1 Great Lakes Wisconsin Aquatic Technology and Environmental Research (WATER) Institute, University of Wisconsin-Milwaukee, Milwaukee, Wisconsin
2 Pacific Biological Station, Fisheries and Oceans Canada, Nanaimo
3 Centre for Biomedical Research, University of Victoria, Victoria
4 Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, British Columbia, Canada
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ABSTRACT |
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Salmo salar; salmonid rickettsial septicemia; antioxidant
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INTRODUCTION |
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P. salmonis occurs within membrane-bound vacuoles in various cell types (31) including phagocytes. The mechanisms used by the bacterium for survival and replication within host cells are not known. Microarray-based gene expression studies of cultured mammalian macrophages infected with intracellular, nonrickettsial bacterial pathogens identified suites of responsive host genes, pointing to cellular processes (e.g., inflammation, signal transduction, apoptosis) that may be altered to prevent pathogen destruction (13, 15). The work contained herein, utilizing genomics resources developed by the Genomic Research on Atlantic Salmon Project (GRASP) (36), is the first microarray-based study that considers and compares the gene expression responses of isolated macrophages and their tissue of origin, the hematopoietic salmon kidney, following infection with P. salmonis (Fig. 1, A and B). A comparison of in vivo and in vitro expression studies leads to hypotheses regarding host molecular pathways potentially altered by P. salmonis infection. Candidate molecular biomarkers of P. salmonis infection, derived from lists of informative, functionally annotated transcripts with relatively high levels of induction or suppression, may aid in the development of anti-piscirickettsial vaccines and therapeutics.
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MATERIALS AND METHODS |
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To confirm P. salmonis in Atlantic salmon tissues and in cell culture, DNA was extracted from kidney and from culture supernatants (Qiagen DNEasy kit) for use as template in a nested polymerase chain reaction (PCR). The primers (EubA, EubB, PS2S, and PS2A2) and methods followed Mauel et al. (30). In addition, the organism was identified in tissue sections and imprints using an indirect fluorescent antibody test (IFAT) described by Almendras et al. (2).
Atlantic salmon parr received an intraperitoneal injection of infected tissue culture supernatant diluted 1:10 with MEM-10. The titer of P. salmonis in the inoculum was determined on CHSE-214 cells using the method of Kärber (23). Control salmon received an intraperitoneal injection with MEM-10 alone. After 14 days, the head kidney was dissected from 10 control and 10 infected salmon. The organs were plunged into liquid nitrogen immediately following dissection and subsequently stored at 80°C.
P. salmonis infections in cultured macrophages.
Separate suspensions of hematopoietic kidney (head kidney) leukocytes were obtained from six naive Atlantic salmon (300 g) that had been reared in freshwater. Briefly, the head kidney from each fish was pressed through a sterile 100-µm mesh nylon screen in the presence of ice-cold RPMI 1640 medium supplemented with 25 mM HEPES, 0.3 µg/ml amphotericin B, 10 U/ml heparin, and 0.1% FBS (cRPMI). The cell suspension was layered onto a 2.5-ml bed of 54% Percoll and centrifuged at 4°C for 30 min at 650 g. Viable leucocytes were counted by hemocytometer in the presence of trypan blue and adjusted in cRPMI to 5.0 x 106 cells/ml.
Sterile, round, glass coverslips were aseptically placed into three wells in 12-well polystyrene tissue culture plates. Leukocyte cultures were incubated overnight at 15°C, and nonadherent cells were removed by washing three times with cold, unsupplemented RPMI. The medium in three of the four wells containing cells from each salmon (including the coverslipped well) was replaced with 1.0 ml of P. salmonis culture supernatant diluted 1:10 with cRPMI, containing 5% fetal bovine serum (FBS) (cRPMI-5). The medium in the fourth well was replaced with 1.0 ml cRPMI-5. Plates were incubated in a sealed humid chamber at 15°C.
Cells from each fish were harvested after 6 h and 24 h incubation. Three harvesting methods were followed. 1) Cells in the uninfected well and in one infected well were lysed with 250 µl MicroPoly (A)Pure lysis solution (Ambion). The lysate was transferred to a sterile tube and stored at 80°C. 2) Cells from the second infected well were scraped from an infected well and centrifuged for 4 min at 12,000 g, and the cell pellet fixed in 2% glutaraldehyde. Fixed cells were processed for routine transmission electron microscopy. 3) Cells from the third infected well and adherent to the glass coverslip were fixed in 100% alcohol and stained with Giemsa stain. The dried coverslip was inverted and mounted to a glass slide using Permount.
