Integrative analysis of microRNA and mRNA expression profiles in MARC-145 cells infected with PRRSV

Porcine reproductive and respiratory syndrome virus (PRRSV) causes tremendous economic losses to the swine industry worldwide. miRNAs are crucial regulators of gene expression and a wide range of complex interactions of miRNAs–mRNAs is possible during virus infection. However, there is no comprehensive integrated study of miRNA and mRNA networks in MARC-145 cells after infection with PRRSV. We analyzed the differential expressions, co-relations, annotations, and putative functions of miRNA and mRNA networks in PRRSV-infected MARC-145 cells. Based on the filtering criterion, 22 differentially expressed miRNAs (DEmiRs) (15 up- and 7 downregulated) were filtered out. miRNA–mRNA interaction networks were constructed. For the 18 selected miRNAs, 390 potential target genes were predicted from the differentially expressed mRNAs (DEmRs). GO and KEGG pathway annotations predicted 34 KEGG pathways, 12 of which are known to be involved in virus infection. Real-time PCR validated the RNA-seq results. Our analysis showed that miR-27a-5p and miR-21-3p downregulate the expression of two of their potential target genes–SPARC, CLIC1, and cofilin-1, COX7A2, respectively. Further experiments proved that miR-21-3p and miR-27a-5p can promote PRRSV replication significantly. It is the first report that these two miRNAs participate in the interaction of host cells with PRRSV. Our results provide insights into the role of miRNAs in response to PRRSV infection, which will aid the research for developing novel therapies against PRRSV.