Transcriptomic Insights into Heat and Hypoxia Stress in Rainbow Trout: A Meta-Analysis of Public RNA-Seq Data

Background Rainbow trout ( Oncorhynchus mykiss ) is a commercially important species that faces physiological stress under environmental challenges. Although numerous studies have used RNA-Seq to investigate the responses of rainbow trout to heat and hypoxic stress, a comprehensive analysis identifying common genes and pathways is still lacking. This study presents a meta-analysis of four RNA-Seq datasets from O. mykiss to identify conserved molecular responses to heat and hypoxia stress. Result The meta-analysis identified 1,009 (555 upregulated and 451 downregulated) protein-coding differentially expressed genes (DEGs). Among them, five genes, cdkn1ba, znf395a, klf9, irs2b, and tsc22d3, were commonly regulated under both stress conditions, indicating their shared roles in cellular homeostasis. The meta-analysis revealed highly regulated heat shock protein (hsp) family genes and hypoxia-inducible factor (HIF) genes. GO enrichment analysis revealed that DEGs under heat and hypoxia stress were associated primarily with the cell cycle, DNA metabolic processes, catalytic activity, and membrane components. KEGG analysis revealed key stress-adaptive pathways, including the cell cycle, oxidative phosphorylation, cellular senescence, p53, and FoxO signaling, which govern stress sensing, damage control, and cell survival. Conclusion This meta-analysis revealed conserved gene expression patterns and key regulatory pathways driving rainbow trout adaptation to heat and hypoxia, providing valuable insights for enhancing stress resistance in aquaculture.