The impact of breed and tissue compartment on the response of pig macrophages to lipopolysaccharide
© Kapetanovic et al.; licensee BioMed Central Ltd. 2013
Received: 4 April 2013
Accepted: 6 August 2013
Published: 28 August 2013
The draft genome of the domestic pig (Sus scrofa) has recently been published permitting refined analysis of the transcriptome. Pig breeds have been reported to differ in their resistance to infectious disease. In this study we examine whether there are corresponding differences in gene expression in innate immune cells
We demonstrate that macrophages can be harvested from three different compartments of the pig (lungs, blood and bone-marrow), cryopreserved and subsequently recovered and differentiated in CSF-1. We have performed surface marker analysis and gene expression profiling on macrophages from these compartments, comparing twenty-five animals from five different breeds and their response to lipopolysaccharide. The results provide a clear distinction between alveolar macrophages (AM) and monocyte-derived (MDM) and bone-marrow-derived macrophages (BMDM). In particular, the lung macrophages express the growth factor, FLT1 and its ligand, VEGFA at high levels, suggesting a distinct pathway of growth regulation. Relatively few genes showed breed-specific differential expression, notably CXCR2 and CD302 in alveolar macrophages. In contrast, there was substantial inter-individual variation between pigs within breeds, mostly affecting genes annotated as being involved in immune responses.
Pig macrophages more closely resemble human, than mouse, in their set of macrophage-expressed and LPS-inducible genes. Future research will address whether inter-individual variation in macrophage gene expression is heritable, and might form the basis for selective breeding for disease resistance.
Macrophages are the first line of defence against many pathogens . They discriminate self from non-self through the recognition of pathogen-associated molecular patterns (PAMPs) that are not present in the host. The most-studied PAMP is lipopolysaccharide (LPS), a structural component of the cell wall of gram negative bacteria recognised by toll-like receptor (TLR) 4, which elicits much of the pathology of gram-negative septicaemia. Macrophages respond to LPS with a sequential cascade of altered gene expression that leads first to inflammation and elimination of the pathogen, and then to resolution of tissue damage [2–4]. The laboratory mouse has been used extensively as a model for the study of macrophage biology and the response to pathogens. However, mice and humans differ rather fundamentally in the nature of their innate effector pathways. Even amongst strict orthologs numerous inducible genes are regulated in one species and not the other, due in large measure to differences in promoter sequences . For example, human macrophages do not induce the effector enzyme, inducible nitric oxide synthase (iNOS or NOS2), which generates the toxic radical nitric oxide, but instead induce indoleamine dioxygenase (IDO) in response to LPS [6, 7]. These differences are also evident when one compares gene expression profiles of mouse inflammatory models with human disease . Of course, aside from divergent expression of orthologous genes, a feature of the evolution of the immune system across species, and even within species, is the gain and loss of individual genes, especially within gene families . Such differences further undermine the utility of the mouse as a model.
The domestic pig (Sus scrofa) has been used extensively in medical research , and in contrast to experimental animals, is economically important; the most important meat-producing livestock species world-wide (from OECD-FAO Agricultural Outlook 2011–2020). Because of the intensive mode of production, they are highly susceptible to pathogen epidemics that can cause huge economic losses. Viral (e.g. influenza A, African swine fever, classical swine fever, porcine adenovirus, porcine respiratory and reproductive syndrome (PRRS), parainfluenza) and bacterial (e.g. Salmonella spp, Yersinia enterocolitica, Mycoplasma hypopneumoniae, Actinobacillus pleuropneumoniae) pathogens often target the macrophage for replication and alter their gene expression. Many of these agents are zoonotic. One advantage of mouse models is the availability of inbred lines that can be used to map disease-susceptibility loci. Pig breeds may offer some of the same advantages. Studies of viral (PRRS) and bacterial (actinobacillus) infections suggest that variation in disease susceptibility or pathology between breeds, or between individuals within a breed, is correlated with differences in macrophage activation [11–13]. Such breed-specific variation also offers opportunities to breed for disease resistance or tolerance.
