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Kumar R, Kamboj H, Dhanda S, Verma A, Chander Y, Nehra K, Bhati A, Dedar RK, Sharma DK, Barua S, Tripathi BN, Sharma S, Kumar N. Identification of miR-29a as a novel biomarker for lumpy skin disease virus exposure in cattle. Virulence 2024; 15:2324711. [PMID: 38527940 PMCID: PMC10965105 DOI: 10.1080/21505594.2024.2324711] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2023] [Accepted: 02/04/2024] [Indexed: 03/27/2024] Open
Abstract
Micro RNAs (miRNAs) have been implicated in the regulation of maturation, proliferation, differentiation, and activation of immune cells. In this study, we demonstrated that miR-29a antagonizes IFN-γ production at early times post-LSDV infection in cattle. miR-29a was predicted to target upstream IFN-γ regulators, and its inhibition resulted in enhanced IFN-γ production in sensitized peripheral blood mononuclear cells (PBMCs). Further, stimulation of PBMCs with LSDV antigen exhibited lower levels of miR-29a, concomitant with a potent cell-mediated immune response (CMI), characterized by an increase in LSDV-specific CD8+ T cell counts and enhanced levels of IFN-γ, which eventually facilitated virus clearance. In addition, a few immunocompromised cattle (developed secondary LSDV infection at ~ 6 months) that failed to mount a potent cell-mediated immune response, were shown to maintain higher miR-29a levels. Furthermore, as compared to the sensitized crossbred cattle, PBMCs from sensitized Rathi (a native Indian breed) animals exhibited lower levels of miR-29a along with an increase in CD8+ T cell counts and enhanced levels of IFN-γ. Finally, we analysed that a ≥ 60% decrease in miR-29a expression levels in the PBMCs of sensitized cattle correlated with a potent CMI response. In conclusion, miR-29a expression is involved in antagonizing the IFN-γ response in LSDV-infected cattle and may serve as a novel biomarker for the acute phase of LSDV infection, as well as predicting the functionality of T cells in sensitized cattle. In addition, Rathi cattle mount a more potent CMI response against LSDV than crossbred cattle.
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Affiliation(s)
- Ram Kumar
- National Centre for Veterinary Type Cultures, ICAR-National Research Centre on Equines, Hisar, India
| | - Himanshu Kamboj
- National Centre for Veterinary Type Cultures, ICAR-National Research Centre on Equines, Hisar, India
| | - Shweta Dhanda
- National Centre for Veterinary Type Cultures, ICAR-National Research Centre on Equines, Hisar, India
| | - Assim Verma
- National Centre for Veterinary Type Cultures, ICAR-National Research Centre on Equines, Hisar, India
| | - Yogesh Chander
- National Centre for Veterinary Type Cultures, ICAR-National Research Centre on Equines, Hisar, India
| | - Kuldeep Nehra
- Livestock Research Station, Rajasthan University of Veterinary and Animal Sciences, Nohar, Rajasthan, India
| | | | - Ramesh Kumar Dedar
- National Centre for Veterinary Type Cultures, ICAR-National Research Centre on Equines, Hisar, India
| | - Deepak Kumar Sharma
- Department of Veterinary Microbiology, Rajasthan University of Veterinary and Animal Sciences, Udaipur, India
| | - Sanjay Barua
- National Centre for Veterinary Type Cultures, ICAR-National Research Centre on Equines, Hisar, India
| | - Bhupendra N. Tripathi
- National Centre for Veterinary Type Cultures, ICAR-National Research Centre on Equines, Hisar, India
| | - Shalini Sharma
- National Centre for Veterinary Type Cultures, ICAR-National Research Centre on Equines, Hisar, India
| | - Naveen Kumar
- National Centre for Veterinary Type Cultures, ICAR-National Research Centre on Equines, Hisar, India
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Pandita S, Verma A, Kamboj H, Kumar R, Chander Y, Barua S, Tripathi BN, Kumar N. miRNA profiling of primary lamb testicle cells infected with lumpy skin disease virus. Arch Virol 2023; 168:290. [PMID: 37955695 DOI: 10.1007/s00705-023-05917-0] [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: 05/02/2023] [Accepted: 09/27/2023] [Indexed: 11/14/2023]
Abstract
In this study, miRNA profiling of cells infected with lumpy skin disease virus (LSDV) was conducted for the first time. When compared to mock-infected cells, LSDV-infected primary lamb testicle (LT) cells showed dysregulation of 64, 85, and 85 miRNAs at 12 hours postinfection (hpi), 48 hpi, and 72 hpi, respectively. While some of these miRNAs were found to be dysregulated at a particular time point following LSDV infection, others were dysregulated at all three time points. Analysis of the differentially expressed miRNA-mRNA interaction networks, Gene Ontology analysis of the predicted targets, and KEGG analysis of highly enriched pathways revealed several cellular factors/pathways involved in protein/ion/enzyme binding, cell differentiation, movement of subcellular components, calcium reabsorption, aldosterone synthesis and secretion, and melanogenesis. Some selected upregulated (oar-mir-379-5p, oar-let-7d, Chr10-18769, Chr2_5162 and oar-miR-493-5p) and downregulated (ChrX-33741, Chr3_8257 and Chr26_32680) miRNAs were further confirmed by quantitative real-time PCR. These findings contribute to our understanding of virus replication, virus-host interactions, and disease pathogenesis, and the differentially expressed miRNAs and their cellular targets may serve as biomarkers as well as novel targets for therapeutic intervention against LSDV.
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Affiliation(s)
- Sakshi Pandita
- National Centre for Veterinary Type Cultures, ICAR-National Research Centre on Equines, Hisar, Haryana, 125001, India
- Lala Lajpat Rai University of Veterinary and Animal Sciences, Hisar, Haryana, 125004, India
| | - Assim Verma
- National Centre for Veterinary Type Cultures, ICAR-National Research Centre on Equines, Hisar, Haryana, 125001, India
| | - Himanshu Kamboj
- National Centre for Veterinary Type Cultures, ICAR-National Research Centre on Equines, Hisar, Haryana, 125001, India
| | - Ram Kumar
- National Centre for Veterinary Type Cultures, ICAR-National Research Centre on Equines, Hisar, Haryana, 125001, India
| | - Yogesh Chander
- National Centre for Veterinary Type Cultures, ICAR-National Research Centre on Equines, Hisar, Haryana, 125001, India
| | - Sanjay Barua
- National Centre for Veterinary Type Cultures, ICAR-National Research Centre on Equines, Hisar, Haryana, 125001, India
| | - Bhupendra Nath Tripathi
- National Centre for Veterinary Type Cultures, ICAR-National Research Centre on Equines, Hisar, Haryana, 125001, India
| | - Naveen Kumar
- National Centre for Veterinary Type Cultures, ICAR-National Research Centre on Equines, Hisar, Haryana, 125001, India.
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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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Non-Coding Transcriptome Provides Novel Insights into the Escherichia coli F17 Susceptibility of Sheep Lamb. BIOLOGY 2022; 11:biology11030348. [PMID: 35336723 PMCID: PMC8945857 DOI: 10.3390/biology11030348] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/09/2022] [Revised: 02/11/2022] [Accepted: 02/18/2022] [Indexed: 01/16/2023]
Abstract
Simple Summary Diarrhea and vomiting caused by Escherichia coli (E. coli) F17 are considered significant threats to animal farming. In the present study, RNA-Seq was performed to investigate the potential circRNA and miRNA biomarkers for E. coli F17-antagonism (AN) and -sensitive (SE) lambs. The results indicated that circRNA and miRNA expression is closely associated with the susceptibility of E. coli F17 in lambs. Numbers of circRNAs and miRNAs may serve as potential biomarkers for intestinal inflammatory response against E. coli F17 infection. Our study can provide a preliminary understanding of the underlying mechanisms of intestinal immunity. Abstract It has long been recognized that enterotoxigenic Escherichia coli (ETEC) is the major pathogen responsible for vomiting and diarrhea. E. coli F17, a main subtype of ETEC, is characterized by high morbidity and mortality in young livestock. However, the transcriptomic basis underlying E. coli F17 infection has not been fully understood. In this study, RNA sequencing was performed to explore the expression profiles of circRNAs and miRNAs in the jejunum of E. coli F17-antagonism (AN) and -sensitive (SE) lambs. A total of 16,534 circRNAs and 271 miRNAs (125 novel miRNAs and 146 annotated miRNAs) were screened, and 214 differentially expressed (DE) circRNAs and 53 DE miRNAs were detected between the AN and SE lambs (i.e., novel_circ_0025840, novel_circ_0022779, novel_miR_107, miR-10b). Functional enrichment analyses showed that source genes of DE circRNAs were mainly involved in metabolic-related pathways, while target genes of DE miRNAs were mainly enriched in the immune response pathways. Then, a two-step machine learning approach combining Random Forest (RF) and XGBoost (candidates were first selected by RF and further assessed by XGBoost) was performed, which identified 44 circRNAs and 39 miRNAs as potential biomarkers (i.e., novel_circ_0000180, novel_circ_0000365, novel_miR_192, oar-miR-496-3p) for E. coli infection. Furthermore, circRNA-related and lncRNA-related ceRNA networks were constructed, containing 46 circRNA-miRNA-mRNA competing triplets and 630 lncRNA-miRNA-mRNA competing triplets, respectively. By conducting a serious of bioinformatic analyses, our results revealed important circRNAs and miRNAs that could be potentially developed as candidate biomarkers for intestinal inflammatory response against E. coli F17 infection; our study can provide novel insights into the underlying mechanisms of intestinal immunity.
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Valverde A, Seal A, Nares S, Shukla D, Naqvi AR. Human herpesvirus-encoded MicroRNA in host-pathogen interaction. Adv Biol Regul 2021; 82:100829. [PMID: 34560402 DOI: 10.1016/j.jbior.2021.100829] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2021] [Revised: 08/28/2021] [Accepted: 09/13/2021] [Indexed: 11/17/2022]
Abstract
Human herpesviruses (HHV) are ubiquitous, linear dsDNA viruses that establish lifelong latency, disrupted by sporadic reactivation. HHV have evolved diverse ingenious mechanisms to evade robust host defenses. Incorporation of unique stem loop sequences that generate viral microRNAs (v-miRs) exemplifies one such evolutionary adaptation in HHV. These noncoding RNAs can control cellular and viral transcriptomes highlighting their ability in shaping host-HHV interactions. We summarize recent developments in functional characterization of HHV-encoded miRNAs in shaping the outcome of host-pathogen interaction. Non-immunogenic dissemination of v-miRs through exosomes confer added advantage to HHV in incessant modulation of host microenvironment. This review delineates the mechanistic role of v-miRs in facilitating viral persistence and tropism by targeting genes associated with cellular (apoptosis, angiogenesis, cell migration, etc.) and viral life cycle (latency, lytic and reactivation). Burgeoning evidences indicate plausible association of v-miRs in various immune-mediated diseases (nasopharyngeal carcinoma, neurological disorders, periodontal diseases, etc.) and herpesvirus-related malignancies indicating their broad-spectrum impact on host cellular pathways. We propose to exploit tisssue and systemic levels of v-miRs as diagnostic and prognostic markers for cancers and immune-mediated diseases. Therapeutic targeting of v-miRs will advance the promising outcomes of preclinical discoveries to bedside application.
