Transcriptome profiling the gills of amoebic gill disease (AGD)-affected Atlantic salmon (Salmo salar L.): a role for tumor suppressor p53 in AGD pathogenesis?

Comparative analysis of the acute response of the trout, O. mykiss, head kidney to in vivo challenge with virulent and attenuated infectious hematopoietic necrosis virus and LPS-induced inflammation

BACKGROUND

The response of the trout, O. mykiss, head kidney to bacterial lipopolysaccharide (LPS) or active and attenuated infectious hematopoietic necrosis virus (IHNV and attINHV respectively) intraperitoneal challenge, 24 and 72 hours post-injection, was investigated using a salmonid-specific cDNA microarray.

RESULTS

The head kidney response to i.p. LPS-induced inflammation in the first instance displays an initial stress reaction involving suppression of major cellular processes, including immune function, followed by a proliferative hematopoietic-type/biogenesis response 3 days after administration. The viral response at the early stage of infection highlights a suppression of hematopoietic and protein biosynthetic function and a stimulation of immune response. In fish infected with IHNV a loss of cellular function including signal transduction, cell cycle and transcriptional activity 72 hours after infection reflects the tissue-specific pathology of IHNV infection. attIHNV treatment on the other hand shows a similar pattern to native IHNV infection at 24 hours however at 72 hours a divergence from the viral response is seen and replace with a recovery response more similar to that observed for LPS is observed.

CONCLUSION

In conclusion we have been able to identify and characterise by transcriptomic analysis two different types of responses to two distinct immune agents, a virus, IHNV and a bacterial cell wall component, LPS and a 'mixed' response to an attenuated IHNV. This type of analysis will lead to a greater understanding of the physiological response and the development of effective immune responses in salmonid fish to different pathogenic and pro-inflammatory agents.

Transgenic fish resistant to infectious diseases, their risk and prevention of escape into the environment and future candidate genes for disease transgene manipulation

Transgenic fish have been produced that have improved growth, disease resistance, survival in cold and body composition, have altered color, that can act as bioindicators for estrogenic pollutants and that can produce pharmaceutical proteins. The largest amount of transgenic research has focused on growth hormone transfer. A relatively small amount of research has focused on enhancing disease resistance, but significant enhancement has been accomplished. Pleiotropic effects from the transfer of other transgenes, particularly growth hormone gene can alter disease resistance in both positive and negative ways. Most negative effects for all transgenes appear to lower fitness traits, which is positive for biological containment. Transgenic fish appear to pose little environmental risk, but this research is not fully conclusive. To expedite commercialization and minimize environmental risk, transgenic sterilization research is underway. A large amount of functional genomics research has resulted in a much better understanding of gene expression when fish are experiencing disease epizootics. This information may allow the future design of more effective transgenic approaches to address disease resistance.

Microarray analysis of gene expression in the blue catfish liver reveals early activation of the MHC class I pathway after infection with Edwardsiella ictaluri

The acute nature of disease outbreaks in aquaculture settings has served to emphasize the importance of the innate immune response of fish for survival and led to the recent identification and characterization of many of its components. Catfish, the predominant aquaculture species in the United States, is an important model for the study of the teleost immune system. However, transcriptomic-level studies of disease-related gene expression in catfish have only recently been initiated, and understanding of immune responses to pathogen infections is limited. Here, we have developed and utilized a 28K in situ oligonucleotide microarray composed of blue catfish (Ictalurus furcatus) and channel catfish (Ictalurus punctatus) transcripts. While channel catfish accounts for the majority of commercial production, the closely related blue catfish possesses several economically important phenotypic traits. Microarray analysis of gene expression changes in blue catfish liver after infection with Gram-negative bacterium Edwardsiella ictaluri indicated the strong upregulation of several pathways involved in the inflammatory immune response and potentially in innate disease resistance. A multifaceted response to infection could be observed, encompassing the complement cascade, iron regulation, inflammatory cell signaling, and antigen processing and presentation. The induction of several components of the MHC class I-related pathway following infection with an intracellular bacterium is reported here for the first time in fish. A comparison with previously published expression profiles in the channel catfish liver was also made and the microarray results extended by use of quantitative RT-PCR. Our results add to the understanding of the teleost immune responses and provide a solid foundation for future functional characterization, genetic mapping, and QTL analysis of immunity-related genes from catfish.

