華聯產品: Mouse OneArray
Nuclear factor-kB bioluminescence imaging-guided transcriptomic analysis for the assessment of host?Vbiomaterial interaction in vivo.
Biomaterials 2009, 30(17):3042-9. doi: 10.1016/j.biomaterials.2009.02.016
Establishment of a comprehensive platform for the assessment of host-biomaterial interaction in vivo is an important issue. Nuclear factor-kappaB (NF-kappaB) is an inducible transcription factor that is activated by numerous stimuli. Therefore, NF-kappaB-dependent luminescent signal in transgenic mice carrying the luciferase genes was used as the guide to monitor the biomaterials-affected organs, and transcriptomic analysis was further applied to evaluate the complex host responses in affected organs in this study. In vivo imaging showed that genipin-cross-linked gelatin conduit (GGC) implantation evoked the strong NF-kappaB activity at 6h in the implanted region, and transcriptomic analysis showed that the expressions of interleukin-6 (IL-6), IL-24, and IL-1 family were up-regulated. A strong luminescent signal was observed in spleen on 14 d, suggesting that GGC implantation might elicit the biological events in spleen. Transcriptomic analysis of spleen showed that 13 Kyoto Encyclopedia of Genes and Genomes pathways belonging to cell cycles, immune responses, and metabolism were significantly altered by GGC implants. Connectivity Map analysis suggested that the gene signatures of GGC were similar to those of compounds that affect lipid or glucose metabolism. GeneSetTest analysis further showed that host responses to GGC implants might be related to diseases states, especially the metabolic and cardiovascular diseases. In conclusion, our data provided a concept of molecular imaging-guided transcriptomic platform for the evaluation and the prediction of host-biomaterial interaction in vivo.
華聯產品: Mouse OneArray
Transcriptomic analysis of EGb 761-regulated neuroactive receptor pathway in vivo.
Journal of Ethnopharmacology 2009, 123(1):68-73. doi: 10.1016/j.jep.2009.02.027
Although EGb 761 exhibits neuroprotective effects and exerts beneficial effects on many neurological disorders, its mechanism on the neuronal functions is unclear so far. In this study, we used oligonucleotide microarray technique to investigate the effect of EGb 761 on the transcriptional profile of mouse genes. RNA samples were obtained from frontal cortex, straitum, and kidneys after the oral administration of EGb 761 for seven consecutive days. Our data showed that EGb 761 significantly altered the neuroactive ligand-receptor interaction pathway in frontal cortex but not in straitum and kidney. Then we analyzed 26 receptor genes that were significantly altered by EGb 761 in this pathway and found that EGb 761 treatment highly up-regulated the subgroup of dopamine receptors, especially dopamine receptor 1a (Drd1a), in frontal cortex. Quantitative real-time reverse transcription-polymerase chain reaction and immunohistochemical staining confirmed the increased level of Drd1a expression after EGb 761 treatment. In summary, we investigated for the first time the overall effects of EGb 761 on the gene expression in brain using a powerful systemic biological technique. Our results suggested that EGb 761 altered unique pathways and regulated the expressions of some specific neuronal receptor genes exclusively in frontal cortex.
華聯產品: Mouse OneArray
Interactive transcriptome analysis of enterohemorrhagic Escherichia coli+H23 (EHEC) O157:H7 and intestinal epithelial HT-29 cells after bacterial attachment.
International Journal of Food Microbiology 2009, 131(2-3):224-32. doi: 10.1016/j.ijfoodmicro.2009.03.002
Here, the gene expression profiles of EHEC O157:H7 and HT-29 during the attachment stage were investigated by using duplex whole transcriptome analysis. After the initial attachment (3 h), the gene regulation systems of both the EHEC O157:H7 and HT-29 host cells were immediately remodeled. A total of 326 genes of the HT-29 cells, which involved proteins associated with the detoxification process, stress response proteins, anti-apoptosis/inflammation proteins, immune response protein, and oxidative stress proteins, were differentially regulated by more than 2.0-fold during EHEC attachment. In contrast, when HT-29 was attached to EHEC the expression of 611 genes was induced and the expression of 384 genes was reduced by more than twofold when compared to RPMI 1640-grown EHEC (16.14% of the total hybridized genes). Among the genes that were classified according to biological function, the mRNA levels of the genes involved in stress response, oxidative stress, cell signaling and cell surface proteins were significantly altered after the attachment of EHEC O157:H7. Therefore, the results of this study provide crucial insight into the genetic networks that provide host cell protection and the strategy of EHEC O157:H7 pathogenesis in gastro-intestinal (GI) tracts.
