Lumpfish are cleaner fish widely used for parasite (sea-lice) control in large scale Atlantic salmon (Salmo salar) farming. Aeromonas salmonicida is a prevalent Gram-negative bacterial pathogen that directly impacts lumpfish survival. In this study, the whole transcriptome-wide response in lymphoid tissue such as head kidney, spleen and liver were studied after administering a lethal dose of A. salmonicida. The samples were collected at zero, three, and ten days post-infection (dpi). RNA sequencing (RNA-seq) based transcriptomic profiling revealed several transcripts and genes to understand the immune mechanisms in fish during pathogenic infection.
Trinity and Trinotate software performed de novo assembly and annotation of the transcriptome. RSEM software was used to quantify transcript expression before identifying differentially expressed transcripts (DETs) using DESeq2 and egdeR. The samples collected at three dpi is a critical time point to study the crosstalk between both the innate and adaptive immune response. The most DE transcripts (|FC| > 2 and adj. P-value ≤ 0.05) between three dpi vs zero dpi is 1789 (720 up-regulated and 1069 down-regulated). We further identified 450, 1049 and 224 unique DETs in Head Kidney (234 up-regulated and 216 down-regulated), Spleen (370 up-regulated and 679 down-regulated), and liver (105 up-regulated and 119 down-regulated) respectively between three dpi vs zero dpi.
Antimicrobial peptides (innate immunity), such as hepcidin (hamp), hemopexin (hpx), and haptoglobin (hp) have a significant role in regulating inflammatory response during bacterial infection. We identified several significant transcripts of hamp, hpx, and hp overexpressed in all the three central lymphoid tissue. We also identified heparanase (hpse) transcript (down-regulated) that is critical to effective wound healing process. The complement system defence mechanism is diverse, and it triggers inflammation, attract phagocytes to the infection site and plays a role in the activation of naive B-lymphocytes. Interestingly, we observed complement system 3 and 6 up-regulated in head kidney and spleen, respectively, while complement system 5 down-regulated in liver. We also found several DETs involved in pathways of complement activation. We further catalogued innate immune genes such as hck, malt1, aimp1, ccl13, il1b, stat3, acod1, pik3cg, and lbp response. These results provided with novel insights of A. salmonicida infection and how the fish innate immune system is highjack during infection.