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Chip Analysis (chip + analysis)
Selected AbstractsThe histone deacetylase inhibitor MS-275 induces p21WAF1/Cip1 expression in human Hep3B hepatoma cellsDRUG DEVELOPMENT RESEARCH, Issue 2 2007Haiyuan Zhang Abstract MS-275 is a novel synthetic benzamide derivative histone deacetylase (HDAC) inhibitor, that has demonstrated antiproliferative activity in a variety of in vitro human cancer cell lines including breast, colon, lung, myeloma, ovary, pancreas, prostate, and leukemia. Currently, little information is available concerning the effects of MS-275 on liver cancer cells. In the current study, MS-275 was found to have potent actions against human hepatoma Hep3B cells including inhibition of cell proliferation and induction of apoptosis. MS-275 selectively up-regulated a cyclin-dependent kinase inhibitor, p21WAF1/Cip1 without alteration of p27WAF1. Expression of p21WAF1/Cip1 is considered to play a pivotal role in Hep3B cell growth arrest and induction of apoptosis. Induction of p21WAF1/Cip1 expression was accompanied by an accumulation of acetylated histones H3 and H4 associated specifically with p21WAF1/Cip1 gene. ChIP analysis revealed remarkable alterations in protein components bound to the promoter region of p21WAF1/Cip1 gene in response to MS-275 treatment. These included the degradation of HDAC1, HDAC3, and c-Myc, and as well as increased p300 and RNA polymerase II. The selective effect of MS-275 on the up-regulation of the p21WAF1/Cip1 gene whose expression was suppressed in the hepatoma cancer cell line indicated that it would be a very attractive approach in clinical liver cancer therapy. Drug Dev Res 68:61,70, 2007. © 2007 Wiley-Liss, Inc. [source] Characterization and gene expression profiling in glioma cell lines with deletion of chromosome 19 before and after microcell-mediated restoration of normal human chromosome 19GENES, CHROMOSOMES AND CANCER, Issue 10 2009Kristen L. Drucker Nearly 10% of human gliomas are oligodendrogliomas. Deletion of chromosome arm 19q, often in conjunction with deletion of 1p, has been observed in 65,80% of these tumors. This has suggested the presence of a tumor suppressor gene located on the 19q arm. Chromosome 19 deletion is also of interest due to the better prognosis of patients with deletion, including longer survival and better response to chemotherapy, compared with patients without deletion. Two glioma cell lines with deletion of 19q were used for chromosome 19 microcell-mediated transfer, to assess the effect of replacing the deleted segment. Complementation with chromosome 19 significantly reduced the growth rate of the hybrid cells compared with the parental cell lines. Affymetrix U133 Plus 2.0 Gene Chip analysis was performed to measure and compare the expression of the chromosome 19 genes in the chromosome 19 hybrid cell lines to the parental cell line. Probes were considered significantly different when a P value <0.01 was seen in all of the cell line comparisons. Of 345 probes within the commonly deleted 19q region, seven genes (APOE, RCN3, FLJ10781, SAE1, STRN4, CCDC8, and BCL2L12) were identified as potential candidate genes. RT-PCR analysis of primary tumor specimens showed that several genes had significant differences when stratified by tumor morphology or deletion status. This suggests that one or more of these candidates may play a role in glioma formation or progression. © 2009 Wiley-Liss, Inc. [source] Mobile phone base station-emitted radiation does not induce phosphorylation of Hsp27BIOELECTROMAGNETICS, Issue 2 2007H. Hirose Abstract An in vitro study focusing on the effects of low-level radiofrequency (RF) fields from mobile radio base stations employing the International Mobile Telecommunication 2000 (IMT-2000) cellular system was conducted to test the hypothesis that modulated RF fields act to induce phosphorylation and overexpression of heat shock protein hsp27. First, we evaluated the responses of human cells to microwave exposure at a specific absorption rate (SAR) of 80 mW/kg, which corresponds to the limit of the average whole-body SAR for general public exposure defined as a basic restriction in the International Commission on Non-Ionizing Radiation Protection (ICNIRP) guidelines. Second, we investigated whether continuous wave (CW) and Wideband Code Division Multiple Access (W-CDMA) modulated signal RF fields at 2.1425 GHz induced activation or gene expression of hsp27 and other heat shock proteins (hsps). Human glioblastoma A172 cells were exposed to W-CDMA radiation at SARs of 80 and 800 mW/kg for 2,48 h, and CW radiation at 80 mW/kg for 24 h. Human IMR-90 fibroblasts from fetal lungs were exposed to W-CDMA at 80 and 800 mW/kg for 2 or 28 h, and CW at 80 mW/kg for 28 h. Under the RF field exposure conditions described above, no significant differences in the expression levels of phosphorylated hsp27 at serine 