Change in Long Non-Coding RNA Expression Profile Related to the Antagonistic Effect of Clostridium perfringens Type C on Piglet Spleen

SIMPLE SUMMARY: Clostridium perfringens (C. perfringens) type C is a spore-forming pathogenic bacterium characterized by the secretion of fatal toxins, which are absorbed into the body, causing diarrhea. Diarrhea has already brought about tremendous economic losses in pig farms worldwide. However, the understanding of lncRNAs’ regulatory mechanisms of the spleen in piglets challenged by C. perfringens type C is still limited. This paper aimed to identify antagonistic lncRNAs associated with the spleen in piglets challenged by C. perfringens type C. The study found that four lncRNAs are involved in immune-/inflammation-related pathways to regulate cytokine genes against C. perfringens type C infection. ABSTRACT: LncRNAs play important roles in resisting bacterial infection via host immune and inflammation responses. Clostridium perfringens (C. perfringens) type C is one of the main bacteria causing piglet diarrhea diseases, leading to major economic losses in the pig industry worldwide. In our previous studies, piglets resistant (SR) and susceptible (SS) to C. perfringens type C were identified based on differences in host immune capacity and total diarrhea scores. In this paper, the RNA-Seq data of the spleen were comprehensively reanalyzed to investigate antagonistic lncRNAs. Thus, 14 lncRNAs and 89 mRNAs were differentially expressed (DE) between the SR and SS groups compared to the control (SC) group. GO term enrichment, KEGG pathway enrichment and lncRNA-mRNA interactions were analyzed to identify four key lncRNA targeted genes via MAPK and NF-κB pathways to regulate cytokine genes (such as TNF-α and IL-6) against C. perfringens type C infection. The RT-qPCR results for six selected DE lncRNAs and mRNAs are consistent with the RNA-Seq data. This study analyzed the expression profiling of lncRNAs in the spleen of antagonistic and sensitive piglets and found four key lncRNAs against C. perfringens type C infection. The identification of antagonistic lncRNAs can facilitate investigations into the molecular mechanisms underlying resistance to diarrhea in piglets.