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At least 973 records · Page 54Linked to original sources
PubMed2006

Microarray-based method for monitoring yeast overexpression strains reveals small-molecule targets in TOR pathway.

Identification of the cellular targets of small-molecule hits in phenotypic screens is a central challenge in the development of small molecules as biological tools and potential therapeutics. To facilitate the process of small-molecule target identification, we developed a global, microarray-based method for monitoring the growth of pools of yeast strains, each overexpressing a different protein, in the presence of small molecules. Specifically, the growth of Saccharomyces cerevisiae strains harboring approximately 3,900 different overexpression plasmids was monitored in the presence of rapamycin, which inhibits the target of rapamycin (TOR) proteins. TOR was successfully identified as a candidate rapamycin target, and many additional gene products were implicated in the TOR signaling pathway. We also characterized the mechanism of LY-83583, a small-molecule suppressor of rapamycin-induced growth inhibition. These data enabled functional links to be drawn between groups of genes implicated in the TOR pathway, identified several candidate targets for LY-83583, and suggested a role for mitochondrial respiration in mediating rapamycin sensitivity.

Aminoquinolines↗
PubMed2005

Multivalent recombinant proteins for probing functions of leucocyte surface proteins such as the CD200 receptor.

CD200 (OX2) is a membrane glycoprotein that interacts with a structurally related receptor (CD200R) involved in the regulation of macrophage function. The interaction is of low affinity (K(D) approximately 1 microm) but can be detected using CD200 displayed in a multivalent form on beads or with dimeric fusion proteins consisting of the extracellular region of CD200 and immunoglobulin Fc regions. We prepared putative pentamers and trimers of mouse CD200 with sequences from cartilage oligomeric matrix protein (COMP) and surfactant protein D (SP-D), respectively. The COMP protein gave high-avidity binding and was a valuable tool for showing the interaction whilst the SP-D protein gave weak binding. In vivo experiments showed that an agonistic CD200R monoclonal antibody caused some amelioration in a model of experimental autoimmune encephalomyelitis but the COMP protein was cleared rapidly and had minimal effect. Pentameric constructs also allowed detection of the rat CD48/CD2 interaction, which is of much lower affinity (K(D) approximately 70 microm). These reagents may have an advantage over Fc-bearing hybrid molecules for probing cell surface proteins without side-effects due to the Fc regions. The CD200-COMP gave strong signals in protein microarrays, suggesting that such reagents may be valuable in high throughput detection of weak interactions.

Animals↗
PubMed2004

Leukotriene B4 strongly increases monocyte chemoattractant protein-1 in human monocytes.

OBJECTIVE: Leukotriene B4 (LTB4), a product of the 5-lipoxygenase (5-LO) pathway of arachidonic acid metabolism, has been implicated in atherosclerosis. However, the molecular mechanisms for the atherogenic effect of LTB4 are not well understood. This study is to determine candidate mechanisms. METHOD AND RESULTS: Primary human monocytes were treated with LTB4 and the supernatant was analyzed for cytokine/chemokine production by an immuno-protein array. This analysis revealed a strong increase of the monocyte chemoattractant protein-1 (MCP-1), a proinflammatory cytokine. Follow-up analyses with MCP-1 enzyme-linked immunosorbent assay (for quantitation of MCP-1 protein) and real-time polymerase chain reaction (PCR) (for MCP-1 mRNA) demonstrated that LTB4 strongly induced expression of MCP-1 protein and mRNA in a time-dependent and dose-dependent fashion. This induction was effectively abolished by CP-105,696, an antagonist for the LTB4 receptor BLT1. Selective inhibitors of ERK1/2 or JNK MAPK effectively blocked the LTB4-induced MCP-1 production. Furthermore, LTB4 increased NF-[kappa]B DNA binding activity, which was blocked by CP-105,696. CONCLUSIONS: LTB4 strongly induces MCP-1 production in primary human monocytes. This induction is mediated through the BLT1 pathway increasing MCP-1 transcription. Activation of ERK1/2 or JNK MAPK is essential for this induction. The NF-[kappa]B activation may be involved in LTB4-increased MCP-1 expression. The LTB4-induced MCP-1 in human monocytes may play a critical role in the atherogenicity of LTB4.

