Cells consistently face stressful conditions, which cause them to modulate a variety of intracellular processes and adapt to these environmental changes via regulation of gene expression. Hyperosmotic and oxidative stresses are significant stressors that induce cellular damage, and finally cell death. In this study, oligonucleotide microarrays were employed to investigate mRNA level changes in cells exposed to hyperosmotic or oxidative conditions. In addition, since heat shock protein 70 (HSP70) is one of the most inducible stress proteins and plays pivotal role to protect cells against stressful condition, we performed microarray analysis in HSP70 overexpressing cells to identify the genes expressed in a HSP70 dependent manner. Under hyperosmotic or oxidative stress conditions, a variety of genes showed altered expression. Down regulation of protein phosphatase1 beta (PP1 beta) and sphingosine 1 phosphate phosphatase 1 (SPPase1) was detected in both stress conditions. Microarray analysis of HSP70 overexpressing cells demonstrated that diverse mRNA species depend on the level of cellular HSP70. Genes encoding lysyl oxidase, thrombospondin 1, and procollagen displayed altered expression in all tested conditions. The results of this study will be useful to construct networks of stress response genes.
Cell Death ; Down-Regulation ; Gene Expression Regulation ; Gene Expression* ; Heat-Shock Proteins ; HSP70 Heat-Shock Proteins ; Microarray Analysis ; Oligonucleotide Array Sequence Analysis ; Oxidative Stress* ; Procollagen ; Protein-Lysine 6-Oxidase ; RNA, Messenger ; Sphingosine ; Thrombospondin 1

OBJECTIVES: Methyl-CpG binding protein 2 (MeCP2) is a ubiquitous epigenetic factor that represses gene expression by modifying chromatin. Mutations in the MeCP2 gene cause Rett syndrome, a progressive neurodevelopmental disorder. Recent studies also have shown that MeCP2 plays a role in carcinogenesis. Specifically, functional ablation of MeCP2 suppresses cell growth and leads to the proliferation of cancer cells. However, MeCP2's function in adult tissues remains poorly understood. We utilized a weight matrix-based comparison software to identify transcription factor binding site (TFBS) of MeCP2-regulated genes, which were recognized by cDNA microarray analysis. METHODS: MeCP2 expression was silenced using annealed siRNA in HEK293 cells, and then a cDNA microarray analysis was performed. Functional analysis was carried out, and transcriptional levels in target genes regulated by MeCP2 were investigated. TFBS analysis was done within genes selected by the cDNA microarray analysis, using a weight matrix-based program and the TRANSFAC 6.0 database. RESULTS: Among the differentially expressed genes with a change in expression greater than two-fold, 189 genes were up-regulated and 91 genes were down-regulated. Genes related to apoptosis and cell proliferation (JUN, FOSL2, CYR61, SKIL, ATF3, BMABI, BMPR2, RERE, and FALZ) were highly up-regulated. Genes with anti-apoptotic and anti-proliferative functions (HNRPA0, HIS1, and FOXC1) were down-regulated. Using TFBS analysis within putative promoters of novel candidate target genes of MeCP2, disease-related transcription factors were identified. CONCLUSIONS: The present results provide insights into the new target genes regulated by MeCP2 under epigenetic control. This information will be valuable for further studies aimed at clarifying the pathogenesis of Rett syndrome and neoplastic diseases.
Adult ; Apoptosis ; Binding Sites ; Carcinogenesis ; Carrier Proteins ; Cell Proliferation ; Chromatin ; Epigenomics ; Gene Expression ; HEK293 Cells ; Humans* ; Methyl-CpG-Binding Protein 2 ; Microarray Analysis ; Oligonucleotide Array Sequence Analysis ; Rett Syndrome ; RNA, Small Interfering ; Transcription Factors

