genomewide characterization of host-pathogen interactions by ...

Maren Depke
Results
Host Cell Gene Expression Pattern in an in vitro Infection Model
transcriptome level at the 2.5 h time point. PTGS2 transcription is positively influenced by
IL-6. All three genes, IL6, PTGS2, and PTGER4, are indirectly induced by endothelin, EDN1, which
also has vasoconstrictor functions and itself was induced 2.5 h after start of infection (fold
change 4.2). The influence on expression is at least in parts mediated by ERK1/2, which was not
regulated itself (Fig. R.4.6).
Fig. R.4.6:
Interactions of IL-6, PTGS2,
PTGER4, EDN1, ERK1/2, IFNB1,
IFIT2, and IFIT3 in a custom
pathway design (modified from
IPA, www.ingenuity.com).
Red color indicates induction of
gene expression in infected
samples compared to control 2.5 h
after start of infection. More
intense shade of color is used for
higher absolute fold change
values. Dashed lines indicate
indirect influence on expression
(E), activation (A), phosphorylation
(P), and secretion (S), the solid line
binding (B).
These genes illustrated a beginning pro-inflammatory response. Another interesting candidate
which is assigned an important role at the interface of neuronal and immune system, the
leukemia inhibitory factor LIF, was increased in infected cells (fold change 1.6) already 2.5 h after
start of infection (and stayed induced at the 6.5 h time point). LIF belongs to the IL-6 family of
cytokines and recruits, like IL-6, the ubiquitous glycoprotein gp130 as second subunit of its
receptor.
Several genes for signal transduction molecules and transcription factors were included in the
small set of 40 differentially expressed genes 2.5 h after start of infection. An increased
expression was observed for NR4A2 (fold change 3.5), NFKBIZ (3.0), KLF4 (2.1), ATF3 (2.1), BCL6
(1.7), MYC (1.7), ZFP36L2 (1.6), and KLF6 (1.5).
Increased expression was recorded for TNFAIP3 (2.3), a gene thought to be critical for limiting
inflammation, and for ZC3H12C (1.5), a member of a family of negative regulators in macrophage
activation. In addition, CD274 (B7-H1), ligand for the immunoinhibitory receptor PD-1 on
activated B and T cells and on monocytes, was higher expressed in infected samples than in
controls. These gene expression changes alluded to a role in counterregulatory processes during
the beginning of infection and inflammation.
Other genes like NEDD9 (2.0), TNC (1.6), and RND3 (1.5) are involved in cell adhesion,
rounding and cytoskeleton organization, indicating the beginning of morphological changes in the
infected cells.
Even more, cell cycle progression seems to be negatively affected by the infection, as seen by
increased transcription of KLF4 (2.1), PPP1R15A (2.1), and MYC (1.7). Strikingly, 7 of 40 genes
were repressed 2.5 h after start of infection and all of them are functionally associated with cell
cycle progression: AURKA (−1.9), PLK1 (−1.8), HIST1H2AB (−1.6), BUB1 (−1.5) C13ORF34/BORA
(−1.5), CDCA2 (−1.5), and CDCA8 (−1.5).
About two thirds of regulated genes in the 2.5 h samples were still regulated 6.5 h after
infection, and the absolute fold change was even increased for almost all of these genes at the
later time point (Fig. R.4.7). Only one exception with reversed direction of regulation occurred,
and PTGS2 had a smaller fold change after 6.5 h than after 2.5 h although its expression still was
increased. To conclude, the changes started in the early time point were enforced in the later
time point.
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