling. A total of 19,606 miRNA-mRNA pairs with negatively correlated expression patterns were identified in miRNA-mRNA networks constructed on the basis of these DEMs and DEGs. Moreover, immune-related pathways, including the cytokine-cytokine receptor interaction, apoptosis, Toll-like receptor, Jak-STAT, and RIG-I-like receptor signaling pathway, were significantly enriched through analyzing functions of mRNAs in the network in response to DHAV-3 infection. Furthermore, apl-miR-32-5p, apl-miR-125-5p, apl-miR-128-3p, apl-miR-460-5p, and novel-m0012-3p were identified as potential regulators in the immune-related signaling pathways during DHAV-3 infection. And some host miRNAs were predicted to target the DHAV-3 genome. Conclusions This is the first integrated analysis of miRNA and mRNA in DHAV-3-infected ducklings. The results indicated the important roles of miRNAs in regulating immune response genes and revealed the immune related miRNA-mRNA regulation network in the DHAV-3-infected duckling liver. These findings increase our knowledge of the roles of miRNAs and their target genes in DHAV-3 replication and pathogenesis. They also aid in the understanding of host-virus interactions.
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Affiliation(s)
- Fengyao Wu
- Institute of Veterinary Medicine, Jiangsu Academy of Agricultural Sciences, Nanjing, Jiangsu Province, China.,Key Laboratory of Veterinary Biological Engineering and Technology, Ministry of Agriculture, Nanjing, Jiangsu Province, China
| | - Fengying Lu
- Institute of Veterinary Medicine, Jiangsu Academy of Agricultural Sciences, Nanjing, Jiangsu Province, China.,Key Laboratory of Veterinary Biological Engineering and Technology, Ministry of Agriculture, Nanjing, Jiangsu Province, China
| | - Xin Fan
- Institute of Veterinary Medicine, Jiangsu Academy of Agricultural Sciences, Nanjing, Jiangsu Province, China.,Academy of Animal Sciences, Tibet Agriculture and Animal Husbandry University, Linzhi, Tibet Province, China
| | - Jin Chao
- Institute of Veterinary Medicine, Jiangsu Academy of Agricultural Sciences, Nanjing, Jiangsu Province, China.,College of Animal Science and Technology, Anhui Agricultural University, Hefei, Anhui Province, China
| | - Chuanmin Liu
- Institute of Veterinary Medicine, Jiangsu Academy of Agricultural Sciences, Nanjing, Jiangsu Province, China.,Key Laboratory of Veterinary Biological Engineering and Technology, Ministry of Agriculture, Nanjing, Jiangsu Province, China
| | - Qunxing Pan
- Institute of Veterinary Medicine, Jiangsu Academy of Agricultural Sciences, Nanjing, Jiangsu Province, China.,Key Laboratory of Veterinary Biological Engineering and Technology, Ministry of Agriculture, Nanjing, Jiangsu Province, China
| | - Huawei Sun
- Institute of Veterinary Medicine, Jiangsu Academy of Agricultural Sciences, Nanjing, Jiangsu Province, China.,Key Laboratory of Veterinary Biological Engineering and Technology, Ministry of Agriculture, Nanjing, Jiangsu Province, China
| | - Xiaofei Zhang
- Institute of Veterinary Medicine, Jiangsu Academy of Agricultural Sciences, Nanjing, Jiangsu Province, China. .,Key Laboratory of Veterinary Biological Engineering and Technology, Ministry of Agriculture, Nanjing, Jiangsu Province, China.
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15
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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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16
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Samir M, Vidal RO, Abdallah F, Capece V, Seehusen F, Geffers R, Hussein A, Ali AAH, Bonn S, Pessler F. Organ-specific small non-coding RNA responses in domestic (Sudani) ducks experimentally infected with highly pathogenic avian influenza virus (H5N1). RNA Biol 2019; 17:112-124. [PMID: 31538530 DOI: 10.1080/15476286.2019.1669879] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
The duck represents an important reservoir of influenza viruses for transmission to other avian and mammalian hosts, including humans. The increased pathogenicity of the recently emerging clades of highly pathogenic avian influenza (HPAI) viruses of the H5N1 subtype in ducks features systemic viral spread and organ-to-organ variation in viral transcription and tissue damage. We previously reported that experimental infection of Sudani ducks (Cairina moschata) with an Egyptian HPAI (H5N1) virus (clade 2.2.1.2) features high viral replication and severe tissue damage in lung, but lower viral replication and only mild histological changes in brain. Little is known about the involvement of miRNA in organ-specific responses to H5N1 viruses in ducks, and involvement of the other classes of small noncoding RNA (sncRNA) has not been investigated so far. Following RNA sequencing, we have annotated the duck sncRNome and compared global expression changes of the four major sncRNA classes (miRNAs, piRNAs, snoRNAs, snRNAs) between duck lung and brain during a 120 h time course of infection with this HPAI strain. We find major organ-specific differences in miRNA, piRNA and snoRNA populations even before infection and substantial reprogramming of all sncRNA classes throughout infection, which was less pronounced in brain. Pathway prediction analysis of miRNA targets revealed enrichment of inflammation-, infection- and apoptosis-related pathways in lung, but enrichment of metabolism-related pathways (including tryptophan metabolism) in brain. Thus, organ-specific differences in sncRNA responses may contribute to differences in viral replication and organ damage in ducks infected with isolates from this emerging HPAI clade, and likely other strains.