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Affiliation(s)
- Araceli Valverde
- Department of Periodontics, College of Dentistry, University of Illinois at Chicago, United States
| | - Alexandra Seal
- Department of Periodontics, College of Dentistry, University of Illinois at Chicago, United States
| | - Salvador Nares
- Department of Periodontics, College of Dentistry, University of Illinois at Chicago, United States
| | - Deepak Shukla
- Department of Microbiology and Immunology, University of Illinois at Chicago, Chicago, IL, United States; Department of Ophthalmology and Visual Sciences, University of Illinois Medical Center, Chicago, IL, United States
| | - Afsar Raza Naqvi
- Department of Periodontics, College of Dentistry, University of Illinois at Chicago, United States.
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Gennart I, Petit A, Wiggers L, Pejaković S, Dauchot N, Laurent S, Coupeau D, Muylkens B. Epigenetic Silencing of MicroRNA-126 Promotes Cell Growth in Marek's Disease. Microorganisms 2021; 9:microorganisms9061339. [PMID: 34205549 PMCID: PMC8235390 DOI: 10.3390/microorganisms9061339] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2021] [Revised: 06/12/2021] [Accepted: 06/14/2021] [Indexed: 12/30/2022] Open
Abstract
During latency, herpesvirus infection results in the establishment of a dormant state in which a restricted set of viral genes are expressed. Together with alterations of the viral genome, several host genes undergo epigenetic silencing during latency. These epigenetic dysregulations of cellular genes might be involved in the development of cancer. In this context, Gallid alphaherpesvirus 2 (GaHV-2), causing Marek’s disease (MD) in susceptible chicken, was shown to impair the expression of several cellular microRNAs (miRNAs). We decided to focus on gga-miR-126, a host miRNA considered a tumor suppressor through signaling pathways controlling cell proliferation. Our objectives were to analyze the cause and the impact of miR-126 silencing during GaHV-2 infection. This cellular miRNA was found to be repressed at crucial steps of the viral infection. In order to determine whether miR-126 low expression level was associated with specific epigenetic signatures, DNA methylation patterns were established in the miR-126 gene promoter. Repression was associated with hypermethylation at a CpG island located in the miR-126 host gene epidermal growth factor like-7 (EGFL-7). A strategy was developed to conditionally overexpress miR-126 and control miRNAs in transformed CD4+ T cells propagated from Marek’s disease (MD) lymphoma. This functional assay showed that miR-126 restoration specifically diminishes cell proliferation. We identified CT10 regulator of kinase (CRK), an adaptor protein dysregulated in several human malignancies, as a candidate target gene. Indeed, CRK protein levels were markedly reduced by the miR-126 restoration.
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Affiliation(s)
- Isabelle Gennart
- Integrated Veterinary Research Unit (URVI), Namur Research Institute for Life Sciences (NARILIS), Université de Namur, 61 Rue de Bruxelles, 5000 Namur, Belgium; (I.G.); (L.W.); (S.P.); (D.C.)
| | - Astrid Petit
- Integrated Veterinary Research Unit (URVI), Namur Research Institute for Life Sciences (NARILIS), Université de Namur, 61 Rue de Bruxelles, 5000 Namur, Belgium; (I.G.); (L.W.); (S.P.); (D.C.)
- Correspondence: (A.P.); (B.M.)
| | - Laetitia Wiggers
- Integrated Veterinary Research Unit (URVI), Namur Research Institute for Life Sciences (NARILIS), Université de Namur, 61 Rue de Bruxelles, 5000 Namur, Belgium; (I.G.); (L.W.); (S.P.); (D.C.)
| | - Srđan Pejaković
- Integrated Veterinary Research Unit (URVI), Namur Research Institute for Life Sciences (NARILIS), Université de Namur, 61 Rue de Bruxelles, 5000 Namur, Belgium; (I.G.); (L.W.); (S.P.); (D.C.)
| | - Nicolas Dauchot
- Unit of Research in Plant Cellular and Molecular Biology (URBV), Université de Namur, 61 Rue de Bruxelles, 5000 Namur, Belgium;
| | - Sylvie Laurent
- Département Santé Animale, Institut National de la Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Centre Val de Loire, 37380 Nouzilly, France;
| | - Damien Coupeau
- Integrated Veterinary Research Unit (URVI), Namur Research Institute for Life Sciences (NARILIS), Université de Namur, 61 Rue de Bruxelles, 5000 Namur, Belgium; (I.G.); (L.W.); (S.P.); (D.C.)
| | - Benoît Muylkens
- Integrated Veterinary Research Unit (URVI), Namur Research Institute for Life Sciences (NARILIS), Université de Namur, 61 Rue de Bruxelles, 5000 Namur, Belgium; (I.G.); (L.W.); (S.P.); (D.C.)
- Correspondence: (A.P.); (B.M.)
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Song N, Wang W, Wang Y, Guan Y, Xu S, Guo MY. Hydrogen sulfide of air induces macrophage extracellular traps to aggravate inflammatory injury via the regulation of miR-15b-5p on MAPK and insulin signals in trachea of chickens. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 771:145407. [PMID: 33548704 DOI: 10.1016/j.scitotenv.2021.145407] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/19/2020] [Revised: 01/16/2021] [Accepted: 01/20/2021] [Indexed: 06/12/2023]
Abstract
Hydrogen sulfide (H2S) is an environmental contaminant to cause the airway damage. The release of macrophage extracellular traps (METs) is the mechanism of immune protection to harmful stimulation via microRNAs, but excessive METs cause the injury. However, few studies have attempted to interpret the mechanism of an organism injury due to H2S via METs in chickens. Here, we investigated the transcriptome profiles, pathological morphologic changes and METs release from chicken trachea after H2S exposure. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis revealed that 10 differentially expressed genes were related to the METs release, the MAPK and insulin signaling pathways. Morphological and immunofluorescence analysis showed that H2S caused airway injury and MET release. H2S activated the targeting effect of miRNA-15b-5p on activating transcription factor 2 (ATF2). Western blotting and real time quantitative PCR results showed that H2S down-regulated the levels of dual specificity protein phosophatase1 (DUSP1) but up-regulated p38 MAP Kinase (p38) in the MAPK signal pathway. And the expression of phosphoinositide-dependent protein kinase 1 (PDK1), serine/threonine kinase (Akt), and protein kinase ζ subtypes (PKCζ) in the insulin signal pathway were increased after H2S exposure. These promoted the release of myeloperoxidase (MPO) and degradation histone 4 (H4) to induce the release of METs. Taken together, miR-15b-5p targeted ATF2 to mediate METs release, which triggered trachea inflammatory injury via MAPK and insulin signals after H2S exposure. These results will provide new insights into the toxicological mechanisms of H2S and environmental ecotoxicology.
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Affiliation(s)
- Nuan Song
- College of Veterinary Medicine, Northeast Agricultural University; Key Laboratory of the Provincial Education Department of Heilongjiang for Common Animal Disease Prevention and Treatment, Harbin 150030, China
| | - Wei Wang
- College of Veterinary Medicine, Northeast Agricultural University; Key Laboratory of the Provincial Education Department of Heilongjiang for Common Animal Disease Prevention and Treatment, Harbin 150030, China
| | - Yue Wang
- College of Veterinary Medicine, Northeast Agricultural University; Key Laboratory of the Provincial Education Department of Heilongjiang for Common Animal Disease Prevention and Treatment, Harbin 150030, China
| | - Yalin Guan
- College of Life Science, Northeast Agricultural University, Harbin 150030, China
| | - Shiwen Xu
- College of Veterinary Medicine, Northeast Agricultural University; Key Laboratory of the Provincial Education Department of Heilongjiang for Common Animal Disease Prevention and Treatment, Harbin 150030, China
| | - Meng-Yao Guo
- College of Veterinary Medicine, Northeast Agricultural University; Key Laboratory of the Provincial Education Department of Heilongjiang for Common Animal Disease Prevention and Treatment, Harbin 150030, China.
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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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Smith J, Lipkin E, Soller M, Fulton JE, Burt DW. Mapping QTL Associated with Resistance to Avian Oncogenic Marek's Disease Virus (MDV) Reveals Major Candidate Genes and Variants. Genes (Basel) 2020; 11:genes11091019. [PMID: 32872585 PMCID: PMC7564597 DOI: 10.3390/genes11091019] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2020] [Revised: 08/20/2020] [Accepted: 08/26/2020] [Indexed: 01/13/2023] Open
Abstract
Marek’s disease (MD) represents a significant global economic and animal welfare issue. Marek’s disease virus (MDV) is a highly contagious oncogenic and highly immune-suppressive α-herpes virus, which infects chickens, causing neurological effects and tumour formation. Though partially controlled by vaccination, MD continues to have a profound impact on animal health and on the poultry industry. Genetic selection provides an alternative and complementary method to vaccination. However, even after years of study, the genetic mechanisms underlying resistance to MDV remain poorly understood. The Major Histocompatability Complex (MHC) is known to play a role in disease resistance, along with a handful of other non-MHC genes. In this study, one of the largest to date, we used a multi-facetted approach to identify quantitative trait locus regions (QTLR) influencing resistance to MDV, including an F6 population from a full-sib advanced intercross line (FSIL) between two elite commercial layer lines differing in resistance to MDV, RNA-seq information from virus challenged chicks, and genome wide association study (GWAS) from multiple commercial lines. Candidate genomic elements residing in the QTLR were further tested for association with offspring mortality in the face of MDV challenge in eight pure lines of elite egg-layer birds. Thirty-eight QTLR were found on 19 chicken chromosomes. Candidate genes, microRNAs, long non-coding RNAs and potentially functional mutations were identified in these regions. Association tests were carried out in 26 of the QTLR, using eight pure lines of elite egg-layer birds. Numerous candidate genomic elements were strongly associated with MD resistance. Genomic regions significantly associated with resistance to MDV were mapped and candidate genes identified. Various QTLR elements were shown to have a strong genetic association with resistance. These results provide a large number of significant targets for mitigating the effects of MDV infection on both poultry health and the economy, whether by means of selective breeding, improved vaccine design, or gene-editing technologies.
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Affiliation(s)
- Jacqueline Smith
- The Roslin Institute and Royal (Dick) School of Veterinary Studies R(D)SVS, University of Edinburgh, Easter Bush, Midlothian EH25 9RG, UK
| | - Ehud Lipkin
- Department of Genetics, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat Ram, Jerusalem 91904, Israel
| | - Morris Soller
- Department of Genetics, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat Ram, Jerusalem 91904, Israel
| | - Janet E Fulton
- Hy-Line International, P.O. Box 310, 2583 240th St., Dallas Center, IA 50063, USA
| | - David W Burt
- The Roslin Institute and Royal (Dick) School of Veterinary Studies R(D)SVS, University of Edinburgh, Easter Bush, Midlothian EH25 9RG, UK
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10
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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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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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Selection of the Most Stable Endogenous Control Genes for Microrna Quantitation in Chicken Ovarian Follicles. ANNALS OF ANIMAL SCIENCE 2020. [DOI: 10.2478/aoas-2019-0070] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Abstract
MicroRNAs (miRNAs or miRs) belong to a class of small non-coding RNAs of 19 to 24 nucleotides long that act as negative gene regulators at the post-transcriptional level. Quantitative PCR (q-PCR) is a commonly used technique in the profiling of miRs, and identification of reliable endogenous controls is crucial for proper data normalisation. To date, no study has been performed on reference miRs for the normalisation of miR expression in chicken ovarian tissues. Therefore, the aim of the present study was to experimentally identify the most stable reference mirs for normalisation of miR q-PCR expression data in the chicken ovary. Relying on high-throughput sequencing, five putative reference miR (let-7a-3p, miR-140a-3p, miR-22-5p, miR-33-5p, miR-99a-3p) were identified and subsequently analysed in a total of 66 tissue samples. The stability of candidate endogenous controls validated by the most widely used algorithms, geNorm, NormFinder, and BestKeeper, showed that let-7a-3p, miR-140a-3p, and miR-22-5p are the most appropriate choice of reference genes. Application of different normalisation approaches to the relative quantitation of randomly chosen miR-1552-5p in chicken ovarian follicles indicated the impact of the selected reference genes on miR expression. Further, the results revealed a downregulation of miR-1552-5p. In summary, the three identified endogenous reference miRs are suitable for profiling the miR expression in ovarian tissues of laying hens. Our findings provide valuable information for future miR expression studies in the avian ovary.