Microarray fabrication and quality control.
Microarray construction and initial testing were previously described (36). Briefly, 3,557 clones from 18 high-complexity salmonid cDNA libraries were selected with an emphasis on immune-relevant transcripts. Clones were robotically re-arrayed from daughter glycerol stock 384-well plates into 96-well plates prefilled with 7% glycerol in Luria broth + ampicillin, incubated overnight at 37°C, and checked for uniform optical density. Plasmid inserts were PCR amplified in a Tetrad PTC-200 thermocycler (MJ Research) using 1 µl overnight culture, 0.2 µM M13/pUC forward primer (5'-CCCAGTCACGACGTTGTAAAACG-3'), 0.2 µM M13/pUC reverse primer (5'-AGCGGATAACAATTTCACACAGG-3'), 2 mM MgCl2, 10 mM Tris·HCl, 50 mM KCl, 250 µM dNTPs, 1 U AmpliTaq (PerkinElmer), and nuclease-free H2O (Invitrogen) to 100 µl. PCR conditions were as follows: 2 min 95°C denaturation; 35 cycles of 95°C 30 s, 60°C 45 s, 72°C 3 min; 7 min 72°C. Five microliters of each PCR product was run on a 1% agarose gel to assess yield and quality. Of 3,557 salmonid clones, there were 3,312 strong, single bands (93%), 170 absent (5%), and 75 multiple bands (2%). Five exogenous genome (Arabidopsis) cDNAs were amplified from the following clones kindly provided by the Arabidopsis Information Resource (http://www.arabidopsis.org/): rubisco activase, protochlorophyllide reductase, chlorophyll a/b-binding protein CP29, PSII oxygen-evolving complex protein 2, and tonoplast intrinsic protein root-specific RB7. Arabidopsis cDNAs were spotted in quadruplicate on each microarray and used for thresholding (determining number of transcripts present). PCR products were robotically cleaned (Qiagen) and consolidated into 384-well plates, lyophilized by SpeedVac, and resuspended in 15 µl of 3x SSC.
All cDNAs were printed as double, side-by-side spots on aminosilane slides (ez-rays, Matrix) with a BioRobotics MicroGrid II microarray printer (Apogent Discoveries). MicroSpot 10K quill pins (BioRobotics) in a 48-pin tool were used to deposit 0.5 nl (0.2 ng cDNA) per spot onto the slide. Resulting microarrays have a 4-by-12 subgrid layout with 182 spots per subgrid, each spot having approximate diameter and pitch of 100 µm and 250 µm, respectively. The slides were cross-linked in a UV Stratalinker 2400 (Stratagene) at 120 mJ. Spot morphology was assessed by visual inspection or SYBR Green 1 (Molecular Probes) staining. To check clone tracking, 42 high-quality sequences were obtained from randomly selected wells of the consolidated plates used for microarray printing. All 42 had BLAST identifiers matching gene IDs predicted from the re-array spreadsheet, indicating accurate clone tracking throughout microarray fabrication.
RNA amplification, and microarray hybridization and analysis.
