Immune-relevant components of two Genome Canada supported projects (entitled “Biomarker Platform for Commercial Aquaculture Feed Development”, and “Integrated Pathogen Management of Co-infection in Atlantic Salmon”) will be presented. These projects involved close collaborations between academic (e.g. Memorial, UPEI) and industry (Cargill) researchers using transcriptomics, lipid biochemistry, and complementary techniques to identify and validate molecular biomarkers of Atlantic salmon responses to diet ingredients and immunogenic stimuli [e.g. exposure to pathogens or pathogen-associated molecular patterns (PAMPs)]. Experimental diets were designed and formulated by Cargill, and feeding and immune challenge trials were run in Memorial, UPEI, and Cargill facilities. In addition to in vivo analyses, in vitro methods were developed to study the impact of feed ingredients on salmon macrophage function. 44K microarrays, mRNA and miRNA sequencing, multiplex PCR, and real-time quantitative PCR (qPCR) were used to identify transcripts that respond to diet (e.g. varying DHA+EPA levels; with and without immunostimulant such as CpG) and/or immune challenges [e.g. co-infection with sea lice and ISAV; or exposure to PAMPs such as poly(I:C) or bacterin]. Selected publications from these projects (see below) will be discussed. Applications of biomarkers (e.g. mRNA, miRNA, lipid/fatty acid) identified in these research projects include the development of novel, sustainable diets that improve Atlantic salmon resistance to infections and co-infections.
Caballero-Solares A, Xue X, Cleveland BM, Foroutani MB, Parrish CC, Taylor RG, and Rise ML. 2020. Diet-induced physiological responses in the liver of Atlantic salmon (Salmo salar) inferred using multiplex PCR platforms. Marine Biotechnology 22(4), 511-525.
Caballero-Solares A, Xue X, Parrish CC, Foroutani MB, Taylor RG, and Rise ML. 2018. Changes in the liver transcriptome of farmed Atlantic salmon (Salmo salar) fed experimental diets based on terrestrial alternatives to fish meal and fish oil. BMC Genomics 19(1), 796.
Cai W, Kumar S, Navaneethaiyer U, Caballero-Solares A, Carvalho LA, Whyte SK, Purcell Sl, Gagne N, Hori TS, Allen M, Taylor RG, Balder R, Parrish CC, Rise ML and Fast MD. 2022. Transcriptome analysis of Atlantic salmon (Salmo salar) skin in response to sea lice and infectious salmon anemia virus co-infection under different experimental functional diets. Frontiers in Immunology 12, 787033.
Eslamloo K, Xue X, Hall JR, Smith NC, Caballero-Solares A, Parrish CC, Taylor RG and Rise ML. 2017. Transcriptome profiling of antiviral immune and dietary fatty acid dependent responses of Atlantic salmon macrophage-like cells. BMC Genomics 18, 706.
Xue X, Hall JR, Caballero-Solares A, Eslamloo K, Taylor RG, Parrish CC, and Rise ML. 2020. Liver transcriptome profiling reveals that dietary DHA and EPA levels influence suites of genes involved in metabolism, redox homeostasis, and immune function in the Atlantic salmon (Salmo salar). Marine Biotechnology 22(2), 263-284.
Xue X, Woldemariam NT, Caballero-Solares A, Umasuthan N, Fast MD, Taylor RG, Rise ML, and Andreassen R. 2019. Dietary immunostimulant CpG modulates microRNA biomarkers associated with immune responses in Atlantic salmon (Salmo salar). Cells 8(12), 1592.