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Comprehensive transcriptome analysis of CIAV infected MDCC-MSB1 cells [RNA-seq]

ABSTRACT: Chicken infectious anaemia (CIA) is an immunosuppressive disease caused by chicken infectious anaemia virus (CIAV). Due to immunosuppression, the disease is often leads to mixed infections and secondary infections, exacerbating viral, bacterial, and fungal infections, which can be highly detrimental. Therefore, it is imperative to identify the immune genes involved in regulating CIAV infection. In this study, comprehensive transcriptome sequencing was employed to determine the expression levels of regulated immune genes including mRNAs, microRNAs, lncRNAs, and circRNAs in CIAV-infected MDCC-MSB1 cells. A total of 2590 differentially expressed genes were identified in CIAV-infected MDCC-MSB1 cells, of which 526 were up-regulated. There were 539 differentially expressed mRNAs, including 166 up-regulated mRNAs, 38 differentially expressed microRNAs, including 22 up-regulated microRNAs, 1957 differentially expressed lncRNAs, including 295 up-regulated lncRNAs, and 56 differentially expressed circRNAs, including 43 up-regulated circRNAs. Subsequently, we selected the top 20 significantly up-regulated differentially expressed genes (GEM, ODF1, ARHGEF12, DOC2B, ZP2, gga-miR-1306-5p_L-1R-2, gga-miR-6615-3p, gga-mir-3535-p5, gga-miR-726-5p_1ss4AG, gga-miR-458a-3p, ENSGALG00010010181, ENSGALG00010002366, ENSGALG00010019353, ENSGALG00010029120, ENSGALG00010026718, circMAP3K5, ENSGALG00010015867, circGALNT1, circMCTP2, circPTEN) among the 526 up-regulated differentially expressed genes for Gene Ontology (GO) annotation and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis, and we found that those 20 genes were significantly enriched in key pathways such as apoptosis, transcriptional regulation, MAPK signaling pathway, p53 signaling pathway and phosphatidylinositol signaling system. qRT-PCR was used to further verify the accuracy of RNA sequencing at the transcriptional level. In summary, this study provides a theoretical foundation for future prevention and control strategies against CIAV, while further investigation is required to elucidate the functions and mechanisms underlying these significantly differentially expressed genes.

ORGANISM(S): Gallus gallus

PROVIDER: GSE270913 | GEO | 2024/07/02

REPOSITORIES: GEO

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Project description:Chicken infectious anaemia (CIA) is an immunosuppressive disease caused by chicken infectious anaemia virus (CIAV). Due to immunosuppression, the disease is often leads to mixed infections and secondary infections, exacerbating viral, bacterial, and fungal infections, which can be highly detrimental. Therefore, it is imperative to identify the immune genes involved in regulating CIAV infection. In this study, comprehensive transcriptome sequencing was employed to determine the expression levels of regulated immune genes including mRNAs, microRNAs, lncRNAs, and circRNAs in CIAV-infected MDCC-MSB1 cells. A total of 2590 differentially expressed genes were identified in CIAV-infected MDCC-MSB1 cells, of which 526 were up-regulated. There were 539 differentially expressed mRNAs, including 166 up-regulated mRNAs, 38 differentially expressed microRNAs, including 22 up-regulated microRNAs, 1957 differentially expressed lncRNAs, including 295 up-regulated lncRNAs, and 56 differentially expressed circRNAs, including 43 up-regulated circRNAs. Subsequently, we selected the top 20 significantly up-regulated differentially expressed genes (GEM, ODF1, ARHGEF12, DOC2B, ZP2, gga-miR-1306-5p_L-1R-2, gga-miR-6615-3p, gga-mir-3535-p5, gga-miR-726-5p_1ss4AG, gga-miR-458a-3p, ENSGALG00010010181, ENSGALG00010002366, ENSGALG00010019353, ENSGALG00010029120, ENSGALG00010026718, circMAP3K5, ENSGALG00010015867, circGALNT1, circMCTP2, circPTEN) among the 526 up-regulated differentially expressed genes for Gene Ontology (GO) annotation and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis, and we found that those 20 genes were significantly enriched in key pathways such as apoptosis, transcriptional regulation, MAPK signaling pathway, p53 signaling pathway and phosphatidylinositol signaling system. qRT-PCR was used to further verify the accuracy of RNA sequencing at the transcriptional level. In summary, this study provides a theoretical foundation for future prevention and control strategies against CIAV, while further investigation is required to elucidate the functions and mechanisms underlying these significantly differentially expressed genes.

Project description:Avian pathogenic Escherichia coli (APEC) is considered one of the most common infectious bacterial diseases resulting in significant economic losses in poultry industry worldwide. In order to investigate the association between host immune resistance and miRNA expression in the pathogenic process induced by APEC, miRNA expression profiles in broilers spleen were performed by Solexa deep sequencing from three different treatment groups including non-challenged (NC), challenged-mild pathology (MD), and challenged-severe pathology (SV).In total, 3 462 706, 3 586 689, and 3 591 027 clean reads were obtained for NC, MD, and SV, respectively. After comparing the miRNA expression patterns, 27 differentially expressed miRNAs were identified among the three response groups, which included 13 miRNAs between NC and MD, 17 between NC and SV, and 14 between MD and SV. For these miRNAs, different expression in MD and SV suggested they may have resistance activity in APEC infection. Through integrated analysis of miRNA and mRNA expression patterns, 43 negative pairs between miRNA and mRNA (r < -0.80) were obtained. 4 miRNAs were validated to be significant negatively correlated to targets by quantitative real time PCR: gga-miR-21 (CLEC3B and GGTLA1), gga-miR-429 (TMEFF2, CDC20, SHISA2 and NOX4), gga-miR-146b (LAT2 and WNK1), and gga-miR-215 (C7 and ASL2). Additionally, the expression of gga-miR-21 and gga-miR-146b was significantly up-regulated by LPS induced in HD11 macrophage cell. In contrast, gga-miR-429 has no significant change. In summary, we present the first report that characterized the miRNA profiles of chicken spleen in response to APEC infection, and identified several candidate miRNAs which might accelerate host immune response through down-regulating their specific target genes. Through the intra-air sac route into the left thoracic air sac, 240 non-vaccinated males at 4 weeks of age were challenged with 0.1 ml APEC O1 (10^8 colony forming units) and another 120 non-vaccinated males were non-challenged but treated with 0.1 ml PBS. Detailed information on the APEC O1 strain and challenge process was described by previously described study. Necropsy was performed at 1 day post challenge, and a summarized lesion ranging from 0 to 7 was determined for each APEC-challenged bird. Birds with lesions scoring 0-2 were regarded as mild infection, and those scoring 4-7 were designated as severe infection. The mild and severe pathology meant that birds were resistant and susceptible to APEC infection, respectively. Then, spleens from three groups, consisting of non-challenged, challenged-mild pathology and challenged-severe pathology were subjected to Solexa deep sequencing to investigate the dynamics of chicken miRNA expression.

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Comprehensive transcriptome analysis of CIAV infected MDCC-MSB1 cells [RNA-seq]

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