Long-term, proteome-scale analysis of rainbow trout immune proteins: Implications for aquaculture vaccine development

Infectious diseases pose a significant threat to the economic stability and expansion of finfish aquaculture. Vaccination is widely considered the best prevention strategy, but evaluation of immune protection typically relies on measuring immune gene expression at the mRNA level from terminally-acquired tissue samples. However, mRNA expression does not always correlate with tissue protein levels, providing an incomplete representation of the nature and kinetics of the immune response. In addition, inter-individual variation necessitates the use of large numbers of experimental animals to obtain sufficient statistical power. To overcome these limitations, we used a long-term, proteome-scale approach to identify and quantify changes in immune protein levels in rainbow trout (Oncorhynchus mykiss) plasma. These changes provide an indication of fish health and immune status, while also permitting non-lethal sampling. Although all experimental fish mounted an antigen-specific humoral response, the timing and magnitude of this, and the response trajectories of most immune-relevant proteins, differed markedly between individuals. However, certain immunological proteins were found to be more consistently expressed across all fish, and may represent useful biomarkers of the immune response. Together our data emphasise the importance both of judicious selection of immunological biomarkers, and of careful assessment of changes in the expression of such proteins over longer-term study periods, when considering whether or not an effective antigen-specific immune response has been mounted. More generally, this approach offers a useful tool to monitor fish immune responses, while dramatically reducing the number of experimental animals required.