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Results for “expression profiling”

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PubMed2005

[Effect of NGX6 on gene expression profile of colon carcinoma cell line HT-29].

BACKGROUND & OBJECTIVE: Colon cancer is one of the most common malignant tumors, but the mechanism involved in its pathogenesis is not fully understood. Under the foundation of early study, we intended to explore the effects of NGX6 on the gene expression profile of colon carcinoma cell line HT-29. METHODS: pcDNA3.1-NGX6-transfected HT-29 cells were used as the test, and empty vector-transfected HT-29 cells were used as the control. Differentially expressed genes were screened with high-throughout BiostarH-80sx1 DNA microarray; part of the results of DNA microarray was confirmed by reverse transcription-polymerase chain reaction (RT-PCR). RESULTS: NGX6 transfection induced wide changes of the gene expression profile of HT-29 cells. A total of 377 genes were up-regulated or down-regulated by more than 3 folds, which were involved in cell signal transduction, cell cycle controlling, cell apoptosis, cytokinetics, gene transcription and translation, DNA damage and repairing, protein synthesis, metabolism, and so on. Some of them belonged to some important signal pathways related with cell proliferation and metastasis, such as DDK1, ILK, MMP-1 and COL11A1 in Wnt/beta-catenin signal pathway, ILK in ILK signal pathway, EpHB2 in Eph-Ephrins signal pathway, ROCK2 in RhoA signal pathway, RANBP1 in RanGTPase signal pathway, and RBBP1 in RB/RBBP1 signal pathway. CONCLUSION: NGX6 transfection leads to molecular changes of some important signal pathways, and may suppress cell proliferation and metastasis of tumor by regulating these signal pathways.

Cell Proliferation↗

PubMed2004

Hunting drug targets by systems-level modeling of gene expression profiles.

Structural learning of Bayesian networks applied to sets of genome-wide expression patterns has been recently discovered as a potentially useful tool for the systems-level statistical description of gene interactions. We train and analyze Bayesian networks with the goal of inferring biological aspects of gene function. Our two-component approach focuses on supporting the drug discovery process by identifying genes with central roles for the network operation, which could act as drug targets. The first component, referred to as scale-free analysis, uses topological measures of the network-related to a high-traffic load of genes-as estimators for their functional importance. The second component, referred to as generative inverse modeling, is a method of estimating the effect of a simulated drug treatment or mutation on the global state of the network, as measured in the expression profile. We show for a dataset from acute lymphoblastic leukemia patients that both approaches are suitable for finding genes with central cellular functions. In addition, generative inverse modeling correctly identifies a known oncogene in a purely data-driven way.

Algorithms↗

PubMed2002

Gene expression profiles of poor-prognosis primary breast cancer correlate with survival.

The extensive heterogeneity of breast cancer complicates the precise assessment of tumour aggressiveness, making therapeutic decisions difficult and treatments inappropriate in some cases. Consequently, the long-term metastasis-free survival rate of patients receiving adjuvant chemotherapy is only 60%. There is a genuine need to identify parameters that might accurately predict the effectiveness of this treatment for each patient. Using cDNA arrays, we profiled tumour samples from 55 women with poor-prognosis breast cancer treated with adjuvant anthracycline-based chemotherapy. Gene expression monitoring was applied to a set of about 1000 candidate cancer genes. Differences in expression profiles provided molecular evidence of the clinical heterogeneity of disease. First, we confirmed the capacity of a 23-gene predictor set, identified in a previous study, to distinguish between tumours associated with different survival. Second, using a refined gene set derived from the previous one, we distinguished, among the 55 clinically homogeneous tumours, three classes with significantly different clinical outcome: 5-year overall survival and metastasis-free survival rates were respectively 100% and 75% in the first class, 65% and 56% in the second and 40% and 20% in the third. This discrimination resulted from the differential expression of two clusters of genes encoding proteins with diverse functions, including the estrogen receptor (ER). Another finding was the identification of two ER-positive tumour subgroups with different survival. These results indicate that gene expression profiling can predict clinical outcome and lead to a more precise classification of breast tumours. Furthermore, the characterization of discriminator genes might accelerate the development of new specific and alternative therapies, allowing more rationally tailored treatments that are potentially more efficient and less toxic.

Breast Neoplasms↗

PubMed2001

Optimal procedure for extracting RNA from human ocular tissues and expression profiling of the congenital glaucoma gene FOXC1 using quantitative RT-PCR.