These microarray experiments were designed to comply with MIAME guidelines (7). MicroPoly(A)Pure kits (Ambion) were used to prepare mRNA from P. salmonis-infected and control Atlantic salmon macrophages and head kidney. To have adequate quantities of template for microarray target syntheses, infected and control (24 h incubation) macrophage mRNA samples were subjected to two rounds of amplification using the MessageAmp aRNA kit (Ambion) according to the manufacturers instructions. Initial macrophage mRNA isolations yielded 0.91.8 µg of mRNA per sample. Four hundred nanograms of macrophage mRNA was used as template in the first round of amplification, yielding 8.1 µg of infected macrophage amplified RNA (aRNA) and 7.8 µg of control macrophage aRNA. One microgram of first-round macrophage aRNA was used as template in the second round of amplification, yielding 81.2 µg of infected macrophage aRNA and 83.3 µg of control macrophage aRNA. Head kidney mRNA samples were prepared from pooled (n = 10) infected or control kidney. Since the amounts of kidney mRNAs available were inadequate for running a microarray experiment (1.5 µg of control and 7.6 µg of infected head kidney mRNA), these samples were subjected to one round of amplification. Two hundred nanograms of infected or control head kidney mRNA was used as template in aRNA synthesis reactions. Two infected head kidney samples were pooled to yield 8.9 µg of aRNA, and a single control head kidney sample contained 8.4 µg of aRNA. Infected and control macrophage and head kidney aRNA samples were visualized on agarose gels to check quality and quantity (data not shown). Except for the amounts of aRNA and reverse transcription (RT) primer used, macrophage and head kidney target labeling reactions and microarray hybridizations were identical. Macrophage target syntheses used 5 µg of second-round aRNA and 5 µg of random primers (Roche), and head kidney target syntheses used 2 µg of aRNA and 2 µg of random primers (Roche). RT primers were mixed with aRNA samples, and nuclease-free H2O (Invitrogen) was added to make 10 µl total volume. Samples were incubated at 70°C 4 min, then placed on ice. RT reactions included 50 mM Tris·HCl, pH 8.3, 75 mM KCl, 3 mM MgCl2, 10 mM DTT; 0.5 mM each of dATP, dCTP, and dGTP; 0.2 mM dTTP, 0.05 mM Cy3-dUTP or Cy5-dUTP (Amersham), 40 U RNAguard ribonuclease inhibitor (Amersham), and 400 U SuperScript II RNase H reverse transcriptase (Invitrogen). RT reactions were incubated at 42°C for 2.5 h, followed by addition of 0.025 U RNase A (Sigma) and 1.5 U RNase H (New England BioLabs) and incubation at 37°C for 30 min. Labeled targets were cleaned using the QIAquick PCR purification kit (Qiagen) and precipitated, with 300 mM sodium acetate, 1 µl of 20 µg/µl glycogen (Invitrogen), and 2.5 vol of 100% ethanol, at 20°C overnight. Each labeled target was recovered by centrifugation (14,000 rpm, 4°C, 1 h), washed in 70% ethanol, air-dried, and resuspended in 60 µl of hybridization buffer: 50% deionized formamide, 5x SSC, 0.1% SDS, 5 µl of 5 µg/µl oligo dT (5'T18[Q-N]3'), 5 µl of 2 µg/µl BSA (Pierce), and 2 µl of 10 µg/µl sonicated human placental DNA (Sigma). Targets were incubated at 96°C for 3 min and then at 65°C until applied to microarrays. Microarrays were prepared for hybridization by washing twice for 5 min each wash in 0.1% SDS, washing five times for 1 min each time in MilliQ H2O, immersing 3 min in 95°C MilliQ H2O, and drying by centrifugation (2,000 rpm, 5 min, in 50-ml conical tube). Microarray hybridizations were run in the dark under HybriSlips hybridization covers (Grace Biolabs) in slide hybridization chambers (Corning) submerged in a 45°C water bath for 16 h. Coverslips were floated off at 45°C in 1x SSC, 0.2% SDS, and arrays were washed once for 10 min at 45°C in 1x SSC, 0.2% SDS, three times for 4 min each time at room temperature in 0.1x SSC, 0.1% SDS, and four times for 4 min each time at room temperature in 0.1x SSC. Slides were dried by centrifugation as before.
