genomewide characterization of host-pathogen interactions by ...

Maren Depke
Results
Host Cell Gene Expression Pattern in an in vitro Infection Model
Differentially abundant proteins in infected samples compared to medium-treated controls
[Melanie Gutjahr]
Samples for transcriptome analysis were generated from the same experiments which yielded
samples for a proteome study (Melanie Gutjahr). Here, a gel-free mass spectrometric analysis
was performed, which allowed the identification of 1049 proteins in all analyzed samples. Of
these, Melanie Gutjahr classified 112 and 224 as different in abundance 2.5 h and 6.5 h after start
of infection, respectively. At the 2.5 h time point, reduced abundance prevailed with 73 proteins
in comparison to 39 proteins with increased abundance. In contrary, 96 reduced and 128
increased proteins were observed 6.5 h after start of infection. The common signature of both
2.5 h and 6.5 h time point included 63 proteins, whereas 49 and 161 proteins were specifically
regulated at the 2.5 h and 6.5 h time point, respectively. Reverse regulation at both time points
did not exist.
UniProt accession numbers of proteins exhibiting differential abundance were mapped to
EntrezGene IDs using the UniProt ID mapping tool (www.uniprot.org). The majority of these
EntrezGene IDs was available as annotation for sequences of the GeneChip Human Gene 1.0 ST
array in Rosetta Resolver software. Finally, 98 regulated proteins were available for comparison
with transcriptome data from samples 2.5 h after infection, and at the 6.5 h time point, 198
regulated proteins could be compared to array results (Table R.4.2).
Table R.4.2: Mapping of UniProt entries to EntrezGene IDs and EntrezGene records in Rosetta Resolver software.
time
point
UniProt accession numbers
of regulated proteins
EntrezGene IDs
after ID mapping
EntrezGene IDs available in Rosetta Resolver software
for the GeneChip Human Gene 1.0 ST array
2.5 h 112 110 98
6.5 h 224 221 198
Comparison of differentially abundant proteins with differentially expressed genes
[in cooperation with Melanie Gutjahr]
At the first time point 2.5 h after start of infection, the small list of differentially expressed
genes did not overlap with the list of regulated proteins.
When comparing transcriptome and proteome results of the 6.5 h time point, an overlap of 11
genes/proteins was discernible. These included 7 (ALCAM, APOL2, ERAP1, IFIT2, IFIT3, OASL,
WARS) and 3 (FASN, KPNA2, PPME1) genes/proteins which exhibited in both analysis methods
up- and down-regulation, respectively. The remaining gene/protein DYNC1H1 was induced at
transcript level and reduced in protein abundance.
The comparison between differentially expressed genes at the earlier 2.5 h time point with
regulated proteins at the later 6.5 h time point revealed that for 2 (IFIT2, IFIT3) increased
proteins the transcripts already were induced 2.5 h after start of infection.
When the comparison was performed in reversion, i. e. when the 2.5 h time point regulated
proteins were compared with the later 6.5 h time point’s gene expression changes, 4 (CNP,
DYNC1H1, IFIT1, ZC3HAV1) proteins were reduced at 2.5 h whereas gene transcripts were
induced at 6.5 h. Furthermore, one protein (ALCAM) was increased after 2.5 h, but the transcript
was induced only at the 6.5 h time point. This gene/protein was already included in a list
mentioned above. Finally, the protein FASN was reduced 2.5 h after start of infection, but the
transcript was repressed after 6.5 h. The FASN gene/protein was already included in the list of
gene and protein repression at the 6.5 h time point (Table R.4.3).
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