Benzopyrans↗
PubMedDate not supplied

ProteinChip system technology: a powerful tool to analyze expression differences in tissue-engineered blood vessels.

At the time of implantation, tissue-engineered constructs should resemble native tissues as closely as possible. At present, histology and biochemical methods are commonly used to compare tissue-engineered constructs with native tissue. A ProteinChip system based on surface-enhanced laser desorption/ionization time of flight mass spectrometry (SELDI) has been developed that allows visualization of complex protein profiles from biological samples. The aim of this study was to determine whether the ProteinChip system is a suitable tool with which to compare the protein expression profiles of tissue-engineered aortic blood vessels with native tissues. Tissue-engineered blood vessel substitutes were fabricated with poly-4-hydroxybutyrate scaffolds, ovine vascular cell seeding, and dynamic tissue culture conditions. Engineered, ovine aortic, and carotid tissues were homogenized and total protein was extracted. Samples were analyzed on ProteinChip arrays. Analysis yielded reproducible protein profiles from all samples. About 150 distinct protein peaks were detected. Comparative analysis with ProteinChip software revealed that the protein profiles from native aorta and native carotid arteries were similar whereas early tissue-engineered samples displayed more distinct deviations. In conclusion, ProteinChip system technology is rapid, reproducible, and highly sensitive in highlighting differentially expressed proteins in tissue-engineered blood vessel substitutes.

Animals↗
PubMed2004

Evaluation of MafG interaction with Maf recognition element arrays by surface plasmon resonance imaging technique.

Specific interactions between transcription factors and cis-acting DNA sequence motifs are primary events for the transcriptional regulation. Many regulatory elements appear to diverge from the most optimal recognition sequences. To evaluate affinities of a transcription factor to various suboptimal sequences, we have developed a new detection method based on the surface plasmon resonance (SPR) imaging technique. Transcription factor MafG and its recognition sequence MARE (Maf recognition elements) were adopted to evaluate the new method. We modified DNA immobilization procedure on to the gold chip, so that a double-stranded DNA array was successfully fabricated. We further found that a hydrophilic flexible spacer composed of the poly (ethylene glycol) moiety between DNA and alkanethiol self-assembled monolayers on the surface is effective for preventing nonspecific adsorption and facilitating specific binding of MafG. Multiple interaction profiles between MafG and six of MARE-related sequences were observed by the SPR imaging technique. The kinetic values obtained by SPR imaging showed very good correlation with those obtained from electrophoretic gel mobility shift assays, although absolute values were deviated from each other. These results demonstrate that the double-stranded DNA array fabricated with the modified multistep procedure can be applied for the comprehensive analysis of the transcription factor-DNA interaction.

Binding Sites↗
PubMed2006

Identification of protein expression signatures associated with Helicobacter pylori infection and gastric adenocarcinoma using recombinant antibody microarrays.

Antibody microarray based technology is a powerful emerging tool in proteomics, target discovery, and differential analysis. Here, we report the first study where recombinant antibody fragments have been used to construct large scale antibody microarrays, composed of 127 different antibodies against mostly immunoregulatory antigens. The arrays were based on single framework recombinant antibody fragments (SinFabs) designed for high on-chip stability and functionality and were used for the analysis of malignant and normal stomach tissue samples from Helicobacter pylori-positive and -negative patients. Our results demonstrate that distinct tumor- as well as infection-associated protein expression signatures could be identified from these complex tissue proteomes, as well as biomarkers such as IL-9, IL-11, and MCP-4, previously not found in these diseases. In a longer perspective, this study may improve the understanding of H. pylori-induced stomach cancer and lead to development of improved diagnostics.

