Swine blood transcriptomics: Application and advancement

Background: Breeding pig for improved feed efficiency is of practical interest. However, it is not clear whether selection for improved feed efficiency by selection for low residual feed intake (RFI), a measure of feed efficiency, compromises a pig‟s immune response to pathogens or inflammatory stimuli. In this study, we intramuscularly injected pigs from two lines divergently selected for RFI with lipopolysaccharide (LPS) to investigate whether these two lines responded to LPS stimulation differently. And we also aimed to determine to what extent transcriptomic response to endotoxemia in pigs and humans are similar. Results: Intramuscular injection of LPS induced systemic inflammation in pigs of both lines (n = 4 per line), but no significant differences in dynamics of body temperature, complete blood count (CBC), and levels of several cytokines in plasma were detected between the lines during the first 24 hours post injection (hpi). Profiling peripheral blood transcriptomes at baseline and at 2, 6, and 24 hpi by RNA-seq revealed that LPS induced dramatic transcriptomewide changes, with 5,871 genes differentially expressed for at least one time point post LPS injection compared to baseline for the average line (|log2(FC)| ≥ log2(1.2), q < 0.05). However, 24 we detected only a very small number of genes that were differentially expressed between the two lines at baseline, and at 2, 6, and 24 hpi, with negligible line-by-time interaction effects on gene expression. Gene set enrichment analyses suggested that at the pathway level the two lines were largely similar in transcriptomic response to LPS stimulation, although the low RFI line had a slightly lower level of inflammatory response than the high RFI line at each time point post LPS injection. Genes involved in protein translation, defense and immune response, and signaling formed individual co-expression clusters. Compared to the inflammatory response induced by intravenous LPS infusion in humans, swine inflammatory response observed in this pig study was much weaker, although a much higher dosage of LPS was used in pigs than in humans. While hundreds of key pathways and biological processes were shared between the two species during LPS response, any pathways and biological processes were specifically involved in human response, but only a few were pig-specific. In total, 1,543 porcine genes and their human orthologs were differentially expressed in response to LPS stimulation in both species. Nearly one third of these genes shared a very similar dynamic expression pattern over the time course in these species. These conserved genes mainly functioned in biological processes including translation, RNA catabolism, signaling, apoptosis, immune response and inflammatory response. Conclusions: The pig lines divergently selected for RFI responded very similarly to systemic inflammation triggered by intramuscular LPS injection, though the low-RFI line had a lower level of inflammation response than the high-RFI line at every time point post LPS injection. Pigs and humans shared similarity in response to systematic inflammation triggered by LPS at both the gene and pathway levels, although the response to LPS in pigs was much weaker than previously reported in humans. But caution should be taken to interpret the differences seen 25 in humans and pigs due to differences in routes of LPS administration, dosage and sources of LPS, blood fractionation, expression profiling platforms, and completeness of genome annotation in both species. Our work indicates that selection for feed efficient pigs does not compromise a pig‟s ability to handle acute systemic inflammation, and also offered another line of evidence that pigs can be used as models for human inflammatory disease.