OBJECTIVES: Methyl-CpG binding protein 2 (MeCP2) is a ubiquitous epigenetic factor that represses gene expression by modifying chromatin. Mutations in the MeCP2 gene cause Rett syndrome, a progressive neurodevelopmental disorder. Recent studies also have shown that MeCP2 plays a role in carcinogenesis. Specifically, functional ablation of MeCP2 suppresses cell growth and leads to the proliferation of cancer cells. However, MeCP2's function in adult tissues remains poorly understood. We utilized a weight matrix-based comparison software to identify transcription factor binding site (TFBS) of MeCP2-regulated genes, which were recognized by cDNA microarray analysis. METHODS: MeCP2 expression was silenced using annealed siRNA in HEK293 cells, and then a cDNA microarray analysis was performed. Functional analysis was carried out, and transcriptional levels in target genes regulated by MeCP2 were investigated. TFBS analysis was done within genes selected by the cDNA microarray analysis, using a weight matrix-based program and the TRANSFAC 6.0 database. RESULTS: Among the differentially expressed genes with a change in expression greater than two-fold, 189 genes were up-regulated and 91 genes were down-regulated. Genes related to apoptosis and cell proliferation (JUN, FOSL2, CYR61, SKIL, ATF3, BMABI, BMPR2, RERE, and FALZ) were highly up-regulated. Genes with anti-apoptotic and anti-proliferative functions (HNRPA0, HIS1, and FOXC1) were down-regulated. Using TFBS analysis within putative promoters of novel candidate target genes of MeCP2, disease-related transcription factors were identified. CONCLUSIONS: The present results provide insights into the new target genes regulated by MeCP2 under epigenetic control. This information will be valuable for further studies aimed at clarifying the pathogenesis of Rett syndrome and neoplastic diseases.
Adult ; Apoptosis ; Binding Sites ; Carcinogenesis ; Carrier Proteins ; Cell Proliferation ; Chromatin ; Epigenomics ; Gene Expression ; HEK293 Cells ; Humans* ; Methyl-CpG-Binding Protein 2 ; Microarray Analysis ; Oligonucleotide Array Sequence Analysis ; Rett Syndrome ; RNA, Small Interfering ; Transcription Factors

BACKGROUND: Uterine leiomyomas are common benign smooth muscle tumors among the reproductive aged-women. The research has been aimed to identify the differentially expressed genes between normal myometrium and leiomyoma and to investigate the effects of E2 on their expression. METHODS: Gene microarray analysis was performed to identify the differentially expressed genes between normal myomerium and leiomyoma. The data was confirmed at protein level by tissue microarray. RESULTS: Gene microarray analysis revealed 792 upregulated genes in leiomyoma. Four genes (tropomyosin 4 [TPM4], collagen, type IV, alpha 2 [COL4alpha2], insulin-like growth factor binding protein 5 [IGFBP5], tripartite motif-containing 28 [TRIM28]) showed the most dramatic upregulation in all leiomyoma samples. Tissue microarray analyses of 262 sample pairs showed significantly elevated expression of TPM4, IGFBP5, estrogen receptor-alpha, and progesterone receptor (PR) protein in leiomyoma from the patients in their forties, COL4alpha2 in the forties and fifties age-groups, and TRIM28 in the thirties age-group. PR, insulin-like growth factor 1 (IGF-1), IGF-1 receptor (IGF-1R) and IGFBP5 were induced by E2 in in vitro culture of tissue explants from which cells migrated throughout the plate. Among these, PR, IGF-1, IGFBP5 genes showed higher expression in tissue compared to cells-derived from tissue in leiomyoma and IGF-1R in leiomyoma cell. CONCLUSIONS: This observation implies the importance of the whole tissue context including the cells-derived from tissue in the research for the understanding of molecular mechanism of leiomyoma. Here, we report higher expression of TRIM28 in leiomyoma for the first time and identify E2-responsive genes that may have important roles in leiomyoma development.
Animals ; Collagen Type IV ; Estrogens ; Female ; Gene Expression ; Humans ; Immunohistochemistry ; Insulin-Like Growth Factor Binding Protein 5 ; Insulin-Like Growth Factor I ; Leiomyoma ; Mice ; Microarray Analysis ; Myometrium ; Oligonucleotide Array Sequence Analysis ; Receptor, IGF Type 1 ; Receptors, Progesterone ; Smooth Muscle Tumor ; Tissue Array Analysis ; Transcriptome ; Up-Regulation ; Uterus

