LncRNA activates immune response against Vibrio anguillarum in the intestine-liver axis of turbot (Scophthalmus maximus L.) by sponging miRNA in a ceRNA regulatory network

Vibriosis, most commonly caused by the bacterium Vibrio anguillarum, is one of the most important diseases affecting the marine aquaculture industry throughout the world. The intestine is the main entry portal of V. anguillarum into host fishes. Although there has been extensive research on the immunity of the gut-associated lymphoid tissue (GALT) in teleost, the mechanisms underlying the immunity of the intestine-liver during bacterial infections are still not well understood. This study conducted an integrative analysis of the transcriptome in turbot (Scopthalmus maximus L.) intestine and liver after V. anguillarum infection. To provide evidence of immunological collaboration in the turbot intestine-liver axis, we constructed the immune gene libraries, and conducted the functional annotation and enrichment analyses of immune genes that were jointly expressed in both turbot intestine and liver. Additionally, we administered the bioinformatic analyses of transcriptomic data to investigate regulatory relationships between non-coding RNAs (ncRNAs) and their target immune genes, based on the ceRNA theory. The recognition and binding abilities to bacteria were activated by the Toll-like receptor (TLR) signaling pathway. Subsequently, NF-κB was activated by the TLR/MyD88 signaling, and its target genes were induced to up-regulate in intestine and associated tissues to the digestive tract to enhance disease resistance through the production of inflammation. Histology of the intestine and liver of infected fish showed pathological changes consistent with inflammation. Bioinformatic analysis suggested that ceRNA regulatory networks play a pivotal role in the regulation of TLR genes, and RT-qPCR analyses and dual-luciferase reporter assays showed confirmed evidence to verify these hypothesized regulatory relationships. Overall, the results in this study demonstrated that a lncRNA (LNC_002468) activated the TLR signaling pathway by upregulating the TLR9 gene through sponging miRNA (novel_709). This study provides a strong indication that ncRNAs play regulatory roles in the antibacterial immune response of teleost fishes. However, further functional verification is required of the key immune genes and their regulatory relationship with miRNAs and lncRNAs. •Total of 225 genes were differentially expressed in both turbot intestine and liver infected by bacteria at an early stage.•The regulations between the ceRNAs of TLR9/novel_709/LNC_002468 axis was determined.•A hyp