82 (hsp27[pS82]) were observed between the test groups exposed to W-CDMA or CW signal and the sham-exposed negative controls, as evaluated immediately after the exposure periods by bead-based multiplex assays. Moreover, no noticeable differences in the gene expression of hsps were observed between the test groups and the negative controls by DNA Chip analysis. Our results confirm that exposure to low-level RF field up to 800 mW/kg does not induce phosphorylation of hsp27 or expression of hsp gene family. Bioelectromagnetics © 2006 Wiley-Liss, Inc. [source] Glucose-dependent cell size is regulated by a G protein-coupled receptor system in yeast Saccharomyces cerevisiaeGENES TO CELLS, Issue 3 2005Hisanori Tamaki In the yeast, Saccharomyces cerevisiae, cell size is affected by the kind of carbon source in the medium. Here, we present evidence that the Gpr1 receptor and Gpa2 G, subunit are required for both maintenance and modulation of cell size in response to glucose. In the presence of glucose, mutants lacking GPR1 or GPA2 gene showed smaller cells than the wild-type strain. Physiological studies revealed that protein synthesis rate was reduced in the mutant strains indicating that reduced growth rate, while the level of mRNAs for CLN1, 2 and 3 was not affected in all strains. Gene chip analysis also revealed a down-regulation in the expression of genes related to biosynthesis of not only protein but also other cellular component in the mutant strains. We also show that GPR1 and GPA2 are required for a rapid increase in cell size in response to glucose. Wild-type cells grown in ethanol quickly increased in size by addition of glucose, while little change was observed in the mutant strains, in which glucose-dependent cell cycle arrest caused by CLN1 repression was somewhat alleviated. Our study indicates that the yeast G-protein coupled receptor system consisting of Gpr1 and Gpa2 regulates cell size by affecting both growth rate and cell division. [source] Developmental and activity-dependent genomic occupancy profiles of CREB in monkey area V1GENES, BRAIN AND BEHAVIOR, Issue 2 2009J. Lalonde The mammalian neocortex displays significant plastic rearrangement in response to altered sensory input, especially during early postnatal development. It is believed that cyclic AMP-response element-binding (CREB) plays an important role in orchestrating the molecular events that guide neuroplastic change, although the details of its genomic targets during normal postnatal development or in response to sensory deprivation remain unknown. Here, we performed CREB chromatin immunoprecipitation (ChIP) from monkey area V1 tissue and hybridized enriched DNA fragments to promoter microarrays (ChIP chip analysis). Our goal was to determine and categorize the CREB regulon in monkey area V1 at two distinct developmental stages (peak of critical period vs. adulthood) and after 5 days of monocular enucleation (ME) at both ages. Classification of enriched candidates showed that the majority of isolated promoter loci (n = 795) were common to all four conditions. A particularly interesting group of candidates (n = 192) was specific to samples derived from enucleated infant area V1. Gene ontology analysis of CREB targets during early postnatal development showed a subgroup of genes implicated in cytoskeleton-based structural modification. Analysis of messenger RNA expression (quantitative real-time,polymerase chain reaction) of candidate genes showed striking differences in expression profiles between infant and adult area V1 after ME. Our study represents the first extensive genomic analysis of CREB DNA occupancy in monkey neocortex and provides new insight into the multifaceted transcriptional role of CREB in guiding neuroplastic change. [source] Microarray profile of micro-ribonucleic acid in tumor tissue from cervical squamous cell carcinoma without human papillomavirusJOURNAL OF OBSTETRICS AND GYNAECOLOGY RESEARCH (ELECTRONIC), Issue 5 2009YanLiang Zhang Abstract Aims:, Micro-ribonucleic acid (miRNA) are noncoding RNA molecules of 21 to 24 nt that regulate the expression of target genes in a post-transcriptional manner. Evidence indicates that miRNA play essential roles in embryogenesis, cell differentiation and pathogenesis of human diseases. This study describes a comparison between the microRNA profile of human-papillomavirus-negative cervical squamous cell carcinoma patients and controls, in order to develop further understanding of the pathogenesis of cervical squamous cell carcinomas. Methods:, MiRNA were isolated from tumor tissues of five human-papillomavirus-negative cervical squamous cell carcinoma patients and five healthy controls in order to perform miRNA microarray chip analysis. The chip results were then confirmed by northern blot analysis. Results:, A total of 27 miRNA differentially expressed between the squamous cell carcinoma patients and the