The identification of differential gene expression between gray and black hairs is an important study in modern hair pigment research. In this experiment, the authors have applied new methods by the integration of three updated molecular biological tools, T7 RNA polymerase-based RNA amplification, representational difference analysis (RDA), and microarray analysis, to screen the differentially expressed genes in gray and black hairs. The genes more abundantly expressed in black hairs were pigment related proteins, such as Pmel17, 95kD melanocyte-specific secreted glycoprotein, MART-1, tyrosinase, tyrosinase-related protein 1 etc. Also, expression of the selenium-binding protein (hSBP) gene and the spast gene for spastin protein were up-regulated in black hairs compared to those in gray hairs. In gray hairs, many kinds of genes related with keratin, trichohyalin and transmembrane glycoprotein were more expressed. In particular ch 17, hRPK.142_H_19 was expressed in gray hairs as high signal intensity.
DNA* ; Gene Expression* ; Glycoproteins ; Hair* ; Mass Screening* ; Microarray Analysis ; Monophenol Monooxygenase ; Oligonucleotide Array Sequence Analysis* ; RNA

OBJECTIVE: To examine the mechanism for the inhibited differentiation of osteoclasts in rheumatoid arthritis synovial CD14+ osteoclast precursors, the different expressions of the osteoclastogenesis-related genes in rheumatoid arthritis (RA) synovial fluid CD14+ osteoclast precursors were compared with those of normal peripheral blood (PB) CD14+ osteoclast precursors. METHODS: The expression of osteoclastogenesis-related genes were examined using a gene expression oligonucleotide microarray. To validate the results of the microarray analysis, the mRNA expressions of osteoclastogenesis-related genes were measured by real-time PCR. RESULTS: Comparative analysis of the mRNA profiles showed significantly different expression of osteoclastogenesis- related genes, such as MafB, Id3 and LILRB4, in the RA synovial CD14+ osteoclast precursors, compared to that of normal PB CD14+ osteoclast precursors. CONCLUSION: The expression of the osteoclastogenesis-related genes in RA synovial CD14+ osteoclast precursors is different from that of the normal PB CD14+ osteoclast precursors. These results suggest that the different expression of osteoclastogenesis-related genes might be involved in the altered osteoclastogenesis in RA synovial osteoclast precursors.
Arthritis, Rheumatoid ; Genes, vif ; Macrophages ; Microarray Analysis ; Oligonucleotide Array Sequence Analysis ; Osteoclasts ; RNA, Messenger ; Synovial Fluid

The establishment of DNA microarray technology has enabled high-throughput analysis and molecular profiling of various types of cancers. By using the gene expression data from microarray analysis we are able to investigate diagnostic applications at the molecular level. The most important step in the application of microarray technology to cancer diagnostics is the selection of specific markers from gene expression profiles. In order to select markers of immortalization and transformation we used c-myc and H-ras(V12) oncogene-transfected NIH3T3 cells as our model system. We have identified 8751 differentially expressed genes in the immortalization/transformation model by multivariate permutation F-test (95% confidence, FDR <0.01). Using the support vector machine algorithm, we selected 13 discriminative genes which could be used to predict immortalization and transformation with perfect accuracy. We assayed H-ras(V12)-transfected "transformed" cells to validate our immortalization/transformation classification system. The selected molecular markers generated valuable additional information for tumor diagnosis, prognosis and therapy development.
Classification ; Diagnosis ; Gene Expression ; Microarray Analysis ; Oligonucleotide Array Sequence Analysis ; Prognosis ; Transcriptome ; Support Vector Machine

OBJECTIVES: Alteration of hippocampus was demonstrated in the maternal social separation(MSS) pups, separated from dams on postnatal day(pnd) 14 and placed alone. Therefore, to understand the molecular events involved in the MSS, we have initiated a search for gene profiles that are up or down-regulated in the hippocampus of MSS pups. METHODS: Analysis of cDNA microarray was performed by using total RNA extracted from the hippocampus of control and MSS pups on pnd 17. Also, passive-avoidance test was demonstrated on pnd 35. RESULTS: Up-regulation of Nedd4a was observed in the hippocampus of MSS pups. Also, MSS rats showed less elongation of latency in passive avoidance test. CONCLUSION: We suggest that environmental effects of MSS may be altered the neural and/or glial differentiation and synapse formation-related genes which may lead cognitive alterations in MSS rats.
Animals ; Gene Expression* ; Hippocampus* ; Memory ; Microarray Analysis* ; Oligonucleotide Array Sequence Analysis ; Rats* ; RNA ; Synapses ; Up-Regulation