Adenocarcinoma↗
PubMed2004

Towards a comprehensive understanding of Bacillus subtilis cell physiology by physiological proteomics.

Using Bacillus subtilis as a model system for functional genomics, this review will provide insights how proteomics can be used to bring the virtual life of genes to the real life of proteins. Physiological proteomics will generate a new and broad understanding of cellular physiology because the majority of proteins synthesized in the cell can be visualized. From a physiological point of view two major proteome fractions can be distinguished: proteomes of growing cells and proteomes of nongrowing cells. In the main analytical window almost 50% of the vegetative proteome expressed in growing cells of B. subtilis were identified. This proteomic view of growing cells can be employed for analyzing the regulation of entire metabolic pathways and thus opens the chance for a comprehensive understanding of metabolism and growth processes of bacteria. Proteomics, on the other hand, is also a useful tool for analyzing the adaptational network of nongrowing cells that consists of several partially overlapping regulation groups induced by stress/starvation stimuli. Furthermore, proteomic signatures for environmental stimuli can not only be applied to predict the physiological state of cells, but also offer various industrial applications from fermentation monitoring up to the analysis of the mode of action of drugs. Even if DNA array technologies currently provide a better overview of the gene expression profile than proteome approaches, the latter address biological problems in which they can not be replaced by mRNA profiling procedures. This proteomics of the second generation is a powerful tool for analyzing global control of protein stability, the protein interaction network, protein secretion or post-translational modifications of proteins on the way towards the elucidation of the mystery of life.

Bacillus subtilis↗
PubMed2006

Pathobiological characteristics of intestinal and diffuse-type gastric carcinoma in Japan: an immunostaining study on the tissue microarray.

AIM: To investigate the pathobiological features of intestinal and diffuse-type gastric carcinomas in the Japanese population. METHODS: The expression of fragile histine triad (FHIT), phosphatase and tensin homology deleted from human chromosome 10 (PTEN), caspase-3, Ki-67, mutant p53, matrix metalloproteinase (MMP)-2, MMP-9, and extracellular matrix metalloproteinase inducer (EMMPRIN) on tissue microarrays of gastric carcinomas by immunostaining was examined in comparison with the clinicopathological characteristics between intestinal and diffuse-type cases. RESULTS: Intestinal-type carcinoma frequently occurred in old men, whereas the diffuse type comparatively occurred more in young women (p<0.05). The diffuse-type carcinoma was more inclined to invasion into muscularis propria, lymphatic invasion and lymph node metastasis, and belonged to higher International Union against Cancer (UICC) staging (p<0.05) compared with intestinal-type counterparts. Expression of FHIT, PTEN, Ki-67, caspase-3, mutant p53 and EMPPRIN was higher in intestinal-type carcinomas than in diffuse-type carcinomas (p<0.05). Kaplan-Meier analysis indicated that patients with intestinal-type carcinomas had a higher cumulative survival rate (p<0.05). CONCLUSION: Intestinal-type gastric carcinomas with a more favourable prognosis frequently show high levels of proliferation and apoptosis, and always accompany strong expression of FHIT, PTEN and mutant p53 and EMMPRIN. EMMPRIN expression might underlie the molecular basis of liver metastasis and higher proliferation of intestinal-type gastric carcinomas in Japan. Lauren's classification thus proved pathologically relevant for the clinical treatment of gastric carcinomas.

Acid Anhydride Hydrolases↗
PubMed2006

CCN1/Cyr61 is regulated by the canonical Wnt signal and plays an important role in Wnt3A-induced osteoblast differentiation of mesenchymal stem cells.

