Pathway-specific differences between tumor cell lines and normal and tumor tissue cells

BACKGROUND: Cell lines are used in experimental investigation of cancer but their capacity to represent tumor cells has yet to be quantified. The aim of the study was to identify significant alterations in pathway usage in cell lines in comparison with normal and tumor tissue. METHODS: This study utilized a pathway-specific enrichment analysis of publicly accessible microarray data and quantified the gene expression differences between cell lines, tumor, and normal tissue cells for six different tissue types. KEGG pathways that are significantly different between cell lines and tumors, cell lines and normal tissues and tumor and normal tissue were identified through enrichment tests on gene lists obtained using Significance Analysis of Microarrays (SAM). RESULTS: Cellular pathways that were significantly upregulated in cell lines compared to tumor cells and normal cells of the same tissue type included ATP synthesis, cell communication, cell cycle, oxidative phosphorylation, purine, pyrimidine and pyruvate metabolism, and proteasome. Results on metabolic pathways suggested an increase in the velocity nucleotide metabolism and RNA production. Pathways that were downregulated in cell lines compared to tumor and normal tissue included cell communication, cell adhesion molecules (CAMs), and ECM-receptor interaction. Only a fraction of the significantly altered genes in tumor-to-normal comparison had similar expressions in cancer cell lines and tumor cells. These genes were tissue-specific and were distributed sparsely among multiple pathways. CONCLUSION: Significantly altered genes in tumors compared to normal tissue were largely tissue specific. Among these genes downregulation was a major trend. In contrast, cell lines contained large sets of significantly upregulated genes that were common to multiple tissue types. Pathway upregulation in cell lines was most pronounced over metabolic pathways including cell nucleotide metabolism and oxidative phosphorylation. Signaling pathways involved in adhesion and communication of cultured cancer cells were downregulated. The three way pathways comparison presented in this study brings light into the differences in the use of cellular pathways by tumor cells and cancer cell lines

Modeling Surface and Subsurface Pesticide Transport Under Three Field Conditions Using PRZM-3 and GLEAMS

Contaminant transport models should be evaluated over a wide range of conditions to determine their limitations. The models PRZM and GLEAMS have been evaluated many times, but few studies are available in which predicted movement in runoff and percolate were simultaneously evaluated against field data. Studies of this type are essential because pesticide leaching and runoff are mutually dependent processes. For this reason, PRZM-3 and GLEAMS were evaluated for their ability to predict metribuzin concentrations in runoff, sediment, subsurface soil, and pan lysimeters under three field conditions (yard waste compost amended, no-till, and conventional-till) on a Lowell silt loam soil. Sensitive input parameters were either site specific (climatic, soil, and chemical) or calibrated (K-factor, C-factor, curve number). In general, both models under-predicted metribuzin concentration in runoff water, runoff sediment, subplow layer soil (15-75 cm), and pan lysimeter water (75 cm). Contrary to field data, both models predicted that a large percentage (\u3e 50%) of metribuzin would move below the “mixing zone” (top 1 cm) during the first rainfall event after application. Relatively little metribuzin was predicted to move beyond the plow layer (top 15 cm) into the pan lysimeters or subsurface soil throughout the simulation period, possibly due to the lack of a macropore component in the models. High metribuzin concentrations in sediment (field data) indicated that relatively little metribuzin moved below the “mixing zone”, possibly because of hysteresis but much of the metribuzin that did move was quickly transported into the pan lysimeters, probably due to macropore flow. GLEAMS more accurately predicted pesticide concentration in sediment and PRZM predicted subsurface soil concentration somewhat more accurately than GLEAMS. Little difference in accuracy was detected between models on metribuzin concentration in runoff or metribuzin concentration in percolate. Although both models generally under-predicted metribuzin concentration in runoff, runoff transport (mass of metribuzin in runoff) for the study period was over-predicted by both models which emphasizes the importance of accurately predicting herbicide concentration and runoff volume soon after application when the surface pesticide concentrations are highest

Role of E-cadherin in the response of tumor cell aggregates to lymphatic, venous and arterial flow: measurement of cell-cell adhesion strength

Defects in the expression or function of the calcium dependent cell-cell adhesion molecule E-cadherin are common in invasive, metastatic carcinomas. In the present study the response of aggregates of breast epithelial cells and breast and colon carcinoma cells to forces imposed by laminar flow in a parallel plate flow channel was examined. Although E-cadherin negative tumor cells formed cell aggregates in the presence of calcium, these were significantly more likely than E-cadherin positive cell aggregates to disaggregate in response to low shear forces, such as those found in a lymphatic vessel or venule (\u3c 3.5 dyn/cm2). E-cadherin positive normal breast epithelial cells and E-cadherin positive breast tumor cell aggregates could not be disaggregated when exposed to shear forces in excess of those found in arteries (\u3e 100 dyn/cm2). E-cadherin negative cancer cells which had been transfected with E-cadherin exhibited large increases in adhesion strength only if the expressed protein was appropriately linked to the cytoskeleton. These results show that E-cadherin negative tumor cells, or cells in which the adhesion molecule is present but is inefficiently linked to the cytoskeleton, are far more likely than E-cadherin positive cells to detach from a tumor mass in response to low shear forces, such as those found in a lymphatic vessel or venule. Since a primary route of dissemination of many carcinoma cells is to the local lymph nodes these results point to a novel mechanism whereby defects in cell-cell adhesion could lead to carcinoma cell dissemination

Novel Stromal Biomarkers in Human Breast Cancer Tissues Provide Evidence for the More Malignant Phenotype of Estrogen Receptor-Negative Tumors

