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Integrated miRNA and mRNA transcriptomes of porcine alveolar macrophages (PAM cells) identifies strain-specific miRNA molecular signatures associated with H-PRRSV and N-PRRSV infection

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Abstract

Porcine reproductive and respiratory syndrome (PRRS) is one of the most significant viral diseases in swine, which causes large economic losses to the swine industry worldwide. There is considerable strain variation in PRRSV and two examples of this are the highly virulent Chinese-type PRRSV (H-PRRSV) and the classical North American type PRRSV (N-PRRSV), both with different pathogenesis. These differences may be due in part to genetic and phenotypic differences in virus replication, but also interaction with the host cell. MicroRNAs (miRNAs) are crucial regulators of gene expression and play vital roles in virus and host interactions. However, the regulation role of miRNAs during PRRSV infection has not been systematically investigated. In order to better understand the differential regulation roles of cellular miRNAs in the host response to PRRSV, miRNA expression and a global mRNA transcriptome profile was determined in primary cells infected with either H-PRRSV or N-PRRSV as multiple time points during the viral lifecycle. miRNA-mRNA interactome networks were constructed by integrating the differentially expressed miRNAs and inversely correlated target mRNAs. Using gene ontology and pathway enrichment analyses, cellular pathways associated with deregulated miRNAs were identified, including immune response, phagosome, autophagy, lysosome, autolysis, apoptosis and cell cycle regulation. To our knowledge, this is the first global analysis of strain-specific host miRNA molecular signatures associated with H- and N-PRRSV infection by integrating miRNA and mRNA transcriptomes and provides a new perspective on the contribution of miRNAs to the pathogenesis of PRRSV infection.

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Acknowledgments

We thank the Beijing Institute of Genomics (BIG) of Chinese Academy of Sciences (CAS) and Novel Bioinformatics Co. Ltd. for providing technical assistance in deep sequencing and bioinformatics analysis. This work was supported by National Natural Science Foundation of China (Grant No. 31101690) and Open Project grant of the State Key Laboratory of Biocontrol (Grant No. SKLBC12K13).

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Authors and Affiliations

  1. State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, China

    Peiqing Cong, Shuqi Xiao, Yaosheng Chen, Liangliang Wang, Jintao Gao, Ming Li, Zuyong He, Yunxue Guo, Guangyin Zhao, Xiaoyu Zhang, Luxi Chen, Delin Mo & Xiaohong Liu

  2. College of Veterinary Medicine, Northwest A&F University, Yangling, 712100, Shaanxi, China

    Shuqi Xiao

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  1. Peiqing Cong
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Correspondence to Shuqi Xiao.

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Peiqing Cong and Shuqi Xiao have contributed equally to this work.

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Cong, P., Xiao, S., Chen, Y. et al. Integrated miRNA and mRNA transcriptomes of porcine alveolar macrophages (PAM cells) identifies strain-specific miRNA molecular signatures associated with H-PRRSV and N-PRRSV infection. Mol Biol Rep 41, 5863–5875 (2014). https://doi.org/10.1007/s11033-014-3460-7

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