Integrated analysis of circRNA- and lncRNA-mediated ceRNA regulatory networks reveals early immune responses induced by Vibrio anguillarum vaccine in turbot (Scophthalmus maximus) intestine.

Competitive endogenous RNAs (ceRNAs) represent a class of transcripts comprising protein-coding mRNAs and various non-coding RNAs such as miRNAs, lncRNAs, and circRNAs, which interact through mutual post-transcriptional regulation mediated by their competition for common miRNA binding sites. Compared to traditional chemical drugs and antibiotics, vaccine is a desirable alternative not only for effective prevention of infectious diseases, but also ensures environmental safety and food safety. Understanding the functional interplay of miRNA, lncRNA and circRNA in the early stages of vaccination will provide new insights for the process of early immune response in teleosts. In this study, non-coding RNAs (ncRNAs) in turbot intestine were analyzed at 2 h, 12 h, and 48 h post-vaccination with inactivated Vibrio anguillarum vaccine. Comparative analysis between vaccinated and control groups identified 59 differentially expressed circular RNAs (DE-circRNAs), 425 differentially expressed microRNAs (DE-miRNAs), 169 differentially expressed long non-coding RNAs (DE-lncRNAs), and 338 differentially expressed messenger RNAs (DEGs), representing four classes of RNAs with altered expression patterns. The co-localization analysis between DE-lncRNAs and their corresponding co-expressed mRNAs was performed, followed by functional enrichment assessments using GO and KEGG pathway analyses. To investigate the regulatory functions of non-coding RNAs in the immune response mechanisms of V. anguillarum, both circRNA-miRNA-mRNA and lncRNA-miRNA-mRNA interaction networks were established. Among which, Cathepsin B (CTSB), one member of the cathepsin superfamily, was predicted to be regulated by miRNA (dre-miR-1788-3p) and lncRNA. The experimental data demonstrated a strong concordance between qRT-PCR measurements and RNA-Seq profiling outcomes, indicating that the Illumina sequencing data is reliable for gene expression analysis. This study aims to clarify the molecular mechanisms by which non-coding RNAs regulate the piscine immune response to pathogenic infection, thereby providing the theoretical basis for developing targeted prevention and control strategies against aquatic animal diseases.