Research efforts were focused on genetic alterations in epithelial cancer cells. Epithelial-stromal interactions play a crucial role in cancer initiation, progression, invasion, angiogenesis, and metastasis; however, the active role of stroma in human breast tumorigenesis in relation to estrogen receptor (ER) status of epithelial cells has not been explored. Using proteomics and biochemical approaches, we identified two stromal proteins in ER-positive and ER-negative human breast cancer tissues that may affect malignant transformation in breast cancer. Two putative biomarkers, T-cell receptor alpha (TCR-α) and zinc finger and BRCA1-interacting protein with a KRAB domain (ZBRK1), were detected in leukocytes of ER-positive and endothelial cells of ER-negative tissues, respectively. Our data suggest an immunosuppressive role of leukocytes in invasive breast tumors, propose a multifunctional nature of ZBRK1 in estrogen receptor regulation and angiogenesis, and demonstrate the aggressiveness of ER-negative human breast carcinomas. This research project may identify new stromal drug targets for the treatment of breast cancer patients

Control of TCF-4 Expression by VDR and Vitamin D in the Mouse Mammary Gland and Colorectal Cancer Cell Lines

BACKGROUND: The vitamin D receptor (VDR) pathway is important in the prevention and potentially in the treatment of many cancers. One important mechanism of VDR action is related to its interaction with the Wnt/beta-catenin pathway. Agonist-bound VDR inhibits the oncogenic Wnt/beta-catenin/TCF pathway by interacting directly with beta-catenin and in some cells by increasing cadherin expression which, in turn, recruits beta-catenin to the membrane. Here we identify TCF-4, a transcriptional regulator and beta-catenin binding partner as an indirect target of the VDR pathway. METHODOLOGY/PRINCIPAL FINDINGS: In this work, we show that TCF-4 (gene name TCF7L2) is decreased in the mammary gland of the VDR knockout mouse as compared to the wild-type mouse. Furthermore, we show 1,25(OH)2D3 increases TCF-4 at the RNA and protein levels in several human colorectal cancer cell lines, the effect of which is completely dependent on the VDR. In silico analysis of the human and mouse TCF7L2 promoters identified several putative VDR binding elements. Although TCF7L2 promoter reporters responded to exogenous VDR, and 1,25(OH)2D3, mutation analysis and chromatin immunoprecipitation assays, showed that the increase in TCF7L2 did not require recruitment of the VDR to the identified elements and indicates that the regulation by VDR is indirect. This is further confirmed by the requirement of de novo protein synthesis for this up-regulation. CONCLUSIONS/SIGNIFICANCE: Although it is generally assumed that binding of beta-catenin to members of the TCF/LEF family is cancer-promoting, recent studies have indicated that TCF-4 functions instead as a transcriptional repressor that restricts breast and colorectal cancer cell growth. Consequently, we conclude that the 1,25(OH)2D3/VDR-mediated increase in TCF-4 may have a protective role in colon cancer as well as diabetes and Crohn's disease

Enabling Metabolomics Based Biomarker Discovery Studies Using Molecular Phenotyping Of Exosome-like Vesicles

Identification of sensitive and specific biomarkers with clinical and translational utility will require smart experimental strategies that would augment expanding the breadth and depth of molecular measurements within the constraints of currently available technologies. Exosomes represent an information rich matrix to discern novel disease mechanisms that are thought to contribute to pathologies such as dementia and cancer. Although proteomics and transcriptomic studies have been reported using Exosomes-Like Vesicles (ELVs) from different sources, exosomal metabolome characterization and its modulation in health and disease remains to be elucidated. Here we describe methodologies for UPLC-ESI-MS based small molecule profiling of ELVs from human plasma and cell culture media. In this study, we present evidence that indeed ELVs carry a rich metabolome that could not only augment the discovery of low abundance biomarkers but may also help explain the molecular basis of disease progression. This approach could be easily translated to other studies seeking to develop predictive biomarkers that can subsequently be used with simplified targeted approaches

The Molecular Basis of Vitamin D Receptor and β-Catenin Crossregulation

The signaling/oncogenic activity of β-catenin can be repressed by activation of the vitamin D receptor (VDR). Conversely, high levels of β-catenin can potentiate the transcriptional activity of 1,25-dihydroxyvitamin D3 (1,25D). We show here that the effects of β-catenin on VDR activity are due to interaction between the activator function-2 (AF-2) domain of the VDR and C terminus of β-catenin. Acetylation of the β-catenin C terminus differentially regulates its ability to activate TCF or VDR-regulated promoters. Mutation of a specific residue in the AF-2 domain, which renders the VDR trancriptionally inactive in the context of classical coactivators, still allows interaction with β-catenin and ligand-dependent activation of VDRE-containing promoters. VDR antagonists, which block the VDRE-directed activity of the VDR and recruitment of classical coactivators, do allow VDR to interact with β-catenin, which suggests that these and perhaps other ligands would permit those functions of the VDR that involve β-catenin interaction.The authors wish to acknowledge the support of National Institutes of Health grants DK058196 and U54 CA100971 (S.W.B.), the AACR-Bristol Myers Squibb Translational Fellowship in Colon Cancer (S.S.), and the following LCCC Core Facilities: macromolecular analysis, microscopy, and tissue culture

Development and Evaluation of a 193nm Immersion Generation-Three Fluid Candidates

The need to extend 193nm immersion lithography necessitates the development of a third generation (Gen-3) of high refractive index (RI) fluids that will enable approximately 1.7 numerical aperture (NA) imaging. A multi-pronged approach was taken to develop these materials. One approach investigated the highest-index organic thus far discovered. The second approach used a very high refractive index nanoparticle to make a nanocomposite fluid. This report will describe the chemistry of the best Gen-3 fluid candidates and the systematic approach to their identification and synthesis. Images obtained with the Gen-3 fluid candidates will also be presented for a NA ≥ 1.7