Transcriptomic Analysis of Gene Expression in Immune Pathways in the Spleen of Takifugu rubripes After Infection with Scuticociliate Uronema marinum

Abstract

This study employed Illumina HiSeq™ 2000 sequencing to compare spleen transcriptomes of Uronema marinum-infected and healthy Takifugu rubripes. High-throughput analysis generated 25.6 Gb (infected) and 23.39 Gb (control) high-quality reads, meeting stringent quality standards (Q20 ≥ 98.3%, Q30 ≥ 95.1%). DESeq analysis identified 238 differentially expressed genes (116 upregulated/122 downregulated), functionally categorized into Gene Ontology (GO) domains: biological processes (54.03%), molecular functions (31.78%), and cellular components (14.19%). Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment revealed 62 signaling cascades, with 80% of the top 20 pathways involving immune regulation—including cytokine-receptor interactions, focal adhesion, Jak-STAT signaling, and IgA-mediated immunity. Core immune components (CXCR4, CCR9/CCL19, IL6R/IL12RB2) demonstrated coordinated regulation with ECM-RTK complexes and cytoskeletal modulators (RhoGAP, Paxillin). Mechanistically, PI3K-AKT/PKB signaling cascades emerged as central regulators, interacting with SHP2 phosphatases and Sprouty inhibitors to orchestrate anti-parasitic responses. Quantitative validation confirmed transcriptomic patterns, revealing > 85% concordance in immune gene expression. As the first comprehensive analysis of teleost immunity against scuticociliates, this work delineates evolutionarily conserved defense mechanisms in marine fish, including three novel regulatory axes: Toll-like receptor signaling for pathogen recognition, complement-mediated lysis cascades, and antigen processing/presentation pathways. These findings identify candidate molecular targets and immune pathway interactions, laying groundwork for future development of targeted anti-parasitic strategies in aquaculture systems.