Stage-specific modular responses reveal mechanisms and biomarkers of phoxim toxicity in Carassius auratus

Phoxim, a typical organophosphorus pesticide widely used in agriculture and aquaculture, poses significant ecotoxicological risks to fish species due to its environmental residues. In this study, we focused on the liver, the core detoxification organ, systematically investigated the transcriptomic responses of Carassius auratus exposed to different concentrations (low, medium, high) of phoxim for 24 h and 96 h. Integrating WGCNA with qRT-PCR validation, we elucidated the dynamic, stage-specific toxic mechanisms and adaptive responses. The results demonstrated that phoxim toxicity exhibits marked time-dependent accumulation and concentration dependence. A total of 30,540 differentially expressed genes (DEGs) were enriched at 24 h (defense phase), increasing to 38,320 DEGs at 96 h (adaptation phase). With increasing concentration, the number of DEGs decreased at 24 h but increased at 96 h. GO and KEGG enrichment analyses revealed that 24 h exposure triggered broad cellular stress and defense responses, whereas 96 h exposure shifted toward concentration-dependent pathological processes: low concentrations continuously activated detoxification and tissue remodeling pathways, medium concentrations were dominated by sustained signaling pathway perturbations, and high concentrations exhibited energy depletion and amino acid metabolic disorders. WGCNA identified functionally distinct co-expression modules, constructing a dynamic model spanning homeostasis (Cyan module), defense (Blue, Green, and Purple modules), and adaptation (Yellow module). qRT-PCR validation of key CYP450 isoforms showed concentration- and time-dependent induction patterns, with sustained high expression even at 96 h under high concentration, corroborating the significant enrichment of the drug metabolism-cytochrome P450 pathway in the Yellow module. This study presents comprehensive analysis of time- and concentration-dependent phoxim effect on C. auratus liver cells gene transcription modulation.