Comparative transcriptome analysis of CaIRF1-associated immune responses in Chromileptes altivelis during Vibrio harveyi infection.

Vibrio harveyi is a major bacterial pathogen in marine aquaculture, posing a serious threat to fish health. IRF1 is a conserved regulator of teleost immunity; however, the transcriptional regulatory networks associated with IRF1 during bacterial infection remain incompletely understood. To characterize CaIRF1-associated transcriptional responses during Vibrio harveyi infection, Chromileptes altivelis were injected with PBS (Control group, ControlVa), pCaIRF1 (CaIRF1 overexpression group, VpCaIRF1), or siCaIRF1 (CaIRF1 knockdown group, VsiCaIRF1), and then infected with V. harveyi. Transcriptome analysis was performed in VpCaIRF1 vs. ControlVa and VsiCaIRF1 vs. ControlVa. In VpCaIRF1 vs. ControlVa and VsiCaIRF1 vs. ControlVa, 2495 and 3650 differentially expressed genes (DEGs) were identified; furthermore, 1498 DEGs were shared, enriched in immune-related pathways, such as Toll-like receptors (TLRs), interferons (IFNs), cytokines, and tumor necrosis factor (TNF) signaling. Gene Ontology (GO) enrichment analysis indicated that these DEGs were mainly involved in immune responses, antigen processing and presentation, and oxidative stress regulation. KEGG pathway analysis showed that CaIRF1 overexpression was associated with enrichment of cytokine-mediated signaling, apoptosis, and metabolic pathways, whereas CaIRF1 knockdown was associated with enrichment of pathogen-recognition pathways, including TLR, NOD-like receptor, RIG-I-like receptor, and cytosolic DNA-sensing pathways. Additionally, CaIRF1-associated candidate genes were identified, among which multiple immune-related genes, including TLR1, Cyclic GMP-AMP Synthase (CGAS), Class II Major Histocompatibility Complex Transactivator (CIITA), and Tumor Necrosis Factor Receptor Superfamily Member 11b (TNFRSF11b) etc., were involved in pathogen recognition, inflammatory signaling, antigen presentation, and immune cell regulation. Quantitative real-time PCR analysis confirmed the reliability of the transcriptome data, showing consistent expression patterns of key immune-related genes. Collectively, CaIRF1 modulation was associated with broad transcriptional changes in immune-related processes during V. harveyi infection, including pathogen recognition, cytokine signaling, apoptosis, and oxidative stress responses. This study provides a transcriptomic characterization of CaIRF1-associated immune responses and identifies candidate pathways for subsequent functional validation in teleost fish.