PURPOSE: To develop methods for obtaining high quality RNA from human donor eyes and to determine the expression profile of the congenital glaucoma gene FOXC1 in human ocular tissues. METHODS: To obtain high quality RNA from donor eyes, several different preservation methods were tested including storing eyes on ice, freezing eyes, and placing eyes in the commercial fixative RNAlaterTM prior to dissection and RNA extraction. Nine different ocular tissues from human donors were dissected and examined. Pigment-free total RNA was isolated and used for quantitative real-time RT-PCR using FOXC1 and GAPDH (internal standard) primers to assess the quality and expression of FOXC1. RESULTS: An expression profile of FOXC1 in human ocular tissues was determined using quantitative PCR of RNA isolated using a simple and effective procedure for ocular tissue preservation and pigment-free RNA isolation. Higher quality RNA was obtained from human donor eyes preserved in RNAlaterTM compared to RNA extracted from eyes stored on ice or frozen at -80 degrees C. RNA extraction techniques that removed interfering pigment from ocular tissues produced RNA that could be easily amplified by PCR. In the adult human eye, expression of FOXC1 was greatest in the trabecular meshwork (TM) followed by the optic nerve head, choroid/RPE, ciliary body, cornea, and iris. FOXC1 expression levels were much lower in other non-ocular human tissues, such as liver, muscle, lung, heart, and kidney. CONCLUSIONS: Using an optimized donor eye preservation method and tissue RNA isolation procedure, we show that the FOXC1 transcription factor gene, which is known to be associated with developmental glaucoma, also may have an important role in the adult eye.

Aged↗

PubMed2003

Quick gene expression profiling of promyelocytic cell line HL-60.

OBJECTIVE: A number of techniques have been developed to perform gene expression profiling. We report preliminary results from our exploratory study, using sequential analysis of gene expression (SAGE) technique, to profile the undifferentiated and differentiated HL-60 cells in line with our interest to characterize the cancer phenotype. The aim of the study is to evaluate the technique and to understand the molecular bases of these 2 states of cells. METHODS: HL-60 cells were differentiated after treatment with dimethyl sulfoxide. Tag libraries were prepared from the messenger RNAs of the undifferentiated and differentiated cells according to the SAGE protocol. The search for genes corresponding to the tags was carried out using SAGE software. The tags and the genes from the 2 libraries were compared for their levels of expression. The study was carried out at the King Faisal Specialist Hospital and Research Centre, Riyadh, Kingdom of Saudi Arabia during the year 2001. RESULTS: A comparison of tags from the 2 libraries revealed that 151 tags corresponding to 57 genes expressed differentially: 60 tags were elevated and 59 were repressed in the undifferentiated cells. Thirty-two tags were equally expressed in both types of cells. Of the corresponding genes, 25 were expressed at higher, 17 at lower, while 15 were expressed at comparable levels in both cell types. In the profile of undifferentiated cells, the genes involved in mitochondrial function and protein synthesis were prominent, while in the differentiated cells, the genes coding for proteins associated with cell membranes, signal transduction and for cell specific functions were prominent. The genes, expressed equally in both the cell types, were concerned with the maintenance of the living state. CONCLUSION: Sequential analysis of gene expression is a useful technique for gene expression profiling. As previously indicated by others, a dedicated team can generate useful data within reasonable time limits.

Cell Differentiation↗

PubMed2005

[Effects of cyclosporin A on gene expression profiles of NIT-1 pancreatic beta cell line].

OBJECTIVE: To observe the effects of cyclosporin A (CsA) on gene expression profiles of NIT-1 pancreatic beta cells cell line using microarray technique. METHODS: NIT-1 cells were exposed to cyclosporin A treatment (10 micromol/L) for 24 h and the differential gene expressions were assessed using microarray technique. RESULTS: After 24h of CsA treatment, 38 of the 4096 genes tested were up-regulated, including 13 genes with known functions involving stress response, cell growth and protein synthesis. Meanwhile 46 genes were down-regulated, including 25 genes with known functions involving cell growth and maturation, oxidative phosphorylation and protein synthesis. Changes of gene expression of Zfr,Tpi and Pax6 were confirmed by semi-quantitative reverse transcription polymerase chain reaction. CONCLUSIONS: CsA treatment for 24 h induces changes in the gene expression profiles of NIT-1 pancreatic beta cells. Down-regulation of the genes related to cell growth and maturation, oxidative phosphorylation and protein synthesis may partly explain the mechanisms that CsA inhibits the release of insulin from pancreatic beta cells.

Animals↗

PubMed2006

Hierarchical gene expression profiles of HUVEC stimulated by different lipid A structures obtained from Porphyromonas gingivalis and Escherichia coli.