Fluorescent images of hybridized arrays were acquired immediately at 10 µm resolution using ScanArray Express (PerkinElmer). The Cy3 and Cy5 cyanine fluors were excited at 543 nm and 633 nm, respectively, and the same laser power (90%) and photomultiplier tube (PMT) settings were used for all slides in a study (PMT 72 Cy3, PMT 63 or 64 Cy5 for macrophage study; PMT 75 Cy3, PMT 63 or 64 Cy5 for head kidney study). Fluorescent intensity data were extracted from TIF images using ImaGene 5.5 software (BioDiscovery). Quality statistics were compiled in Excel from raw ImaGene fluorescence intensity report files. Elements were sorted (7,356 salmonid spots representing 3,557 different cDNAs, 20 Arabidopsis spots representing 5 different cDNAs, and 1,356 other control spots), for each microarrays Cy3 and Cy5 data. Median signal values from the 20 Arabidopsis control spots were used to calculate threshold (mean plus 3 standard deviations), and mean numbers of salmonid elements passing threshold were determined for Cy3 and Cy5 data separately. All quality statistics for microarrays used in this report, as well as all scanned microarray TIF images, an ImaGene grid, the gene identification file, and ImaGene quantified data files, are available online from the University of Victoria Centre for Biomedical Research (http://web.uvic.ca/cbr/grasp). In addition, all microarray raw (TIF images) and extracted (ImaGene files) data have been deposited at the National Center for Biotechnology Information (NCBI) in the Gene Expression Omnibus database (GEO; http://www.ncbi.nlm.nih.gov/geo/). The GEO platform accession number is GPL966, and the sample accession numbers are GSM15897 (slide CL012.003), GSM15898 (CL012.004), GSM15899 (CL012.005), GSM16101 (DD035.031), GSM16389 (DD035.032), GSM16390 (DD035.033), and GSM16391 (DD035.034). Data transformation (background correction, and setting background corrected values < 0.01 to 0.01), normalization (Lowess), and analysis (formation and manipulation of fold change transcript lists) were performed in GeneSpring 5 (Silicon Genetics).
Real-time quantitative PCR (QPCR).
Poly(A) RNA (mRNA) was prepared from flash-frozen P. salmonis-infected (pooled, n = 10) and noninfected (pooled, n = 10) head kidney and from P. salmonis-infected and noninfected macrophages (24 h incubation time), using MicroPoly(A) Pure kits (Ambion). Head kidney mRNA was subjected to one round of amplification; microarray targets were synthesized from first-round aRNA, and QPCR cDNA templates were synthesized from mRNA. Macrophage mRNA was subjected to two rounds of amplification; microarray targets were synthesized from second-round aRNA, and QPCR templates were synthesized from first-round aRNA. Two hundred nanograms of mRNA each from infected and control head kidney was reverse transcribed using 200 ng oligo dT primer (5'T18[Q-N]3'). Two hundred nanograms of first-round aRNA each from infected and control macrophage was reverse transcribed using 200 ng random primers (Roche). RT reactions included 40 U RNase inhibitor (Promega), 500 µM dNTPs, 10 mM DTT, and 400 U SuperScript II RNase H reverse transcriptase (Invitrogen) with the manufacturers buffer. First-strand cDNAs were diluted 1:20 and used as templates for QPCR analysis. QPCR used two PCR primers per transcript of interest (TOI) and SYBR Green I dye. Ubiquitin was selected as the normalizer gene, since its expression was stable (background-corrected, Lowess normalized Cy5/Cy3 ratios were within 2-fold lines of scatter plots) in all microarrays used in this report. QPCR primer pairs for TOI and ubiquitin were designed from EST FASTA files using Primer3 (from the Whitehead Institute for Biomedical Research, http://www-genome.wi.mit.edu/cgi-bin/primer/primer3_www.cgi) and the following guidelines: product size 150250 bp, Tm 60 ± 1°C, at least three of the 3' terminal six bases G/C. For each TOI, sequences of the forward and reverse QPCR primers are given in the table in Fig. 2. Primers used for ubiquitin were: 5'-ATGTCAAGGCCAAGATCCAG-3' and 5'-ATAATGCCTCCACGAAGACG-3'. Reactions (50 µl total volume) containing 2 µl diluted template, 200 nM each primer, and 1x Brilliant SYBR Green QPCR Master Mix (Stratagene) were run in triplicate using the Mx3000P real-time PCR system (Stratagene) and the following cycling parameters: 95°C for 9 min; then 40 cycles of 95°C for 15 s, 52°C for 30 s, 72°C for 45 s. Controls (no template) were run for all primer pairs.
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RT-PCR confirmation of P. salmonis infection.
