genomewide characterization of host-pathogen interactions by ...

Maren Depke
Results
Host Cell Gene Expression Pattern in an in vitro Infection Model
Differential expression of apoptosis associated genes has already been observed in the data
evaluation with Ingenuity Pathway Analysis tools (see pathway “Death Receptor Signaling”,
page 120). Further apoptosis related genes were found when manually filtering the list of
differentially expressed genes at the 6.5 h time point (Table R.4.7). Genes for apoptosis inducing
proteins B-cell CLL/lymphoma 10 (BCL10, 1.7) and apoptosis facilitator BCL2-like 11 (BCL2L11,
2.0) were increased in infected samples. The proteins belong to the group of BH3-only proteins
and achieve their apoptotic effect by binding to proteins of the Bcl-2 family. The mechanism is
discussed to take effect by activating pro-apoptotic members or inactivating pro-survival
members in a de-repression mode (Bouillet/Strasser 2002, Adams 2003, Fletcher/Huang 2006).
Also apolipoprotein L1 (APOL1) is a BH3-only protein whose accumulation leads to autophagy
(Wan et al. 2008, Zhaorigetu et al. 2008) and is postulated to be linked to apoptosis
(Vanhollebeke/Pays 2006). Its expression was increased by a factor of 3.4 in infected samples at
the 6.5 h time point. Interestingly, four other apolipoprotein L genes, which do not possess a
secretion signal peptide like APOL1 and therefore are thought to be localized intracellularly
(Duchateau et al. 1997, Page et al. 2001), showed increased expression: APOL2 (4.6), APOL3 (3.7),
APOL4 (1.9), and APOL6 (4.2). Expression of APOL5 was absent (p > 0.01 on intensity profile level
in Rosetta Resolver analysis) in all 16 infected and control S9 cell samples of this study. These
other APOL proteins also contain BH3-domains and are supposed to be associated with
programmed cell death and immune response (Liu Z et al. 2005). Most interestingly, APOL1 is the
target protein of the antagonistic Trypanosoma brucei rhodesiense protein SRA which helps the
pathogen to evade the immune response. Further pro-apoptotic genes were induced in infected
S9 cells like BH3-like motif containing, cell death inducer (BLID; 2.3), BCL2-antagonist/killer 1
(BAK1; 1.9), caspase 4, apoptosis-related cysteine peptidase (CASP4; 2.8), but also an antiapoptotic
gene, BCL2-associated athanogene (BAG1; 1.8; Table R.4.7).
Table R.4.7: Overview on selected differentially expressed apoptosis related genes in S9 cells 6.5 h after start of infection with
S. aureus RN1HG GFP.
Rosetta Resolver annotation
fold change a
gene
name
description
Entrez
Gene ID
BCL10 B-cell CLL/lymphoma 10 8915 CLAP, mE10, CIPER, c-E10, CARMEN 1.7
BCL2L11 BCL2-like 11 (apoptosis facilitator) 10018
BAM, BIM, BOD, BimL, BimEL, BIMbeta6,
BIM-beta7, BIM-alpha6
2.0
APOL1 apolipoprotein L, 1 8542 APOL, APO-L, APOL-I 3.4
APOL2 apolipoprotein L, 2 23780 APOL3, APOL-II 4.5
APOL3 apolipoprotein L, 3 80833 CG12-1, APOLIII 3.7
APOL4 apolipoprotein L, 4 80832 APOLIV,APOL-IV 1.9
APOL6 apolipoprotein L, 6 80830 APOLVI, APOL-VI 4.2
BLID BH3-like motif containing, cell death inducer 414899 BRCC2 2.3
BAK1 BCL2-antagonist/killer 1 578 CDN1, BCL2L7, BAK-LIKE 1.9
CASP4 caspase 4, apoptosis-related cysteine peptidase 837 TX, ICH-2, Mih1/TX, ICEREL-II 2.8
BAG1 BCL2-associated athanogene 573 RAP46 1.8
a Fold change values were calculated for the comparison of infected GFP + S9 cell with the baseline of medium control samples.
alias
6.5 h
Manual filtering revealed induced cytokines and cytokine receptors 6.5 h after start of
infection, some of which have already been mentioned in the context of IFN signaling or pattern
recognition receptors (Table R.4.8). Only IFNB1 and IL6 were already induced at the 2.5 h time
point. In total, the induced genes revealed a pro-inflammatory response: the acute phase
response and fever mediator IL-6, inducers of MHC-I molecules and antiviral/antibacterial
mechanisms (IFNB1, IL28B), chemoattractants for monocytes, T cells, denditic cells and
granulocytes (CCL2, CCL5, CXCL10, CXCL11, CXCL16), B and T cell activating cytokines (IL-7,
TNFSF13B), macrophage growth factor (CSF1), inducer of other cytokines and immune cell
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