Neoparamoeba perurans n. sp., an agent of amoebic gill disease of Atlantic salmon (Salmo salar)

Amoebic gill disease (AGD) is a potentially fatal disease of some marine fish. Two amphizoic amoebae Neoparamoeba pemaquidensis and Neoparamoeba branchiphila have been cultured from AGD-affected fish, yet it is not known if one or both are aetiological agents. Here, we PCR amplified the 18S rRNA gene of non-cultured, gill-derived (NCGD) amoebae from AGD-affected Atlantic salmon (Salmo salar) using N. pemaquidensis and N. branchiphila-specific oligonucleotides. Variability in PCR amplification led to comparisons of 18S rRNA and 28S rRNA gene sequences from NCGD and clonal cultured, gill-derived (CCGD) N. pemaquidensis and N. branchiphila. Phylogenetic analyses inferred from either 18S or 28S rRNA gene sequences unambiguously segregated a lineage consisting of NCGD amoebae from other members of the genus Neoparamoeba. Species-specific oligonucleotide probes that hybridise 18S rRNA were designed, validated and used to probe gill tissue from AGD-affected Atlantic salmon. The NCGD amoebae-specific probe bound AGD-associated amoebae while neither N. pemaquidensis nor N. branchiphila were associated with AGD-lesions. Together, these data indicate that NCGD amoebae are a new species, designated Neoparamoeba perurans n.sp. and this is the predominant aetiological agent of AGD of Atlantic salmon cultured in Tasmania, Australia.

Molecular cloning and expression analysis of tumour necrosis factor-alpha in amoebic gill disease (AGD)-affected Atlantic salmon (Salmo salar L.)

Tumour necrosis factor-alpha (TNF-alpha) is a key mediator of inflammation during amoebiasis of humans and mice. Atlantic salmon (Salmo salar L.) are also susceptible to infection by amoebae (Neoparamoeba spp.), inflicting a condition known as amoebic gill disease (AGD). Here, the role of TNF-alpha in AGD-pathogenesis was examined. Two Atlantic salmon TNF-alpha transcripts designated TNF-alpha1 and TNF-alpha2 together with their respective genes were cloned and sequenced. TNF-alpha1 is 1379 bp and consists of a 738 bp open reading frame (ORF) translating into a predicted protein of 246 amino acids. TNF-alpha2 is 1412 bp containing an ORF and translated protein the same lengths as TNF-alpha1. An anti-rainbow trout TNF-alpha polyclonal antibody that bound recombinant Atlantic salmon TNF-alpha1 and TNF-alpha2 was used to detect constitutive and inducible expression of TNF-alpha in various tissues. The anti-TNF-alpha antibody bound to a TNF-like protein approximately 60 kDa that was constitutively expressed in a number of tissues in healthy Atlantic salmon. However, this protein was not detected in lysates from mitogen-stimulated head kidney leucocytes, despite up-regulation of TNF-alpha mRNAs under the same conditions. During the early onset of AGD in Atlantic salmon, there were no demonstrable differences in the gill tissue expression of TNF-alpha1, TNF-alpha2 nor the interleukin-1 beta (IL-1beta), inducible nitric oxide synthase (iNOS) and interferon gamma (IFN-gamma) mRNAs compared to tissue from healthy fish. In Atlantic salmon with advanced AGD, IL-1beta but not TNF-alpha1 or TNF-alpha2 mRNAs was up-regulated and was lesion-restricted. Given that Neoparamoeba spp. modulated both TNF-alpha2 and IL-1beta in head kidney leucocytes in vitro, it appears that rather than being recalcitrant to Neoparamoeba spp.-mediated TNF-alpha expression, either the parasite can influence the cytokine response during infection, there is ineffective signalling for TNF-alpha expression, or there are too few cells at the site of infection with the capacity to produce TNF-alpha. These data support our previous observation that IL-1beta mRNA expression is up-regulated in AGD-affected tissue and that TNF-alpha is not intrinsic in AGD-pathogenesis.

Interferon type I and type II responses in an Atlantic salmon (Salmo salar) SHK-1 cell line by the salmon TRAITS/SGP microarray

Interferons (IFNs) are cytokines that have proinflammatory, antiviral, and immunomodulatory effects and play a central role during a host response to pathogens. The IFN family contains both type I and type II molecules. While there are a number of type I IFNs, there is only one type II IFN. Recently both type I and type II IFN genes have been cloned in salmonid fish and recombinant proteins produced showing IFN activity. We have stimulated an Atlantic salmon cell line (SHK-1) with both type I and type II recombinant salmonid IFNs and analyzed the transcriptional response by microarray analysis. Cells were exposed to recombinant IFNs for 6 or 24 h or left unexposed as controls. RNA was hybridized to an Atlantic salmon cDNA microarray (salmon 17K feature TRAITS/SGP array) in order to assess differential gene expression in response to IFN exposure. For IFN I and II, 47 and 72 genes were stimulated, respectively; most genes were stimulated by a single IFN type, but some were affected by both IFNs, indicating coregulation of the IFN response in fish. Real-time PCR analysis was employed to confirm the microarray results for selected differentially expressed genes in both a cell line and primary leukocyte cultures.

Directional responses following recombinant cytokine stimulation of rainbow trout (Oncorhynchus mykiss) RTS-11 macrophage cells as revealed by transcriptome profiling

Background

The early stages of the immune response are regulated by key cytokines including both interleukin 1β (IL-1β) and interferon-γ (IFN-γ) which stimulate panels of responsive genes via conserved signal transduction pathways. To further our understanding of the transcriptional response to these cytokines in lower vertebrates we have utilized microarray analysis to characterize the transcriptional response to recombinant rainbow trout IL-1β and IFN-γ in the trout macrophage cell line RTS-11.