Two hundred nanograms of P. salmonis-infected and control macrophage mRNA was reverse transcribed with 200 ng random primer (Roche), and 5 µl (33 ng) of cDNA was used as template in PCR. Two hundred nanograms of P. salmonis infected and control head kidney mRNA were reverse transcribed using MessageAmp aRNA kit reagents and instructions (Ambion). Head kidney cDNAs were purified and eluted in 100 µl nuclease-free water, and 1 µl (
2 ng) was used as template in PCR. Fifty-microliter PCR reactions were run using P. salmonis-specific primers PS2S and PS2A2 (30), 1x Q solution (Qiagen), dNTPs (200 µM each), 1x PCR buffer (Qiagen), 1.25 U HotStarTaq DNA polymerase (Qiagen), and the following cycling parameters: 95°C for 15 min; then 40 cycles of 94°C for 1 min, 50°C for 2 min, 72°C for 2 min. Positive controls (using P. salmonis DNA) and negative controls (no template) were run. Ten microliters of each RT-PCR product or negative control, and 2.5 µl of positive control reaction, were visualized by agarose gel electrophoresis (Fig. 1C).
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RESULTS |
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Effects of P. salmonis infection on host macrophage and head kidney gene expression.
Differential gene expression in P. salmonis-infected and noninfected Atlantic salmon macrophages (24 h incubation), and in P. salmonis-infected and noninfected Atlantic salmon head kidney (14 days postinjection), was determined using a microarray containing 3,557 different cDNAs selected from high-complexity, salmonid (primarily Atlantic salmon) cDNA libraries (36). Since the strong, P. salmonis-specific RT-PCR product in 24-h infected macrophages suggested a level of infection that may be altering the host cell transcriptome to allow intracellular survival of the pathogen (Fig. 1C), this time point was chosen for microarray analysis. On the salmonid elements, average Cy3 mean signal/mean background (s/b) was 13.0 (SE 1.2) and average Cy5 s/b was 10.8 (SE 1.3) in the macrophage study, while average Cy3 s/b was 11.2 (SE 0.1) and average Cy5 s/b was 12.3 (SE 0.5) in the head kidney study (Supplemental Table S1; at http://web.uvic.ca/cbr/grasp). In the macrophage study, an average of 67.3% (SE 2.1) of Cy3-labeled transcripts passed threshold and were therefore deemed "present" (see MATERIALS AND METHODS) and an average of 69.8% (SE 3.8) of Cy5-labeled transcripts passed threshold; in the head kidney study, these values were 73.0% (SE 0.9) and 80.6% (SE 1.1), respectively (Supplemental Table S1; http://web.uvic.ca/cbr/grasp).
Salmonid cDNAs having significant (E < 105) BLASTX or BLASTN hits against the current GenBank nr or nt databases, as well as unknowns (cDNAs with no significant BLAST hits), are described for transcripts responding reproducibly (>2-fold up- or downregulated in all slides of a study) to P. salmonis infection (Tables 14). Changes in transcription of informative genes and the degree of similarity (length and percent identity over aligned region) between the translation of each salmonid cDNAs expressed sequence tag (EST) and its top (most negative E-value) BLASTX hit, or between ESTs and their top BLASTN hits, are also shown (Tables 14) and serve to identify potentially informative transcripts.
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Thirty-one different transcripts were reproducibly downregulated in P. salmonis-infected macrophages (Fig. 1A, Table 2). Transcripts in Table 2 are listed by descending control macrophage signal values from one slide in the study. In infected macrophages, the most abundant downregulated transcript was 1-microglobulin (Table 2). There were two K18 simple type I keratin, two 14.5-kDa translational inhibitor, and two kidney dicarbonyl reductase entries in the transcript list from which Table 2 was derived (Supplemental Table S3, http://web.uvic.ca/cbr/grasp). From microarray data, the most highly suppressed (>4.2-fold) macrophage transcripts with significant BLASTX hits were selenoprotein P (30.7-fold, SE 3.6), 14.5-kDa translational inhibitor (26.8-fold, SE 19.2), collagen
1 (7.1-fold, SE 2.2), cysteine proteinase (5.8-fold, SE 2.2),
1-microglobulin (5.4-fold, SE 0.4), retinoid X receptor-
(4.7-fold, SE 0.2), cysteine-rich protein 1 (4.5-fold, SE 0.3), N-formylpeptide receptor-like 2 (4.4-fold, SE 0.1), and lysophospholipase (4.3-fold, SE 0.4) (Table 2). QPCR with these samples showed a 43.8-fold suppression of selenoprotein P (SE 3.3), a 4.9-fold suppression of retinoid X receptor-
(SE 0.1), a 4.7-fold suppression of N-formylpeptide receptor-like 2 (SE 0.1), and a 4.7-fold suppression of lysophospholipase (SE 0.3) in infected macrophages (table in Fig. 2).