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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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He G, Wu J, Kong H, Zhang Y, Li Y, Cai M, Shaduhan G, Yan Y, Zheng Y, Ding J. Comparative analysis of miRNAs in exosomes released by sheeppox virus-infected ovine testicular cells. Comp Immunol Microbiol Infect Dis 2019; 67:101363. [PMID: 31600681 DOI: 10.1016/j.cimid.2019.101363] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2019] [Accepted: 09/25/2019] [Indexed: 12/14/2022]
Abstract
Exosomes, secreted by various cells, are nanometer-scale vesicles with the functions in intercellular communication. To understand a role of exosomal miRNAs in the sheeppox virus infection, exosomes were isolated from sheeppox virus-infected sheep testicular cells 0 h, 24 h and 72 h post infection. The results of transmission electron microscopy and size distribution showed that all three exosome samples were spherical particles with negatively-stained membrane, ranging from 39 nm to 127 nm in diameter. A total of 106 known and 279 novel miRNAs were identified, and 78 known and 54 novel miRNAs were commonly detected in three exosome samples. Compared with the exosomes by the uninfected controls, a total of 34 known miRNAs were aberrantly expressed in the exosomes from infected cells. In agreement with the sequencing data, the expression of oar-miR-21 and oar-miR-10b was shown to be the highest in exosomes at 24 h after SPPV-infected, and the expression of oar-let-7f was the highest in exosomes at 72 h. Conversely, the expression of oar-let-7b and oar-miR-221 was significantly decreased 24 h and 72 h post infection compared with 0 h. The analysis results also revealed that differentially expressed miRNAs were mostly involved in an immune system process and stimulus response. These results provide rich data to further investigate a role of exosomal miRNAs in SPPV-host interactions.
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Affiliation(s)
- Guitian He
- College of Life Science and Technology, Xinjiang University, Urumqi, 830046, China
| | - Jin'en Wu
- State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Veterinary Parasitology of Gansu Province, Lanzhou Veterinary Research Institute, CAAS, Lanzhou, 730046, China
| | - Helei Kong
- College of Life Science and Technology, Xinjiang University, Urumqi, 830046, China
| | - Yong'e Zhang
- State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Veterinary Parasitology of Gansu Province, Lanzhou Veterinary Research Institute, CAAS, Lanzhou, 730046, China
| | - Yating Li
- College of Life Science and Technology, Xinjiang University, Urumqi, 830046, China
| | - Mengting Cai
- College of Life Science and Technology, Xinjiang University, Urumqi, 830046, China
| | - Gulinazi Shaduhan
- College of Life Science and Technology, Xinjiang University, Urumqi, 830046, China
| | - Yuting Yan
- College of Life Science and Technology, Xinjiang University, Urumqi, 830046, China
| | - Yadong Zheng
- State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Veterinary Parasitology of Gansu Province, Lanzhou Veterinary Research Institute, CAAS, Lanzhou, 730046, China; Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou, 225009, China.
| | - Juntao Ding
- College of Life Science and Technology, Xinjiang University, Urumqi, 830046, China.
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Pasquini G, Kunej T. A Map of the microRNA Regulatory Networks Identified by Experimentally Validated microRNA-Target Interactions in Five Domestic Animals: Cattle, Pig, Sheep, Dog, and Chicken. OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY 2019; 23:448-456. [PMID: 31381467 DOI: 10.1089/omi.2019.0082] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Domestic animals are members of the broader ecological context, in which humans are situated. Yet, genomics and systems science research have lagged behind and been relatively underappreciated in domestic animals compared to human genetics/genomics. Harnessing big data calls for omics data mapping studies in a broad range of mammals. To this end, microRNAs (miRNAs) regulate posttranscriptional expression of target genes, hence, governing different biological pathways and physiological processes. The knowledge of miRNA regulatory networks and maps is important for understanding regulation of gene expression and functions in both humans and domestic animals. However, complete miRNA regulatory networks have not yet been described in all species, particularly in domestic animals. We report here an original analysis so as to map the miRNA regulatory networks in domestic animals based on miRNA-target interactions (MTIs). Validated MTIs for five species; cattle, pig, sheep, dog, and chicken were extracted from the miRTarBase. miRNA regulomes were visualized using the Cytoscape software. The data in cattle, chicken, and pig were sufficient to visualize networks, identify central molecules, and subnetworks associated with the same phenotype; however, the MTI data in dog and sheep are still limited. We found several hub genes with large number of interactions, for example, 1 miRNA (bta-miR-17-5p) interacting with 27 genes and 7 miRNAs interacting with the same gene (tumor necrosis factor [TNF]) in cattle. In addition, two single-nucleotide polymorphisms were identified within the seed region of a previously demonstrated MTI, namely, between HMGB3 (high mobility group box 3) gene and bta-miR-17-5p. In summary, this miRNA regulome mapping study will enable and guide further studies of genome function in mammals with a view to applications in human as well as veterinary medicine. Furthermore, these miRNA regulomes can help to clarify fundamental pathways in cell biology and reveal molecular insights on phenotypic trait variability in common complex diseases and response phenotypes of drugs or other health interventions for precision medicine in the future.
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Affiliation(s)
- Giacomo Pasquini
- Department of Animal Science, Biotechnical Faculty, University of Ljubljana, Domzale, Slovenia
| | - Tanja Kunej
- Department of Animal Science, Biotechnical Faculty, University of Ljubljana, Domzale, Slovenia
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16
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Gao S, Jiang H, Sun J, Diao Y, Tang Y, Hu J. Integrated Analysis of miRNA and mRNA Expression Profiles in Spleen of Specific Pathogen-Free Chicken Infected with Avian Reticuloendotheliosis Virus Strain SNV. Int J Mol Sci 2019; 20:ijms20051041. [PMID: 30818863 PMCID: PMC6429403 DOI: 10.3390/ijms20051041] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2019] [Revised: 02/15/2019] [Accepted: 02/23/2019] [Indexed: 01/06/2023] Open
Abstract
The Reticuloendotheliosis virus (REV) primarily causes avian severe immunosuppression, in addition to other symptoms, which include avian dwarfing syndrome and chronic tumors in lymphoid and other tissue. To date, REV’s molecular mechanisms leading to immunosuppression have not been fully elucidated. In the current study, we aimed to elucidate the role of microRNAs (miRNA) in regulating gene expression during REV infections. Therefore, we used a high-dose spleen necrosis virus (SNV) model of REV to inoculate one-day-old specific pathogen-free (SPF) chickens, thereby inducing congenital infections. We analyzed miRNA and mRNA expression profiles using Next Generation Sequencing (NGS) in a total of 19 spleen samples that were collected at 7, 14, and 21 days post infection (dpi). The results showed that 63 differentially expressed miRNAs (DEmiRNAs) (30 known miRNAs and 33 novel miRNAs) and 482 differentially expressed target genes (DETGs) were identified. Integration analysis identified 886 known miRNA–mRNA and 580 novel miRNA–mRNA interaction pairs, which involved miRNAs that were inversely correlated with the above DETGs. Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis revealed that the DETGs were considerably enriched in the immune-relevant pathways category, such as immune system, cell growth and death, signaling molecules and interaction, signal transduction, etc. We further verified selected immune-relevant miRNA and their DETGs while using quantitative RT-PCR (qRT-PCR). Overall, our data revealed valuable immune-related miRNA–mRNA interaction information that occurred during REV infections, thereby broadening our understanding of the REV-induced immunosuppression.
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Affiliation(s)
- Shuo Gao
- College of Animal Science and Veterinary Medicine, Shandong Agricultural University, No. 61 Daizong Street, Tai’an 271018, Shandong, China; (S.G.); (H.J.); (J.S.); (Y.D.)
- Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, Shandong Agricultural University, No. 61 Daizong Street, Tai’an 271018, Shandong, China
- Shandong Provincial Engineering Technology Research Center of Animal Disease Control and Prevention, Shandong Agricultural University, No. 61 Daizong Street, Tai’an 271018, Shandong, China
| | - Hao Jiang
- College of Animal Science and Veterinary Medicine, Shandong Agricultural University, No. 61 Daizong Street, Tai’an 271018, Shandong, China; (S.G.); (H.J.); (J.S.); (Y.D.)
- Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, Shandong Agricultural University, No. 61 Daizong Street, Tai’an 271018, Shandong, China
- Shandong Provincial Engineering Technology Research Center of Animal Disease Control and Prevention, Shandong Agricultural University, No. 61 Daizong Street, Tai’an 271018, Shandong, China
| | - Jie Sun
- College of Animal Science and Veterinary Medicine, Shandong Agricultural University, No. 61 Daizong Street, Tai’an 271018, Shandong, China; (S.G.); (H.J.); (J.S.); (Y.D.)
- Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, Shandong Agricultural University, No. 61 Daizong Street, Tai’an 271018, Shandong, China
- Shandong Provincial Engineering Technology Research Center of Animal Disease Control and Prevention, Shandong Agricultural University, No. 61 Daizong Street, Tai’an 271018, Shandong, China
| | - Youxiang Diao
- College of Animal Science and Veterinary Medicine, Shandong Agricultural University, No. 61 Daizong Street, Tai’an 271018, Shandong, China; (S.G.); (H.J.); (J.S.); (Y.D.)
- Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, Shandong Agricultural University, No. 61 Daizong Street, Tai’an 271018, Shandong, China
- Shandong Provincial Engineering Technology Research Center of Animal Disease Control and Prevention, Shandong Agricultural University, No. 61 Daizong Street, Tai’an 271018, Shandong, China
| | - Yi Tang
- College of Animal Science and Veterinary Medicine, Shandong Agricultural University, No. 61 Daizong Street, Tai’an 271018, Shandong, China; (S.G.); (H.J.); (J.S.); (Y.D.)
- Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, Shandong Agricultural University, No. 61 Daizong Street, Tai’an 271018, Shandong, China
- Shandong Provincial Engineering Technology Research Center of Animal Disease Control and Prevention, Shandong Agricultural University, No. 61 Daizong Street, Tai’an 271018, Shandong, China
- Correspondence: (Y.T.); (J.H.); Tel.: +86-13127277623 (Y.T.); +86-15949803926 (J.H.)
| | - Jingdong Hu
- College of Animal Science and Veterinary Medicine, Shandong Agricultural University, No. 61 Daizong Street, Tai’an 271018, Shandong, China; (S.G.); (H.J.); (J.S.); (Y.D.)
- Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, Shandong Agricultural University, No. 61 Daizong Street, Tai’an 271018, Shandong, China
- Shandong Provincial Engineering Technology Research Center of Animal Disease Control and Prevention, Shandong Agricultural University, No. 61 Daizong Street, Tai’an 271018, Shandong, China
- Correspondence: (Y.T.); (J.H.); Tel.: +86-13127277623 (Y.T.); +86-15949803926 (J.H.)
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Zhang F, Sun X, Zhu Y, Qin W. Downregulation of miR-146a inhibits influenza A virus replication by enhancing the type I interferon response in vitro and in vivo. Biomed Pharmacother 2019; 111:740-750. [PMID: 30611999 DOI: 10.1016/j.biopha.2018.12.103] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2018] [Revised: 12/17/2018] [Accepted: 12/23/2018] [Indexed: 12/13/2022] Open
Abstract
Albeit microRNAs (miRNAs) have become increasingly appreciated for their essential roles in innate immune responses to viral infections; however, it is unknown how host miRNAs regulate influenza A virus (IAV)-induced inflammation. The aim of our study was to investigate the role of miR-146a in IAV replication in vitro and in vivo. In vitro, we found miR-146a was significantly upregulated in A549 cells with IAV infection. Overexpression of miR-146a promoted IAV replication, while downregulation of miR-146a repressed replication. We found that miR-146a diminished type I interferon (IFN) responses by decreasing IFN-β production and IFN-stimulated gene (ISG) expression. Furthermore, we found the IFNs level and IAV replication regulated by miR-146a inhibitor was partially reversed by depletion of interferon receptor (IFNAR) 1 or 2. In addition, we found that miR-146a directly targets tumor necrosis factor receptor association factor 6 (TRAF6), which is involved in the production of type I IFN, and TRAF6 overexpression reversed the replication-promoting effect of miR-146a on IAV. In vivo, inhibition of miR-146a alleviated IAV-induced mice lung injury and promoted survival rates by promoting type I antiviral activities. It is, therefore, concluded that downregulation of miR-146a inhibits IAV replication by enhancing type I IFN response through its target gene TRAF6 in vitro and in vivo, suggesting miR-146a antagomir might be a potential therapeutic target during IAV infection.
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Affiliation(s)
- Fuming Zhang
- Clinical Laboratory, Henan Provincial People's Hospital, People's Hospital of Zhengzhou University, Zhengzhou, Henan, 450003, China
| | - Xiaofang Sun
- Clinical Laboratory, Henan Provincial People's Hospital, People's Hospital of Zhengzhou University, Zhengzhou, Henan, 450003, China
| | - Ya Zhu
- Clinical Laboratory, Henan Provincial People's Hospital, People's Hospital of Zhengzhou University, Zhengzhou, Henan, 450003, China
| | - Wangsen Qin
- Clinical Laboratory, Henan Provincial People's Hospital, People's Hospital of Zhengzhou University, Zhengzhou, Henan, 450003, China.
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18
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Zampiga M, Flees J, Meluzzi A, Dridi S, Sirri F. Application of omics technologies for a deeper insight into quali-quantitative production traits in broiler chickens: A review. J Anim Sci Biotechnol 2018; 9:61. [PMID: 30214720 PMCID: PMC6130060 DOI: 10.1186/s40104-018-0278-5] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2018] [Accepted: 07/03/2018] [Indexed: 12/12/2022] Open
Abstract
The poultry industry is continuously facing substantial and different challenges such as the increasing cost of feed ingredients, the European Union's ban of antibiotic as growth promoters, the antimicrobial resistance and the high incidence of muscle myopathies and breast meat abnormalities. In the last decade, there has been an extraordinary development of many genomic techniques able to describe global variation of genes, proteins and metabolites expression level. Proper application of these cutting-edge omics technologies (mainly transcriptomics, proteomics and metabolomics) paves the possibility to understand much useful information about the biological processes and pathways behind different complex traits of chickens. The current review aimed to highlight some important knowledge achieved through the application of omics technologies and proteo-genomics data in the field of feed efficiency, nutrition, meat quality and disease resistance in broiler chickens.
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Affiliation(s)
- Marco Zampiga
- Department of Agricultural and Food Sciences, Alma Mater Studiorum - University of Bologna, Via del Florio, 2, 40064 Ozzano dell’Emilia, Italy
| | - Joshua Flees
- Center of Excellence for Poultry Science, University of Arkansas, Fayetteville, AR 72701 USA
| | - Adele Meluzzi
- Department of Agricultural and Food Sciences, Alma Mater Studiorum - University of Bologna, Via del Florio, 2, 40064 Ozzano dell’Emilia, Italy
| | - Sami Dridi
- Center of Excellence for Poultry Science, University of Arkansas, Fayetteville, AR 72701 USA
| | - Federico Sirri
- Department of Agricultural and Food Sciences, Alma Mater Studiorum - University of Bologna, Via del Florio, 2, 40064 Ozzano dell’Emilia, Italy
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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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Gga-miR-130b-3p inhibits MSB1 cell proliferation, migration, invasion, and its downregulation in MD tumor is attributed to hypermethylation. Oncotarget 2018; 9:24187-24198. [PMID: 29849932 PMCID: PMC5966247 DOI: 10.18632/oncotarget.24679] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2017] [Accepted: 02/27/2018] [Indexed: 01/07/2023] Open
Abstract
Marek's disease is an oncogenic and lymphoproliferative disease of chickens caused by Marek's disease virus. Hypermethylation or hypomethylation of CpG islands in gene promoter region are involved in the initiation and progression of carcinogenesis. In this study, we analyzed differential methylation levels of upstream region of gga-miR-130b-3p gene between Marek's disease virus-infected tumorous and non-infected spleens. Around the upstream 1 kb of gga-miR-130b-3p gene, two amplicons were designed that covered 616 bp. There were forty-eight CpG sites in this region. CpG sites in this region presented higher methylation level in tumorous spleens compared with that in non-infected ones. There were eight CpG sites significantly hypermethylated in tumorous spleens. The expression level of three DNA methyltransferases including DNMT1, DNMT3a and DNMT3b increased and the expression level of Tet ten-eleven translocation protein 2 remarkably decreased in tumorous spleens. Hypermethylation in the upstream region of gga-miR-130b-3p gene might be a direct reason for its downregulation in MD tumorous tissues. Moreover, cell proliferation of Marek's disease lymphoblastoid cell line MDCC-MSB1 was remarkably inhibited at 24, 36, 48, 60 and 72 h post-gga-miR-130b-3p-agomir transfection. The transwell migration assay indicated cell number of migration was significantly lower in miRNA agomir transfection group. Matrix metalloproteinases MMP2 and MMP9 are involved in tumor invasion, and their protein levels were significantly downregulated at 72 h post-miRNA-agomir transfection. Collectively, these results indicated that hypermethylation in upstream region of gga-miR-130b-3p gene contributed to its downregulation in tumorous tissues. Gga-miR-130b-3p plays an inhibitory role in lymphomatous cell transformation.
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Wu X, Jia R, Zhou J, Wang M, Chen S, Liu M, Zhu D, Zhao X, Sun K, Yang Q, Wu Y, Yin Z, Chen X, Wang J, Cheng A. Virulent duck enteritis virus infected DEF cells generate a unique pattern of viral microRNAs and a novel set of host microRNAs. BMC Vet Res 2018; 14:144. [PMID: 29704894 PMCID: PMC5923184 DOI: 10.1186/s12917-018-1468-2] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2017] [Accepted: 04/20/2018] [Indexed: 12/12/2022] Open
Abstract
Background Duck enteritis virus (DEV) belongs to the family Herpesviridae and is an important epornitic agent that causes economic losses in the waterfowl industry. The Chinese virulent (CHv) and attenuate vaccines (VAC) are two different pathogenic DEV strains. MicroRNAs (miRNAs) are a class of non-coding RNAs that regulate gene expression in viral infection. Nonetheless, there is little information on virulent duck enteritis virus (DEV)-encoded miRNAs. Results Using high-throughput sequencing, we identified 39 mature viral miRNAs from CHv-infected duck embryo fibroblasts cells. Compared with the reported 33 VAC-encoded miRNAs, only 13 miRNA sequences and 22 “seed sequences” of miRNA were identical, and 8 novel viral miRNAs were detected and confirmed by stem-loop RT-qPCR in this study. Using RNAhybrid and PITA software, 38 CHv-encoded miRNAs were predicted to target 41 viral genes and formed a complex regulatory network. Dual luciferase reporter assay (DLRA) confirmed that viral dev-miR-D8-3p can directly target the 3’-UTR of CHv US1 gene (p < 0.05). Gene Ontology analysis on host target genes of viral miRNAs were mainly involved in biological regulation, cellular and metabolic processes. In addition, 598 novel duck-encoded miRNAs were detected in this study. Thirty-eight host miRNAs showed significant differential expression after CHv infection: 13 miRNAs were up-regulated, and 25 miRNAs were down-regulated, which may affect viral replication in the host cell. Conclusions These data suggested that CHv encoded a different set of microRNAs and formed a unique regulatory network compared with VAC. This is the first report of DEF miRNAs expression profile and an analysis of these miRNAs regulatory mechanisms during DEV infection. These data provide a basis for further exploring miRNA regulatory roles in the pathogenesis of DEV infection and contribute to the understanding of the CHv-host interaction at the miRNA level. Electronic supplementary material The online version of this article (10.1186/s12917-018-1468-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Xianglong Wu
- Research Center of Avian Disease, College of Veterinary, Medicine of Sichuan Agricultural University, Wenjiang District, Chengdu, 611130, Sichuan Province, China.,Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Wenjiang District, Chengdu, 611130, Sichuan Province, China
| | - Renyong Jia
- Research Center of Avian Disease, College of Veterinary, Medicine of Sichuan Agricultural University, Wenjiang District, Chengdu, 611130, Sichuan Province, China. .,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Wenjiang District, Chengdu, 611130, Sichuan Province, China. .,Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Wenjiang District, Chengdu, 611130, Sichuan Province, China.