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Affiliation(s)
- Mohamed Samir
- Department of Zoonoses, Faculty of Veterinary Medicine, Zagazig University, Zagazig, Egypt.,Research Group Biomarkers for Infectious Diseases, TWINCORE, Centre for Experimental and Clinical Infection Research, Hannover, Germany
| | - Ramon O Vidal
- Group of Computational Systems Biology, German Center for Neurodegenerative Diseases, Goettingen, Germany.,Department of Genomics, Max-Delbrück-Centrum für Molekulare Medizin (MDC), Berlin, Germany
| | - Fatma Abdallah
- Department of Virology, Faculty of Veterinary Medicine, Zagazig University, Zagazig, Egypt
| | - Vincenzo Capece
- Group of Computational Systems Biology, German Center for Neurodegenerative Diseases, Goettingen, Germany.,ID Research IT Platforms, Swiss Federal Institute of Technology (ETH), Zurich, Switzerland
| | - Frauke Seehusen
- Department of Pathology, University of Veterinary Medicine (TiHo), Hannover, Germany
| | - Robert Geffers
- Genome Analytics, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Ashraf Hussein
- Department of Avian and Rabbit Medicine, Faculty of Veterinary Medicine, Zagazig University, Zagazig, Egypt
| | - Ahmed A H Ali
- Department of Virology, Faculty of Veterinary Medicine, Zagazig University, Zagazig, Egypt
| | - Stefan Bonn
- Group of Computational Systems Biology, German Center for Neurodegenerative Diseases, Goettingen, Germany.,Institute of Medical Systems Biology, Center for Molecular Neurobiology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany.,German Center for Neurodegenerative Diseases, Tuebingen, Germany
| | - Frank Pessler
- Research Group Biomarkers for Infectious Diseases, TWINCORE, Centre for Experimental and Clinical Infection Research, Hannover, Germany.,Research Group Biomarkers for Infectious Diseases, Helmholtz Centre for Infection Research, Braunschweig, Germany.,Centre for Individualized Infection Medicine, Hannover, Germany
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17
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Huo L, Wang B, Zheng M, Zhang Y, Xu J, Yang G, Guan Q. miR-128-3p inhibits glioma cell proliferation and differentiation by targeting NPTX1 through IRS-1/PI3K/AKT signaling pathway. Exp Ther Med 2019; 17:2921-2930. [PMID: 30906475 PMCID: PMC6425241 DOI: 10.3892/etm.2019.7284] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2017] [Accepted: 11/03/2017] [Indexed: 12/23/2022] Open
Abstract
It has been reported that glioma has a higher morbidity and mortality than other types of malignant brain tumor. While glioma has been extensively researched, the exact molecular mechanisms of its genesis and progression have remained to be fully elucidated. In order to explore a novel glioma-associated pathway which may represent a therapeutic target, 61 pairs of tumor tissues and adjacent normal tissues of glioma patients were collected and subjected to reverse-transcription quantitative polymerase chain reaction analysis, indicating that the relative expression of microRNA (miR)-128-3p was significantly decreased in the tumor tissues. However, the expression of neuronal pentraxin 1 (NPTX1) was obviously elevated. Through a bioinformatics analysis using Targetscan and transfection experiments, it was confirmed that NPTX1 was targeted by miR-128-3p. In the U251 human glioma cell line, transfection with miR-128-3p mimics increased the levels of phosphorylated insulin receptor substrate 1 (p-IRS-1), phosphoinositide-3 kinase (PI3K) and p-AKT, as demonstrated by western blot analysis. In addition, the proliferation rate of the cells was notably decreased following transfection with miR-128-3p mimics. Conversely, transfection with miR-128-3p inhibitor significantly increased the levels of p-IRS-1, PI3K and p-AKT, accompanied by an elevated proliferation rate of the cells. Therefore, it was indicated that miR-128-3p could reversely regulate NPTX1 expression. After the expression of NPTX1 was inhibited with specific small interfering RNA, the levels of p-IRS-1, PI3K and p-AKT were obviously decreased, while the expression of miR-128-3p was not significantly changed. Overall, it was concluded that miR-128-3p suppresses glioma through the NPTX1/IRS-1/PI3K/AKT signaling pathway.