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Overlap and QPCR confirmation of macrophage and head kidney microarray studies.
Seven transcripts (immune-responsive gene 1, amebocyte aggregation factor, an unknown similar to a previously identified S. salar kidney cDNA sequence, C-type lectin 2-1, an unknown with no significant BLAST hits, type 1 cytokeratin enveloping layer, and O-methyltransferase) were reproducibly greater than twofold upregulated in both infected macrophages and infected head kidney (Fig. 1B, Tables 1 and 3). Four transcripts (1-microglobulin, selenoprotein P, B-cell translocation gene 1, and hemopexin-like) were reproducibly greater than twofold downregulated in both infected macrophages and infected head kidney (Fig. 1B, Tables 2 and 4). The selection of transcripts of interest for QPCR confirmation was based on their potential utility as molecular biomarkers of P. salmonis infection. Preference was given to those S. salar transcripts with significant and functionally annotated BLASTX hits and relatively high fold differences in expression between infected and noninfected samples (Fig. 1, Tables 14, and table in Fig. 2). The characterization and evaluation of potential biomarker transcripts lacking significant BLASTX hits (i.e., with only significant BLASTN hits, or with no significant BLAST hits) is ongoing. QPCR was performed in triplicate by relative quantification for 19 transcripts of interest normalized to ubiquitin (table in Fig. 2; Supplemental Tables S6A and S6B). QPCR products of the predicted sizes were obtained for all transcripts of interest and ubiquitin, and no PCR products were observed in no-template controls. Microarray results were considered confirmed if, for a TOI, the direction of change in expression (e.g., >2-fold upregulated in infected macrophages relative to noninfected macrophages) shown by QPCR matched that seen in microarray experiments (table in Fig. 2 and Supplemental Table S6A).
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DISCUSSION |
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Responses to lipopolysaccharide and oxidative stress.
Activated macrophages respond to bacterial infection and to lipopolysaccharide (LPS) by using NADPH oxidase to reduce oxygen to superoxide (O2), which may then be converted to reactive oxygen intermediates such as free radicals and singlet oxygen (3, 42). This "respiratory burst" protects the host against invading microorganisms by creating a toxic intracellular environment. The host cell protects itself from oxidative damage partly through the synthesis of glutathione, a potent antioxidant (45). The expression of at least 10 genes involved in response to oxidative stress (glutathione S-transferase, glutathione reductase, glutathione peroxidase, cytochrome b558 - and ß-subunits, myeloid-specific peroxidase, hydroxyprostaglandin dehydrogenase 15, 20ß-hydroxysteroid dehydrogenase, ribonucleotide reductase r2 class I, and cytochrome P450 4F2) is consistently upregulated in P. salmonis-infected macrophages by up to sixfold (Table 1). Of known antioxidants, only two (selenoprotein P and kidney dicarbonyl reductase) are reproducibly downregulated in infected macrophages (Table 2). Interestingly, both the most highly induced antioxidant (glutathione peroxidase, Table 1) and the most highly repressed antioxidant (selenoprotein P, Table 2 and table in Fig. 2) in P. salmonis-infected macrophages are functionally dependent upon selenium. Selenoprotein P is also downregulated in infected head kidney (Table 4 and table in Fig. 2).
IB
is reproducibly induced in P. salmonis-infected macrophages (Table 1 and table in Fig. 2) but not in infected head kidney (table in Fig. 2). I
B
is an endogenous inhibitor of nuclear factor
B (NF-
B), an evolutionarily conserved, redox-sensitive transcription factor that regulates the expression of many genes (e.g., cytokines) involved in the innate and adaptive immune responses (43). NF-
B is often activated in infected host cells. Some pathogenic microorganisms interfere with NF-
B activation, thereby evading the host immune response and allowing intracellular survival of the pathogen (44). NF-
B, with other transcription factors, upregulates inducible nitric oxide synthase (iNOS) transcription in LPS-stimulated mouse macrophages (25), increasing the synthesis of reactive nitrogen intermediates that contribute to the killing of phagocytosed bacteria (9). LPS stimulation also induces iNOS transcription in teleost macrophages (40). The upregulation of I
B
transcription in P. salmonis-infected macrophages suggests that this pathogen may be interfering with NF-
B activation, with subsequent repression of genes controlled by NF-
B (e.g., iNOS) hypothetically forming part of the mechanism by which P. salmonis evades the macrophage immune response. The hypotheses that selenium imbalance and NF-
B inhibition may play roles in P. salmonis pathogenesis are strengthened by the recent finding that selenium status affects LPS-induced iNOS expression in mouse macrophages, potentially through increased activation of NF-
B (35).