BACKGROUND AND OBJECTIVES: Mucin hypersecretion is one of the main symptoms of inflammatory diseases in the respiratory tract. The authors previously reported that pleiotypic pro-inflammatory cytokine, interleukin (IL)-1beta, plays significant roles in the respiratory tract inflammation by inducing mucins (MUC2, MUC5AC, MUC8). However, the molecular mechanism for mucin hypersecretion in the respiratory tract is still unclear. MATERIALS AND METHOD: In order to understand the mechanisms of mucin hypersecretion in the airway epithelium, the differentially expressed proteins and genes in the lung mucoepidermoid carcinoma cell line (NCI-H292 cells), which were treated for 6 and 24 hours with IL-1beta (10 ng/ml), were identified using 2-dimensional polyacrylamide gel electrophoresis (2-D PAGE) proteomics and cDNA microarray analysis (8.6 K). RESULTS: In the 2-D PAGE, 8 differentially expressed proteins and 14 post-translational modification proteins were identified 6 and 24 hrs after the IL-1beta treatment. Microarray analysis identified a total of 413 genes (6.6%) in the 6-hour treatment group and 115 genes (2.0%) in the 24-hour treatment group that were regulated after the IL-1beta treatment. The differentially expressed genes that were regulated by the IL-1beta treatment were mostly found in the metabolic pathway rather than in the regulatory pathway. A comparison of the proteomic and microarray data showed that there was a large discrepancy between the protein expression and the gene expression levels. Among the genes encoding the proteins secreted in the airway, MUC5B was down-regulated but sialomucin CD 164, lysozyme, and the secretory leukocyte protease inhibitor (SLPI) were up-regulated. CONCLUSION: These results clearly show that the transcript levels have little value in predicting the extent of protein expression. Genomics and proteomics have different evaluation fields. Therefore, they may not provide all the information on the gene and protein profiles.
Carcinoma, Mucoepidermoid ; Cell Line ; Electrophoresis, Polyacrylamide Gel ; Epithelial Cells* ; Epithelium ; Gene Expression ; Genomics ; Inflammation ; Interleukin-1beta* ; Interleukins ; Lung ; Metabolic Networks and Pathways ; Microarray Analysis ; Mucins ; Mucus ; Muramidase ; Oligonucleotide Array Sequence Analysis ; Protein Processing, Post-Translational ; Proteomics ; Respiratory System ; Secretory Leukocyte Peptidase Inhibitor ; Sialomucins

Objetives: Identification of target genes for ethanol in neurons is important for understanding its molecular and cellular mechanism of action and the neuropathological changes seen in alcoholics. The purpose of this study is to identify of altered gene expression after acute treatmet of ethanol in rat gliom cells. METHODS: We used high density cDNA microarray chip to measure the expression patterns of multiple genes in cultured rat glioma cells. DNA microarrays allow for the simultaneous measurement of the expression of several hundreds of genes. RESULTS: After comparing hybridized signals between control and ethanol treated groups, we found that treatment with ethanol increased the expression of 15 genes and decreased the expression of 12 genes. Upregulated genes included Orthodenticle(Drosophila) homolog 1, procollagen type II, adenosine A2a receptor, GATA-bindning protein 2. Downregulated genes included diacylglycerol kinase beta, PRKC, Protein phosphatase 1, clathrin-associated protein 17, nucleoporin p58, proteasome. CONCLUSION: The gene changes noted were those related to the regulation of transcription, signal transduction, second messenger systems. modulation of ischemic brain injury, and neurodengeneration.Although some of the genes were previously known to be ethanol responsive, we have for the most part identified novel genes involved in the brain response to ethanol.
Alcoholics ; Animals ; Brain ; Brain Injuries ; Collagen Type II ; Diacylglycerol Kinase ; Ethanol* ; Gene Expression* ; Glioma* ; Humans ; Microarray Analysis* ; Neurons ; Nuclear Pore Complex Proteins ; Oligonucleotide Array Sequence Analysis ; Proteasome Endopeptidase Complex ; Protein Phosphatase 1 ; Rats* ; Receptor, Adenosine A2A ; Second Messenger Systems ; Signal Transduction