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Affiliation(s)
- Leiming Huo
- Department of Neurosurgery, The First Hospital of Lanzhou University, Lanzhou, Gansu 730000, P.R. China
| | - Bin Wang
- Department of Neurosurgery, The First People's Hospital of Longxi County, Dingxi, Gansu 730050, P.R. China
| | - Maohua Zheng
- Department of Neurosurgery, The First Hospital of Lanzhou University, Lanzhou, Gansu 730000, P.R. China
| | - Yonghong Zhang
- Department of Neurosurgery, The First Hospital of Lanzhou University, Lanzhou, Gansu 730000, P.R. China
| | - Jiguang Xu
- Department of Neurosurgery, The First Hospital of Lanzhou University, Lanzhou, Gansu 730000, P.R. China
| | - Gang Yang
- Department of Neurosurgery, The First Hospital of Lanzhou University, Lanzhou, Gansu 730000, P.R. China
| | - Quanlin Guan
- Department of Neurosurgery, The First Hospital of Lanzhou University, Lanzhou, Gansu 730000, P.R. China
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18
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Qi X, Wang T, Xue Q, Li Z, Yang B, Wang J. MicroRNA expression profiling of goat peripheral blood mononuclear cells in response to peste des petits ruminants virus infection. Vet Res 2018; 49:62. [PMID: 30012212 PMCID: PMC6048839 DOI: 10.1186/s13567-018-0565-3] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2018] [Accepted: 05/29/2018] [Indexed: 12/21/2022] Open
Abstract
Peste des petits ruminants virus (PPRV) belongs to the genus Morbillivirus that causes an acute and highly contagious disease in goats and sheep. Virus infection can trigger the change in the cellular microRNA (miRNA) expression profile, which play important post-transcriptional regulatory roles in gene expression and can greatly influence viral replication and pathogenesis. Here, we employed deep sequencing technology to determine cellular miRNA expression profile in goat peripheral blood mononuclear cells (PBMC) infected with Nigeria 75/1 vaccine virus, a widely used vaccine strain for mass vaccination programs against Peste des petits ruminants. Expression analysis demonstrated that PPRV infection can elicit 316 significantly differentially expressed (DE) miRNA including 103 known and 213 novel miRNA candidates in infected PBMC at 24 hours post-infection (hpi) as compared with a mock control. Target prediction and functional analysis of these DEmiRNA revealed significant enrichment for several signaling pathways including TLR signaling pathways, PI3K-Akt, endocytosis, viral carcinogenesis, and JAK-STAT signaling pathways. This study provides a valuable basis for further investigation of the roles of miRNA in PPRV replication and pathogenesis.
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Affiliation(s)
- Xuefeng Qi
- College of Veterinary Medicine, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Ting Wang
- College of Veterinary Medicine, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Qinghong Xue
- China Institute of Veterinary Drug Control, Beijing, 100000, China
| | - Zhen Li
- College of Veterinary Medicine, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Bo Yang
- College of Veterinary Medicine, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Jingyu Wang
- College of Veterinary Medicine, Northwest A&F University, Yangling, 712100, Shaanxi, China.