The generalized upregulation of antioxidant transcripts in P. salmonis-infected macrophages (Table 1) was largely absent in P. salmonis-infected head kidney (Table 3). Glutathione S-transferase was upregulated in infected macrophages (Table 1 and table in Fig. 2), but not in infected head kidney (Table 4 and table in Fig. 2). In human endothelial cells infected with the rickettsial agent of Rocky Mountain spotted fever, decreased levels of reduced glutathione and increased peroxide levels correlated with signs of cell damage (14). Similarly, P. salmonis infection may alter the host antioxidant system, resulting in the cell death and necrosis observed in infected head kidney and other tissues (1). Treatment of rickettsia-infected human endothelial cells with an antioxidant increased intracellular levels of reduced glutathione and prevented oxidative injury (14). The possibility that treatment with antioxidants could decrease cellular damage caused by rickettsial infection in salmonids requires further investigation.
Innate and adaptive immune responses.
In addition to antioxidants, other innate immune-relevant genes were regulated by P. salmonis infection in macrophages and head kidney (Tables 14 and table in Fig. 2). C-type lectin 2-1 and immune-responsive gene 1 (Irg1) were upregulated in infected macrophages (Table 1 and table in Fig. 2) and infected head kidney (Table 3 and table in Fig. 2). MARCO, a macrophage receptor that binds both gram-positive and gram-negative bacteria, was downregulated in infected macrophages (Table 2 and table in Fig. 2). One complement component C3-like transcript was downregulated in infected macrophages (Table 2), while a different complement component C3-like putative paralog was upregulated in infected head kidney (Table 3). Induction of ferritin H-3 and transferrin in infected macrophages suggests altered iron ion homeostasis. Since transferrin appears to be a positive acute phase protein in rainbow trout (5), upregulation of this gene in P. salmonis infected macrophages may signify a host attempt to control bacterial proliferation by limiting available iron. Genes involved in iron homeostasis did not appear to be regulated by P. salmonis infection in head kidney (Tables 3 and 4). Alternatively, transferrin induction may be indicative of an autocrine macrophage activating pathway in salmonids as in cyprinid fish (41). Four immune-relevant transcripts that were reproducibly upregulated in P. salmonis-infected head kidney (C-type lectin 2-1, chemotaxin, differentially regulated trout protein 1, and complement component C3) (Table 3) were also identified in a subtractive library enriched for rainbow trout liver transcripts responding to Vibrio infection (4) and are considered putative acute phase proteins (5). These data suggest that P. salmonis infection induced inflammatory and acute phase responses in head kidney, potentially contributing to cell death and necrosis.
Six transcripts encoding antibody components (immunoglobulin heavy chain constant and variable regions and immunoglobulin light chain) were reproducibly upregulated in P. salmonis-infected macrophage cultures (Table 1). These results were likely due to the presence of lymphocytes in these cell cultures. Interestingly, no immunoglobulin transcripts were induced (Table 3) and one immunoglobulin heavy chain transcript was repressed (Table 4) in P. salmonis-infected head kidney. Several other transcripts involved in adaptive (lymphoid) immune responses were reproducibly downregulated in P. salmonis-infected head kidney (Table 4). These include a T cell receptor -chain transcript, a salmon transcript related to a gene expressed in activated human lymphocytes, and a salmon transcript similar to C-C chemokine receptor 7 (a lymphocyte-specific, G protein-coupled receptor for the macrophage inflammatory protein 3-ß chemokine) (Table 4). These results may point to a compromised adaptive immune response in infected head kidney and may reflect in vitro lymphocyte activation by macrophage-derived cytokines.
Evolutionary conservation in transcriptomic responses to infection.
