Identification of Differentially Expressed microRNAs Associated with PRRSV Infection

Porcine reproductive and respiratory syndrome (PRRS) is characterized by respiratory disease and abortions in pregnant sows, particularly in young pigs.  The causative agent of PRRS is the arterivirus, porcine reproductive and respiratory syndrome virus (PRRSV).  Determination of alterations in host gene expression upon infection will provide a better understanding of PRRSV pathogenesis.  It is well-established that small RNAs, particularly microRNA (miRNA), are an important class of post-transcriptional gene regulators. The objective of this study was to fully characterize differentially expressed miRNAs induced in PRRSV infected macrophage cells. Swine alveolar macrophages (SAMs) were isolated from three 7-week-old pigs and then either mock infected or infected with PRRSV strain VR-2332. Total RNA was isolated at 0 hpi, 12 hpi, 24 hpi, and 48 hpi. Small RNA populations were enriched and subjected to deep sequencing using an Illumina GAIIX platform.  The resulting sequences were then searched against miRBase and Rfam to determine sequence reads representing known miRNAs and other types of small RNA.  Our results show at least 200 known miRNAs were identified at each time point. Among these, miR-451 was significantly down-regulated at 12hpi.  In humans, miR-451 is known to target macrophage migration inhibitory factor (MIF), a pro-inflammatory cytokine that suppresses anti-inflammatory glucocorticords in macrophages.  MiR-30a-3p was significantly down-regulated at 24 hpi and 48 hpi.  Target prediction analysis suggests that miR-30a-3p is involved in regulating host response to dsRNA and GTPase activity, as well as leukocyte differentiation and activation.  Our results suggest that miRNAs are likely participants in PRRSV pathogenesis.