Genome-wide integrated analysis of miRNA and mRNA expression profiles to identify differentially expressed miR-22-5p and miR-27b-5p in response to classical swine fever vaccine virus

Elucidation of novel SNPs affecting immune response to classical swine fever vaccination in pigs using immunogenomics approach

The host genetic makeup plays a significant role in causing the within-breed variation among individuals after vaccination. The present study was undertaken to elucidate the genetic basis of differential immune response between high and low responder Landlly (Landrace X Ghurrah) piglets vis-à-vis CSF vaccination. For the purpose, E2 antibody response against CSF vaccination was estimated in sampled animals on the day of vaccination and 21-day post-vaccination as a measure of humoral immune response. Double-digestion restriction associated DNA (ddRAD) sequencing was undertaken on 96 randomly chosen Landlly piglets using Illumina HiSeq platform. SNP markers were called using standard methodology. Genome-wide association study (GWAS) was undertaken in PLINK program to identify the informative SNP markers significantly associated with differential immune response. The results revealed significant SNPs associated with E2 antibody response against CSF vaccination. The genome-wide informative SNPs for the humoral immune response against CSF vaccination were located on SSC10, SSC17, SSC9, SSC2, SSC3 and SSC6. The overlapping and flanking genes (500Kb upstream and downstream) of significant SNPs were CYB5R1, PCMTD2, WT1, IL9R, CD101, TMEM64, TLR6, PIGG, ADIPOR1, PRSS37, EIF3M, and DNAJC24. Functional enrichment and annotation analysis were undertaken for these genes in order to gain maximum insights into the association of these genes with immune system functionality in pigs. The genetic makeup was associated with differential immune response against CSF vaccination in Landlly piglets while the identified informative SNPs may be used as suitable markers for determining variation in host immune response against CSF vaccination in pigs.

Role of microRNAs in host defense against porcine reproductive and respiratory syndrome virus infection: a hidden front line

Porcine reproductive and respiratory syndrome virus (PRRSV) is one of the most globally devastating viruses threatening the swine industry worldwide. Substantial advancements have been achieved in recent years towards comprehending the pathogenesis of PRRSV infection and the host response, involving both innate and adaptive immune responses. Not only a multitude of host proteins actively participate in intricate interactions with viral proteins, but microRNAs (miRNAs) also play a pivotal role in the host response to PRRSV infection. If a PRRSV-host interaction at the protein level is conceptualized as the front line of the battle between pathogens and host cells, then their fight at the RNA level resembles the hidden front line. miRNAs are endogenous small non-coding RNAs of approximately 20-25 nucleotides (nt) that primarily regulate the degradation or translation inhibition of target genes by binding to the 3'-untranslated regions (UTRs). Insights into the roles played by viral proteins and miRNAs in the host response can enhance our comprehensive understanding of the pathogenesis of PRRSV infection. The intricate interplay between viral proteins and cellular targets during PRRSV infection has been extensively explored. This review predominantly centers on the contemporary understanding of the host response to PRRSV infection at the RNA level, in particular, focusing on the twenty-six miRNAs that affect viral replication and the innate immune response.

Transcriptomics analysis reveals key lncRNAs and genes related to the infection of feline kidney cell line by panleukopenia virus

Feline panleukopenia virus (FPV) can cause a viral disease and is responsible for severe leukopenia, gastroenteritis, and nervous signs with significant economic losses. Biochemically long non-coding RNAs (lncRNAs) can regulate the expression of mRNA in different ways, thereby causing the functional changes in host cells in response to viral infection. However, no attention has been paid until now to investigate the link between FPV pathogenesis and lncRNA. Here, through RNA sequencing, we performed a comprehensive analysis of lncRNA and mRNA in F81 cells after FPV-BJ04 strain infection. Consistent with previous studies, our data showed that lncRNAs have distinct features from mRNA. A total of 291 lncRNAs and 873 mRNAs were differentially expressed in F81 cells after FPV-BJ04 infection. GO and KEGG enrichment analysis showed that the differentially upregulated lncRNAs target genes were mainly involved in the positive regulation of transcription by RNA polymerase II and MAPK signaling pathway. The differentially downregulated lncRNAs target genes were mainly involved in the mRNA splicing and endocytosis. In addition, the differentially expressed immune pathway related genes that are targeted by lncRNA were also screened out to construct a lncRNA-miRNA-mRNA axes as a potential novel biomarkers in regulating the immune response of feline against FPV infection. Our results contribute to understand the basic role of lncRNA in F81 cells during FPV infection and lay the foundation for following research.