Marrow mesenchymal stem cells are pluripotent progenitors that can differentiate into bone, cartilage, muscle, and fat cells. Wnt signaling has been implicated in regulating osteogenic differentiation of mesenchymal stem cells. Here, we analyzed the gene expression profile of mesenchymal stem cells that were stimulated with Wnt3A. Among the 220 genes whose expression was significantly changed by 2.5-fold, we found that three members of the CCN family, CCN1/Cyr61, CCN2/connective tissue growth factor (CTGF), and CCN5/WISP2, were among the most significantly up-regulated genes. We further investigated the role of CCN1/Cyr61 in Wnt3A-regulated osteogenic differentiation. We confirmed that CCN1/Cyr61 was up-regulated at the early stage of Wnt3A stimulation. Chromatin immunoprecipitation analysis indicates that CCN1/Cyr61 is a direct target of canonical Wnt/beta-catenin signaling. RNA interference-mediated knockdown of CCN1/Cyr61 expression diminished Wnt3A-induced osteogenic differentiation. Furthermore, exogenously expressed CCN1/Cyr61 was shown to effectively promote mesenchymal stem cell migration. These findings suggest that tightly regulated CCN1/Cyr61 expression may play an important role in Wnt3A-induced osteoblast differentiation of mesenchymal stem cells.

Adenoviridae↗
PubMed2002

Antibody microarrays: promises and problems.

Antibody microarrays have enormous potential for becoming a tool that will allow, at the protein level, the type of global characterization of molecular mixtures that DNA microarrays already make possible at the RNA and DNA level. However, the much higher complexity of proteins both in terms of their sheer number and their structural and biochemical diversity necessitates an even more sophisticated analysis process. Its eventual realization will be demanding to achieve and requires further developments on many technical aspects, not in the least because the understanding of proteins is still comparatively less comprehensive than that of nucleic acids prior to the emergence of array technologies.

Antibodies↗
PubMed2004

Toward immobilized antibody microarray optimization: print buffer and storage condition comparisons on performance.

Performance issues in protein arrays differ substantially from DNA microarrays because of the different intrinsic construction and stability of proteins versus DNA, and the impact on biological recognition phenomena required for assay from a surface-immobilized state. Maintenance of the capture bioactivity and performance of antibodies on microarray substrates for relatively long periods (under storage or shipping) requires carefully designed and optimized print buffer and storage conditions. We have focused on selection of several additives added to antibody print buffers with different concentrations, and storage of printed antibody slides under different temperatures from 1 day to 4 weeks. Activities of these slides were compared in capture assay formats in order to compare the effects of print buffer and storage conditions of antibody microarrays. Commercial polymer-coated Optarray slides exhibited better performance over Codelink slides in terms of activity of anti-human TNF alpha and IL-1 beta. IL-1 beta antibodies immobilized on both commercial surfaces showed much higher activity than TNF alpha antibodies, regardless of source or vendor. Addition of 1% (v/v) PEO to the print buffer increased the printed analyte capture activity of IL-1 beta on Optarray slides compared to standard print buffer without any additives. This helps to maintain antibody immobilized analyte capture activity for 4 weeks when stored at -70 degrees C.

Adsorption↗
PubMed2002

High-throughput molecular profiling of high-grade astrocytomas: the utility of fluorescence in situ hybridization on tissue microarrays (TMA-FISH).

Due to recent biological and technical advances, the list of potentially useful candidate genes is rapidly expanding in the study of brain tumors. However, traditional methods of screening individual genes in individual samples are slow and tedious, often with consumption of precious resources after only a few experiments. This study evaluates the feasibility of high-throughput molecular analysis using fluorescence in situ hybridization (FISH) on glioma tissue microarrays (TMA). A single microarray paraffin block was constructed using 65 WHO grade III and IV astrocytomas, sampled in duplicate with 0.6-mm-diameter punch cores. FISH was used to detect common alterations, such as EGFR amplification, chromosome 7, 9, and 10 aneusomies and deletions of 1p, 19q, PTEN, DMBT1, and p16. Of 585 hybridization sets, 508 (87%) yielded interpretable data, with hybridization failure in 33 (5.5%) and dislodged tissue in 44 sets (7.5%), respectively. Glioblastomas harbored significantly more alterations than anaplastic astrocytomas, with the overall frequencies of alterations similar to those reported using other techniques. The overall concordance rate between paired tumor core samples was 93%. We conclude that TMA-FISH is an efficient and reliable method for detecting molecular alterations in high-grade astrocytomas.