| | - Jiakun Zhou
- Research Center of Avian Disease, College of Veterinary, Medicine of Sichuan Agricultural University, Wenjiang District, Chengdu, 611130, Sichuan Province, China.,Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Wenjiang District, Chengdu, 611130, Sichuan Province, China
| | - Mingshu Wang
- Research Center of Avian Disease, College of Veterinary, Medicine of Sichuan Agricultural University, Wenjiang District, Chengdu, 611130, Sichuan Province, China.,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Wenjiang District, Chengdu, 611130, Sichuan Province, China.,Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Wenjiang District, Chengdu, 611130, Sichuan Province, China
| | - Shun Chen
- Research Center of Avian Disease, College of Veterinary, Medicine of Sichuan Agricultural University, Wenjiang District, Chengdu, 611130, Sichuan Province, China.,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Wenjiang District, Chengdu, 611130, Sichuan Province, China.,Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Wenjiang District, Chengdu, 611130, Sichuan Province, China
| | - Mafeng Liu
- Research Center of Avian Disease, College of Veterinary, Medicine of Sichuan Agricultural University, Wenjiang District, Chengdu, 611130, Sichuan Province, China.,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Wenjiang District, Chengdu, 611130, Sichuan Province, China.,Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Wenjiang District, Chengdu, 611130, Sichuan Province, China
| | - Dekang Zhu
- Research Center of Avian Disease, College of Veterinary, Medicine of Sichuan Agricultural University, Wenjiang District, Chengdu, 611130, Sichuan Province, China.,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Wenjiang District, Chengdu, 611130, Sichuan Province, China.,Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Wenjiang District, Chengdu, 611130, Sichuan Province, China
| | - Xinxin Zhao
- Research Center of Avian Disease, College of Veterinary, Medicine of Sichuan Agricultural University, Wenjiang District, Chengdu, 611130, Sichuan Province, China.,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Wenjiang District, Chengdu, 611130, Sichuan Province, China.,Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Wenjiang District, Chengdu, 611130, Sichuan Province, China
| | - Kunfeng Sun
- Research Center of Avian Disease, College of Veterinary, Medicine of Sichuan Agricultural University, Wenjiang District, Chengdu, 611130, Sichuan Province, China.,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Wenjiang District, Chengdu, 611130, Sichuan Province, China.,Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Wenjiang District, Chengdu, 611130, Sichuan Province, China
| | - Qiao Yang
- Research Center of Avian Disease, College of Veterinary, Medicine of Sichuan Agricultural University, Wenjiang District, Chengdu, 611130, Sichuan Province, China.,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Wenjiang District, Chengdu, 611130, Sichuan Province, China.,Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Wenjiang District, Chengdu, 611130, Sichuan Province, China
| | - Ying Wu
- Research Center of Avian Disease, College of Veterinary, Medicine of Sichuan Agricultural University, Wenjiang District, Chengdu, 611130, Sichuan Province, China.,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Wenjiang District, Chengdu, 611130, Sichuan Province, China.,Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Wenjiang District, Chengdu, 611130, Sichuan Province, China
| | - Zhongqiong Yin
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Wenjiang District, Chengdu, 611130, Sichuan Province, China
| | - Xiaoyue Chen
- Research Center of Avian Disease, College of Veterinary, Medicine of Sichuan Agricultural University, Wenjiang District, Chengdu, 611130, Sichuan Province, China.,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Wenjiang District, Chengdu, 611130, Sichuan Province, China
| | - Jue Wang
- BGI Genomics Co,shenzhen Ltd, Shenzhen, 518083, Guangdong Province, China
| | - Anchun Cheng
- Research Center of Avian Disease, College of Veterinary, Medicine of Sichuan Agricultural University, Wenjiang District, Chengdu, 611130, Sichuan Province, China. .,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Wenjiang District, Chengdu, 611130, Sichuan Province, China. .,Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Wenjiang District, Chengdu, 611130, Sichuan Province, China.
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22
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Wang H, Liu L, Liu X, Zhang M, Li X. Correlation between miRNAs and target genes in response to Campylobacter jejuni inoculation in chicken. Poult Sci 2018; 97:485-493. [DOI: 10.3382/ps/pex343] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2017] [Accepted: 10/14/2017] [Indexed: 12/19/2022] Open
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23
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Long intergenic non-coding RNA GALMD3 in chicken Marek's disease. Sci Rep 2017; 7:10294. [PMID: 28860661 PMCID: PMC5579197 DOI: 10.1038/s41598-017-10900-2] [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: 03/24/2017] [Accepted: 08/16/2017] [Indexed: 12/18/2022] Open
Abstract
Long intergenic non-coding RNAs (lincRNAs) are transcribed from non-coding DNA sequences. Studies have revealed that aberrant expressions of lincRNAs are associated with various types of cancers and neurological disorders. Marek's disease (MD) is a highly contagious T-cell lymphoid neoplasia of chicken induced by Marek's disease virus (MDV). In this study, we first identified and validated linc-GALMD3 highly expressed in MDV-infected CD4+ T cells by RNA-Seq and qRT-PCR. By RNA-Seq analysis in MDCC-MSB1 cells after loss of function of linc-GALMD3 by shRNA, we found that linc-GALMD3 could positively cis-regulate its downstream gga-miR-223 gene expression. In contrast, it could trans-regulate the 748 differentially expressed genes (FDR < 0.01) that were mainly enriched into mitochondrial structure and cell cycle processes using GO analysis. Of these, the most significantly expressed gene EPYC might cause iris lesion in MD. The other eight genes, NDUFA4, NDUFB6, NDUFV1, NDUFS8, SDHB, UQCRC1, UQCRC2, and COX7A2, actively participated in oxidative phosphorylation in mitochondrial dysfunction and cell death. Most importantly, we found that the MDV replication was repressed when linc-GALMD3 was knocked down in CEF cells. Our results suggested that linc-GALMD3 might be a critical regulator in chicken MD and could be used as a candidate-promising mark for MD prevention, diagnosis, and treatment.
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24
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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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25
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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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26
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Paces J, Nic M, Novotny T, Svoboda P. Literature review of baseline information to support the risk assessment of RNAi‐based GM plants. ACTA ACUST UNITED AC 2017. [PMCID: PMC7163844 DOI: 10.2903/sp.efsa.2017.en-1246] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Jan Paces
- Institute of Molecular Genetics of the Academy of Sciences of the Czech Republic (IMG)
| | | | | | - Petr Svoboda
- Institute of Molecular Genetics of the Academy of Sciences of the Czech Republic (IMG)
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27
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Lai AG, Aboobaker AA. Comparative genomic analysis of innate immunity reveals novel and conserved components in crustacean food crop species. BMC Genomics 2017; 18:389. [PMID: 28521727 PMCID: PMC5437397 DOI: 10.1186/s12864-017-3769-4] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2017] [Accepted: 05/07/2017] [Indexed: 12/17/2022] Open
Abstract
BACKGROUND Growing global demands for crustacean food crop species have driven large investments in aquaculture research worldwide. However, large-scale production is susceptible to pathogen-mediated destruction particularly in developing economies. Thus, a thorough understanding of the immune system components of food crop species is imperative for research to combat pathogens. RESULTS Through a comparative genomics approach utilising extant data from 55 species, we describe the innate immune system of the class Malacostraca, which includes all food crop species. We identify 7407 malacostracan genes from 39 gene families implicated in different aspects of host defence and demonstrate dynamic evolution of innate immunity components within this group. Malacostracans have achieved flexibility in recognising infectious agents through divergent evolution and expansion of pathogen recognition receptors genes. Antiviral RNAi, Toll and JAK-STAT signal transduction pathways have remained conserved within Malacostraca, although the Imd pathway appears to lack several key components. Immune effectors such as the antimicrobial peptides (AMPs) have unique evolutionary profiles, with many malacostracan AMPs not found in other arthropods. Lastly, we describe four putative novel immune gene families, potentially representing important evolutionary novelties of the malacostracan immune system. CONCLUSION Our analyses across the broader Malacostraca have allowed us to not only draw analogies with other arthropods but also to identify evolutionary novelties in immune modulation components and form strong hypotheses as to when key pathways have evolved or diverged. This will serve as a key resource for future immunology research in crustacean food crops.
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Affiliation(s)
- Alvina G Lai
- Department of Zoology, University of Oxford, Tinbergen Building, South Parks Road, Oxford, OX1 3PS, UK.
| | - A Aziz Aboobaker
- Department of Zoology, University of Oxford, Tinbergen Building, South Parks Road, Oxford, OX1 3PS, UK.
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28
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Integrated host and viral transcriptome analyses reveal pathology and inflammatory response mechanisms to ALV-J injection in SPF chickens. Sci Rep 2017; 7:46156. [PMID: 28401895 PMCID: PMC5388866 DOI: 10.1038/srep46156] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2016] [Accepted: 03/09/2017] [Indexed: 12/31/2022] Open
Abstract
Avian leukosis virus (ALV) is detrimental to poultry health and causes substantial economic losses from mortality and decreased performance. Because tumorigenesis is a complex mechanism, the regulatory architecture of the immune system is likely to include the added dimensions of modulation by miRNAs and long-noncoding RNA (lncRNA). To characterize the response to ALV challenge, we developed a novel methodology that combines four datasets: mRNA expression and the associated regulatory factors of miRNA and lncRNA, and ALV gene expression. Specific Pathogen-Free (SPF) layer chickens were infected with ALV-J or maintained as non-injected controls. Spleen samples were collected at 40 days post injection (dpi), and sequenced. There were 864 genes, 7 miRNAs and 17 lncRNAs differentially expressed between infected and non-infected birds. The combined analysis of the 4 RNA expression datasets revealed that ALV infection is detected by pattern-recognition receptors (TLR9 and TLR3) leading to a type-I IFN mediated innate immune response that is modulated by IRF7 and IRF1. Co-expression network analysis of mRNA with miRNA, lncRNA and virus genes identified key elements within the complex networks utilized during ALV response. The integration of information from the host transcriptomic, epigenetic and virus response also has the potential to provide deeper insights into other host-pathogen interactions.
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29
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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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30
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Wu N, Gaur U, Zhu Q, Chen B, Xu Z, Zhao X, Yang M, Li D. Expressed microRNA associated with high rate of egg production in chicken ovarian follicles. Anim Genet 2016; 48:205-216. [PMID: 27781291 DOI: 10.1111/age.12516] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/01/2016] [Indexed: 01/28/2023]
Abstract
MicroRNA (miRNA) is a highly conserved class of small noncoding RNA about 19-24 nucleotides in length that function in a specific manner to post-transcriptionally regulate gene expression in organisms. Tissue miRNA expression studies have discovered a myriad of functions for miRNAs in various aspects, but a role for miRNAs in chicken ovarian tissue at 300 days of age has not hitherto been reported. In this study, we performed the first miRNA analysis of ovarian tissues in chickens with low and high rates of egg production using high-throughput sequencing. By comparing low rate of egg production chickens with high rate of egg production chickens, 17 significantly differentially expressed miRNAs were found (P < 0.05), including 11 known and six novel miRNAs. We found that all 11 known miRNAs were involved mainly in pathways of reproduction regulation, such as steroid hormone biosynthesis and dopaminergic synapse. Additionally, expression profiling of six randomly selected differentially regulated miRNAs were validated by quantitative real-time polymerase chain reaction (RT-qPCR). Some miRNAs, such as gga-miR-34b, gga-miR-34c and gga-miR-216b, were reported to regulate processes such as proliferation, cell cycle, apoptosis and metastasis and were expressed differentially in ovaries of chickens with high rates of egg production, suggesting that these miRNAs have an important role in ovary development and reproductive management of chicken. Furthermore, we uncovered that a significantly up-regulated miRNA-gga-miR-200a-3p-is ubiquitous in reproduction-regulation-related pathways. This miRNA may play a special central role in the reproductive management of chicken, and needs to be further studied for confirmation.