The study of pig macrophage biology has recently been expedited by the completion of a draft genome sequence , comprehensive annotation of the pig immunome , the development of a comprehensive expression array platform , methodology for cultivation of macrophages  and identification and characterisation of subsets of monocytes . Using these tools we demonstrated that pig macrophages are much more similar to human than to mouse (and correspondingly, inducible promoters are more conserved) , and also provided preliminary evidence for distinct gene expression profiles amongst resident tissue macrophage populations . The macrophages of the lung are of particular interest because this is a major portal of pathogen entry. There is evidence that they are specifically adapted to the airway environment  and these cells are not readily accessed in large numbers from experimental animals.
In the current study, we have combined the available tools to extend the knowledge of the macrophage biology of the domestic pig. We have compared the expression profiles of macrophages from different tissue compartments, and their response to bacterial LPS, in multiple individuals from five divergent pig breeds. Analysis of the entire dataset using the network analysis tool Biolayout Express3D serves to highlight clusters of genes that share regulatory patterns across genetic and cellular variation. The data identify variation between individual pigs and breeds, and confirm the similarities between pigs and humans that support the use of the pig as a more predictive model than the mouse in biomedical research.
Preliminary characterisation of the response to LPS in different macrophage populations
To enable the study of the macrophages from the twenty-five animals at the same time and under the same conditions, AM, PBMC and BMC were frozen as described previously  on the day of the harvest and used a few weeks later. PBMC and BMC were cultured for 5 to 7 days in the presence of rhCSF-1 until differentiation into macrophages . The three types of macrophages were seeded at 1×106 cells/ml, cultivated overnight before removing non-adherent cells, replacing the medium, and cultivating with or without LPS (100 ng/ml). Morphologically, the BMDM and MDM were more spread on the substratum by comparison to AM, where a subpopulation of cells is non-adherent (Figure 1C, D, E). Each of the populations expressed the macrophage markers CD14 and CD16, albeit at varying levels (Figure 1F-K). In order to control for the efficacy of LPS stimulation in each experiment, prior to expression profiling, TNF concentration was measured in the supernatant of the culture at 0 and 7 h (Figure 1L). With the exception of AM from HAM and LW, there were no obvious differences between the breeds in terms of the magnitude of this response. The higher production of TNF by AM from these 2 breeds appeared to be due to a higher percentage of adherent macrophages amongst the cells from the broncho-alveolar lavage, which would not interfere with the microarray analysis.
Alveolar macrophages show a distinct expression profile from BMDM and MDM
The recently published pig gene expression atlas  included replicates of AM, BMDM and MDM from two individual crossbred pigs, but did not compare the populations in detail. We inferred that AM were distinct from macrophages in the wall of the gut, notably in their expression of C-type lectin receptor genes.. The current dataset permits comparison in much greater depth, with the macrophages isolated from the same animals, and with 25-fold replication of the comparison. PCA analysis of the data based upon cell compartment clearly distinguishes AM from BMDM and MDM which are very similar to each other (Figure 2B).
The second supercluster (407 nodes) is made up of clusters of genes down-regulated after LPS stimulation, such as cluster 05 and 23 (Figure 3E-F). These two clusters contain genes encoding proteins linked to intracellular signalling, kinase and phosphatase (PKC, PIK3IP1, TRAK2, DNM3, PLEK). The full list of clusters and the probes within them can be found in the Additional file 1.
Differential regulation of LPS-responsive genes in AM
We selected the genes significantly regulated by LPS in AM, BMDM and MDM with a p adj. value <0.01 and a fold change >2 or <-2 (Figure 5 B, C respectively). There was again a substantial overlap between these lists in BMDM and MDM. These gene lists include the up-regulation of IDO1, IRG1 CXCL11, CXCL9 and CXCL20. As expected the 3 types of macrophages share significant up-regulation of genes encoding inflammatory mediators such as TNF, CCL20, IL23A, IL27 and G-CSF. A small set of genes induced only in the AM included GM-CSF (CSF2), LIF or IL19. The former is of interest because of the extensive literature on the specific function of GM-CSF in lung macrophage homeostasis . IL19 has also been implicated in lung injury in septic shock . As already shown in Figure 3, AM have a higher basal expression of inducible genes such TNF suggesting that they are primed for an inflammatory response. Indeed, there were only 91 genes significantly up-regulated in AM after LPS stimulation compare to the 1,400 in BMDM and 942 in MDM. The complete list of DR genes in the 3 populations of macrophage after LPS stimulation is listed in the Additional file 3.
