genomewide characterization of host-pathogen interactions by ...

Maren Depke
Results
Host Cell Gene Expression Pattern in an in vitro Infection Model
(1.6), but CASP9, the link to the intrinsic mitochondrial apoptosis pathway, was repressed (−1.6).
Possibly, S9 cells were prepared to react to external apoptosis signals or give signals to infection
relevant immune cells like neutrophils or macrophages. Of course, such situation does not occur
in the S9 cell in vitro infection setting.
Similarly, antigen presentation will not find any reaction partner in vitro. This canonical
pathway was significantly overrepresented in the infection-dependent genes which were
differentially expressed 6.5 h after start of infection (p = 1.21E−02; ratio = 8/39; Fig. R.4.9).
Antigen presentation is divided into two parts, presentation of intracellular and extracellular
antigens. Intracellular antigens are digested by cytosolic proteasome with sequential transport of
peptides into the endoplasmatic reticulum (ER). These peptides are loaded to MHC-I molecules
and transported via the Golgi to the cell surface for presentation. The immune-proteasome gene
PSMB8 (LMP7), coding for a protein in the 20S-core of the proteasome, was induced (fold change
1.8). PSMB9 (LMP2) with a fold change of 1.499 was just marginally below the cutoff and could
be regarded as induced, too. Both induced genes lead to an immune response-specific
reorganization of the proteasomes’ catalytic center. Induced were the peptide transporters TAP1
(2.4) and TAP2 (2.2), the TAP-binding protein tapasin/TPN (TAPBP; 1.5), which attaches the TAP
molecules to the MHC-I complex, and the ER aminopeptidases ERAP1 (1.6) and ERAP2 (4.4),
which are responsible for N-terminal trimming of the peptide in the ER. At the end of this
pathway, MHC-I molecules HLA-E (1.7) and HLA-F (1.8) and MHC class I-related molecule MR1
(2.0) were induced. MR1, a non-classical MHC-gene, features a strong homology to MHC-I
molecules, is highly conserved in human and mouse, ubiquitously transcribed in different tissue
or cell types, and speculated to present an unknown invariant ligand to certain “innate” mucosaassociated
invariant T cells (MAIT cells) expressing an invariant T cell receptor (TCR) similar as
innate natural killer T cells (iNKT) (Riegert et al. 1998, Hansen TH et al. 2007). Beta-2-
microglobulin (B2M; MHC-I-β) as the second subunit of the MHC-I complex showed a trend of
induction with a fold change of 1.3, but was not significant in statistical testing.
Fig. R.4.9: Antigen Presentation (modified from IPA, www.ingenuity.com). Red color indicates increase of expression.
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