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19
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Brogaard L, Larsen LE, Heegaard PMH, Anthon C, Gorodkin J, Dürrwald R, Skovgaard K. IFN-λ and microRNAs are important modulators of the pulmonary innate immune response against influenza A (H1N2) infection in pigs. PLoS One 2018; 13:e0194765. [PMID: 29677213 PMCID: PMC5909910 DOI: 10.1371/journal.pone.0194765] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2017] [Accepted: 02/02/2018] [Indexed: 11/19/2022] Open
Abstract
The innate immune system is paramount in the response to and clearance of influenza A virus (IAV) infection in non-immune individuals. Known factors include type I and III interferons and antiviral pathogen recognition receptors, and the cascades of antiviral and pro- and anti-inflammatory gene expression they induce. MicroRNAs (miRNAs) are increasingly recognized to participate in post-transcriptional modulation of these responses, but the temporal dynamics of how these players of the antiviral innate immune response collaborate to combat infection remain poorly characterized. We quantified the expression of miRNAs and protein coding genes in the lungs of pigs 1, 3, and 14 days after challenge with swine IAV (H1N2). Through RT-qPCR we observed a 400-fold relative increase in IFN-λ3 gene expression on day 1 after challenge, and a strong interferon-mediated antiviral response was observed on days 1 and 3 accompanied by up-regulation of genes related to the pro-inflammatory response and apoptosis. Using small RNA sequencing and qPCR validation we found 27 miRNAs that were differentially expressed after challenge, with the highest number of regulated miRNAs observed on day 3. In contrast, the number of protein coding genes found to be regulated due to IAV infection peaked on day 1. Pulmonary miRNAs may thus be aimed at fine-tuning the initial rapid inflammatory response after IAV infection. Specifically, we found five miRNAs (ssc-miR-15a, ssc-miR-18a, ssc-miR-21, ssc-miR-29b, and hsa-miR-590-3p)-four known porcine miRNAs and one novel porcine miRNA candidate-to be potential modulators of viral pathogen recognition and apoptosis. A total of 11 miRNAs remained differentially expressed 14 days after challenge, at which point the infection had cleared. In conclusion, the results suggested a role for miRNAs both during acute infection as well as later, with the potential to influence lung homeostasis and susceptibility to secondary infections in the lungs of pigs after IAV infection.
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Affiliation(s)
- Louise Brogaard
- Section for Protein Science and Signaling Biology, Department of Biotechnology and Biomedicine, Technical University of Denmark, Kongens Lyngby, Denmark
- * E-mail:
| | - Lars E. Larsen
- Division of Diagnostics and Scientific Advice–Virology, National Veterinary Institute, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Peter M. H. Heegaard
- Section for Protein Science and Signaling Biology, Department of Biotechnology and Biomedicine, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Christian Anthon
- Center for non-coding RNA in Technology and Health (RTH), Department of Veterinary and Animal Science, University of Copenhagen, Frederiksberg, Denmark
| | - Jan Gorodkin
- Center for non-coding RNA in Technology and Health (RTH), Department of Veterinary and Animal Science, University of Copenhagen, Frederiksberg, Denmark
| | - Ralf Dürrwald
- Department of Infectious Diseases, Robert Koch Institute, Berlin, Germany
| | - Kerstin Skovgaard
- Section for Protein Science and Signaling Biology, Department of Biotechnology and Biomedicine, Technical University of Denmark, Kongens Lyngby, Denmark
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20
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Dong H, Gao Q, Peng X, Sun Y, Han T, Zhao B, Liu Y, Wang C, Song X, Wu J, Yang L. Circulating MicroRNAs As Potential Biomarkers for Veterinary Infectious Diseases. Front Vet Sci 2017; 4:186. [PMID: 29209619 PMCID: PMC5701639 DOI: 10.3389/fvets.2017.00186] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2017] [Accepted: 10/17/2017] [Indexed: 12/15/2022] Open
Abstract
MicroRNAs (miRNAs) are a kind of small non-coding RNA molecules that could regulate multiple biological pathways at posttranscriptional level. Over 2,000 miRNAs have so far been discovered in humans, and many of them are found to be linked to various kinds of diseases. Thus, miRNAs are being considered as clinical diagnostic and therapeutic targets. With the discovery of high stability of circulating miRNAs in various kinds of mammalian body fluids, the potential of circulating miRNAs as diagnostic/prognostic biomarkers of infectious diseases aroused great interest among researchers. As far as human diseases are concerned, some biomarkers based on circulating miRNAs have been progressed to clinical application. In veterinary fields, however, this concept is only beginning to come into view. In this review, we summarize an update of preclinical studies on using circulating miRNAs as diagnostic biomarkers to combat infectious diseases that affect domestic animals.
