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Characterization and Analysis of Whole Transcriptome of Ningxiang Pig Spleens Reveal Potential Mechanism for Transcriptional Regulation in Immunity [miRNA-Seq]

ABSTRACT: we comprehensively analyzed the whole transcriptome of the spleen from three important developmental nodes(30d, 90d and 210d) of Ningxiang pig (a Chinese indigenous breed). A total of 812, 364 and 865 differentially expressed (DE) mRNAs, 98, 37 and 97 DE miRNAs, 278, 220 and 271 DE lncRNAs, and 113, 96 and 96 DE circRNAs were identified between 90d and 30d, 210d and 30d, and 210d and 90d, respectively. And their molecular characterization, spatio temporal expression pattern, potential function and interaction with miRNAs were analyzed. Additionally, co-expression network analysis identified the potential non coding RNAs(ncRNAs) related to immunomodulation, e.g., ssc-miRNA-150, ssc-miRNA-497, MSTRG.24160, MSTRG.18646. Furthermore, our results also revealed that miRNAs and circRNAs may have evolved to regulate a large set of biological processes of Ningxiang pigs spleens, and circRNAs may play the role of miRNA sponges. Our study provides new insights into the expression changes of RNAs during the spleen development process of Chinese indigenous breed Ningxiang pigs, which might contribute to the phenotypic formation of immune function in Chinese native pig breeds. These results greatly improved our understanding of the molecular mechanisms which regulate the immune function of the spleen of Ningxiang pigs.

ORGANISM(S): Sus scrofa

PROVIDER: GSE152087 | GEO | 2022/06/06

REPOSITORIES: GEO

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Project description:Porcine reproductive and respiratory syndrome caused by porcine reproductive and respiratory syndrome virus (PRRSV) is an infectious disease characterized by severe reproductive deficiency in pregnant sows, respiratory symptoms in piglets, and high mortality. In this study, we employed Affymetrix microarray chip technology to compare the gene expression profiles of lung tissue samples from Dapulian (DPL) pigs (a Chinese indigenous pig breed) and Duroc×Landrace×Yorkshire (DLY) pigs after infection with PRRSV. During infection with PRRSV, the DLY pigs exhibited the range of clinical features that typify the disease, while the DPL pigs exhibited only mild signs of the disease. The percentage of CD8+ T cells in the DPL pigs was significantly higher than that in the DLY pigs at 21 days post-infection (dpi) (p< 0.05). Interleukin (IL) 1 beta (IL-1β) and IL-2 levels showed significant differences between the DPL and DLY pigs at 0 and 7 dpi (p< 0.01). For IL-10, the DLY pigs had significantly higher values than the DPL pigs at 0 and 7 dpi (p< 0.01). Significant differences were apparent between the DPL and DLY pigs in terms of their tumor necrosis factor-alpha (TNF-α) and interferon (IFN)-gamma (IFN-γ) levels at 0 and 7 dpi (p< 0.01). Microarray data revealed 16 differentially expressed genes in the lung tissue samples from the DLY and DPL pigs (q≤5%), of which LOC100516029 and LOC100523005 were up-regulated in the PRRSV-infected DPL pigs, while the other 14 genes were down-regulated in the PRRSV-infected DPL pigs compared with the PRRSV-infected DLY pigs. The expression levels of 10 of the 16 genes, namely CCDC84, C6ORF52, THYMOSIN, PRVE, HSPCB, CYP2J2, AMPD3, TOR1AIP2, PTGES3, and ACOX3, were validated by real-time quantitative RT-PCR. This study provides a platform for further investigation of the molecular mechanisms underlying the differential immune responses to PRRSV infection in different breeds or lines of pig. We investigated the response of lung tissues from Dapulian (DPL) pigs (a Chinese indigenous pig breed) and Duroc×Landrace×Yorkshire (DLY) pigs infected with porcine reproductive and respiratory syndrome virus (strain JXA1) by using the Affymetrix Porcine Genome Array.

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Characterization and Analysis of Whole Transcriptome of Ningxiang Pig Spleens Reveal Potential Mechanism for Transcriptional Regulation in Immunity [miRNA-Seq]

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