The ability of lipid A structural variants to elicit unique endothelial cell gene expression was examined by measuring global gene expression profiles in human umbilical cord vein endothelial cells (HUVEC) using Affymetrix full genome chips. Two lipid A structural variants obtained from Porphyromonas gingivalis designated PgLPS(1435/1449) and PgLPS(1690) as well as LPS obtained from Escherichia coli wild type and an E. coli msbB mutant (missing myristic acid in the lipid A) were examined. Each of these lipid A structures has been shown to interact with TLR4; however, PgLPS(1435/1449) and E. coli msbB LPS have been shown to be TLR4 antagonists while PgLPS(1690) and wild-type E. coli LPS are TLR4 agonists. It was found that PgLPS(1435/1449) and PgLPS(1690) as well as E. coli msbB LPS activated a subset of those genes significantly transcribed in response to E. coli wild-type LPS. Furthermore, the subset of genes expressed in response to the different lipid A structural forms were those most significantly activated by wild-type E. coli LPS demonstrating a hierarchy in TLR4-dependent endothelial cell gene activation. A unique gene expression profile for the weak TLR4 agonist PgLPS(1690) was observed and represents a TLR4 hierarchy in endothelial cell gene activation.

Cell Line↗

PubMed2006

TCDD-induced alterations in gene expression profiles of the developing mouse paw do not influence morphological differentiation of this potential target tissue.

The aryl-hydrocarbon receptor (AhR) is a ligand-dependent transcription factor that mediates the toxicity of certain halogenated aromatic hydrocarbons including 2,3,7,8-tetra-chlorodibenzo-p-dioxin (TCDD). These compounds are potent developmental toxicants that can alter gene expression and disrupt processes of proliferation and differentiation. It has not yet been determined which tissues during development are most sensitive to these compounds, nor which genes are directly associated with the toxicities. We developed a transgenic (TG) mouse model to delineate the temporal and spatial context of transcriptionally active AhR by utilizing a dioxin responsive element-linked LacZ reporter system. The present study focuses on the pattern of TCDD-induced transgene expression localized to the footpad and digits of the paws between gestational days (GD) 13 and 18. Paw morphology was evaluated at several developmental stages following TCDD exposure. Gene expression profiles acquired by microarray technology were evaluated in the paws of fetuses exposed at GD 14.5. The results showed that TCDD exposure in utero induced LacZ expression in the developing paws. This expression appeared to be localized to the mesenchymal cell layer. Gross morphological changes were not observed in the paws prior to or after birth following TCDD exposure in utero. However, significant alterations in gene expression profiles in the developing paws were observed at 24 h following TCDD exposure in utero. These results indicate that the developing paw is a target tissue of TCDD in terms of altered gene expression, further validating the use of this AhR responsive reporter gene TG mouse model in studying AhR ligand-mediated responsiveness. However, the linkage of these changes to detectable biological outcomes in the paw remains unclear.

Animals↗

PubMedDate not supplied

Monitoring gene expression profile changes in bladder transitional cell carcinoma using cDNA microarray.

PURPOSE: Differential gene expression profiles between normal bladder mucosas and bladder transitional cell carcinomas TCC were detected. MATERIALS AND METHODS: cDNA microarrays were prepared by spotting PCR products of 12,800 human genes onto specially treated glass slides. The cDNA probes were prepared by labeling normal bladder mucosa mRNA and TCC tissue mRNA with Cy3-dUTP and Cy5-dUTP respectively through reverse transcription. The arrays were then hybridized against the cDNA probe mixture and the fluorescent signals were scanned. The ratios of Cy5/Cy3 were computed. Northern analysis was used to confirm the results of microarray hybridization. RESULTS: Eighty-three genes (0.65%), whose ratios of Cy5/Cy3 were greater than 4.0 or less than 0.25, were screened out after 10 groups of hybridization. In the cancerous tissues 28 of them showed higher expression and 55 lower. Twenty-three genes are unregistered in GenBank. These differentially expressed genes are always involved in the physiological processes such as signal transduction, apoptosis and cell cycle, etc. CONCLUSIONS: This technique provides a powerful method for quantitative analysis of the expression levels of thousands of genes in parallel, and is used to identify genes involved in TCC carcinogenesis. The data obtained by this means are comparable to those obtained by other methods. Using cDNA microarrays to define alterations in gene expression associated with a specific cancer may be an efficient way to uncover the clues to specific molecular derangements that account for its pathogenesis and thus identify potential targets for therapeutic intervention.

Aged↗

PubMed2003

Analyzing tumor gene expression profiles.