Agglutinins↗
PubMed2005

Immunoassays based on microelectrodes arrayed on a silicon chip for high throughput screening of liver fibrosis markers in human serum.

A novel immunoassays for screening of disease markers in human serum are presented by miniaturizing interdigitated array (IDA) of microelectrodes via micro electro-mechanical system (MEMS) on a silicon chip for multi-channel electrochemical measurement. Different selected antibodies (Abs) are incorporated site-specifically into the electrochemically deposited polypyrrole (PPy) formed on the IDA of the silicon chip, which was characterized by fluorescence microscope photo and the electrochemical quartz crystal microbalance (EQCM) measurements. The selective recognition of Ab to the corresponding antigen (Ag) is monitored through the measurable conductivity change, which is directly visualized by cyclic voltammograms (CVs) in presence of the redox probe, Fe (CN)6(3-/4-). By using the strategy presented here, three liver fibrosis markers, hyaluronic acid (HA), lamin (LN) and collagen type IV (IV-C), are detected simultaneously and specifically at the surface of the chip with calibration curves, y = 21.75 + 0.84x (R = 0.995), y = 57.54 + 0.47x (R = 0.999) and y = 37.92 + 0.28x (R = 0.999), separately. Either the standard or the serum samples can be detected at ng/mL concentration level in a tiny amount of volume, approximately 50 microL. The chip-based immunoassay shows the advantages of high sensitivity, good specificity, high throughput, low sample consumption, and the stability offered via batch production by MEMS as well, which is expected to benefit the multi-target screening of desired clinical analytes.

Biomarkers↗
PubMed2004

[Evaluation of p63 expression in lung cancer by use of complementary DNA and tissue microarray].

OBJECTIVE: To study p63 expression at mRNA transcript and protein levels in human lung cancers, including squamous cell lung carcinoma (SCC), adenocarcinoma, large cell lung carcinoma (LCLC) and small cell lung carcinoma (SCLC), or the corresponding metastatic foci. The relationship of p63 expression and alterations in p63 locus at chromosomal 3q27-29 was also determined. METHODS: p63 gene expression in 72 cases of SCC, adenocarcinoma, LCLC and SCLC was analyzed by cDNA microarray technology. Tissue microarray of specimens from 150 cases of primary lung cancer was prepared for immunohistochemical study for p63 protein. Possible chromosomal alterations at the p63 locus in 70 cases of primary lung cancer were studied by comparative genomic hybridization (CGH) technology. RESULTS: p63 mRNA transcript expression was significantly increased by more than 10-fold in SCC, as compared with that in other histologic subtypes including adenocarcinoma, LCLC and SCLC. p63 mRNA expression in metastatic foci was also remarkably higher than that in their primary tumors (P < 0.001). Immunostaining showed that p63 protein expression was observed in 94.64% of SCC, whereas only one lung adenocarcinoma (1.79%) was positive. Immunopositivity was also demonstrated in 2 of the 4 LCLC cases studied. None of the SCLC cases was positive. There was a statistically significant difference in p63 expression between pT1 and pT2 tumors (P < 0.05). The CGH results showed that overrepresentation of p63 locus at chromosomal 3q27-29 was a typical finding in SCC. p63 immunopositivity also correlated significantly with pronounced gains of p63 locus at chromosomal 3q27-q29 (P < 0.000 1), suggesting that strong expression of p63 in lung SCC was associated with increased gene amplification. CONCLUSION: p63 may play a role in oncogenesis of human lung squamous cell carcinoma and development of metastasis.

