Transcriptomic Profiling of the Adaptive and Innate Immune Responses of Atlantic Salmon to Renibacterium salmoninarum Infection

Abstract

Bacterial Kidney Disease (BKD), which is caused by a Gram-positive, intracellular bacterial pathogen (Renibacterium salmoninarum), affects salmonids including Atlantic salmon (Salmo salar). However, the transcriptome response of Atlantic salmon to BKD remained unknown before the current study. We used a 44K salmonid microarray platform to characterise the global gene expression response of Atlantic salmon to BKD. Fish (∼54 g) were injected with a dose of R. salmoninarum (H-2 strain, 2 × 10 8 CFU per fish) or sterile medium (control), and then head kidney samples were collected at 13 days post-infection/injection (dpi). Firstly, infection levels of individuals were determined through quantifying the R. salmoninarum level by RNA-based TaqMan qPCR assays. Thereafter, based on the qPCR results for infection level, fish (n = 5) that showed no (control), higher (H-BKD), or lower (L-BKD) infection level at 13 dpi were subjected to microarray analyses. We identified 6,766 and 7,729 differentially expressed probes in the H-BKD and L-BKD groups, respectively. There were 357 probes responsive to the infection level (H-BKD vs. L-BKD). Several adaptive and innate immune processes were dysregulated in R. salmoninarum-infected Atlantic salmon. Adaptive immune pathways associated with lymphocyte differentiation and activation (e.g., lymphocyte chemotaxis, T-cell activation, and immunoglobulin secretion), as well as antigen-presenting cell functions, were shown to be differentially regulated in response to BKD. The infection level-responsive transcripts were related to several mechanisms such as the JAK-STAT signalling pathway, B-cell differentiation and interleukin-1 responses. Sixty-five microarray-identified transcripts were subjected to qPCR validation, and they showed the same fold-change direction as microarray results. The qPCRvalidated transcripts studied herein play putative roles in various immune processes including pathogen recognition (e.g., tlr5), antibacterial activity (e.g., hamp and camp), regulation of immune responses (e.g., tnfrsf11b and socs1), T-/B-cell differentiation (e.g., ccl4, irf1 and ccr5), T-cell functions (e.g., rnf144a, il13ra1b and tnfrsf6b), and Eslamloo et al. Atlantic Salmon Response to BKD antigen-presenting cell functions (e.g., fcgr1). The present study revealed diverse immune mechanisms dysregulated by R. salmoninarum in Atlantic salmon, and enhanced the current understanding of Atlantic salmon response to BKD. The identified biomarker genes can be used for future studies on improving the resistance of Atlantic salmon to BKD.

Lumpfish (Cyclopterus lumpus) Is Susceptible to Renibacterium salmoninarum Infection and Induces Cell-Mediated Immunity in the Chronic Stage

“…Significant downregulation of cd74 (an invariant polypeptide involved in major histocompatibility complex-II (MHC-II) formation and transport) (Figure 6K) in lumpfish head kidney at 28 dpi suggests that the T-cell responses could be modified towards an enhanced MHC-I and a reduced MHC-II dependent pathway, perhaps caused by an increased amount of MSA, similar to R. salmoninarum infection in rainbow trout (32,105). This skewing towards the MHC-I pathway in lumpfish at the early stages of R. salmoninarum infection correlates with the BKD-dependent major histocompatibility-1 (mh1) induction observed in Atlantic salmon at 13 dpi (46). Further, Rozas-Serri et al (106) demonstrated that the humoral and cellmediated adaptive immune responses against R. salmoninarum in Atlantic salmon pre-smolts were significantly downregulated at the later stage of infection (55 dpi) (106), which agrees with our findings at 28 dpi.…”

“…Lumpfish were intraperitoneally (i.p.) injected with 100 ml of 10 7 , 10 8 , or 10 9 cells of R. salmoninarum dose -1 , similar to infection studies in salmonids and other fish species (44)(45)(46)(47). A duplicate group of lumpfish i.p.…”

Transcriptome Profiling of Atlantic Salmon Adherent Head Kidney Leukocytes Reveals That Macrophages Are Selectively Enriched During Culture

“…For example, il1b, tnfrsf6b, tnfrsf11b and tlr9 were downregulated in Day 5 HKLs compared to Day 1 HKLs. These genes have been demonstrated to be responsive to bacterial and viral challenges in various fish species (92)(93)(94). The upregulation of some pathogenresponsive genes, and the downregulation of others, in Day 5 HKLs compared with Day 1 HKLs, suggests that these cells are likely changing in their responsiveness to pathogens over time in culture.…”

Comparative Transcriptome Analysis Reveals the Molecular Immunopathogenesis of Chinese Soft-Shelled Turtle (Trionyx sinensis) Infected with Aeromonas hydrophila

“…RNA-sequencing (RNA-Seq) using next-generation sequencing is one of the most useful methods to survey the character of a transcriptome because it offers the whole data on gene expression. To date, transcriptome profiling using next-generation sequencing technologies has provided new insights into pathogen–host immunity interaction in many aquaculture fish species, such as Nile tilapia ( Oreochromis niloticus ) [ 24 ], Gold fish ( Carassius auratus L.) [ 25 ], Ussuri catfish ( Pseudobagrus ussuriensis ) [ 26 ], Yellow catfish ( Pelteobagrus fulvidraco ) [ 27 ], and Atlantic salmon ( Salmo salar ) [ 28 ]. More and more studies have used this high-throughput sequencing approach to identify the expression differences of immune molecules between the resistant and susceptible fish to pathogen infection.…”