Identification of gene expression patterns in superficial and invasive human bladder cancer
ABSTRACT Multiple transcriptional events take place when normal urothelium is transformed into tumor tissue. These can now be monitored simultaneously by the use of oligonucleotide arrays, and expression patterns of superficial and invasive tumors can be established. Single-cell suspensions were prepared from bladder biopsies (36 normal, 29 tumor). Pools of cells were made from normal urothelium and from pTa grade I and II and pT2 grade III and IV bladder tumors. From these suspensions, and from 10 single-tumor biopsies, labeled cRNA was hybridized to oligonucleotide arrays carrying probes for 6500 genes. The obtained expression data were sorted according to a weighting scheme and were subjected to hierarchical cluster analysis of tissues and genes. Northern blotting was used to verify the array data, and immunohistology was used to correlate between RNA and protein levels. Hierarchical clustering of samples correctly identified the stage using both 4076 genes and a subset of 400 genes covarying with the stages and grades of tumors. Hierarchical clustering of gene expression levels identified several stage-characteristic, functionally related clusters, encoding proteins that were related to cell proliferation, oncogenes and growth factors, cell adhesion, immunology, transcription, proteinases, and ribosomes. Northern blotting correlated well with array data. Immunohistology showed a good concordance between transcript level and protein staining. The study indicates that gene expression patterns may be identified in bladder cancer by combining oligonucleotide arrays and cluster analysis. These patterns give new biological insight and may form a basis for the construction of molecular classifiers and for developing new therapy for bladder cancer.
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- "Among our identified candidate migration/progression genes, versican, ephrin-B2 and E-cadherin are well known to be associated with tumor transformation and progression . We also identified E-cadherin and fibronectin 1 as biomarkers for both cell migration and tumor stage consistent with data from other microarrays (Thykjaer et al., 2001; Modlich et al., 2004). Elevated levels of ECM versican are also predictive of poor prognosis in patients with prostate cancer, endometrial cancer and oral squamous cell carcinoma (Ricciardelli et al., 1999; Kodama et al., 2007; Pukkila et al., 2007). "
ABSTRACT: Cell migration is essential to cancer invasion and metastasis and is spatially and temporally integrated through transcriptionally dependent and independent mechanisms. As cell migration is studied in vitro, it is important to identify genes that both drive cell migration and are biologically relevant in promoting invasion and metastasis in patients with cancer. Here, gene expression profiling and a high-throughput cell migration system answers this question in human bladder cancer. In vitro migration rates of 40 microarray-profiled human bladder cancer cell lines were measured by radial migration assay. Genes whose expression was either directly or inversely associated with cell migration rate were identified and subsequently evaluated for their association with cancer stage in 61 patients. This analysis identified genes known to be associated with cell invasion such as versican, and novel ones, including metallothionein 1E (MT1E) and nicotinamide N-methyltransferase (NNMT), whose expression correlated positively with cancer cell migration and tumor stage. Using loss of function analysis, we show that MT1E and NNMT are necessary for cancer cell migration. These studies provide a general approach to identify the clinically relevant genes in cancer cell migration and mechanistically implicate two novel genes in this process in human bladder cancer.Oncogene 09/2008; 27(52):6679-89. DOI:10.1038/onc.2008.264
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- "Total RNA was extracted using the RNeasy Minikit (Qiagen, Hilden, Germany) and cRNA was prepared as described previously (Thykjaer et al., 2001). Briefly, RNA was isolated from tissue culture flasks. "
ABSTRACT: The probiotic Escherichia coli strain Nissle 1917 (EcN) has been used for decades in human medicine in Central Europe for the treatment and prevention of intestinal disorders and diseases. However, the molecular mechanisms underlying its beneficial effects are only partially understood. To identify molecular responses induced by EcN that might contribute to its probiotic properties polarized T84 cells were investigated employing DNA microarrays, quantitative RT-PCR, Western blotting, immunofluorescence and specific protein kinase C (PKC) inhibitors. Polarized T84 epithelial cell monolayers were used as a model to monitor barrier disruption by infection with the enteropathogenic E. coli (EPEC) strain E2348/69. Co-incubation of EPEC with EcN or addition of EcN following EPEC infection abolished barrier disruption and, moreover, restored barrier integrity as monitored by transepithelial resistance. DNA-microarray analysis of T84 cells incubated with EcN identified 300+ genes exhibiting altered expression. EcN altered the expression, distribution of zonula occludens-2 (ZO-2) protein and of distinct PKC isotypes. ZO-2 expression was enhanced in parallel to its redistribution towards the cell boundaries. This study provides evidence that EcN induces an overriding signalling effect leading to restoration of a disrupted epithelial barrier. This is transmitted via silencing of PKCzeta and the redistribution of ZO-2. We suggest that these properties contribute to the reported efficacy in the treatment of inflammatory bowel diseases and in part rationalize the probiotic nature of EcN.Cellular Microbiology 04/2007; 9(3):804-16. DOI:10.1111/j.1462-5822.2006.00836.x
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- "The chips were scanned with an HP-laserscanner and the data were analysed with GeneChip microarray Suite 5.0 software (Affymetrix). Each microarray was scaled to " 150 " as previously described (Thykjaer et al. 2001). All of the data were also normalised by using the robust multiarray analysis (RMA) normalisation approach in the Bioconductor Affy package in the R project for statistical computing (Irizarry et al. 2003). "
ABSTRACT: We have investigated the effect of bismuth by autometallography, cell viability, TUNEL assay and microarray analysis of a macrophage cell line. The cells accumulate bismuth in their lysosomes in a time- and dose-dependent manner. Cell viability assays show a significant decrease in the number of viable cells related to both bismuth concentrations and exposure time. TUNEL assays after 12 h and 24 h at a bismuth-citrate concentration of 50 microM revealed the presence of 30% and 70% TUNEL-positive cells, respectively, compared with 8% in the controls. We have analysed gene expression profiles for cells exposed to 50 microM bismuth-citrate and for untreated controls at 12 h and 24 h by microarray analysis, which confirmed that bismuth is a powerful metallothionein inducer. A number of glycolytic enzymes are induced by bismuth, suggesting that bismuth is able to induce "hypoxia-like" stress. BCL2/adenovirus E1B 19-kDa-interacting protein 3 (Bnip3) has been suggested as a regulator of hypoxia-induced cell death independent of caspase-3 activation and cytochrome c release. Bnip3 is up-regulated indicating the involvement of Bnip3 as a possible mechanism for bismuth-induced cell death. Differences have been noticed in cell viability and in the modification of the mRNA expression levels at 12 and 24 h. Only 13 genes are modified at both these times, suggesting a time-dependent molecular cascade in which bismuth-exposed cells enter a dormant stage with mRNA down-regulation being followed by cell death of susceptible cells.Cell and Tissue Research 09/2005; 321(2):195-210. DOI:10.1007/s00441-005-1103-y