Transcriptome analysis reveals differential immune related genes expression in bovine viral diarrhea virus-2 infected goat peripheral blood mononuclear cells (PBMCs)

Abstract

Background Bovine viral diarrhea virus (BVDV) is an economically important viral pathogen of domestic and wild ruminants. Apart from cattle, small ruminants (goats and sheep) are also the susceptible hosts for BVDV. BVDV infection could interfere both of the innate and adaptive immunity of the host, while the genes and mechanisms responsible for these effects have not yet been fully understood. Peripheral blood mononuclear cells (PBMCs) play a pivotal role in the immune responses to viral infection, and these cells were the target of BVDV infection. In the present study, the transcriptome of goat peripheral blood mononuclear cells (PBMCs) infected with BVDV-2 was explored by using RNA-Seq technology. Results Goat PBMCs were successfully infected by BVDV-2, as determined by RT-PCR and quantitative real-time RT-PCR (qRT-PCR). RNA-Seq analysis results at 12 h post-infection (hpi) revealed 499 differentially expressed genes (DEGs, fold-change ≥ ± 2, p < 0.05) between infected and mock-infected PBMCs. Of these genes, 97 were up-regulated and the remaining 352 genes were down-regulated. The identified DEGs were found to be significantly enriched for locomotion/ localization, immune response, inflammatory response, defense response, regulation of cytokine production, etc., under GO enrichment analysis. Cytokine-cytokine receptor interaction, TNF signaling pathway, chemokine signaling pathway, etc., were found to be significantly enriched in KEGG pathway database. Protein-protein interaction (PPI) network analysis indicated most of the DEGs related to innate or adaptive immune responses, inflammatory response, and cytokine/chemokine-mediated signaling pathway. TNF, IL-6, IL-10, IL-12B, GM-CSF, ICAM1, EDN1, CCL5, CCL20, CXCL10, CCL2, MAPK11, MAPK13, CSF1R and LRRK1 were located in the core of the network and highly connected with other DGEs. Conclusions BVDV-2 infection of goat PBMCs causes the transcription changes of a series of DEGs related to host immune responses, including inflammation, defense response, cell locomotion, cytokine/chemokine-mediated signaling, etc. The results will be useful for exploring and further understanding the host responses to BVDV-2 infection in goats. Electronic supplementary material The online version of this article (10.1186/s12864-019-5830-y) contains supplementary material, which is available to authorized users.

RNA Sequencing (RNA-Seq) Based Transcriptome Analysis in Immune Response of Holstein Cattle to Killed Vaccine against Bovine Viral Diarrhea Virus Type I

“…Bovine viral diarrhea virus (BVDV) is an economically important pathogen of domestic and wild ruminants affecting multiple organ systems, incurring most economic losses due to respiratory diseases, low reproductive performance (due to reduced conception rates), early embryonic deaths, abortion, congenital weak calves, and high costs of control programs [1][2][3][4]. BVDV belongs to the genus Pestivirus within the family Flaviviridae, with two species, namely BVDV1 and BVDV2; both consist of strains, belonging to biotypes non-cytopathogenic or cytopathogenic, based on cell-cultured characteristics [5].…”

“…In addition, recent studies reported that the immunosuppressive ability of BVDV heightens other viral disease potentiators, particularly the bovine respiratory disease [8][9][10]. The differences in genotypes and biotypes of BVDV, a wide range of susceptible hosts, the ability to induce persistent infection, and intervene with both innate and adaptive immunity, makes the prevention and control program difficult [4].…”

“…Numerous studies focusing on the transcriptomic analysis of animals infected with various diseases were carried out. In the study of Li et al [4], various differentially expressed genes (DEGs) related to goat immune response, including inflammation, defense response, cell locomotion, and cytokine/chemokine-mediated signaling were revealed by transcriptome analysis with samples from BVDV2 artificially infected goat peripheral blood mononuclear cells (PBMCs). Similar methodology was done in the study of Singh et al [14], where various significant DEGs related to the immune system processes of goat and sheep against bluetongue virus serotype 16 (BTV-16) were revealed, such as NFκB, MAPK, Ras, NOD, RIG, TNF, TLR, JAK-STAT, and VEGF signaling pathways.…”

Transcriptome analysis reveals differentially expressed genes for improving survival of dormant Apostichopus japonicus in response to high temperature

“…As shown in many studies, high-throughput RNA-Sequencing (RNA-Seq) technology is an excellent approach to study the transcriptional levels of large numbers of genes in tissues or organisms. The results of sequencing data can provide the "whole picture" of the gene expression profile in the organisms [18][19][20][21]. Obtained genes were annotated upon Protein family (Pfam), Superfamily, Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) database for characterizing their functions at the molecular and cellular levels [22][23][24][25].…”

“…Moreover, Venn diagram analysis was used to study the special expression of genes in each group, and then performed GO and KEGG enrichment to analyze functional categories [5,22]. Therefore, the database of Search Tool for the Retrieval of Interacting Genes (STRING) was used to study functional interaction of proteins (including stable complexes, metabolic pathways and a bewildering array of direct and indirect regulatory interactions), which was also usually used to analyze the transcriptomic profile [19,26]. Therefore, our study employed transcriptome sequencing to investigate the alteration of physiological metabolism and immune in the aestivation stage, and then analyze the potential associations between them.…”