RNA Seq analysis for transcriptome profiling in response to classical swine fever vaccination in indigenous and crossbred pigs

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.

Single cell RNA-seq: a novel tool to unravel virus-host interplay

Over the last decade, single cell RNA sequencing (scRNA-seq) technology has caught the momentum of being a vital revolutionary tool to unfold cellular heterogeneity by high resolution assessment. It evades the inadequacies of conventional sequencing technology which was able to detect only average expression level among cell populations. In the era of twenty-first century, several epidemic and pandemic viruses have emerged. Being an intracellular entity, viruses totally rely on host. Complex virus-host dynamics result when the virus tend to obtain factors from host cell required for its replication and establishment of infection. As a prevailing tool, scRNA-seq is able to understand virus-host interplay by comprehensive transcriptome profiling. Because of technological and methodological advancement, this technology is capable to recognize viral genome and host cell response heterogeneity. Further development in analytical methods with multiomics approach and increased availability of accessible scRNA-seq datasets will improve the understanding of viral pathogenesis that can be helpful for development of novel antiviral therapeutic strategies.

Differences in Immune Characteristics and Related Gene Expression in Spleen among Ningxiang, Berkshire Breeds and Their Hybrid Pigs

To investigate the differential immunology in Ningxiang and Berkshire pigs and their F1 offspring (F1 offspring), physiological and biochemical indicators in the plasma and spleen were analyzed. Then, transcriptomic analysis of the spleen identified 1348, 408, and 207 differentially expressed genes (DEGs) in comparisons of Ningxiang vs. Berkshire, Berkshire vs. F1 offspring, and Ningxiang vs. F1 offspring, respectively. In Ningxiang vs. Berkshire pigs, the gene ontology (GO) and the Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis indicated that the DEGs included CD163, MARCO, CXCL14, CCL19, and PPBP, which are associated with immunity. GO and KEGG analyses were also conducted comparing F1 offspring and their parents. The DEGs, including BPIFB1, HAVCR2, CD163, DDX3X, CCR5, and ITGB3, were enriched in immune-related pathways. Protein-protein interaction (PPI) analysis indicated that the EGFR and ITGA2 genes were key hub genes. In conclusion, this study identifies significant immune DEGs in different pig breeds, providing data to support the exploration of breeding strategies for disease resistance in local and crossbred pig populations.

Androgen receptor gene deficiency results in the reduction of steroidogenic potential in porcine luteal cells

Luteal steroidogenesis is critical to implantation and pregnancy maintenance in mammals. The role of androgen receptors (AR) in the progesterone (P4) producing luteal cells of porcine corpus luteum (CL) remains unexplored. The aim of the present study was to establish AR gene knock out (KO) porcine luteal cell culture system model by CRISPR/Cas9 genome editing technology and to study the downstream effects of AR gene deficiency on steroidogenic potential and viability of luteal cells. For this purpose, genomic cleavage detection assay, microscopy, RT-qPCR, ELISA, annexin, MTT, and viability assay complemented by bioinformatics analysis were employed. There was significant downregulation (p < 0.05) in the relative mRNA expression of steroidogenic marker genes STAR, CYP11A1, HSD3B1 in AR KO luteal cells as compared to the control group, which was further validated by the significant (p < 0.05) decrease in the P4 production. Significant decrease (p < 0.05) in relative viability on third passage were also observed. The relative mRNA expression of hypoxia related gene HIF1A was significantly (p < 0.05) downregulated in AR KO luteal cells. Protein-protein interaction analysis mapped AR to signaling pathways associated with luteal cell functionality. These findings suggests that AR gene functionality is critical to luteal cell steroidogenesis in porcine.

Ovarian follicle transcriptome dynamics reveals enrichment of immune system process during transition from small to large follicles in cyclic Indian Ghoongroo pigs

Ovarian follicular development is a critical determinant of reproductive performance in litter bearing species like pigs, wherein economic gains depend on litter size. The study aimed to gain insight into the differentially expressed genes (DEGs) and signalling pathways regulating follicular growth and maturation in Ghoongroo pigs. Transcriptome profiling of porcine small follicles (SF) and large follicles (LF) was conducted using NovaSeq600 sequencing platform and DEGs were identified using DESeq2 with threshold of Padj. < 0.05 and log2 fold change cut off 0.58 (LF vs. SF). Functional annotations and bioinformatics analysis of DEGs were performed to find out biological functions, signalling pathways and hub genes regulating follicular dynamics. Transcriptome analysis revealed 709 and 479 genes unique to SF and LF stages, respectively, and 11,993 co-expressed genes in both the groups. In total, 507 DEGs (284 upregulated and 223 downregulated) were identified, which encoded for diverse proteins including transcription factors (TFs). These DEGs were functionally linked to response to stimulus, lipid metabolic process, developmental process, extracellular matrix organisation along with the immune system process, indicating wide-ranging mechanisms associated with follicular transition. The enriched KEGG pathways in LF stage consisted of ovarian steroidogenesis, cholesterol and retinol metabolism, cell adhesion molecules, cytokine receptor interaction and immune signalling pathways, depicting intra-follicular control of varied ovarian function. The hub gene analysis revealed APOE, SCARB1, MMP9, CYP17A1, TYROBP as key regulators of follicular development. This study identified candidate genes and TFs providing steroidogenic advantage to LFs which makes them fit for selection into the ovulatory pool of follicles.

