Integrated Transcriptomic and Metabolomic Analyses Reveal Metabolic Reprogramming and Stress Responses in Spotted Sea Bass Lateolabrax maculatus Under Cold Stress

Low temperature is a major environmental stressor that severely affects the physiology and survival of marine fish. However, the molecular mechanisms underlying cold stress responses in spotted sea bass Lateolabrax maculatus remain poorly understood, particularly from a multi-omics perspective. Here, integrated transcriptomic and metabolomic analyses were performed to systematically investigate hepatic responses to acute cold stress (8 °C). Transcriptomic analysis identified 4116 differentially expressed genes, with significant upregulation of genes involved in energy metabolism (e.g., PCK1) and protein quality control (e.g., heat shock proteins), and marked suppression of immune-related and transmembrane transport genes. Metabolomic profiling revealed 824 differential metabolites, with lipid metabolites accounting for the largest proportion, followed by amino acids and their derivatives. Enrichment analyses indicated activation of glycolysis/gluconeogenesis, the pentose phosphate pathway, and lipid metabolism under cold stress. Integrated multi-omics analysis demonstrated coordinated changes at key metabolic nodes between transcriptional and metabolic reprogramming, highlighting key pathways such as glycolysis/gluconeogenesis, glycerophospholipid metabolism, arginine and proline metabolism, and PPAR signaling. A correlation network suggested a dominant downregulation module enriched for immune-related hub genes. Overall, the transcriptomic and metabolomic signatures suggest that L. maculatus may respond to cold stress through enhanced energy production, lipid remodeling, activation of proteostasis mechanisms, and suppression of immune-related pathways. These findings provide valuable insights into cold stress and candidate pathways for future cold-tolerance breeding programs in aquaculture.