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

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

PURPOSE: Under different culture conditions, periodontal ligament (PDL) stem cells are capable of differentiating into cementoblast-like cells, adipocytes, and collagen-forming cells. Several previous studies reported that because of the stem cells in the PDL, the PDL have a regenerative capacity which, when appropriately triggered, participates in restoring connective tissues and mineralized tissues. Therefore, this study analyzed the genes involved in mineralization during differentiation of human PDL (hPDL) cells, and searched for candidate genes possibly associated with the mineralization of hPDL cells. METHODS: To analyze the gene expression pattern of hPDL cells during differentiation, the hPDL cells were cultured in two conditions, with or without osteogenic cocktails (beta-glycerophosphate, ascorbic acid and dexamethasone), and a DNA microarray analysis of the cells cultured on days 7 and 14 was performed. Reverse transcription-polymerase chain reaction was performed to validate the DNA microarray data. RESULTS: The up-regulated genes on day 7 by hPDL cells cultured in osteogenic medium were thought to be associated with calcium/iron/metal ion binding or homeostasis (PDE1A, HFE and PCDH9) and cell viability (PCDH9), and the down-regulated genes were thought to be associated with proliferation (PHGDH and PSAT1). Also, the up-regulated genes on day 14 by hPDL cells cultured in osteogenic medium were thought to be associated with apoptosis, angiogenesis (ANGPTL4 and FOXO1A), and adipogenesis (ANGPTL4 and SEC14L2), and the down-regulated genes were thought to be associated with cell migration (SLC16A4). CONCLUSIONS: This study suggests that when appropriately triggered, the stem cells in the hPDL differentiate into osteoblasts/cementoblasts, and the genes related to calcium binding (PDE1A and PCDH9), which were strongly expressed at the stage of matrix maturation, may be associated with differentiation of the hPDL cells into osteoblasts/cementoblasts.
Adipocytes ; Adipogenesis ; Apoptosis ; Ascorbic Acid ; Calcium ; Cell Differentiation ; Cell Movement ; Cell Survival ; Connective Tissue ; Durapatite ; Gene Expression ; Gene Expression Profiling ; Homeostasis ; Humans ; Microarray Analysis ; Oligonucleotide Array Sequence Analysis ; Periodontal Ligament ; Stem Cells

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 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

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

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

OBJECTIVE: This study was designed to detect genes specifically expressed in severe preeclamptic placentas. METHODS: Placenta tissues were collected immediately after delivery from 5 preeclamptic patients and 5 normal pregnant women. Total RNAs of each placenta were extracted and hybridized for a cDNA microarray. Of the microarray data, four up-regulated genes (DSCR4, GPA, PCDHGB1, Hemogen) and four down-regulated genes (IL1R2, MGST1, GAS1 GREB1) were selected and reverse transcriptase-polymerase chain reaction was used to confirm the results of cDNA microarray. RESULTS: The expression fold for each up-regulated gene was 2.2 times for DSCR4, 2.7 times for PCDHGB1, 3.5 times for Hemogen, 5.2 times for GPA on the cDNA microarray. The expression fold for each down-regulated gene was 3.3 times for IL1R2, 4.2 times for MGST1, 4.9 times for GAS1 and 2.3 times for GREB1 on the cDNA microarray. The expression fold for each up- regulated gene was 5.21 times for DSCR4, 3.01 times for PCDHGB1, and 4,53 times for Hemogen and 2.2 times for GPA on RT-PCR. The expression fold for each down-regulated gene was 2.7 times for IL1R2, 2.22 times for MGST1, 2.53 times for GAS1 and 1.83 times for GREB1 on the RT-PCR. CONCLUSION: DSCR4, PCDHGB1, Hemogen and GPA as the up-regulated genes and IL1R2, MGST1, GAS1 and GREB1 as the down-regulated genes, which were found and selected by the cDNA microarray, might be considered to be novel biomarkers for preeclampsia.
Biomarkers ; Chimera ; Female ; Gene Expression ; Humans ; Microarray Analysis ; Oligonucleotide Array Sequence Analysis ; Placenta ; Pre-Eclampsia ; Pregnant Women ; RNA

OBJECTIVES: We analyzed gene-expression profiles after 14 day odontogenic induction of human dental pulp cells (DPCs) using a DNA microarray and sought candidate genes possibly associated with mineralization. MATERIALS AND METHODS: Induced human dental pulp cells were obtained by culturing DPCs in odontogenic induction medium (OM) for 14 day. Cells exposed to normal culture medium were used as controls. Total RNA was extracted from cells and analyzed by microarray analysis and the key results were confirmed selectively by reverse-transcriptase polymerase chain reaction (RT-PCR). We also performed a gene set enrichment analysis (GSEA) of the microarray data. RESULTS: Six hundred and five genes among the 47,320 probes on the BeadChip differed by a factor of more than two-fold in the induced cells. Of these, 217 genes were upregulated, and 388 were down-regulated. GSEA revealed that in the induced cells, genes implicated in Apoptosis and Signaling by wingless MMTV integration (Wnt) were significantly upregulated. CONCLUSIONS: Genes implicated in Apoptosis and Signaling by Wnt are highly connected to the differentiation of dental pulp cells into odontoblast.
Apoptosis ; Dental Pulp ; Gene Expression ; Genes, vif ; Humans ; Microarray Analysis ; Odontoblasts ; Oligonucleotide Array Sequence Analysis ; Polymerase Chain Reaction ; RNA