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Affiliation(s)
- Hao Dong
- National Veterinarian Diagnostic Center, China Animal Disease Control Center, Beijing, China
| | - Qiang Gao
- Department of Inspection Technology Research, China Institute of Veterinary Drug Control, Beijing, China
| | - Xiaowei Peng
- Department of Inspection Technology Research, China Institute of Veterinary Drug Control, Beijing, China
| | - Yu Sun
- National Veterinarian Diagnostic Center, China Animal Disease Control Center, Beijing, China
| | - Tao Han
- National Veterinarian Diagnostic Center, China Animal Disease Control Center, Beijing, China
| | - Bolin Zhao
- National Veterinarian Diagnostic Center, China Animal Disease Control Center, Beijing, China
| | - Yufu Liu
- South China Agricultural University, Guangzhou, China
| | - Chuanbin Wang
- National Veterinarian Diagnostic Center, China Animal Disease Control Center, Beijing, China
| | - Xiaohui Song
- National Veterinarian Diagnostic Center, China Animal Disease Control Center, Beijing, China
| | - Jiajun Wu
- National Veterinarian Diagnostic Center, China Animal Disease Control Center, Beijing, China
| | - Lin Yang
- National Veterinarian Diagnostic Center, China Animal Disease Control Center, Beijing, China
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21
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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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22
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Du J, Gao S, Tian Z, Xing S, Huang D, Zhang G, Zheng Y, Liu G, Luo J, Chang H, Yin H. MicroRNA expression profiling of primary sheep testicular cells in response to bluetongue virus infection. INFECTION GENETICS AND EVOLUTION 2017; 49:256-267. [PMID: 28132926 DOI: 10.1016/j.meegid.2017.01.029] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2016] [Revised: 01/20/2017] [Accepted: 01/25/2017] [Indexed: 01/04/2023]
Abstract
Bluetongue virus (BTV) is a member of the genus Orbivirus within the family Reoviridae and causes a non-contagious, insect-transmitted disease in domestic and wild ruminants, mainly in sheep and occasionally in cattle and some species of deer. Virus infection can trigger the changes of the cellular microRNA (miRNA) expression profile, which play important post-transcriptional regulatory roles in gene expression and can greatly influence viral replication and pathogenesis. Here, we employed deep sequencing technology to determine which cellular miRNAs were differentially expressed in primary sheep testicular (ST) cells infected with BTV. A total of 25 known miRNAs and 240 novel miRNA candidates that were differentially expressed in BTV-infected and uninfected ST cells were identified, and 251 and 8428 predicted target genes were annotated, respectively. Nine differentially expressed miRNAs and their mRNA targets were validated by quantitative reverse transcription-polymerase chain reaction. Targets prediction and functional analysis of these regulated miRNAs revealed significant enrichment for several signaling pathways including MAPK, PI3K-Akt, endocytosis, Hippo, NF-kB, viral carcinogenesis, FoxO, and JAK-STAT signaling pathways. This study provides a valuable basis for further investigation on the roles of miRNAs in BTV replication and pathogenesis.
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Affiliation(s)
- Junzheng Du
- State Key Laboratory of Veterinary Etiological Biology, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Xujiaping 1, Lanzhou, Gansu 730046, PR China.
| | - Shandian Gao
- State Key Laboratory of Veterinary Etiological Biology, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Xujiaping 1, Lanzhou, Gansu 730046, PR China
| | - Zhancheng Tian
- State Key Laboratory of Veterinary Etiological Biology, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Xujiaping 1, Lanzhou, Gansu 730046, PR China
| | - Shanshan Xing
- State Key Laboratory of Veterinary Etiological Biology, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Xujiaping 1, Lanzhou, Gansu 730046, PR China
| | - Dexuan Huang
- State Key Laboratory of Veterinary Etiological Biology, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Xujiaping 1, Lanzhou, Gansu 730046, PR China
| | - Guorui Zhang
- State Key Laboratory of Veterinary Etiological Biology, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Xujiaping 1, Lanzhou, Gansu 730046, PR China
| | - Yadong Zheng
- State Key Laboratory of Veterinary Etiological Biology, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Xujiaping 1, Lanzhou, Gansu 730046, PR China
| | - Guangyuan Liu
- State Key Laboratory of Veterinary Etiological Biology, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Xujiaping 1, Lanzhou, Gansu 730046, PR China
| | - Jianxun Luo
- State Key Laboratory of Veterinary Etiological Biology, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Xujiaping 1, Lanzhou, Gansu 730046, PR China
| | - Huiyun Chang
- State Key Laboratory of Veterinary Etiological Biology, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Xujiaping 1, Lanzhou, Gansu 730046, PR China
| | - Hong Yin
- State Key Laboratory of Veterinary Etiological Biology, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Xujiaping 1, Lanzhou, Gansu 730046, PR China; Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou 225009, PR China.
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