Genome-wide transcriptome profiling of CSF virus challenged monocyte-derived macrophages provides distinct insights into immune response of Landrace and indigenous Ghurrah pigs

The present study was undertaken to characterize the distinct immune response in indigenous Ghurrah and exotic Landrace pigs by challenging monocyte-derived macrophages (MDMs) with CSF virus under in-vitro conditions and assessing the variations in the transcriptome profile at 48 h post-infection (hpi). RNA-sequencing was carried out in infected and non-infected MDMs of Ghurrah (n = 3) and Landrace (n = 3) piglets prior- as well as post-stimulation. MDMs of Ghurrah showed greater immune regulation in response to CSF infection with 518 significantly differentially expressed genes (DEG) in infected versus non-infected MDMs, as compared to only 31 DEGs in Landrace MDMs. In Landrace, the principal regulators of inflammation (IL1α, IL1β and TNF) were upregulated in infected cells while in Ghurrah, these were downregulated. Overall, macrophages from indigenous Ghurrah showed more immunological dysregulation in response to virulent CSF virus infection as compared to the exotic Landrace pigs.

Characterisation and comparison of immune response mechanisms in an indigenous and a commercial pig breed after classical swine fever vaccination

The live attenuated classical swine fever (CSF) vaccine has been successfully used to prevent and control CSF outbreaks for 6 decades. However, the immune response mechanisms against the vaccine remain poorly understood. Moreover, very few reports exist regarding the breed differences in the response to CSF vaccine. In this study, we generated the peripheral blood mononuclear cell transcriptomes of indigenous Ghurrah and commercial Landrace pig breeds, before and 7 days after CSF vaccination. Subsequently, between and within-breed differential gene expression analyses were carried out. Results revealed large differences in pre-vaccination peripheral blood mononuclear cell transcriptome profiles of the two breeds, which were homogenised 7 days after vaccination. Before vaccination, gene set enrichment analysis showed that pathways related to antigen sensing and innate immune response were enriched in Ghurrah, while pathways related to adaptive immunity were enriched in Landrace. Ghurrah exhibited greater immunomodulation compared to Landrace following the vaccination. In Ghurrah, cell-cycle processes and T-cell response pathways were upregulated after vaccination. However, no pathways were upregulated in Landrace after vaccination. Pathways related to inflammation were downregulated in both the breeds after vaccination. Key regulators of inflammation such as IL1A, IL1B, NFKBIA and TNF genes were strongly downregulated in both the breeds after vaccination. Overall, our results have elucidated the mechanisms of host immune response against CSF vaccination in two distinct breeds and revealed common key genes instrumental in the global immune response to the vaccine.

Transcriptome profiling of different developmental stages of corpus luteum during the estrous cycle in pigs

To better understand the molecular basis of corpus luteum (CL) development and function RNA-Seq was utilized to identify differentially expressed genes (DEGs) in porcine CL during different physiological stages of the estrous cycle viz. early (EL), mid (ML), late (LL) and regressed (R) luteal. Stage wise comparisons obtained 717 (EL vs. ML), 568 (EL vs. LL), 527 (EL vs. R), 786 (ML vs. LL), 474 (ML vs. R) and 534 (LL vs. R) DEGs with log₂(FC) ≥1 and p < 0.05. The process of angiogenesis, steroidogenesis, signal transduction, translation, cell proliferation and tissue remodelling were significantly (p < 0.05) enriched in EL, ML and LL stages, where as apoptosis was most active in regressed stage. Pathway analysis revealed that most annotated genes were associated with lipid metabolism, translation, immune and endocrine system pathways depicting intra-luteal control of diverse CL function. The network analysis identified genes AR, FOS, CDKN1A, which were likely the novel hub genes regulating CL physiology.