healthy controls were identified. Conclusion:, This work indicates that these miRNA may be potential diagnosis biomarkers and probable factors involved in the pathogenesis of cervical squamous cell carcinomas. [source] Upregulation of CC chemokine ligand 18 and downregulation of CX3C chemokine receptor 1 expression in human T-cell leukemia virus type 1-associated lymph node lesions: Results of chemokine and chemokine receptor DNA chip analysisCANCER SCIENCE, Issue 12 2007Kei Shimizu Adult T-cell leukemia/lymphoma (ATLL) is a human malignancy associated with human T-cell leukemia virus type 1 (HTLV-1). The pathological features of the lymph nodes of ATLL change from those of lymphadenitis to Hodgkin's-like features and those of lymphoma. Chemokines and their receptors are closely associated with T-cell subgroups and immune responses. To clarify the relationship between chemokines and their receptor expression, as well as the development of ATLL, 17 cases with ATLL were analyzed using DNA chips of chemokines and their receptors. All cases showed a varied and mixed pattern of upregulated and downregulated gene expression of Th1, Th2, naïve, and cytotoxic cell-associated chemokine genes. As CC chemokine ligand 18 (CCL18) accounted for the most upregulated gene and CX3C chemokine receptor 1 (CX3CR1) for the most downregulated gene, they were selected for immunohistochemical analysis. Immunohistochemical staining showed expression of the two genes in immunological cells, with a positive expression for reticulum cells, but not for ATLL cells. HTLV-1-associated lymphadenitis type (n = 13) and Hodgkin's-like type (n = 12) cases showed significantly higher CCL18 expression than the non-specific lymphadenitis cases (n = 10) (P < 0.05). However, all HTLV-1-associated cases showed significantly lower CX3CR1 expression than the non-specific lymphadenitis cases (P < 0.05). These results suggest that upregulation of CCL18 expression and downregulation of CX3CR1 expression play a role in immune responses against the ATLL cells. (Cancer Sci 2007; 98: 1875,1880) [source] 2242: Update on ophthalmic molecular geneticsACTA OPHTHALMOLOGICA, Issue 2010E DE BAERE Purpose To provide an overview of the recent technological advances in human molecular genetics that can be applied in ophthalmic genetics. Methods Since the finalization of the Human Genome Project many novel genomic technologies emerged that led to significant advances in gene identification and genetic testing of hereditary eye disorders: (1) genomewide copy number screening (array CGH); (2) genomewide SNP genotyping; (3) next-generation sequencing. Results (1) Microarray comparative genomic hybridisation or array CGH allows genomewide discovery of submicroscopic deletions and duplications in a single experiment. This technique is applied in routine molecular cytogenetic testing. Using array CGH a causal genomic defect can be found in at least 10% of all cases with mental retardation and/or multiple congenital anomalies. In ophthalmic genetics array CGH is mainly useful in the context of developmental eye disorders, with chorioretinal coloboma and anterior segment dysgenesis as an example. (2) Genomewide chip-based SNP genotyping can be used for homozygosity mapping in inbred and outbred pedigrees. Recent successes in gene identification using this approach are illustrated. (3) Next-generation sequencing or NGS. The application of this technology in gene identification and genetic testing of genetically heterogeneous conditions (with LCA as a paradigm) is discussed. Conclusion The rapid progress of genomic technologies such as array CGH, SNP chip analysis and next-generation sequencing lead to a boost in gene identification and genetic testing of both developmental and retinal eye disease. [source] Fluorescence in situ hybridization analysis with a tissue microarray: ,FISH and chips' analysis of pathology archivesPATHOLOGY INTERNATIONAL, Issue 8 2010Haruhiko Sugimura Practicing pathologists expect major somatic genetic changes in cancers, because the morphological deviations in the cancers they diagnose are so great that the somatic genetic changes to direct these phenotypes of tumors are supposed to be correspondingly tremendous. Several lines of evidence, especially lines generated by high-throughput genomic sequencing and genome-wide analyses of cancer DNAs are verifying their preoccupations. This article reviews a comprehensive morphological approach to pathology archives that consists of fluorescence in situ hybridization with bacterial artificial chromosome (BAC) probes and screening with tissue microarrays to detect structural changes in chromosomes (copy number alterations and rearrangements) in specimens of human solid tumors. The potential of this approach in the attempt to provide individually tailored medical practice, especially in terms of cancer therapy, is discussed. [source] | |||||||||||||