Transcriptome profiling analysis of caeca in chicks challenged withSalmonellaTyphimurium reveals differential expression of genes involved in host mucosal immune response

Temporal regulation of global gene expression in the caeca of chickens infected withSalmonellaTyphimurium has not been investigated previously. In this study, we performed the transcriptome analysis of the caeca ofSalmonellaTyphimurium challenged chicks to understand the regulation of the mucosal immune system in a temporal manner. TheSalmonellainfection resulted in the activation of the caecal immune system by the upregulation of the differentially expressed genes (DEGs; false discovery rate (FDR) < 0.05; log(2)fold change > 1) involved in biological pathways such as Toll-like receptor signaling pathway,Salmonellainfection, cytokine-cytokine receptor interaction, phagosome, apoptosis and intestinal immune network for IgA production. The activation of biological pathways such as RIG-I-like receptor signaling pathway, ErbB signaling pathway and cellular senescence showed a time-dependent response of the host immune system. A 49% increase in the DEGs on day 7 compared with day 3 post-infection (p.i.) suggested a time-dependent role of multiple genes such asAvBD1, AvBD2, AvBD7,IL2,IL10, IL21, SIVA1,CD5,CD14andGPR142in the regulation of the immune system. Nested network analysis of the individual biological pathways showed thatIL6played a significant role in the immune system regulation by activating the pathways, including Toll-like receptor signaling pathway,Salmonellainfection, intestinal immune network for IgA production and C-type lectin receptor signaling pathway. The downregulated DEGs (FDR < 0.05; log(2)fold change < -1) showed thatSalmonellachallenge affected the functions of pathways, such as tryptophan metabolism, retinol metabolism, folate biosynthesis and pentose and glucoronate interconversions, suggesting the disruption of cellular mechanisms involved in nutrient synthesis, absorption and metabolism. Overall, the immune response was temporally regulated through the activation of Toll-like signaling receptor pathway, cytokine-cytokine interactions andSalmonellainfection, whereIL6played a significant role in the modulation of caecal immune system againstSalmonellaTyphimurium.