Several similarities were noted between the gene expression responses of P. salmonis-infected salmon macrophages and human macrophages stimulated by LPS or infected by intracellular pathogenic bacteria. The transcription of ferritin H and matrix metalloproteinase 9, among other genes, is upregulated in human macrophages stimulated with LPS (42). Ferritin H-3 and a matrix metalloproteinase were upregulated in P. salmonis-infected salmon macrophages (Table 1 and table in Fig. 2). P. salmonis-infected Atlantic salmon macrophages and mouse macrophages infected with Brucella abortus (a gram-negative, intracellular bacterial pathogen) have several responsive genes in common. C-type lectin, matrix metalloproteinase, Irg1, and IB
were upregulated in both B. abortus-infected mouse macrophages (15) and in P. salmonis-infected salmon macrophages (Table 1 and table in Fig. 2). Of these genes, the expression of C-type lectin, matrix metalloproteinase, and Irg1 was also induced in P. salmonis-infected head kidney (Table 3 and table in Fig. 2). Irg1 was also induced in mouse macrophages infected with Mycobacterium tuberculosis (13). These observations suggest that intracellular bacterial pathogens elicit the expression of conserved immune genes among all vertebrate hosts.
A salmonid transcript belonging to the dermatopontin family was strongly induced in both infected macrophages and infected head kidney (Tables 1 and 3 and table in Fig. 2). The most significant BLASTX hits for this salmonid EST are horseshoe crab (Limulus sp.) hemagglutinin/amebocyte aggregation factor (GenBank nr accession number AAA28272; E value = 9.5e-29), sponge dermatopontin (CAC38786 E = 8.3e-25), and human dermatopontin (CAA80487 E = 9.9e-10). While dermatopontins are abundant in both vertebrate and invertebrate extracellular matrices, their functions remain poorly understood (29, 32). This salmon amebocyte aggregation factor-like cDNA sequence has been previously identified (GenBank nt accession number BG934969), but nothing is known about its expression or function. Limulus amebocytes are immunocompetent hemocytes thought to be functionally homologous to mammalian macrophages, platelets, and B and T lymphocytes (20, 28). The LPS-induced degranulation of Limulus amebocytes, mediated by G protein-linked receptors (39), releases coagulation factors, protease inhibitor, and antimicrobial peptides (18, 21). Amebocyte aggregation factor, also secreted from amebocyte granules, induces the aggregation of amebocytes and the agglutination of erythrocytes (18). These data suggest that amebocyte aggregation factor orthologs may be conserved components of salmon and invertebrate innate immune responses to bacterial invasion. Interestingly, four transcripts involved in G protein-coupled receptor signaling (calmodulin, N-formylpeptide receptor-like 2, complement component C3, and thrombin receptor-like 3) are reproducibly downregulated in infected macrophages (Table 2), but not in infected head kidney (Table 4). Suppression of G protein signaling may be part of the mechanism by which P. salmonis evades macrophage antimicrobial defenses.
Molecular biomarkers for P. salmonis infection.
Nineteen S. salar transcripts, selected because of their relatively high fold differences in expression between infected and noninfected samples as well as the immune-relevant functional annotations of their top BLASTX hits, were confirmed by QPCR (table in Fig. 2). These molecular biomarkers may be useful in research into the molecular pathogenesis of P. salmonis infection. Recent development and testing of vaccines against P. salmonis utilized relative percent survival to gauge vaccine effectiveness (26). We propose that QPCR-based molecular biomarker expression analyses may add sensitivity to current methods of evaluating the efficacies of anti-piscirickettsial vaccines and therapeutics.
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GRANTS |
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ACKNOWLEDGMENTS |
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The URL for the Gene Ontology Consortium is http://www.geneontology.org (2001).
The programs PHRED (v. 0.990722.j) and PHRAP (v. 0.990329) are available from the University of Washington Genome Center (http://www.genome.washington.edu/UWGC/).
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FOOTNOTES |
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Address for reprint requests and other correspondence: B. F. Koop, Centre for Biomedical Research, Univ. of Victoria, PO Box 3020, Victoria, British Columbia V8W 3N5, Canada (E-mail: bkoop{at}uvic.ca).
10.1152/physiolgenomics.00036.2004.
1 The Supplemental Material for this article (Supplemental Tables S1S6) is available online at http://physiolgenomics.physiology.org/cgi/content/full/00036.2004/DC1.
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