Integrative transcriptomic profiling reveals the key pathways in the regulation mechanism of fish intestine-spleen immunity during the bacterial challenges

In teleost, the immune roles of the gut-associated lymphoid tissue (GALT) have been well recognized. The antibacterial functions of the spleen have been also documented in various fish species. However, the mechanism of fish intestine-spleen immunity during bacterial infection still remains largely unknown. In this study, an integrative analysis was conducted in the black rockfish intestine and spleen after Aeromonas salmonicida and Edwardsiella tarda infection on the transcriptomic level. The immune gene libraries were constructed in the intestine and spleen. A total of 211 and 253 differentially expressed genes were observed in the immune gene library of spleen and intestine, respectively. One more category of immune genes was found in the intestine (9 categories) than in the spleen (8 categories). Potential evidence of the cooperation in the intestine-spleen axis was obtained based on the functional annotation and enrichment analyses of joint immune genes between intestine and spleen. In addition, bioinformatic and ceRNA analyses for transcriptomic data were performed. Finally, two key immune genes (CO3 and MRC1) and their related non-coding RNAs were observed in the functions of bacterial recognition and binding. According to the pathway "intestinal immune network for IgA production" predicted in the splenic transcriptome by functional enrichment, a novel regulatory pathway of the immunity of the intestine-spleen axis was hypothesized in black rockfish during bacterial infection. Moreover, the regulatory relationships between the immune transcripts in this pathway were verified preliminarily by RT-qPCR. Dual-luciferase reporter assays were performed to determine the regulations between the ceRNAs of MRC1/miR-23b-5p/LNC_00057980 and CO3/miR-214/LNC_00096415 axis. Overall, our findings demonstrate the key pathways of MRC1/miR-23b-5p/LNC_00057980 and CO3/miR-214/LNC_00096415 in the regulation mechanism of intestine-spleen axis during two different Gram-negative bacteria infection in black rockfish.