Modulation of immune response and tissue repair mechanisms in the gill filaments of Atlantic salmon (Salmo salar) affected by complex gill disease (CGD) in a marine open sea-cage environment
Complex gill disease (CGD) presents significant challenges in Atlantic salmon aquaculture, resulting in reduced growth, higher production costs, and mortality rates of up to 80%. CGD is influenced by a multifactorial interaction of environmental factors and pathogens. Given the impact of CGD and the lack of molecular studies aimed at its characterization and modulation, the objective of this work was to analyze changes in the modulation of genes and biological processes that take place in the CGD-affected gill filaments in Atlantic salmon. Gill samples were taken from CGD-affected fish at an open sea-cage marine farm in the Patagonian fjords of Chile (Aysen Region). Gills were portioned into damaged (CGDdt) and undamaged (CGDndt) tissue for total RNA extraction and subsequent transcriptomic analysis by RNA-Seq, to identify differentially expressed genes and the biological functions they belong to. As a control, gill filaments from healthy fish were also sampled. The results demonstrated a clear distinction in gene expression profiles between CGDdt and CGDndt, with 364 upregulated differentially expressed genes (DEGs) and 332 downregulated, identified with key genes such as mmp9, ccl19, and il8, indicating a promotion of a pro-inflammatory environment. In contrast, underexpression of processes associated with cellular homeostasis, cell communication, and structural development suggests altered tissue homeostasis and regeneration. The comparison between CGDndt and control showed changes in the expression of 5ntla and ca12 that suggest the activation of response mechanisms due to the proximity with the branchial filament affected by CGD. In sum, this study provides valuable insights into the transcriptomic responses of Atlantic salmon to CGD and improves the understanding of tissue repair mechanisms in the mucosal tissues of aquatic organisms. Overall design: RNA-seq profiling of Atlantic salmon gill filament tissue samples from healthy (control) and complex gill disease (CGD) fish, differentiating between damaged tissue (CGDdt) and undamaged tissue (CGDndt).