Classical swine fever virus: the past, present and future

Classical swine fever (CSF) is among the most relevant viral epizootic diseases of swine. Due to its severe economic impact, CSF is notifiable to the world organisation for animal health. Strict control policies, including systematic stamping out of infected herds with and without vaccination, have permitted regional virus eradication. Nevertheless, CSF virus (CSFV) persists in certain areas of the world and has re-emerged regularly. This review summarizes the basic established knowledge in the field and provides a comprehensive and updated overview of the recent advances in fundamental CSFV research, diagnostics and vaccine development. It covers the latest discoveries on the genetic diversity of pestiviruses, with implications for taxonomy, the progress in understanding disease pathogenesis, immunity against acute and persistent infections, and the recent findings in virus-host interactions and virulence determinants. We also review the progress and pitfalls in the improvement of diagnostic tools and the challenges in the development of modern and efficacious marker vaccines compatible with serological tests for disease surveillance. Finally, we highlight the gaps that require research efforts in the future.

Expression profiling of miR-146a-3p and miR-1343 with their target genes after classical swine fever vaccination

The expression profiling of the miRNAs, ssc-miR-146a- 3p and ssc-miR-1343 in the PBMCs of classical swine fever (CSF) vaccinated crossbred pigs were investigated on 7 days post vaccination (7 dpv) as compared to unvaccinated pigs. It was observed that ssc-miR-146a-3p was up-regulated (1.243 Log2 FC) and ssc-miR-1343 was down-regulated (-1.63 Log2 FC) on 7 dpv compared to unvaccinated crossbred pigs which were in concordance with earlier report of miRNA Seq expression profiling. Two target genes, (CD86 for ssc-miR-146a-3p and IFIT1 for ssc-miR-1343) were validated by qRT-PCR and were also found to be in concordance with miRNA expression profile. The CD86 was downregulated with log2 fold changes -5.99, whereas the IFIT1 was upregulated with log2 fold changes 3.19 at 7 dpv. Both of these miRNA was actively involved in cell mediated immune response at 7dpv after CSF vaccination. The CSF vaccine virus triggered the expression of host miRNAs and its target mRNA and enriched immune system processes/pathways.

Signature of genome wide gene expression in classical swine fever virus infected macrophages and PBMCs of indigenous vis-a-vis crossbred pigs

The genetic basis of differential host immune response vis-à-vis transcriptome profile was explored in PBMCs of indigenous (Ghurrah) and crossbred pigs after classical swine fever vaccination and in monocyte derived macrophages (MDMs) challenged with virulent classical swine fever (CSF) virus. The humoral immune response (E2 antibody) was higher (74.87%) in crossbred than indigenous pigs (58.20%) at 21st days post vaccination (21dpv). The rate of reduction of ratio of CD4⁺/CD8⁺ was higher in crossbred pigs than indigenous pigs at 7th days post vaccination (7dpv). The immune genes IFIT1, IFIT5, RELA, NFKB2, TNF and LAT2 were up regulated at 7dpv in RNA seq data set and was in concordance during qRT-PCR validation. The Laminin Subunit Beta 1 (LAMB1) was significantly (p ≤ 0.05) down-regulated in MDMs of indigenous pigs and consequently a significantly (p ≤ 0.01) higher copy number of virulent CSF virus was evidenced in macrophages of crossbred pigs than indigenous pigs. Activation of LXR:RXR pathway at 60 h post infection (60hpi) in MDMs of indigenous versus crossbred pigs inhibited nuclear translocation of NF-κB, resulted into transrepression of proinflammatory genes. But it helped in maintenance of HDL level by lowering down cholesterol/LDL level in MDMs of indigenous pigs. The key immune genes (TLR2, TLR4, IL10, IL8, CD86, CD54, CASP1) of TREM1 signaling pathway were upregulated at 7dpv in PBMCs but those genes were downregulated at 60hpi in MDMs indigenous pigs. Using qRT-PCR, the validation of differentially expressed, immunologically important genes (LAMB1, OAS1, TLR 4, TLR8 and CD86) in MDMs revealed that expression of these genes were in concordance with RNA-seq data.