A brief introduction to high throughput technologies for measuring and analyzing gene expression is given. Various supervised and unsupervised data mining methods for analyzing the produced high-dimensional data are discussed. The main emphasis is on supervised machine learning methods for classification and prediction of tumor gene expression profiles. Furthermore, methods to rank the genes according to their importance for the classification are explored. The approaches are illustrated by exploratory studies using two examples of retrospective clinical data from routine tests; diagnostic prediction of small round blue cell tumors (SRBCT) of childhood and determining the estrogen receptor (ER) status of sporadic breast cancer. The classification performance is gauged using blind tests. These studies demonstrate the feasibility of machine learning-based molecular cancer classification.

Adult↗

PubMed2006

Comparative analysis and integrative classification of NCI60 cell lines and primary tumors using gene expression profiling data.

BACKGROUND: NCI60 cell lines are derived from cancers of 9 tissue origins and have been invaluable in vitro models for cancer research and anti-cancer drug screen. Although extensive studies have been carried out to assess the molecular features of NCI60 cell lines related to cancer and their sensitivities to more than 100,000 chemical compounds, it remains unclear if and how well these cell lines represent or model their tumor tissues of origin. Identification and confirmation of correct origins of NCI60 cell lines are critical to their usage as model systems and to translate in vitro studies into clinical potentials. Here we report a direct comparison between NCI60 cell lines and primary tumors by analyzing global gene expression profiles. RESULTS: Comparative analysis suggested that 51 of 59 cell lines we analyzed represent their presumed tumors of origin. Taking advantage of available clinical information of primary tumor samples used to generate gene expression profiling data, we further classified those cell lines with the correct origins into different subtypes of cancer or different stages in cancer development. For example, 6 of 7 non-small cell lung cancer cell lines were classified as lung adenocarcinomas and all of them were classified into late stages in tumor progression. CONCLUSION: Taken together, we developed and applied a novel approach for systematic comparative analysis and integrative classification of NCI60 cell lines and primary tumors. Our results could provide guidance to the selection of appropriate cell lines for cancer research and pharmaceutical compound screenings. Moreover, this gene expression profile based approach can be generally applied to evaluate experimental model systems such as cell lines and animal models for human diseases.

Carcinoma, Non-Small-Cell Lung↗

PubMed2005

The influence of muscle type and dystrophin deficiency on murine expression profiles.

The phenotypic differences among Duchenne muscular dystrophy patients, mdx mice, and mdx(5cv) mice suggest that despite the common etiology of dystrophin deficiency, secondary mechanisms have a substantial influence on phenotypic severity. The differential response of various skeletal muscles to dystrophin deficiency supports this hypothesis. To explore these differences, gene expression profiles were generated from duplicate RNA targets extracted from six different skeletal muscles (diaphragm, soleus, gastrocnemius, quadriceps, tibialis anterior, and extensor digitorum longus) from wild-type, mdx, and mdx(5cv) mice, resulting in 36 data sets for 18 muscle samples. The data sets were compared in three different ways: (1) among wild-type samples only, (2) among all 36 data sets, and (3) between strains for each muscle type. The molecular profiles of soleus and diaphragm separate significantly from the other four muscle types and from each other. Fiber-type proportions can explain some of these differences. These variations in wild-type gene expression profiles may also reflect biomechanical differences known to exist among skeletal muscles. Further exploration of the genes that most distinguish these muscles may help explain the origins of the biomechanical differences and the reasons why some muscles are more resistant than others to dystrophin deficiency.

Animals↗

PubMed2004

Gene expression profiling of normal and malignant CD34-derived megakaryocytic cells.

Gene expression profiles of bone marrow (BM) CD34-derived megakaryocytic cells (MKs) were compared in patients with essential thrombocythemia (ET) and healthy subjects using oligonucleotide microarray analysis to identify differentially expressed genes and disease-specific transcripts. We found that proapoptotic genes such as BAX, BNIP3, and BNIP3L were down-regulated in ET MKs together with genes that are components of the mitochondrial permeability transition pore complex, a system with a pivotal role in apoptosis. Conversely, antiapoptotic genes such as IGF1-R and CFLAR were up-regulated in the malignant cells, as was the SDF1 gene, which favors cell survival. On the basis of the array results, we characterized apoptosis of normal and ET MKs by time-course evaluation of annexin-V and sub-G1 peak DNA stainings of immature and mature MKs after culture in serum-free medium with an optimal thrombopoietin concentration, and annexin-V-positive MKs only, with decreasing thrombopoietin concentrations. ET MKs were more resistant to apoptosis than their normal counterparts. We conclude that imbalance between proliferation and apoptosis seems to be an important step in malignant ET megakaryocytopoiesis.

Adult↗

PubMed2003

Expression profiling of mouse endometrial cancers microdissected from ethanol-fixed, paraffin-embedded tissues.