華聯產品: Human OneArray
Effect of hydroxyurea on the promoter occupancy profiles of tumor suppressor p53 and p73.
BMC Biology 2009, 7:35. doi: 10.1186/1741-7007-7-35
The p53 tumor suppressor and its related protein, p73, share a homologous DNA binding domain, and mouse genetics studies have suggested that they have overlapping as well as distinct biological functions. Both p53 and p73 are activated by genotoxic stress to regulate an array of cellular responses. Previous studies have suggested that p53 and p73 independently activate the cellular apoptotic program in response to cytotoxic drugs. The goal of this study was to compare the promoter-binding activity of p53 and p73 at steady state and after genotoxic stress induced by hydroxyurea.We employed chromatin immunoprecipitation, the NimbleGen promoter arrays and a model-based algorithm for promoter arrays to identify promoter sequences enriched in anti-p53 or anti-p73 immunoprecipitates, either before or after treatment with hydroxyurea, which increased the expression of both p53 and p73 in the human colon cancer cell line HCT116-3(6). We calculated a model-based algorithm for promoter array score for each promoter and found a significant correlation between the promoter occupancy profiles of p53 and p73. We also found that after hydroxyurea treatment, the p53-bound promoters were still bound by p73, but p73 became associated with additional promoters that that did not bind p53. In particular, we showed that hydroxyurea induces the binding of p73 but not p53 to the promoter of MLH3, which encodes a mismatch repair protein, and causes an up-regulation of the MLH3 mRNA.These results suggest that hydroxyurea exerts differential effects on the promoter-binding functions of p53 and p73 and illustrate the power of model-based algorithm for promoter array in the analyses of promoter occupancy profiles of highly homologous transcription factors.
華聯產品: Mouse OneArray
An essential role for DNA methyltransferase 3a in melanoma tumorigenesis.
Biochemical and Biophysical Research Communications 2009, 387(3):611-6. doi: 10.1016/j.bbrc.2009.07.093
Abnormal DNA methylation and associated silencing of tumor suppressor genes are common to many types of cancers. Among the three coordinate DNA methyltransferases (Dnmts), Dnmt1 and Dnmt3b were both shown to be important for cancer cell survival and tumorigenesis. However, the relationship between Dnmt3a and tumorigenesis is still largely unknown. Here, we show that inhibition of Dnmt3a expression, by stable transfection of a Dnmt3a-RNA interference (RNAi) construct dramatically inhibited melanoma growth and metastasis in mouse melanoma models. Microarray analysis revealed that genes critical for the tumor immune response, were implicated in the inhibition of melanoma growth. Expression of a cluster of class I and class II MHC genes, class II transactivator (Ciita), as well as a subset of 5 chemokines (Cxcl9, Cxcl16, Ccl12, Ccl4, and Ccl2) were up-regulated. Furthermore, we determined that the promoter IV of Ciita was significantly demethylated in Dnmt3a-depleted tumors. In addition, several known tumor-related genes, which are critical for developmental processes and cell cycle, were confirmed to be misregulated, including TgfB1, Socs1, Socs2, E2F6, Ccne1, and Cyr61. The results presented in this report strongly suggest that Dnmt3a plays an essential role in melanoma tumorigenesis, and that the underlying mechanisms include the modulation of the tumor immune response, as well as other processes.
華聯產品: Human OneArray
SOX2 modulates alternative splicing in transitional cell carcinoma.
Biochemical and Biophysical Research Communications 2010, 393(3):420-5. doi: 10.1016/j.bbrc.2010.02.010
Aberrant alternative splicing of key cellular regulators may play a pivotal role in cancer development. To investigate the potential influence of altered alternative splicing on the development of transitional cell carcinoma (TCC), splicing activity in the TCC cell lines TSGH8301 and BFTC905 was examined using the SV40-immortalized uroepithelial cell line SV-HUC-1 as a reference. Our results indicate a significant alteration in splice site selection in the TCC cell lines. By gene expression profiling and subsequent validation, we discovered that sex-determining region Y-box protein 2 (SOX2) is specifically upregulated in BFTC905. Furthermore, ectopic expression of SOX2 modulates alternative splicing of the splicing reporter in vivo. More significantly, using an in vitro pull-down assay, it was found that SOX2 exhibits RNA-binding capability. Our observations suggest that SOX2 modulates alternative splicing by functioning as a splicing factor.