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

The present study was conducted to identify the differentially expressed miRNAs (DE miRNAs) in the peripheral blood mononuclear cells of crossbred pigs in response to CSF vaccination on 7 and 21 days of post vaccination as compared to unvaccinated control (0 dpv). Simultaneously, set of miRNA was predicted using mRNA seq data at same time point. The proportion of CD4^-CD8⁺ and CD4⁺CD8⁺ increased after vaccination, and the mean percentage inhibition was 86.89% at 21 dpv. It was observed that 22 miRNAs were commonly expressed on both the time points. Out of predicted DE miRNAs, it was found that 40 and 35 DE miRNAs were common, obtained from miRNA seq analysis and predicted using mRNA seq data on 7 dpv versus 0 dpv and 21 dpv versus 0 dpv respectively. Two DE miRNAs, ssc-miR-22-5p and ssc-miR-27b-5p, were selected based on their log₂ fold change and functions of their target genes in immune process/pathway of viral infections. The validations of DE miRNAs using qRT-PCR were in concordance with miRNA seq analysis. Two set of target genes, CD40 and SWAP70 (target gene of ssc-miR-22-5p) and TLR4 and Lyn (target gene of ssc-miR-27b-5p), were validated and were in concordance with results of RNA seq analysis at a particular time point (except TLR4). The first report of genome-wide identification of differentially expressed miRNA in response to live attenuated vaccine virus of classical swine fever revealed miR-22-5p and miR-27b-5p were differentially expressed at 7 dpv and 21 dpv.

Transcriptome profile analysis of leg muscle tissues between slow- and fast-growing chickens

Chicken is widely favored by consumers because of some unique features. The leg muscles occupy an important position in the market. However, the specific mechanism for regulating muscle growth speed is not clear. In this experiment, we used Jinghai yellow chickens with different body weights at 300 days as research subjects. The chickens were divided into fast- and slow-growing groups, and we collected leg muscles after slaughtering for use in RNA-seq. After comparing the two groups, 87 differentially expressed genes (DEGs) were identified (fold change ≥ 2 and FDR < 0.05). The fast-growing group had 42 up-regulated genes and 45 down-regulated genes among these DEGs compared to the slow-growing group. Six items were significantly enriched in the biological process: embryo development ending in birth or egg hatching, chordate embryonic development, embryonic skeletal system development, and embryo development as well as responses to ketones and the sulfur compound biosynthetic process. Two significantly enriched pathways were found in the KEGG pathway analysis (P-value < 0.05): the insulin signaling pathway and the adipocytokine signaling pathway. This study provides a theoretical basis for the molecular mechanism of chicken growth and for improving the production of Jinghai yellow chicken.

Exploration of genetic basis of differential immune response to CSF vaccination in desi (indigenous) piglets using RNA-Seq approach

In the present study, the transcriptome profiling of peripheral blood mononuclear cells (PBMCs) of indigenous piglets against classical swine fever (CSF) vaccination was performed for elucidating the genetic basis of their differential humoral immunity. Piglets were vaccinated with lapinised strain of CSF virus (CSFV) followed by measurement of humoral immune response using c-ELISA at 28th day post vaccination (28dpv). The RNA sequencing data was analysed using established pipeline to determine set of differentially expressed genes (DEGs) in high responder as compared to low responder piglet. The differentially expressed important immune molecules were involved in regulating important pathways including antigen processing and presentation, T cell receptor signalling, B cell development, activation and signaling genes. The genes with differential expression also included TLR 3, 6, 7, 8, 9, and antiviral molecules such as MX, and ISG (Interferon stimulated genes) family members. The proteinprotein interaction of the immune genes was extracted for network representation. Most of the immune genes involved showed upregulation except the genes for antigen processing and presentation and T cell receptor signaling that were downregulated in the high responder. The immunologically important genes namely IFIT1, IFIT5, TAPBP, and TLR7 were validated using qRT-PCT and were observed to be in concordance with the RNA Seq results.

Expression profiling of immune genes in classical swine fever vaccinated indigenous and crossbred piglets

Classical swine fever is a highly contagious disease of pigs which courses from life-threatening to asymptomatic, depending on the virulence of the virus strain and the immune-competence of the host. The present study was undertaken to investigate the expression of immunologically important genes, viz. IFNα, IFNβ, SLA, SLA-2, SLA-DR, Ii, SLA-DM, CSK and JUN and to ascertain genetic group differences on the basis of humoral immune response. Blood samples were collected from 5 indigenous and 6 crossbred piglets at pre-vaccination and after 28th day of classical swine fever (CSF) vaccination. On 28th day, the competitive Enzyme Linked Immunosorbent Assay (cELISA) revealed poor humoral immune response (E2 antibodies) in indigenous piglets (84.80%) as compared to crossbred piglets (98.33%) in response to CSF vaccination. The expression level of genes was analyzed in three ways, viz. indigenous 28th day post-vaccination (28dpv) versus pre-vaccination, crossbred 28th day post-vaccination versus pre-vaccination and crossbred 28th day post-vaccination versus indigenous 28th day post-vaccination. The study showed that IFNα, IFNβ, SLA, SLA-2, Ii, SLA-DM, CSK and JUN were significantly upregulated in crossbred piglets than indigenous piglets at 28th day post-vaccination. But the SLA-DR was significantly downregulated in CSF vaccinated crossbred over indigenous piglets.