genomewide characterization of host-pathogen interactions by ...

Maren Depke
Results
Gene Expression Pattern of Bone-Marrow Derived Macrophages after Interferon-gamma Treatment
higher expression in BALB/c BMM. The same direction of difference was observed for arginase
type II (Arg2). Tissue factor pathway inhibitor (Tfpi), coding for a protease inhibitor with anticoagulant
function, was higher expressed in C57BL/6 BMM. Genes of lysosomal, matrix
degrading, and detoxification enzymes were differentially expressed between BMM of the two
mouse strains. Lysosomal enzyme genes showed a mixed pattern with higher expression in
BALB/c BMM for cathepsin E (Ctse) and hyaluronidas (Hyal1) and higher expression in C57BL/6
BMM for cathepsins C and H (Ctsc, Ctsh). Matrix metallopeptidase 14 (Mmp14), which is involved
in degradation of extracellular matrix, and glutathione S-transferases mu 1 and pi 1 (Gstm1,
Gstp1) which are associated with detoxification processes, were detected with higher expression
in C57BL/6 BMM (Table R.3.16).
Strain-specific difference in expression of IFN-γ related genes
BMM of BALB/c and C57BL/6 differ in their ability to eliminate infecting bacteria, especially
after IFN-γ treatment (Breitbach et al. 2006). In this study, the primary reaction of BMM to IFN-γ
in comparison between both strains was analyzed. Therefore, a network centered around the
starting node IFN-γ was created using Ingenuity Pathway Analysis (IPA, www.ingenuity.com). This
network contained 181 genes (Fig. R.3.5 A, B) additionally to the starting node IFN-γ. Genes were
grouped manually into four categories: 1) difference existed between BALB/c BMM and C57BL/6
BMM at both treatment levels, control and after IFN-γ treatment; 2) difference between BMM of
the two strains occurred only at control level; 3) difference between BMM of the two strains
occurred only after IFN-γ treatment; 4) no strain difference was observed, but the gene
expression was influenced at least in BMM of one mouse strain. A second categorization divided
each group exhibiting strain differences into genes higher expressed in BALB/c BMM and into
genes higher expressed in C57BL/6 BMM.
After restricting the network to genes described to be linked to IFN-γ in macrophages or RAW
cells in the Ingenuity Pathway Knowledge Base (IPKB), a list of 132 new macrophage-related
genes out of 181 IFN-γ linked genes could be obtained. Correspondingly, a list of 49 of 181 genes
that are already included in the IPKB as IFN-γ related in macrophages or RAW cells were
exported.
Fig. R.3.5: Ingenuity Pathway Analysis (IPA, www.ingenuity.com) of IFN-γ related genes.
A, B. Network resulting from application of the grow-tool on transcriptome data
To create a network centered around the starting node IFN-γ the grow-tool of IPA‘s pathway function was applied. The addition of
further nodes according to information stored in the so-called Ingenuity Pathway Knowledge Base (IPKB) was restricted to a list of
genes that are differentially expressed in at least 1 of 4 comparisons 1) IFN-γ effects in BALB/c BMM, 2) IFN-γ effects in C57BL/6 BMM,
3) strain difference at non-treated control level and 4) strain difference after IFN-γ treatment. Further restrictions were not included.
Networks are colored according to strain difference at control level (A) or at IFN-γ treated level (B). Green represents a higher
expression in BALB/c BMM than in C57BL/6 BMM whereas red indicates higher expression in C57BL/6 BMM than in BALB/c BMM. The
intensity of color correlates with the magnitude of difference: The shade of color becomes darker with increasing absolute fold
change.
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