Adenocarcinoma↗
PubMed2004

Evaluation of immunohistochemical markers in non-small cell lung cancer by unsupervised hierarchical clustering analysis: a tissue microarray study of 284 cases and 18 markers.

This study has investigated a panel of immunomarkers in non-small cell lung carcinoma (NSCLC). Unsupervised hierarchical clustering analysis was used to investigate the possibility of identifying different subgroups in NSCLC based on their molecular expression profile rather than morphological features. A tissue microarray consisting of 284 cases of NSCLC was constructed. Immunohistochemistry was used to detect the presence of 18 biomarkers including synaptophysin, chromogranin, bombesin, NSE, GFI1, ASH-1, p53, p63, p21, p27, E2F-1, cyclin D1, Bcl-2, TTF-1, CEA, HER2/neu, cytokeratin 5/6, and pancytokeratin. Univariate analysis of all 18 markers for prognostic significance was performed. Immunohistochemical scoring data for NSCLC were analysed by unsupervised hierarchical clustering analysis. Kaplan-Meier survival curves were plotted for the different cluster groups of lung tumours identified by this method. Analysis of the three different World Health Organization (WHO) subtypes (adenocarcinoma, squamous cell carcinoma, large cell carcinoma) of NSCLC individually showed that different markers were significant in different subtypes. For example, p53 and p63 were significant for squamous cell carcinoma (p = 0.007 and p = 0.03, respectively), whereas cyclin D1 and HER2/neu were significant prognostic markers for adenocarcinoma (p = 0.025 and p = 0.015, respectively). These markers were not significant prognostic predictors for NSCLC as a group. Hierarchical clustering analysis of NSCLC produced four separate cluster groups, although the vast majority of cases were found in two cluster groups, one dominated by squamous cell carcinoma and the other by adenocarcinoma. The clinical outcomes of cases from the four cluster groups were not significantly different. Prognostic indicators vary between different morphological subtypes of NSCLC. Unsupervised hierarchical clustering analysis, based on an extended immunoprofile, identifies two main cluster groups corresponding to adenocarcinoma and squamous cell carcinoma; cases of large cell carcinomas are assigned to one of these two groups based on their molecular phenotype.

Adenocarcinoma↗
PubMed2006

Serum proteome profiles identifies parathyroid hormone physiologic response.

Parathyroid hormone (amino acids 1-34) (PTH) regulates bone and calcium homeostasis. The magnitude of the effects of PTH on bone varies in osteoporosis patients. We employed ProteinChip technology to generate protein profiles from sera of mice treated once daily with PTH or vehicle for 3 or 11 days. Data analyses on selected arrays indicated significant increases in serum proteins or peptides in PTH-treated groups, compared to vehicle-controls. The magnitude of change increased with duration of treatment. Anion-exchange fractionation of sera prior to profiling on array surfaces increased the number of proteins detected that were regulated by PTH. The optimized purification conditions developed "on-chip" for subsets of proteins, reflected corresponding behavior with process-compatible chromatographic resins under elution chromatography. We have identified and evaluated subsets of serum proteins regulated by PTH treatment, using a combination of ProteinChip technology, column chromatography, PAGE and LC-MS/MS. Our data demonstrate the feasibility of using a panel of serum proteins to detect PTH responsiveness in humans.

Animals↗
PubMed2005

The fabrication of protein chip based on surface plasmon resonance for detection of pathogens.

Protein chip based on surface plasmon resonance (SPR) was developed for detection of pathogens existing in contaminated environment, such as Escherichia coli O157:H7, Salmonella typhimurium, Legionella pneumophila, and Yersinia enterocolitica. Protein G was immobilized to endow the orientation of antibody molecules on the SPR surface. The pathogen binding of the protein chip was investigated by SPR spectroscopy. Consequently, it was found that the four kinds of pathogen could be selectively detected by using SPR-based protein chip.

Bacteria↗