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Affiliation(s)
- N Wu
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, 610000, China
| | - U Gaur
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, 610000, China
| | - Q Zhu
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, 610000, China
| | - B Chen
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, 610000, China
| | - Z Xu
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, 610000, China
| | - X Zhao
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, 610000, China
| | - M Yang
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, 610000, China
| | - D Li
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, 610000, China
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31
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Samir M, Vaas LAI, Pessler F. MicroRNAs in the Host Response to Viral Infections of Veterinary Importance. Front Vet Sci 2016; 3:86. [PMID: 27800484 PMCID: PMC5065965 DOI: 10.3389/fvets.2016.00086] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2016] [Accepted: 09/12/2016] [Indexed: 12/13/2022] Open
Abstract
The discovery of small regulatory non-coding RNAs has been an exciting advance in the field of genomics. MicroRNAs (miRNAs) are endogenous RNA molecules, approximately 22 nucleotides in length, that regulate gene expression, mostly at the posttranscriptional level. MiRNA profiling technologies have made it possible to identify and quantify novel miRNAs and to study their regulation and potential roles in disease pathogenesis. Although miRNAs have been extensively investigated in viral infections of humans, their implications in viral diseases affecting animals of veterinary importance are much less understood. The number of annotated miRNAs in different animal species is growing continuously, and novel roles in regulating host–pathogen interactions are being discovered, for instance, miRNA-mediated augmentation of viral transcription and replication. In this review, we present an overview of synthesis and function of miRNAs and an update on the current state of research on host-encoded miRNAs in the genesis of viral infectious diseases in their natural animal host as well as in selected in vivo and in vitro laboratory models.
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Affiliation(s)
- Mohamed Samir
- TWINCORE, Center for Experimental and Clinical Infection Research, Hannover, Germany; Department of Zoonoses, Faculty of Veterinary Medicine, Zagazig University, Zagazig, Egypt
| | - Lea A I Vaas
- TWINCORE, Center for Experimental and Clinical Infection Research , Hannover , Germany
| | - Frank Pessler
- TWINCORE, Center for Experimental and Clinical Infection Research, Hannover, Germany; Helmholtz Center for Infection Research, Braunschweig, Germany
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32
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Luo J, Liu J, Liu H, Zhang T, Wang J, He H, Han C. Enrichment and verification of differentially expressed miRNAs in bursa of Fabricius in two breeds of duck. ASIAN-AUSTRALASIAN JOURNAL OF ANIMAL SCIENCES 2016; 30:920-929. [PMID: 27660025 PMCID: PMC5495669 DOI: 10.5713/ajas.16.0325] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/25/2016] [Revised: 06/06/2016] [Accepted: 09/15/2016] [Indexed: 12/03/2022]
Abstract
Objective The bursa of Fabricius (BF) is a central humoral immune organ belonging specifically to avians. Recent studies had suggested that miRNAs were active regulators involved in the immune processes. This study was to investigate the possible differences of the BF at miRNA level between two genetically disparate duck breeds. Methods Using Illumina next-generation sequencing, the miRNAs libraries of ducks were established. Results The results showed that there were 66 differentially expressed miRNAs and 28 novel miRNAs in bursa. A set of abundant miRNAs (i.e., let-7, miR-146a-5p, miR-21-5p, miR-17~92) which are involved in immunity and disease were detected and the predicted target genes of the novel miRNAs were associated with duck high anti-adversity ability. By gene ontology analysis and enriching KEGG pathway, the targets of differential expressed miRNAs were mainly involved in immunity and disease, supporting that there were differences in the BF immune functions between the two duck breeds. In addition, the metabolic pathway had the maximum enriched target genes and some enriched pathways that were related to cell cycle, protein synthesis, cell proliferation and apoptosis. It indicted that the difference of metabolism may be one of the reasons leading the immune difference between the BF of two duck breeds. Conclusion This data lists the main differences in the BF at miRNAs level between two genetically disparate duck breeds and lays a foundation to carry out molecular assisted breeding of poultry in the future.
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Affiliation(s)
- Jun Luo
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Wenjiang, Chengdu 611130, China
| | - Junying Liu
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Wenjiang, Chengdu 611130, China
| | - Hehe Liu
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Wenjiang, Chengdu 611130, China
| | - Tao Zhang
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Wenjiang, Chengdu 611130, China
| | - Jiwen Wang
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Wenjiang, Chengdu 611130, China
| | - Hua He
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Wenjiang, Chengdu 611130, China
| | - Chunchun Han
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Wenjiang, Chengdu 611130, China
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33
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Identification and expression analysis of cellular and viral microRNAs in CyHV3-infected KCF-1 cells. Gene 2016; 592:154-163. [PMID: 27476971 DOI: 10.1016/j.gene.2016.07.064] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2016] [Revised: 07/22/2016] [Accepted: 07/26/2016] [Indexed: 11/22/2022]
Abstract
MicroRNAs (miRNAs) are small non-coding RNAs with approximately 22 nucleotides (nt) that are encoded by a diverse range of metazoan eukaryotes, plants and viruses. CyHV-3 (cyprinid herpesvirus-3) is a member of the Alloherpesviridae virus family and has caused severe economic losses for the common carp and koi carp fishery industries. In this study, a total of 15,987,652 clean reads were generated from a cDNA library of CyHV-3-infected KCF-1 (koi caudal fin) cells using high-throughput sequencing technology. Following annotation and secondary structure prediction, 28 miRNAs were identified as novel candidate miRNAs encoded by common carp (Cyprinus carpio), and seven miRNAs were shown to be encoded by CyHV-3. Next, 19 host miRNAs and seven viral miRNAs were validated by stem-loop real-time PCR. Northern blot analysis confirmed the presence of 14 host miRNAs and five CyHV-3-encoded novel miRNAs. The results of this study expand the knowledge of common carp and CyHV-3 microRNAs and provide a useful theoretical foundation for further study of CyHV-3.
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34
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Han B, Lian L, Li X, Zhao C, Qu L, Liu C, Song J, Yang N. Chicken gga-miR-130a targets HOXA3 and MDFIC and inhibits Marek's disease lymphoma cell proliferation and migration. Mol Biol Rep 2016; 43:667-76. [PMID: 27178573 DOI: 10.1007/s11033-016-4002-2] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2015] [Accepted: 05/04/2016] [Indexed: 12/19/2022]
Abstract
Marek's disease (MD) is an infectious disease of chickens caused by MD virus (MDV), which is a herpesvirus that initiates tumor formation. Studies have indicated that microRNAs (miRNAs) are linked with the development of cancers or tumors. Previously, gga-miR-130a was discovered downregulated in MDV-infected tissues. Here, we aimed to explore the further function of gga-miR-130a in MD. The expression of gga-miR-130a in MDV-infected and uninfected spleens was detected by quantitative real-time PCR (qRT-PCR). Subsequently, proliferation and migration assays of MDV-transformed lymphoid cells (MSB1) were carried out by transfecting gga-miR-130a. The target genes of gga-miR-130a were predicted using TargetScan and miRDB and clustered through Gene Ontology analysis. The target genes were validated by western blot, qRT-PCR, and a dual luciferase reporter assay. Our results show that the expression of gga-miR-130a was reduced in MDV-infected spleens. Gga-miR-130a showed an inhibitory effect on MSB1 cell proliferation and migration. Two target genes, homeobox A3 (HOXA3) and MyoD family inhibitor domain containing (MDFIC), were predicted and clustered to cell proliferation. Results indicate that gga-miR-130a regulates HOXA3 and MDFIC at the protein level but not at the mRNA level. Moreover, the gga-miR-130a binding sites of two target genes have been confirmed. We conclude that gga-miR-130a can arrest MSB1 cell proliferation and migration, and target HOXA3 and MDFIC, which are both involved in the regulation of cell proliferation. Collectively, gga-miR-130a plays a critical role in the tumorigenesis associated with chicken MD.
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Affiliation(s)
- Bo Han
- Department of Animal Genetics and Breeding, National Engineering Laboratory for Animal Breeding College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Ling Lian
- Department of Animal Genetics and Breeding, National Engineering Laboratory for Animal Breeding College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Xin Li
- Department of Animal Genetics and Breeding, National Engineering Laboratory for Animal Breeding College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Chunfang Zhao
- Department of Animal Genetics and Breeding, National Engineering Laboratory for Animal Breeding College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Lujiang Qu
- Department of Animal Genetics and Breeding, National Engineering Laboratory for Animal Breeding College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Changjun Liu
- Division of Avian Infectious Diseases, Harbin Veterinary Research Institute of Chinese Academy of Agricultural Sciences, Harbin, 150001, China
| | - Jiuzhou Song
- Department of Animal & Avian Sciences, University of Maryland, College Park, MD, 20742, USA
| | - Ning Yang
- Department of Animal Genetics and Breeding, National Engineering Laboratory for Animal Breeding College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China.
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Chicken gga-miR-103-3p Targets CCNE1 and TFDP2 and Inhibits MDCC-MSB1 Cell Migration. G3-GENES GENOMES GENETICS 2016; 6:1277-85. [PMID: 26935418 PMCID: PMC4856079 DOI: 10.1534/g3.116.028498] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Marek’s disease (MD) is a highly contagious viral neoplastic disease caused by Marek’s disease virus (MDV), which can lead to huge economic losses in the poultry industry. Recently, microRNAs (miRNAs) have been found in various cancers and tumors. In recent years, 994 mature miRNAs have been identified through deep sequencing in chickens, but only a few miRNAs have been investigated further in terms of their function. Previously, gga-miR-103-3p was found downregulated in MDV-infected samples by using Solexa deep sequencing. In this study, we further verified the expression of gga-miR-103-3p among MDV-infected spleen, MD lymphoma from liver, noninfected spleen, and noninfected liver, by qPCR. The results showed that the expression of gga-miR-103-3p was decreased in MDV-infected tissues, which was consistent with our previous study. Furthermore, two target genes of gga-miR-103-3p, cyclin E1 (CCNE1) and transcription factor Dp-2 (E2F dimerization partner 2) (TFDP2), were predicted and validated by luciferase reporter assay, qPCR, and western blot analysis. The results suggested that CCNE1 and TFDP2 are direct targets of gga-miR-103-3p in chickens. Subsequent cell proliferation and migration assay showed that gga-miR-103-3p suppressed MDCC-MSB1 migration, but did not obviously modulate MDCC-MSB1 cell proliferation. In conclusion, gga-miR-103-3p targets the CCNE1 and TFDP2 genes, and suppresses cell migration, which indicates that it might play an important role in MD tumor transformation.
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Lian L, Li X, Zhao C, Han B, Qu L, Song J, Liu C, Yang N. Chicken gga-miR-181a targets MYBL1 and shows an inhibitory effect on proliferation of Marek's disease virus-transformed lymphoid cell line. Poult Sci 2016; 94:2616-21. [PMID: 26500265 DOI: 10.3382/ps/pev289] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Marek's disease (MD), caused by Marek's disease virus (MDV), is a lymphoproliferative neoplastic disease of chickens and is characterized by MD lymphoma in multiple visceral organs of chicken. It causes great damage to poultry health. Recently, miRNA has been reported to be involved in Marek's disease lymphomagenesis. Our previous study showed that gga-miR-181a was downregulated in MDV-induced lymphoma, and its target gene, v-myb myeloblastosis viral oncogene homolog-like 1 (MYBL1), was predicted. In this study, the interaction between gga-miR-181a and MYBL1 was further verified by detecting protein expression levels of MYBL1 after transfecting miR-181a mimic into MD lymphoma cell line, MSB1. The result showed that protein level of MYBL1 was lower in gga-miR-181a mimic transfecting group than that in the negative control group at 96 h post transfection, which indicated that MYBL1 was a target gene of gga-miR-181a. Additionally, we found that the expression of MYBL1 was higher in MDV-infected samples than that in non-infected controls, which agreed with the proposition that miRNA showed a negatively correlated expression pattern with its target gene. We observed the inhibitory effect of gga-miR-181a on MSB1 cell proliferation. Collectively, the aberrant expression of gga-miR-181a and MYBL1 in MD lymphoma suggested that they might be involved in MD tumor transformation and played important roles.
