Expression profiles of cloned channel catfish (Ictalurus punctatus) lymphoid cell lines and mixed lymphocyte cultures

MicroRNAs and Related Cytokine Factors Quickly Respond in the Immune Response of Channel Catfish to Lipopolysaccharides and β-Glucan Stimulation

MicroRNAs (miRNAs) are well-known as powerful regulators of gene expression, with their potential to serve for immunology widely researched in mammals and birds but rarely in fishes. To better understand fish immunology behavior, we herein investigated nine immune-related miRNAs that were reported in other animals, as well as five related cytokine factors and lysozyme (LZM) in the liver, anterior kidney, and spleen of Channel Catfish Ictalurus punctatus after being stimulated by lipopolysaccharides (LPS) and β-glucan. We also predicated the potential targets of these miRNAs via bioinformatics and further investigated nine of them via quantitative real-time PCR. Results showed that expressions of the nine miRNAs were quickly changed in varying extent after stimulation by LPS, especially for miR-122, miR-142a, miR-155, and miR-223, which were significantly changed in spleen, and the same occurred for the LZM and three cytokine factors TNF-α, IFN-γ and TLR2. Compared with LPS, although most of the miRNAs and the cytokine genes were also affected by β-glucan, the extent of the effect was weak. Bioinformatics analysis revealed many immune-related targets of the miRNAs, with some of them reported by previous studies. For the nine investigated target genes, seven targets (77.8%) were significantly upregulated after the stimulation of LPS. It therefore can be inferred that the immune-related miRNAs, LZM, and cytokine factors elicited quick immune responses of Channel Catfish to LPS stimulation as in other animals, but the regulation mechanism of miRNAs might be complex and diverse. This research will contribute to a better understanding will support further immunology research in fishes.

Expression of Bcl-2 genes in channel catfish after bacterial infection and hypoxia stress

Bcl-2 proteins are of vital importance in regulation of apoptosis, and are involved in a number of biological processes such as carcinogenesis and immune responses. Bcl-2 genes have been well studied in mammals, while they are not well investigated in teleost fish including channel catfish, the major aquaculture species in the United States. In this study, we identified 34 bcl-2 genes from the channel catfish genome, and verified their identities by conducting phylogenetic and syntenic analyses. The expression profiles of the bcl-2 genes in response to bacterial infections (Edwardsiella ictaluri and Flavobacterium columnare) and hypoxia stress were determined by performing meta-analysis using the existing RNA-Seq datasets. Differential expressions of bcl-2 genes were observed after bacterial infections and hypoxia treatment, including 22 bcl-2 genes after E. ictaluri infection, 22 bcl-2 genes after F. columnare infection, and 19 bcl-2 genes after hypoxia stress. Overall, the expression of the pro-apoptotic bcl-2 genes were repressed after bacterial infection and hypoxia stress, indicating that bcl-2 genes are potentially involved in the stress response by reducing cell apoptosis. Some bcl-2 genes, such as bcl2b, mcl1a, bmf1, and bnip3, showed different expression pattern during the E. ictaluri and F. columnare infection, suggesting the difference in the pathogenicity of diseases. This work presented the first systematic identification and annotation of bcl-2 genes in catfish, providing essential genomic resources for further immune and physiological studies.

Impact of feed additives on surface mucosal health and columnaris susceptibility in channel catfish fingerlings, Ictalurus punctatus

One of the highest priority areas for improvement in aquaculture is the development of dietary additives and formulations which provide for complete mucosal health and protection of fish raised in intensive systems. Far greater attention has been paid to dietary impact on gut health than to protective effects at other mucosal surfaces such as skin and gill. These exterior surfaces, however, are important primary targets for pathogen attachment and invasion. Flavobacterium columnare, the causative agent of columnaris disease, is among the most prevalent of all freshwater disease-causing bacteria, impacting global aquaculture of catfish, salmonids, baitfish and aquaria-trade species among others. This study evaluated whether the feeding of a standard catfish diet supplemented with Alltech dietary additives Actigen(®), a concentrated source of yeast cell wall-derived material and/or Allzyme(®) SSF, a fermented strain of Aspergillus niger, could offer protection against F. columnare mortality. A nine-week feeding trial of channel catfish fingerlings with basal diet (B), B + Allzyme(®) SSF, B + Actigen(®) and B + Actigen(®)+Allzyme(®) SSF revealed good growth in all conditions (FCR < 1.0), but no statistical differences in growth between the treatments were found. At nine weeks, based on pre-challenge trial results, basal, B + Actigen(®), and B + Allzyme(®) SSF groups of fish were selected for further challenges with F. columnare. Replicated challenge with a virulent F. columnare strain, revealed significantly longer median days to death in B + Allzyme(®) SSF and B + Actigen(®) when compared with the basal diet (P < 0.05) and significantly higher survival following the eight day challenge period in B + Actigen(®) when compared with the other two diets (P < 0.05). Given the superior protection provided by the B + Actigen(®) diet, we carried out transcriptomic comparison of gene expression of fish fed that diet and the basal diet before and after columnaris challenge using high-throughput RNA-seq. Pathway and enrichment analyses revealed changes in mannose receptor DEC205 and IL4 signaling at 0 h (prior to challenge) which likely explain a dramatic divergence in expression profiles between the two diets soon after pathogen challenge (8 h). Dietary mannose priming resulted in reduced expression of inflammatory cytokines, shifting response patterns instead to favor resolution and repair. Our results indicate that prebiotic dietary additives may provide protection extending beyond the gut to surface mucosa.

