Table 2.
Differential gene expression of Caco-2 cells cocultured with EcN.
| Fold change a | |||||
| Functional category | Gene symbol | GB Acc. No. b | Chip 1 | Chip 2 | Description and/or putative function |
| Immune response | MCP-1 (CCL2) | S69738.1 | 11.1 | 3.1 | Enhances the inflammatory response, upregulated by IL1α and TNFα |
| CD9 | NM_001769.1 | 1.7 | 3.6 | Involved in platelet activation and aggregation; expressed in hematopoetic and epithelial cells | |
| MIP-2α (CXCL2) | M57731.1 | 4.4 | 8.1 | Produced by activated monocytes, expressed at inflammation sites, up-regulated by IL1α and TNFα | |
| MIP-2β (CXCL3) | NM_002090.1 | 6.5 | 10.4 | Plays a role in inflammation, autocrine effect on endothelial cells | |
| NK4 | NM_004221.1 | -1.7 | -2.5 | May play a role in lymphocyte acitivation, angiogenesis inhibitor, putative therapeutic agent for gastric cancer | |
| Signaling | AGT | NM_000029.1 | 1.7 | 2.6 | Serine protease inhibitor |
| CNIH | NM_005776.1 | 2.6 | 6.9 | EGF-signaling in oocyte | |
| DUSP5 | U16996.1 | 13.1 | 3.4 | Hydrolase, negative feedback role in IL-2 signaling, deactivation of mitogen- or stress-activated protein kinases | |
| ID2 | NM_002166.1 | 2.8 | 4.2 | Essential for constitution of the intestinal mucosal barrier, is downregulated by TGFβ | |
| IFNGR2 | NM_005534.1 | 1.8 | 2.4 | Protein translocator | |
| NFκBIA | AI078167 | 6.3 | 3.3 | Downregulation of NF-κB activity, contributed in Crohn's disease | |
| NFκBIE | NM_004556.1 | 3.3 | 2.1 | Inhibits NF-κB | |
| PRDX4 | NM_006406.1 | 1.7 | 3.6 | Regulates the activation of NF-κB by modulation of IκBα phosphorylation | |
| DDIT (RTP801) | NM_019058.1 | 20.9 | 4.0 | HIF-1α responsive proapoptotic protein | |
| TNFαIP3 | NM_006290.1 | 4.3 | 3.3 | Interacts with NAF1 and inhibits TNF-induced NF-κB dependent gene expression | |
| SFN | X57348 | -1.6 | -2.2 | Exonuclease specific for small oligoribonucleotides, sensitive epithelial marker | |
| Transcription and translation | ELF3 | U73844.1 | 3.3 | 1.8 | Epithelial specific ets transcription factor, regulates MIP3α expression which is NF-κB dependent |
| ILF3 | BC003086.1 | -4.3 | -2.0 | May faciliate ds RNA-regulated gene expression | |
| TIEG | NM_005655.1 | 2.5 | 44.7 | Krüppel-like transcription factor, up-regulated by TGFβ | |
| XBP1 | NM_005080.1 | 2.5 | 2.7 | May act as transcription factor in B-cells | |
| Apoptosis | BNIP3 | U15174.1 | 3.0 | 2.7 | Apoptosis inducing protein, binding to BCL2 |
| Differentiation | NDRG1 | NM_006096.1 | 2.4 | 6.8 | Growth inhibitory role, induced app. 20 × during in vitro differentiation of Caco-2 |
| Proliferation | EMP3 | NM_001425.1 | -2.2 | -4.4 | Probably involved in cell proliferation |
| VEGF | H95344 | 2.1 | 2.2 | Induced by mek1, role of vascular endothelial growth factor in IBD | |
a Fold change is the factor of mRNA regulation from EcN-treated cells and non-treated cells according to the signal values itself and to the change value from Affymetrix analysis software. Minus fold change values indicate genes with decreased transcription. Results have been performed by two independent hybridization experiments (Chip 1, Chip 2).
b GB Acc. No. indicates GenBank accession number.