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Affiliation(s)
- Ling Lian
- Department of Animal Genetics and Breeding, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
| | - Xin Li
- Department of Animal Genetics and Breeding, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
| | - Chunfang Zhao
- Department of Animal Genetics and Breeding, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
| | - Bo Han
- Department of Animal Genetics and Breeding, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
| | - Lujiang Qu
- Department of Animal Genetics and Breeding, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
| | - Jiuzhou Song
- Department of Animal & Avian Sciences, University of Maryland, College Park, Maryland 20742, United States
| | - Changjun Liu
- Division of Avian Infectious Diseases, Harbin Veterinary Research Institute of Chinese Academy of Agricultural Sciences, Harbin 150001, China
| | - Ning Yang
- Department of Animal Genetics and Breeding, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
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Dai Z, Ji J, Yan Y, Lin W, Li H, Chen F, Liu Y, Chen W, Bi Y, Xie Q. Role of gga-miR-221 and gga-miR-222 during Tumour Formation in Chickens Infected by Subgroup J Avian Leukosis Virus. Viruses 2015; 7:6538-51. [PMID: 26690468 PMCID: PMC4690879 DOI: 10.3390/v7122956] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2015] [Revised: 11/18/2015] [Accepted: 12/02/2015] [Indexed: 02/02/2023] Open
Abstract
Subgroup J avian leukosis virus (ALV-J) causes a neoplastic disease in infected chickens. Differential expression patterns of microRNAs (miRNAs) are closely related to the formation and growth of tumors. (1) Background: This study was undertaken to understand how miRNAs might be related to tumor growth during ALV-J infection. We chose to characterize the effects of miR-221 and miR-222 on cell proliferation, migration, and apoptosis based on previous microarray data. (2) Methods: In vivo, the expression levels of miR-221 and miR-222 were significantly increased in the liver of ALV-J infected chickens (p < 0.01). Over-expression of gga-miR-221 and gga-miR-222 promoted the proliferation, migration, and growth of DF-1 cells, and decreased the expression of BCL-2 modifying factor (BMF) making cells more resistant to apoptosis. (3) Results: Our results suggest that gga-miR-221 and gga-miR-222 may be tumour formation relevant gene in chicken that promote proliferation, migration, and growth of cancer cells, and inhibit apoptosis. BMF expression was significantly reduced in vivo 70 days after ALV-J infection. They may also play a pivotal role in tumorigenesis during ALV-J infection.
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Affiliation(s)
- Zhenkai Dai
- College of Animal Science, South China Agricultural University & Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, Guangzhou 510642, China.
| | - Jun Ji
- China-UK-NYNU-RRes Joint laboratory of Insect Biology, Nanyang Normal Universiy, Nanyang 473000, China.
| | - Yiming Yan
- College of Animal Science, South China Agricultural University & Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, Guangzhou 510642, China.
| | - Wencheng Lin
- College of Animal Science, South China Agricultural University & Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, Guangzhou 510642, China.
| | - Hongxin Li
- College of Animal Science, South China Agricultural University & Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, Guangzhou 510642, China.
- Institute of Animal Science, Guangdong Academy of Agriculture Sciences, Guangzhou 510640, China.
| | - Feng Chen
- College of Animal Science, South China Agricultural University & Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, Guangzhou 510642, China.
- Institute of Animal Science, Guangdong Academy of Agriculture Sciences, Guangzhou 510640, China.
- Key Laboratory of Animal Health Aquaculture and Environmental Control, Guangzhou 510642, China.
- South China Collaborative Innovation Center for Poultry Disease Control and Product Safety, Guangzhou 510640, China.
| | - Yang Liu
- College of Animal Science, South China Agricultural University & Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, Guangzhou 510642, China.
| | - Weiguo Chen
- College of Animal Science, South China Agricultural University & Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, Guangzhou 510642, China.
- Key Laboratory of Animal Health Aquaculture and Environmental Control, Guangzhou 510642, China.
- South China Collaborative Innovation Center for Poultry Disease Control and Product Safety, Guangzhou 510640, China.
| | - Yingzuo Bi
- College of Animal Science, South China Agricultural University & Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, Guangzhou 510642, China.
- Key Laboratory of Animal Health Aquaculture and Environmental Control, Guangzhou 510642, China.
- South China Collaborative Innovation Center for Poultry Disease Control and Product Safety, Guangzhou 510640, China.
| | - Qingmei Xie
- College of Animal Science, South China Agricultural University & Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, Guangzhou 510642, China.
- China-UK-NYNU-RRes Joint laboratory of Insect Biology, Nanyang Normal Universiy, Nanyang 473000, China.
- Institute of Animal Science, Guangdong Academy of Agriculture Sciences, Guangzhou 510640, China.
- Key Laboratory of Animal Health Aquaculture and Environmental Control, Guangzhou 510642, China.
- South China Collaborative Innovation Center for Poultry Disease Control and Product Safety, Guangzhou 510640, China.
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Ouyang H, He X, Li G, Xu H, Jia X, Nie Q, Zhang X. Deep Sequencing Analysis of miRNA Expression in Breast Muscle of Fast-Growing and Slow-Growing Broilers. Int J Mol Sci 2015; 16:16242-62. [PMID: 26193261 PMCID: PMC4519947 DOI: 10.3390/ijms160716242] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2015] [Revised: 07/03/2015] [Accepted: 07/10/2015] [Indexed: 01/17/2023] Open
Abstract
Growth performance is an important economic trait in chicken. MicroRNAs (miRNAs) have been shown to play important roles in various biological processes, but their functions in chicken growth are not yet clear. To investigate the function of miRNAs in chicken growth, breast muscle tissues of the two-tail samples (highest and lowest body weight) from Recessive White Rock (WRR) and Xinghua Chickens (XH) were performed on high throughput small RNA deep sequencing. In this study, a total of 921 miRNAs were identified, including 733 known mature miRNAs and 188 novel miRNAs. There were 200, 279, 257 and 297 differentially expressed miRNAs in the comparisons of WRRh vs. WRRl, WRRh vs. XHh, WRRl vs. XHl, and XHh vs. XHl group, respectively. A total of 22 highly differentially expressed miRNAs (fold change > 2 or < 0.5; p-value < 0.05; q-value < 0.01), which also have abundant expression (read counts > 1000) were found in our comparisons. As far as two analyses (WRRh vs. WRRl, and XHh vs. XHl) are concerned, we found 80 common differentially expressed miRNAs, while 110 miRNAs were found in WRRh vs. XHh and WRRl vs. XHl. Furthermore, 26 common miRNAs were identified among all four comparisons. Four differentially expressed miRNAs (miR-223, miR-16, miR-205a and miR-222b-5p) were validated by quantitative real-time RT-PCR (qRT-PCR). Regulatory networks of interactions among miRNAs and their targets were constructed using integrative miRNA target-prediction and network-analysis. Growth hormone receptor (GHR) was confirmed as a target of miR-146b-3p by dual-luciferase assay and qPCR, indicating that miR-34c, miR-223, miR-146b-3p, miR-21 and miR-205a are key growth-related target genes in the network. These miRNAs are proposed as candidate miRNAs for future studies concerning miRNA-target function on regulation of chicken growth.
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Affiliation(s)
- Hongjia Ouyang
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science, South China Agricultural University, Guangzhou 510642, China.
- Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding and Key Lab of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture, Guangzhou 510642, China.
| | - Xiaomei He
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science, South China Agricultural University, Guangzhou 510642, China.
- Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding and Key Lab of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture, Guangzhou 510642, China.
| | - Guihuan Li
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science, South China Agricultural University, Guangzhou 510642, China.
- Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding and Key Lab of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture, Guangzhou 510642, China.
| | - Haiping Xu
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science, South China Agricultural University, Guangzhou 510642, China.
- Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding and Key Lab of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture, Guangzhou 510642, China.
| | - Xinzheng Jia
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science, South China Agricultural University, Guangzhou 510642, China.
- Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding and Key Lab of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture, Guangzhou 510642, China.
| | - Qinghua Nie
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science, South China Agricultural University, Guangzhou 510642, China.
- Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding and Key Lab of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture, Guangzhou 510642, China.
| | - Xiquan Zhang
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science, South China Agricultural University, Guangzhou 510642, China.
- Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding and Key Lab of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture, Guangzhou 510642, China.
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Gennart I, Coupeau D, Pejaković S, Laurent S, Rasschaert D, Muylkens B. Marek's disease: Genetic regulation of gallid herpesvirus 2 infection and latency. Vet J 2015; 205:339-48. [PMID: 26067852 DOI: 10.1016/j.tvjl.2015.04.038] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2014] [Revised: 04/27/2015] [Accepted: 04/29/2015] [Indexed: 12/12/2022]
Abstract
Gallid herpesvirus-2 (GaHV-2) is an oncogenic α-herpesvirus that causes Marek's disease (MD), a T cell lymphosarcoma (lymphoma) of domestic fowl (chickens). The GaHV-2 genome integrates by homologous recombination into the host genome and, by modulating expression of viral and cellular genes, induces transformation of latently infected cells. MD is a unique model of viral oncogenesis. Mechanisms implicated in the regulation of viral and cellular genes during GaHV-2 infection operate at transcriptional, post-transcriptional and post-translational levels, with involvement of viral and cellular transcription factors, along with epigenetic modifications, alternative splicing, microRNAs and post-translational modifications of viral proteins. Meq, the major oncogenic protein of GaHV-2, is a viral transcription factor that modulates expression of viral genes, for example by binding to the viral bidirectional promoter of the pp38-pp24/1.8 kb mRNA, and also modulates expression of cellular genes, such as Bcl-2 and matrix metalloproteinase 3. GaHV-2 expresses viral telomerase RNA subunit (vTR), which forms a complex with the cellular telomerase reverse transcriptase (TERT), thus contributing to tumorigenesis, while vTR independent of telomerase activity is implicated in metastasis. Expression of a viral interleukin 8 homologue may contribute to lymphomagenesis. Inhibition of expression of the pro-apoptotic factors JARID2 and SMAD2 by viral microRNAs may promote the survival and proliferation of GaHV-2 latently infected cells, thus enhancing tumorigenesis, while inhibition of interleukin 18 by viral microRNAs may be involved in evasion of immune surveillance. Viral envelope glycoproteins derived from glycoprotein B (gp60 and gp49), as well as glycoprotein C, may also play a role in immune evasion.
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Affiliation(s)
- Isabelle Gennart
- Veterinary Integrated Research Unit, Faculty of Sciences, Namur Research Institute for Life Sciences (NARILIS), University of Namur (UNamur), 5000 Namur, Belgium
| | - Damien Coupeau
- Veterinary Integrated Research Unit, Faculty of Sciences, Namur Research Institute for Life Sciences (NARILIS), University of Namur (UNamur), 5000 Namur, Belgium
| | - Srdan Pejaković
- Veterinary Integrated Research Unit, Faculty of Sciences, Namur Research Institute for Life Sciences (NARILIS), University of Namur (UNamur), 5000 Namur, Belgium
| | - Sylvie Laurent
- Transcription, Lymphome Viro-Induit, University François Rabelais, UFR Sciences et Techniques, Parc de Grandmont, F-37200 Tours, France
| | - Denis Rasschaert
- Transcription, Lymphome Viro-Induit, University François Rabelais, UFR Sciences et Techniques, Parc de Grandmont, F-37200 Tours, France
| | - Benoit Muylkens
- Veterinary Integrated Research Unit, Faculty of Sciences, Namur Research Institute for Life Sciences (NARILIS), University of Namur (UNamur), 5000 Namur, Belgium.