Breed-specific variation in macrophage gene expression
Comparison with other species: the pig as a convenient model for human disease
Investigation on the inter-individual differences between pigs
The variance data are plotted in Figure 8C and D. The genes with highest percentage variance (between 25–50%) are clearly enriched for immune function. In BMDM and MDM the most variable gene is CXCL10 followed by interferon beta, interferon-induced protein with tetratricopeptide repeats (IFIT) 1, DDX58, IDO1, CXCL11, IL7R and IL1RN. In AM, the top genes (>50%) are linked to the immunoglobulin chain, due to the small contamination of B cell from the alveolar lavage. Outside of this set, genes with a variance between 20–50% included IL33, CCR2, IL23A, IGF1, CXCL9 and CXCL10. Genes with a variance > 20% were analysed using the DAVID functional annotation webtool  [http://david.abcc.ncifcrf.gov]. For each compartment and time-point (a total of 6), the biological process clusters were given an enrichment score, ranking the overall importance of the annotation term group (Figure 8E). The score of 1.3 is taken as the threshold for functional importance (red line). Clearly, immune response genes are identified in every comparison.
In this study, we developed ways to harvest macrophages from the lungs, blood and bone-marrow of pigs and to freeze them for later use. This approach provides a convenient basis for analysis of the genetic variation in host pathogen interaction using in vitro challenge models. Morphology, viability, TNF production and expression of surface markers (CD14 and CD16) were unaltered by cryopreservation. Our analysis allowed us to compare 5 different breeds and 3 different compartments (bone-marrow, blood and lungs) in terms of their gene expression profiles and responses to LPS.
The basal gene expression pattern in alveolar macrophages (AM) was clearly distinct from the patterns in monocyte-derived or bone marrow-derived macrophages, regardless of breed. The differences include a relatively high basal expression of IDO1, CXCL2, CCL24 and IL1B. Interestingly, we also found that the genes encoding VEGFA and its receptor FLT1 were also highly expressed in AM. Alveolar macrophages do express the receptor for the macrophage growth factor, CSF-1 (CSF1R). However, unlike most tissue macrophages, in the mouse they do not depend upon continued CSF1R signalling . In the op/op CSF-1 deficient mouse, lung macrophage numbers correct with age  and Flt1 signalling has been attributed a role in age-dependent correction of the bone phenotype in op/op mice . We suggest that VEGF might have specific roles in alveolar macrophage homeostasis.
Pattern recognition receptors also distinguished the macrophage populations regardless of breed background. The high levels of lectin-like receptors noted previously  could contribute to elimination of particulate material in the airways, including bacteria and fungi. AM expressed more TLR4 (Figure 5), suggesting that AM would target mostly bacteria detection. In contrast to AM, the BMDM and MDM expressed more TLR3, TLR7, TLR8 and TLR9 as well as RNA intracellular receptors DDX58 (RIG-1) and IFIH1 (MDA5) suggesting a co-regulated cluster of genes involved in virus detection. There is, of course, a fundamental difference between the AM and the two populations derived by cultivation in CSF-1, the MDM and BMDM. The latter cells expressed cell-cycle-related genes and may also be cell cultured adapted. For the purpose of genetic studies, the culture systems have the advantage that they largely eliminate the effect of in vivo environment including health status, and this is reflected in the relatively consistent gene expression profiles. Nevertheless, Fejer et al.  have recently emphasised the fact that the phenotype of alveolar macrophages in mice can be replicated in vitro to some extent by cultivation of bone marrow cells in GM-CSF, as opposed to CSF-1.
