Transcriptomic analysis of porcine PBMCs in response to FMDV infection

Foot-and-mouth disease (FMD) is a significant zoonotic infectious disease. It has an important economic impact throughout the world. As well, it is a considerable threat to food security. At present, the molecular mechanism of FMDV infection is not clear to a large extent. Innate immune response is the first line of defense against infectious diseases. The systematic analysis of the host immune response to infection has an important role in understanding the pathogenesis of infection. However, there are few reports about effect of immune regulation on virus replication in the interaction of virus and host cellular. High-throughput RNA-seq technology as a powerful and efficient means for transcript analysis provides a new insight into FMDV study. In this study, RNA extracted from pig PBMCs infected with O subtype FMDV at 4 dpi. A total of 29942658 and 31452917 Illumina read pairs were obtained from the non-infected (NI) group and infected (I) group, respectively. The clean bases for all samples are 3.61G (NI group) and 3.79G (I group), respectively. The clean reads of the NI and I group that mapped to pig genome data were 47195073 (81.82%) and 46556714 (76.85%), respectively. Most of the clean reads were distributed in the exon region, followed by intron region and intergenic region. Differently expressed (DE) genes were analyzed using edgeR software. 451 genes were differentially expressed between the infected and the non-infected groups. According to the comparison analysis, more genes were down-regulated in the non-infected samples than in those infected with FMDV.66 out of 451 genes were down-regulated, 385 out of 451 genes were up-regulated following FMDV infection. For function classification and pathway analysis, among 17741 assembled unigenes, there are 349 genes which are different genes of GO notes. Moreover, 49 genes were down-regulated, 300 genes were up-regulated associate with GO term. 1621 were successfully annotated by GO assignments, belonging to one or more of the three categories: biological process, cellular component, and molecular function. According to KEGG analysis,the main pathway was represented including protein processing in endoplasmic reticulum, phagosome, cell cycle and cytokine-cytokine receptor interaction. Some key DE genes related to immune process and signaling pathways were analyzed and quantified by RT-PCR. This is the first systematical transcriptome analysis of pig PBMCs infected by FMDV. These findings will help us better understand the host Cell-FMDV interaction and its relationship to pathogenesis, as well as contribute to the prevention and control of FMDV.