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Hong YH, Dinh H, Lillehoj HS, Song KD, Oh JD. Differential regulation of microRNA transcriptome in chicken lines resistant and susceptible to necrotic enteritis disease. Poult Sci 2014; 93:1383-95. [DOI: 10.3382/ps.2013-03666] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
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Dinh H, Hong YH, Lillehoj HS. Modulation of microRNAs in two genetically disparate chicken lines showing different necrotic enteritis disease susceptibility. Vet Immunol Immunopathol 2014; 159:74-82. [DOI: 10.1016/j.vetimm.2014.02.003] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2013] [Revised: 01/23/2014] [Accepted: 02/03/2014] [Indexed: 10/25/2022]
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Distinct expression pattern of miRNAs in Marek's disease virus infected-chicken splenic tumors and non-tumorous spleen tissues. Res Vet Sci 2014; 97:156-61. [PMID: 24794245 DOI: 10.1016/j.rvsc.2014.04.003] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2013] [Revised: 04/03/2014] [Accepted: 04/13/2014] [Indexed: 11/24/2022]
Abstract
MicroRNAs (miRNAs) are small RNA molecules that regulate gene expression. Emerging evidence suggests that differential miRNA expression is associated with viral infection and tumorigenesis. Recently discovered microRNAs in the Marek's disease virus (MDV) genome have been suggested to have regulatory roles during MDV oncogenesis. To gain more insight into the molecular mechanisms of the tumorigenesis of MDV, we used microarrays to screen host and viral miRNAs that were sensitive to infection by MDV. Microarray analysis showed significant differential expression of 79 miRNAs, which was confirmed by qRT-PCR analysis. These data suggest that differentially expressed miRNAs may have major roles in MDV-induced tumorigenesis. In addition, we found two clades of chicken miRNAs had increased expression in splenic tumors and non-tumorous spleen tissues from GA-infected chickens. Thus, the expression of these miRNAs can be considered signatures for MDV infection and tumorigenesis.
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Labreuche Y, Warr GW. Insights into the antiviral functions of the RNAi machinery in penaeid shrimp. FISH & SHELLFISH IMMUNOLOGY 2013; 34:1002-1010. [PMID: 22732509 DOI: 10.1016/j.fsi.2012.06.008] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/21/2012] [Accepted: 06/11/2012] [Indexed: 06/01/2023]
Abstract
Over the last decade, RNA interference pathways have emerged in eukaryotes as critical regulators of many diverse biological functions including, among others, transcriptional gene regulation, post-transcriptional gene silencing, heterochromatin remodelling, suppression of transposon activity, and antiviral defences. Although this gene silencing process has been reported to be relatively well conserved in species of different phyla, there are important discrepancies between plants, invertebrates and mammals. In penaeid shrimp, the existence of an intact and functional RNAi machinery is supported by a rapidly growing body of evidence. However, the extent to which this process participates to the host immune responses remains poorly defined in this non-model organism. This review summarizes our current knowledge of RNAi mechanisms in shrimp and focuses on their implication in antiviral activities and shrimp immune defences.
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Affiliation(s)
- Yannick Labreuche
- IFREMER, Département Lagons, Ecosystèmes et Aquaculture Durable en Nouvelle-Calédonie, BP 2059, 98846 Nouméa Cedex, New Caledonia, France.
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Chen R, Chang G, Zhang Y, Dai A, Ma T, Li J, Zhai F, Hua D, Xia M, Chen G. Cloning of the quail PIWI gene and characterization of PIWI binding to small RNAs. PLoS One 2012; 7:e51724. [PMID: 23284755 PMCID: PMC3526641 DOI: 10.1371/journal.pone.0051724] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2012] [Accepted: 11/05/2012] [Indexed: 11/19/2022] Open
Abstract
The PIWI protein regulates gene expression at the epigenetic and post-transcriptional level with a variety of endogenous small non-coding RNAs. In poultry, the biological function of the PIWI protein and PIWI binding to small RNAs had not been determined. The present study cloned and analyzed the sequences of the PIWIL1 protein. We also characterized PIWIL1 binding to small RNAs from adult quail testis, where the PIWIL1 protein is specifically expressed. Small RNAs showed a strong peak at 24-27 nt in the testicular RNA library, mapped primarily to repeat sequences and were similar to rasiRNAs. MicroRNAs (miRNAs) were abundant in the ovarian RNA library at a peak of 22 nt.
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Affiliation(s)
- Rong Chen
- College of Animal Science and Technology, Yangzhou University, Yangzhou, China
| | - Guobin Chang
- College of Animal Science and Technology, Yangzhou University, Yangzhou, China
| | - Ying Zhang
- College of Animal Science and Technology, Yangzhou University, Yangzhou, China
| | - Aiqin Dai
- College of Animal Science and Technology, Yangzhou University, Yangzhou, China
| | - Teng Ma
- College of Animal Science and Technology, Yangzhou University, Yangzhou, China
| | - Jianchao Li
- College of Animal Science and Technology, Yangzhou University, Yangzhou, China
| | - Fei Zhai
- College of Animal Science and Technology, Yangzhou University, Yangzhou, China
| | - Dengke Hua
- College of Animal Science and Technology, Yangzhou University, Yangzhou, China
| | - Mingxiu Xia
- College of Animal Science and Technology, Yangzhou University, Yangzhou, China
| | - Guohong Chen
- College of Animal Science and Technology, Yangzhou University, Yangzhou, China
- * E-mail:
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Luo J, Mitra A, Tian F, Chang S, Zhang H, Cui K, Yu Y, Zhao K, Song J. Histone methylation analysis and pathway predictions in chickens after MDV infection. PLoS One 2012; 7:e41849. [PMID: 22848633 PMCID: PMC3406056 DOI: 10.1371/journal.pone.0041849] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2012] [Accepted: 06/29/2012] [Indexed: 01/22/2023] Open
Abstract
Marek's disease (MD) is a lymphoproliferative disease in chicken induced by Marek's disease virus (MDV). Although studies have focused on the genetic differences between the resistant and susceptible chicken, less is known about the role of epigenetic factors in MD. In this study, genome-wide histone modifications in the non-MHC-associated resistant and susceptible chicken lines were examined. We found that tri-methylation at histone H3 Lys4 (H3K4me3) enrichment is positively correlated with the expression of protein coding genes as well as microRNA (miRNA) genes, whereas tri-methylation at histone H3 Lys27 (H3K27me3) exhibits a negative correlation. By identifying line-specific histone modifications in MDV infection, we found unique H3K4me3 islands in the resistant chicken activated genes, which are related to immune response and cell adhesion. Interestingly, we also found some miRNAs from unique H3K27me3 patterns in the susceptible chickens that targeted genes involved in 5-hydroxytryptamine (5-HT)-receptor and adrenergic receptor pathways. In conclusion, dynamic line-specific histone modifications in response to MDV infection suggested that intrinsic epigenetic mechanisms may play a role in MD-resistance and -susceptibility.
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Affiliation(s)
- Juan Luo
- Department of Animal and Avian Sciences, University of Maryland, College Park, Maryland, United States of America
| | - Apratim Mitra
- Department of Animal and Avian Sciences, University of Maryland, College Park, Maryland, United States of America
| | - Fei Tian
- Department of Animal and Avian Sciences, University of Maryland, College Park, Maryland, United States of America
| | - Shuang Chang
- United States Department of Agriculture, ARS, Avian Disease and Oncology Laboratory, East Lansing, Michigan, United States of America
- Department of Animal Science, Michigan State University, East Lansing, Michigan, United States of America
| | - Huanmin Zhang
- United States Department of Agriculture, ARS, Avian Disease and Oncology Laboratory, East Lansing, Michigan, United States of America
| | - Kairong Cui
- Laboratory of Molecular Immunology, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Ying Yu
- Department of Animal and Avian Sciences, University of Maryland, College Park, Maryland, United States of America
| | - Keji Zhao
- Laboratory of Molecular Immunology, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Jiuzhou Song
- Department of Animal and Avian Sciences, University of Maryland, College Park, Maryland, United States of America
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Li H, Ji J, Xie Q, Shang H, Zhang H, Xin X, Chen F, Sun B, Xue C, Ma J, Bi Y. Aberrant expression of liver microRNA in chickens infected with subgroup J avian leukosis virus. Virus Res 2012; 169:268-71. [PMID: 22800510 DOI: 10.1016/j.virusres.2012.07.003] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2012] [Revised: 06/11/2012] [Accepted: 07/04/2012] [Indexed: 12/23/2022]
Abstract
Subgroup J avian leukosis virus (ALV-J) is an oncogenic retrovirus primarily causing myeloid leukosis (ML) in broilers. Although ALV is well under control in a few countries including the USA, poultry industry in many parts of the world continues suffering from serious economic loss due to sporadic or widespread ALV infection, especially ALV-J infection. ALV-J infection of chickens is reportedly mediated by a cellular receptor. So far, however, no genetic variant of the receptor gene that confers resistance to ALV-J has been identified. To advance our understanding on epigenetic factors that are involved in the event of ALV-J infection, we examined the expression of miRNAs in livers of 10-week-old chickens uninfected or infected with ALV-J by miRNA microarray analysis. Our data showed there were 12 miRNAs differentially expressed in liver between the uninfected and infected groups (P<0.01). Of which, the expressions of seven miRNAs (gga-mir-221, gga-mir-222, gga-mir-1456, gga-mir-1704, gga-mir-1777, gga-mir-1790, and gga-mir-2127,) were upregulated by ALV-J infection and may be involved in oncogenicity. The other five miRNAs (gga-let-7b, gga-let-7i, gga-mir-125b, gga-mir-375, and gga-mir-458) were significantly downregulated. The downregulated miRNAs may play important roles in tumor suppression. This finding paves the way for further exploration of epigenetic influence on tumorigenicity upon ALV-J infection.
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Affiliation(s)
- Hongmei Li
- College of Animal Science, South China Agricultural University, Guangzhou 510642, China
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Zhao C, Tian F, Yu Y, Liu G, Zan L, Updike MS, Song J. miRNA-dysregulation associated with tenderness variation induced by acute stress in Angus cattle. J Anim Sci Biotechnol 2012; 3:12. [PMID: 22958451 PMCID: PMC3436641 DOI: 10.1186/2049-1891-3-12] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2011] [Accepted: 05/09/2012] [Indexed: 03/03/2023] Open
Abstract
miRNAs are a class of small, single-stranded, non-coding RNAs that perform post-transcriptional repression of target genes by binding to 3’ untranslated regions. Research has found that miRNAs involved in the regulation of many metabolic processes. Here we uncovered that the beef quality of Angus cattle sharply diversified after acute stress. By performing miRNA microarray analysis, 13 miRNAs were significantly differentially expressed in stressed group compared to control group. Using a bioinformatics method, 135 protein-coding genes were predicted as the targets of significant differentially expressed miRNAs. Gene Ontology (GO) term and Ingenuity Pathway Analysis (IPA) mined that these target genes involved in some important pathways, which may have impact on meat quality and beef tenderness.
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Affiliation(s)
- Chunping Zhao
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, 712100, China.
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