Results

RNA was extracted from stimulated or control cells following 6 h incubation and used to hybridize to a salmonid cDNA microarray containing 16,006 different genes. Analysis of the arrays revealed mRNA transcripts that were differentially expressed as a result of exposure to the recombinant proteins, with some responses common for both cytokines. In general the recombinant IL-1β elicited a response where genes involved in the acute phase response were up-regulated, whilst the recombinant IFN-γ induced strong up-regulation of genes involved in the MHC class I antigen presentation pathway. Key genes were chosen that were differentially regulated and analysed by real time PCR at additional time points, up to 48 h following stimulation. This allowed a deeper insight into the kinetics of the response to the cytokines in this cell line.

Conclusion

We demonstrated that in fish both rIL-1β and rIFN-γ stimulated discrete panels of mRNA transcripts which indicted the cells were being directed towards different cellular functions, with IL-β inducing genes involved in the inflammatory response, whereas IFN-γ induced genes associated with antigen presentation.

Microarray studies of gene expression in fish

The use of microarrays for the study of various aspects of fish physiology has seen a spectacular increase in recent years. From early studies with model species, such as zebrafish, to current studies with commercially important species, such as salmonids, catfish, carp, and flatfish, microarray technology has emerged as a key tool for understanding developmental processes as well as basic physiology. In addition, microarrays are being applied to the fields of ecotoxicology and nutrigenomics. A number of different platforms are now available, ranging from microarrays containing cDNA amplicons to oligomers of various sizes. High-density microarrays containing hundreds of thousands of distinct oligomers have been developed for zebrafish and catfish. As this exciting technology advances, so will our understanding of global gene expression in fish. Furthermore, lessons learned from this experimentally tractable group of organisms can also be applied to more advanced organisms such as humans.

Evidence for changes in the transcription levels of two putative P-glycoprotein genes in sea lice (Lepeophtheirus salmonis) in response to emamectin benzoate exposure

Overexpression of P-glycoproteins (Pgps) is assumed to be a principal mechanism of resistance of nematodes and arthropods to macrocyclic lactones. Quantitative RT-PCR (Q-RT-PCR) was used to demonstrate changes in transcription levels of two putative P-glycoprotein genes, designated here as SL0525 and SL-Pgp1, in sea lice (Lepeophtheirus salmonis) following exposure to emamectin benzoate (EMB). Pre-adult L. salmonis were challenged in an EMB bioassay for 24h and gene expression was studied from lice surviving EMB concentrations of 0, 10, and 30ppb. Gene expression was measured using Q-RT-PCR with elongation factor 1 (eEF1alpha) as an internal reference gene. The results show that both target genes, SL0525 and SL-Pgp1, had significantly increased levels of expression with exposure to 10ppb EMB (p=0.11 and p=0.17, respectively) whereas the group exposed to 30ppb was on the verge of being significant (p=0.053) only in the expression of SL-Pgp1. Gene expression for SL0525 and SL-Pgp1 were increased over five-fold at 10ppb EMB. Therefore, the upregulation of these target genes may offer protection by increasing Pgp expression when lice are exposed to EMB. Our optimized Q-RT-PCR can be used to determine if over-expression of these genes could be the basis for development of resistance in sea lice and thus allow suitable alternative chemotherapeutic options to be assessed.

Expression analysis of the acute phase response in channel catfish (Ictalurus punctatus) after infection with a Gram-negative bacterium

The acute phase response (APR) is a set of metabolic and physiological reactions occurring in the host in response to tissue infection or injury and is a crucial component of the larger innate immune response. The APR is best characterized by dramatic changes in the concentration of a group of plasma proteins known as acute phase proteins (APPs) which are synthesized in the liver and function in a wide range of immunity-related activities. Utilizing a new high-density in situ oligonucleotide microarray, we have evaluated the APR in channel catfish liver following infection with Edwardsiella ictaluri, a bacterial pathogen that causes enteric septicemia of catfish. Our catfish microarray design (28K) builds upon a previous 19K channel catfish array by adding recently sequenced immune transcripts from channel catfish along with 7159 unique sequences from closely related blue catfish. The analysis of microarray results using a traditional 2-fold change in gene expression cutoff and a 10% false-discovery rate revealed a well-developed APR in catfish, with particularly high upregulation (>50-fold) of genes involved in iron homeostasis (i.e. intelectin, hemopexin, haptoglobin, ferritin, and transferrin). Other classical APP genes upregulated greater than 2-fold included coagulation factors, proteinase inhibitors, transport proteins, and complement components. Upregulation of the majority of the complement cascade was observed including the membrane attack complex components and complement inhibitors. A number of pathogen recognition receptors (PRRs) and chemokines were also differentially expressed in the liver following infection. Independent testing of a selection of differentially expressed genes with real-time RT-PCR confirmed microarray results.