Transcriptomic and proteomic analyses of splenic immune mechanisms of rainbow trout (Oncorhynchus mykiss) infected by Aeromonas salmonicida subsp. salmonicida

• We profiled the specific spleen transcriptome and proteome of rainbow trout.
• We identified 17 consistently expressed genes/proteins at RNA and protein levels.
• Immune-related proteins were highly expressed in infected rainbow trout spleen.
• New molecular targets for further immunological research in fish were revealed.

Furunculosis caused by Aeromonas salmonicida subsp. salmonicida is an epidemic disease among salmonids, including rainbow trout (Oncorhynchus mykiss). However, the immune mechanisms that are elicited in rainbow trout against the invasion of A. salmonicida are not yet fully understood. In this study, we examined the spleen to investigate the immune response of rainbow trout at 3 days post-infection by A. salmonicida at the transcriptome and proteome levels by using Illumina-seq and iTRAQ methods, respectively. A total of 1036 genes and 133 proteins were found to undergo differential expression during the immune response of the spleen against A. salmonicida infection. Gene ontology and KEGG analysis were conducted among the differentially expressed genes and proteins, revealing that immune system process and response to stimulus were the top two biological processes, and immune system, signaling molecules and interaction, and immune diseases were the differential pathways activated. Correlation analysis of transcriptomic and proteomic results showed 17 proteins (11 upregulated and 6 downregulated) having consistent expression at RNA and protein levels. Moreover, protein–protein interaction analysis showed that diseases, proteasome, aminoacyl-tRNA biosynthesis, and nucleotide metabolism were the main interactions among the consistently expressed proteins. Consequently, these upregulated proteins, namely, ferritin, CD209, IL13Rα1, VDAC2, GIMAP7, PSMA1, and two ANXA11s could be considered as potential biomarkers for rainbow trout immune responses.Biological significanceThis study provides the first identification of immune markers through an analysis of the differential expression of both genes and their corresponding protein products in the spleen of rainbow trout after infection by A. salmonicida, shedding light on the molecular mechanisms triggered in rainbow trout against A. salmonicida infection and providing new molecular targets for further immunological research in fish.

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