Fish and mammalian phagocytes differentially regulate pro-inflammatory and homeostatic responses in vivo

Phagocytosis is a cellular mechanism that is important to the early induction of antimicrobial responses and the regulation of adaptive immunity. At an inflammatory site, phagocytes serve as central regulators for both pro-inflammatory and homeostatic anti-inflammatory processes. However, it remains unclear if this is a recent evolutionary development or whether the capacity to balance between these two seemingly contradictory processes is a feature already displayed in lower vertebrates. In this study, we used murine (C57BL/6) and teleost fish (C. auratus) in vitro and in vivo models to assess the evolutionary conservation of this dichotomy at a site of inflammation. At the level of the macrophage, we found that teleost fish already displayed divergent pro-inflammatory and homeostatic responses following internalization of zymosan or apoptotic bodies, respectively, and that these were consistent with those of mice. However, fish and mice displayed significant differences in vivo with regards to the level of responsiveness to zymosan and apoptotic bodies, the identity of infiltrating leukocytes, their rate of infiltration, and the kinetics and strength of resulting antimicrobial responses. Unlike macrophages, significant differences were identified between teleost and murine neutrophilic responses. We report for the first time that activated murine, but not teleost neutrophils, possess the capacity to internalize apoptotic bodies. This internalization translates into reduction of neutrophil ROS production. This may play an important part in the recently identified anti-inflammatory activity that mammalian neutrophils display during the resolution phase of inflammation. Our observations are consistent with continued honing of inflammatory control mechanisms from fish to mammals, and provide added insights into the evolutionary path that has resulted in the integrated, multilayered responses that are characteristic of higher vertebrates.

Transcriptome analysis of Frog virus 3, the type species of the genus Ranavirus, family Iridoviridae

Frog virus 3 is the best characterized species within the genus Ranavirus, family Iridoviridae. FV3's large ( approximately 105 kbp) dsDNA genome encodes 98 putative open reading frames (ORFs) that are expressed in a coordinated fashion leading to the sequential appearance of immediate early (IE), delayed early (DE) and late (L) viral transcripts. As a step toward elucidating molecular events in FV3 replication, we sought to identify the temporal class of viral messages. To accomplish this objective an oligonucleotide microarray containing 70-mer probes corresponding to each of the 98 FV3 ORFs was designed and used to examine viral gene expression. Viral transcription was initially monitored during the course of a productive replication cycle at 2, 4 and 9 h after infection. To confirm results of the time course assay, viral gene expression was also monitored in the presence of cycloheximide (CHX), which limits expression to only IE genes, and following infection with a temperature-sensitive (ts) mutant which at non-permissive temperatures is defective in viral DNA synthesis and blocked in late gene expression. Subsequently, microarray analyses were validated by RT-PCR and qRT-PCR. Using these approaches we identified 33 IE genes, 22 DE genes and 36 L viral genes. The temporal class of the 7 remaining genes could not be determined. Comparison of protein function with temporal class indicated that, in general, genes encoding putative regulatory factors, or proteins that played a part in nucleic acid metabolism and immune evasion, were classified as IE and DE genes, whereas those involved in DNA packaging and virion assembly were considered L genes. Information on temporal class will provide the basis for determining whether members of the same temporal class contain common upstream regulatory regions and perhaps allow us to identify virion-associated and virus-induced proteins that control viral gene expression.

Identification and expression analyses of poly [I:C]-stimulated genes in channel catfish (Ictalurus punctatus)

Channel catfish (Ictalurus punctatus) have proven to be an excellent model with which to study immune responses of lower vertebrates. Identification of anti-viral antibodies and cytotoxic cells, as well as both type I and II interferon (IFN), demonstrates that catfish likely mount a vigorous anti-viral immune response. In this report, we focus on other elements of the anti-viral response, and identify more than two dozen genes that are induced following treatment of catfish cells with poly [I:C]. We showed that poly [I:C] induced type I interferon within 2 h of treatment, and that characteristic interferon stimulated genes (ISGs) appeared 6-12 h after exposure. Among the ISGs detected by RT-PCR assay were homologs of ISG15, Mx1, IFN regulatory factor 1 (IRF-1), inhibitor of apoptosis protein-1 (IAP-1) and the chemokine CXCL10. Microarray analyses showed that 13 and 24 cellular genes, respectively, were upregulated in poly [I:C]-treated B cell and fibroblast cultures. Although many of these genes were novel and did not fit the profile of mammalian ISGs, there were several (ISG-15, ubiquitin-conjugating enzyme E2G1, integrin-linked kinase, and clathrin-associated protein 47) that were identified as ISGs in mammalian systems. Taken together, these results suggest that dsRNA, either directly or through the prior induction of IFN, upregulates catfish gene products that function individually and/or collectively to inhibit virus replication.