genomewide characterization of host-pathogen interactions by ...
genomewide characterization of host-pathogen interactions by ...
genomewide characterization of host-pathogen interactions by ...
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Maren Depke<br />
Results<br />
Gene Expression Pattern <strong>of</strong> Bone-Marrow Derived Macrophages after Interferon-gamma Treatment<br />
This analysis revealed expected categories within the IFN-γ dependently regulated genes in<br />
BMM like “Inflammatory Response”, “Antigen Presentation”, “Immune Cell Trafficking” and other<br />
immune response related functions. Furthermore, growth, proliferation, but also cell cyle and cell<br />
death associated genes were included in the set <strong>of</strong> differentially expressed genes.<br />
For a more detailed view, IPA’s canonical pathway analysis was applied (Table R.3.4). Here,<br />
the pathway “Interferon Signaling” appeared with the highest ratio value, i. e. the fraction <strong>of</strong><br />
genes from the pathway, which was also included in the list <strong>of</strong> IFN-γ dependent genes. This<br />
observation nicely proved the relevance <strong>of</strong> the gene expression signature which was recorded<br />
after stimulation <strong>of</strong> BMM with interferon. Further pathways from the group with the highest<br />
ratio values were among others “Antigen Presentation Pathway”, “Role <strong>of</strong> Pattern Recognition<br />
Receptors in Recognition <strong>of</strong> Bacteria and Viruses”, and “Activation <strong>of</strong> IRF <strong>by</strong> Cytosolic Pattern<br />
Recognition Receptors” which fits well into the expected <strong>characterization</strong> <strong>of</strong> the experimental<br />
system. Again, also cell death associated features appeared with the “Retinoic acid Mediated<br />
Apoptosis Signaling” pathway.<br />
Table R.3.4: Canonical pathway analysis <strong>of</strong> IFN-γ dependent genes in BMM <strong>of</strong> at least one strain, BALB/c or C57BL/6, using Ingenuity<br />
Pathway Analysis (Ingenuity Systems, www.ingenuity.com).<br />
Pathway ratio a p-value<br />
Interferon Signaling 11/30 = 0.367 8.34E-12<br />
Antigen Presentation Pathway 11/39 = 0.282 1.61E-09<br />
Role <strong>of</strong> Pattern Recognition Receptors in Recognition <strong>of</strong> Bacteria and Viruses 20/86 = 0.233 5.03E-15<br />
Complement System 8/36 = 0.222 4.09E-07<br />
Retinoic acid Mediated Apoptosis Signaling 9/44 = 0.205 2.42E-08<br />
Role <strong>of</strong> PKR in Interferon Induction and Antiviral Response 9/46 = 0.196 2.95E-07<br />
T Helper Cell Differentiation 8/41 = 0.195 7.42E-06<br />
Activation <strong>of</strong> IRF <strong>by</strong> Cytosolic Pattern Recognition Receptors 14/74 = 0.189 1.51E-11<br />
Allograft Rejection Signaling 8/45 = 0.178 2.34E-05<br />
TREM1 Signaling 12/69 = 0.174 3.84E-09<br />
a Ten pathways with the highest ratio values are cited.<br />
Manual data mining revealed different cytokines and cytokine receptors, which were<br />
differentially expressed in BMM upon treatment with IFN-γ. Here, the induction <strong>of</strong> several<br />
chemotactic chemokines (Ccl5, Ccl12, Ccl22, Cxcl9, Cxcl10, Cxcl11, Cxcl16) was noticeable. Among<br />
the receptors, Ccr5 induction fitted to the induction <strong>of</strong> one <strong>of</strong> its ligands, Ccl5. The induced<br />
receptor Ccrl2 is known to be induced after activation and during differentiation from monocytes<br />
to macrophages, but its function is not described yet. Contrarily, the receptor Cxcr4 was<br />
repressed after treatment <strong>of</strong> BMM with IFN-γ. Two interleukins were included in the<br />
differentially expressed cytokines: IL-15, a regulatory, anti-apoptotic cytokine with structural<br />
similarity to IL-2, and the subunit IL27-p28 <strong>of</strong> the heterodimeric IL-27, a regulatory cytokine<br />
produced <strong>by</strong> antigen presenting cells. Several interleukin receptors or receptor subunits were<br />
induced after IFN-γ treatment. The induction <strong>of</strong> the IL-15 receptor alpha-chain (Il15ra)<br />
corresponded to the already mentioned induction <strong>of</strong> IL-15. Furthermore, the strongly<br />
interdependent receptor subunits Il4ra, Il13ra1, Il21r, and Il2rg were induced. The alpha-chain <strong>of</strong><br />
IL-4 receptor (Il4ra) and the IL-21 receptor (Il21r) employ the IL-2 receptor gamma-chain (Il2rg) as<br />
their second subunit. Similarly, the primary IL-13 binding subunit <strong>of</strong> the IL-13 receptor (Il13ra1)<br />
builds a receptor complex together with the alpha-chain <strong>of</strong> IL-4 receptor (Il4ra). Also Il12rb1,<br />
coding for the low-affinity binding subunit <strong>of</strong> the IL-12 receptor, was induced. The induction <strong>of</strong><br />
Il10ra, high-affinity binding subunit <strong>of</strong> the IL-10 receptor, and <strong>of</strong> Il18bp, cytokine IL-18 binding<br />
protein, is an example for inhibitory processes in BMM after IFN-γ treatment. Repression <strong>of</strong><br />
interleukin receptor subunits was also found after IFN-γ treatment: Il1rl2, receptor for interleukin<br />
1 family member 9, and Il6st alias gp130, signal transducer for several cytokines, e. g. IL-6, were<br />
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