We also compared the inflammatory response in 5 different breeds and identified a small set of genes that could contribute to different disease resistance between breeds. Landrace pigs expressed substantially less IL-8R beta (CXCR2) than the other breeds (Duroc, Hampshire and Piétrain). Ait-Ali et al.  reported that Landrace alveolar macrophages were more resistant to PRRS virus replication and released large amounts of TNF and IL8 into the supernatant. It remains to be seen whether differential expression of the IL8 receptor contributes to this biology. The number of genes differentially expressed between the breeds was relatively small (Figure 6). There was much greater variation between individuals within breeds, which also urges caution upon studies of breed differences based upon relatively small group sizes. Amongst the differences was the apparent absence of expression of SLA6 (Figure 8) and highly variable expression of SLA-DOA. These differences might be associated with polymorphic variation in miRNA recognition sites reported elsewhere . Significant levels of protein-coding polymorphism have already been reported amongst pig pattern intracellular and extracellular recognition receptors [19, 32]. It is striking that such genes are DR between the macrophage populations, and highly variable between individuals. It remains to be determined whether such variation is heritable and can be linked to SNP markers to allow selective breeding. The method we have applied herein, which can be performed on blood and does not require pathogen challenge of the animal, could potentially permit in vitro screening of breeding animals for optimal innate immune responsiveness.
In keeping with our earlier findings, now applied to a much larger data set and macrophages from multiple sites including monocyte-derived macrophages, pigs and humans share innate immune responses that are absent from rodents, and conversely, mice induce pathways that are not shared with large animals [5, 16]. The index genes for these classes of genes are IDO1, expressed only in human and pigs, and NOS2A, expressed only in mouse. Using Biolayout Express3D, we found clusters of genes that share the same expression patterns with these index genes (Figure 3). Analysis of the draft pig genome has highlighted numerous candidate genes underlying human pathology . The findings herein emphasise the applications of understanding pig innate immunity for biomedical research as well as improved livestock production and animal health .
We have examined the differences in cellular markers and gene expression between multiple macrophage populations from 25 pigs of five breeds. The results indicate that individual pigs vary most markedly in their expression of immune-associated inducible genes, whereas there are no major breed-dependent variations. The findings, using the LPS stimulation as an inflammation trigger, suggest that there has been relatively little selection of pigs breeds for immune-associated traits. We show also that pig macrophages are human-like in their inducible gene expression profile, and the pig may therefore provide a superior model for dissection of human inflammatory diseases.
5 pigs at 8–12 weeks old (3 females, 2 males) of 5 different breeds were used in this study: the genome reference breed Duroc (DU), Piétrain (PIE), Large White (LW), Landrace (LR) and Hampshire (HAM). All the pigs spent at least 2 weeks in the same facility at rest before experimentation. Animals have not shown any signs of any infections, did not received any vaccinations and none of the female pig were pregnant. All animal studies were conducted according to University of Edinburgh Guidelines and were approved by the Institutional Ethics Committee.
Cell isolation and cryopreservation
Pigs were injected with a mixture of ketamine (6 mg/kg) and azaperone (1 mg/kg), left undisturbed for 10–15 min then killed by captive bolt. Approximately 400 ml of blood was drawn by cardiac puncture, using a blood bag (Sarstedt, Nümbrecht, Germany). Lungs were then removed and kept on ice after clamping the trachea to avoid blood contamination. Finally, 5 posterior ribs from each side of the animal were removed and kept on ice. To isolate mononuclear cells (PBMC), the blood was centrifuged at 1200 g for 15 min with no brake and the buffy coat was removed and mixed with an equal volume of RPMI-1640 medium (Sigma-Aldrich, USA). PBMC were separated further using Lymphoprep (Axis-Shield, Norway) and centrifuged at 1200 g for 25 min with no brake. The mononuclear cell fraction was washed twice with phosphate buffered saline (PBS) (centrifuged 5 min at 600 g then 400 g). Bone marrow cells were harvested as previously described . In short, the ribs were cleaned with 70% (v/v) ethanol and both extremities were cut. The bone was flushed with RPMI-1640 (containing 5 mM EDTA to prevent clotting) using a 20 ml syringe and a bone marrow biopsy/aspirate needle (Cardinal Health, USA). Alveolar macrophages were extracted by flushing the lungs twice with 500 ml of PBS). The volume recovered was filtered (100 μm) and centrifuged (10 min, 400 g). Red cells were removed by suspension in 5 ml of lysis buffer (10 mM KHCO3, 155 mM NH4Cl, 0.1 M EDTA, sterile 0.2 μM filtered) for 5 min followed by PBS wash. All three type of cells were finally centrifuged at 400 g for 5 min and the pellet was collected, re-suspended in freezing medium (90% FCS, 10% DMSO) and was slow frozen at -80°C in an isopropanol bath. Cells were retained at -155°C for long term storage.
