Identifying transcriptomic profiles after repetitive vaccination in ovine spleen

Aluminum hydroxide, has long been employed as a vaccine adjuvant for its safety profile, although its precise mechanism of action remains elusive. In this study, we investigated the transcriptomic responses in sheep spleen following repetitive vaccination with aluminum adjuvanted vaccines and aluminum hydroxide alone. Notably, this work represents the first exploration of the sheep spleen transcriptome in such conditions. A total of 18 high-depth RNA-seq libraries were sequenced, resulting in a rich dataset which allowed isoform-level analysis also. The comparisons between vaccine-treated and control groups (V vs C) as well as between vaccine-treated and adjuvant-alone groups (V vs A) revealed significant alterations in gene expression profiles, including protein coding genes and long non-coding RNAs. Among the differentially expressed genes, many were associated with processes such as endoplasmic reticulum (ER) stress, immune response, cell cycle, and cellular senescence. The analysis of co-expression modules further indicated a correlation between vaccine treatment and genes related to ER stress and unfolded protein response. Surprisingly, adjuvant-alone treatment had little impact on the spleen transcriptome. Additionally, the role of alternative splicing in the immune response was explored. We identified isoform switches in genes associated with immune regulation and inflammation, potentially influencing protein function. In conclusion, this study provides valuable insights into the transcriptomic changes in sheep spleen following vaccination with aluminum adjuvanted vaccines and aluminum hydroxide alone. These findings shed light on the molecular mechanisms underlying vaccine-induced immune responses and emphasize the significance of antigenic components in aluminum adjuvant mechanism of action. Furthermore, the analysis of alternative splicing revealed an additional layer of complexity in the immune response to vaccination in a livestock species. Overall design: Total RNA profiles were generated by deep sequencing on an Illumina NovaSeq 6000 sequencer, of the spleen of 18 age-matched Rasa Aragonesa sheep divided in three experimental groups of 6 lambs. One group received aluminum-based subcutaneous commercial vaccines (the vaccine group). Another group (the adjuvant group) received equivalent doses of aluminum hydroxide (Alhydrogel, CZ Veterinaria, Spain). The control group only received phosphate-buffered saline (PBS). A total of 19 inoculations were administered in each group during a period of 475 days (from February 2015 to June 2016), following the recommended vaccination schedule. For this study 18 libraries were sequenced (all samples where sequenced in two different sequencing runs).