Integrated Analysis of the lncRNA-miRNA-mRNA ceRNA Network in the Spleen of Acrossocheilus fasciatus Infected with Citrobacter freundii

Acrossocheilus fasciatus is an economically important freshwater fish species in China, and infection with Citrobacter freundii poses a serious threat to the sustainable development of its aquaculture industry. In this study, histopathological examination, TUNEL staining, immune physiological assays, and whole-transcriptome sequencing were integrated to systematically characterize the expression profiles of lncRNAs, circRNAs, miRNAs, and mRNAs in the spleen of A. fasciatus following C. freundii infection. The results showed that infection caused marked tissue damage in the intestine, spleen, and kidney, significantly increased splenic cell apoptosis, and induced pronounced changes in immune physiological parameters. Whole-transcriptome analysis identified 88 differentially expressed lncRNAs, 193 differentially expressed circRNAs, 140 differentially expressed miRNAs, and 1935 differentially expressed mRNAs. KEGG enrichment analysis revealed that the differentially expressed mRNAs were mainly enriched in immune-related pathways, including neutrophil extracellular trap formation, complement and coagulation cascades, antigen processing and presentation, cytokine–cytokine receptor interaction, phagosome, chemokine signaling pathway, and IL-17 signaling pathway. Furthermore, a bioinformatically predicted lncRNA-miRNA-mRNA ceRNA network was constructed, comprising 10 mRNAs, 14 lncRNAs, and 22 miRNAs, which formed 44 putative regulatory interactions. In this network, miR-212-y may mediate the regulation of Il12rb2 and PIK3R1, whereas miR-8-y may be involved in the regulation of Ccr9 and PIK3R1. The qRT-PCR validation results were consistent with the RNA-seq expression trends. This study provides the first comprehensive characterization of non-coding RNA and mRNA expression profiles in the spleen of A. fasciatus after C. freundii infection and identifies potential ceRNA regulatory networks, providing a valuable reference for elucidating antibacterial immune mechanisms and screening candidate molecular markers for disease resistance research in A. fasciatus.