Cells were recovered from -155°C by quickly thawing them at 37°C, then slowly diluting the freezing medium by dropwise addition of 40 ml of warm PBS over 2–3 min to avoid the shock of sudden dilution of DMSO. In order to obtain macrophages, bone-marrow cells and PBMC were cultured 5–7 days in large 100 mm2 sterile petri dishes in 20 ml of complete medium: RPMI-1640, Glutamax supplement (35050–61; Invitrogen), 10% heat-inactivated FCS (PAA Laboratories), penicillin/streptomycin (15140; Invitrogen, Paisley, UK) in the presence of rhCSF-1 (1×104 units/ml; a gift of Chiron, Emeryville, CA). Bone marrow-derived macrophages (BMDM), monocyte-derived macrophages (MDM) or alveolar macrophages (AM) were then seeded at 1×106 cells/ml in 6-wells plates in complete medium with rhCSF-1 and left overnight. The next day, non-adherent cells were removed, fresh complete medium was added and cells were stimulated with LPS from Salmonella enterica serotype minnesota Re 595 (100 ng/ml; L9764; Sigma-Aldrich).
RNA was extracted from AM, BMDM and MDM at 0 h and 7 h after LPS stimulation, using Amsbio RNA-Bee kit, as specified by the manufacturer (Amsbio, Abingdon, U.K.). RNA concentration was measured using ND-1000 Nanodrop (Thermo Scientific). The quality was controlled by running the samples on the RNA 6000 LabChip kit (Agilent Technologies, Waldbronn, Germany) with the Agilent2100 Bioanalyzer in which samples are assigned an integrity classification from 10 (intact RNA) to 1 (highly degraded) by the 2100 Bioanalyzer expert software.
Snowball porcine micro-array
Total RNA was prepared for hybridization using the Ambion's WT Expression Kit (Affymetrix, Santa Clara, CA), following the manufacturer’s instructions, except for the input amount of RNA (500 ng input instead of the recommended 100 ng). We then hybridized in a random order to the Affymetrix Snowball Porcine Array  by ARK-Genomics [http://www.ark-genomics.org]. This array was designed by us, and each probeset is composed of an average of 11 probes dispersed along the transcript to avoid any impact of polymorphism on detection. Statistical analysis of the array data utilised Partek Genomic Suite (Partek, St. Louis, USA). For network analysis, the normalised array data were uploaded to the software Biolayout Express3D [http://www.biolayout.org/] as described previously [15, 33]. The data from the microarray are available at [http://www.macrophages.com] and at Gene Expression Omnibus NCBI [http://www.ncbi.nlm.nih.gov/geo/] - serie GSE45145.
Supernatants from stimulated cells were harvested and stored frozen at -25°C until assayed in a single batch. Porcine TNF was measured by ELISA, following the manufacturer’s instruction (Duoset DY690B; R&D Systems, Minneapolis, MN).
Cells were incubated 15 min in high-block solution (PBS, 0.1% sodium azide, 2% FCS, 0.1% BSA) then washed with low-block solution (PBS, 0.1% sodium azide, 0.2% FCS, 0.1% BSA). Macrophages were stained with either a mouse anti-pig CD14 (clone MCA1218, 1:50; AbD Serotec), a mouse anti-pig CD16 (clone MCA1971, 1:200; AbD Serotec), or an IgG2b or IgG1 isotype control (MCA691 and MCA928PE; AbD Serotec; same concentration as primary Ab) in Low Block. The cells were then washed and resuspended in 500 μl Low Block. Data (10K cells) were acquired using a CyAn ADP Analyzer (Beckman Coulter, High Wycombe, U.K.) and analyzed with Summit software (v4.3).
The authors would like to thanks Dr Helen Brown and Dr Christelle Robert for their help in the statistical analysis. This work was supported by Biotechnology and Biological Sciences Research Council Grant BB/G004013/1 (to RK, LF, DB, DPS, ALA, and DAH) and a Fulbright fellowship (to CKT).
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