Transcriptome profiling of antiviral immune and dietary fatty acid dependent responses of Atlantic salmon macrophage-like cells

Abstract

BackgroundDue to the limited availability and high cost of fish oil in the face of increasing aquaculture production, there is a need to reduce usage of fish oil in aquafeeds without compromising farm fish health. Therefore, the present study was conducted to determine if different levels of vegetable and fish oils can alter antiviral responses of salmon macrophage-like cells (MLCs). Atlantic salmon (Salmo salar) were fed diets containing 7.4% (FO7) or 5.1% (FO5) fish oil. These diets were designed to be relatively low in EPA + DHA (i.e. FO7: 1.41% and FO5: 1%), but near the requirement level, and resulting in comparable growth. Vegetable oil (i.e. rapeseed oil) was used to balance fish oil in experimental diets. After a 16-week feeding trial, MLCs isolated from fish in these dietary groups were stimulated by a viral mimic (dsRNA: pIC) for 6 h (qPCR assay) and 24 h (microarray and qPCR assays).ResultsThe fatty acid composition of head kidney leukocytes varied between the two dietary groups (e.g. higher 20:5n-3 in the FO7 group). Following microarray assays using a 44K salmonid platform, Rank Products (RP) analysis showed 14 and 54 differentially expressed probes (DEP) (PFP < 0.05) between the two diets in control and pIC groups (FO5 vs. FO7), respectively. Nonetheless, Significance Analysis of Microarrays (SAM, FDR < 0.05) identified only one DEP between pIC groups of the two diets. Moreover, we identified a large number (i.e. 890 DEP in FO7 and 1128 DEP in FO5 overlapping between SAM and RP) of pIC-responsive transcripts, and several of them were involved in TLR−/RLR-dependent and cytokine-mediated pathways. The microarray results were validated as significantly differentially expressed by qPCR assays for 2 out of 9 diet-responsive transcripts and for all of the 35 selected pIC-responsive transcripts.Conclusion Fatty acid-binding protein adipocyte (fabp4) and proteasome subunit beta type-8 (psmb8) were significantly up- and down-regulated, respectively, in the MLCs of fish fed the diet with a lower level of fish oil, suggesting that they are important diet-responsive, immune-related biomarkers for future studies. Although the different levels of dietary fish and vegetable oils involved in this study affected the expression of some transcripts, the immune-related pathways and functions activated by the antiviral response of salmon MLCs in both groups were comparable overall. Moreover, the qPCR revealed transcripts responding early to pIC (e.g. lgp2, map3k8, socs1, dusp5 and cflar) and time-responsive transcripts (e.g. scarb1-a, csf1r, traf5a, cd80 and ctsf) in salmon MLCs. The present study provides a comprehensive picture of the putative molecular pathways (e.g. RLR-, TLR-, MAPK- and IFN-associated pathways) activated by the antiviral response of salmon MLCs.Electronic supplementary materialThe online version of this article (10.1186/s12864-017-4099-2) contains supplementary material, which is available to authorized users.

Changes in the liver transcriptome of farmed Atlantic salmon (Salmo salar) fed experimental diets based on terrestrial alternatives to fish meal and fish oil

“…Most vegetable oils are known to be devoid of omega-3 long-chain polyunsaturated fatty acids (ω3 LC-PUFAs) such as eicosapentaenoic acid (EPA) and docosahexaenoic acid (DHA), and to have high content of omega-6 fatty acids (ω6 FAs) [ 25 ], a combination known to be pro-inflammatory [ 26 , 27 ]. Differences in diet ratios of ω6 and ω3 FAs, especially arachidonic acid (ARA)/EPA, have been found to modulate the inflammatory and immune responses of Atlantic salmon [ 28 – 30 ]. Indeed, among all farmed fish species, diet FA composition takes on particular importance for Atlantic salmon producers and consumers.…”

Transcriptomic Profiling in Fins of Atlantic Salmon Parasitized with Sea Lice: Evidence for an Early Imbalance Between Chalimus-Induced Immunomodulation and the Host’s Defense Response

“…The present study addressed this gap of knowledge in the salmon's anti-parasitic immune response using a 44K consortium for Genomic Research on All Salmonids Project (cGRASP) microarray platform [27] which provides good coverage of the salmon transcriptome, together with real-time quantitative polymerase chain reaction (QPCR) for confirmation purposes. We have used this approach in our previous immune-relevant experiments for studying salmon immune transcriptome responses against viral mimic [28] and bacterial antigens [29]. We investigated the initial local host transcriptomic response in pelvic fin, the first dominant attachment sites of L. salmonis copepodids [30], of infected salmon by profiling the gene expression at attachment sites (ATT) and adjacent to chalimus-attachment sites (ADJ) compared to non-infected controls (PRE).…”

Immunomodulatory Effects of Dietary Seaweeds in LPS Challenged Atlantic Salmon Salmo salar as Determined by Deep RNA Sequencing of the Head Kidney Transcriptome

“… Núñez-Acuña et al (2015) investigated the effects of plant-derived additives on the skin and heart kidney transcriptome in sea lice-infested Atlantic salmon. Eslamloo et al (2017) investigated whether vegetable and fish oils can alter antiviral responses of salmon macrophage-like cells by transcriptomic profiling but found similar activation of the immune-related pathways and functions between experimental groups. Caballero-Solares et al (2017) concluded that plant-based diets may enhance the immune response on basis of increased expression of transcripts involved in the synthesis of pro-inflammatory eicosanoids and chemotaxis.…”