Expression-profiling studies have helped define genetic changes associated with carcinogenesis. Determining which alterations in gene expression are causally associated with cancer and which result from the general dysregulation in gene expression that is characteristic of malignancies remains a problem. Transcriptional profiling of early lesions (small cancers or precancers) holds promise for identifying biologically important changes in gene expression. There are, however, technical barriers to the study of small tumors. The total number of cells available for analysis is limiting. It is also often difficult to distinguish cancer cells from normal proliferating cells in frozen sections that are typically used as a source of RNA. Here we describe an ethanol fixation and paraffin-embedding protocol that preserves tissue architecture and cellular morphology of the mouse endometrium, and allows for the recovery of high-quality RNA from microdissected cells. We performed GeneChip expression profiling using RNA from 800 to 4400 cells microdissected from ethanol-fixed, paraffin-embedded uteri. Endometrial adenocarcinomas exhibited changes in the levels of a number of messages known to be abnormally expressed in cancer, and differential expression of additional transcripts not previously implicated in carcinogenesis. We confirmed increased Amd1 expression in RNAs from mouse endometrial carcinomas that were hybridized to GeneChips and validated overexpression of this transcript in additional tumors.

Animals↗

PubMedDate not supplied

Protein expression profile of newly diagnosed acute lymphoblastic leukemia in children developing relapses.

The purpose of this investigation was to evaluate the expression profile of proteins involved in children with newly diagnosed acute lymphoblastic leukemia (ALL) children who are developing relapses. For this reason, the expressions of 10 proteins including proto-oncogene and tumor suppressor gene products, proliferative factors and resistance parameters in 104 initial cases of childhood ALL were analyzed and the proteins correlated with ALL patients who experienced relapses. Applying immunocytochemical assays, we found that 4 out of the 10 parameters revealed a relationship to developing relapses (Fisher's exact tests). These were the oncogene product Fos (p=0.002), the drug resistance proteins glutathione S-transferase (p=0.008) and P-glycoprotein (P-pg/MDR1) (p=0.07) and protein kinase C (p=0.01). By means of hierarchical cluster analysis, we were able to show that the patients could be separated according to their protein expression profile into clusters consisting of patients whose ALL relapsed later and of patients who did not show relapses in the future.

Child↗

PubMed2004

The molecular signature of polycystic ovary syndrome (PCOS) theca cells defined by gene expression profiling.

Polycystic ovary syndrome (PCOS) is characterized by increased ovarian androgen secretion, anovulatory infertility due to arrested folliculogenesis, and is frequently found in association with insulin resistance and obesity. Characterization of PCOS theca cells demonstrated that elevated expression of the steroidogenic enzymes 17alpha hydroxylase/17,20 lyase (CYP17) and P450 side chain cleavage enzyme (CYP11A1) play a role in increased androgen production by 3beta-hydroxysteroid dehydrogenase in the PCOS theca cell. However, the gene networks and signal transduction pathways which cause the altered expansion of the steroid enzymes remain to be determined. In order to identify these gene networks and/or signaling pathways, we carried out global gene expression profiling of normal and PCOS theca cells using subtractive suppressive hybridization and oligonucleotide microarray analysis. These analyses demonstrated that approximately 2% of genes expressed in the theca cell exhibit altered mRNA abundance in PCOS. Characterization of these genes revealed that retinoic acid synthesis and Wnt signal transduction are altered in the PCOS theca cell. In addition, the transcription factor GATA6, which regulates the promoter activity of CYP17 and CYP11A, was increased in the PCOS compared to normal theca cells. Thus, global gene expression profiling has identified potential pathways which may determine the PCOS theca cell phenotype.

Animals↗

PubMed2005

A molecular analysis by gene expression profiling reveals Bik/NBK overexpression in sporadic breast tumor samples of Mexican females.

BACKGROUND: Breast cancer is one of the most frequent causes of death in Mexican women over 35 years of age. At molecular level, changes in many genetic networks have been reported as associated with this neoplasia. To analyze these changes, we determined gene expression profiles of tumors from Mexican women with breast cancer at different stages and compared these with those of normal breast tissue samples. METHODS: 32P-radiolabeled cDNA was synthesized by reverse transcription of mRNA from fresh sporadic breast tumor biopsies, as well as normal breast tissue. cDNA probes were hybridized to microarrays and expression levels registered using a phosphorimager. Expression levels of some genes were validated by real time RT-PCR and immunohistochemical assays. RESULTS: We identified two subgroups of tumors according to their expression profiles, probably related with cancer progression. Ten genes, unexpressed in normal tissue, were turned on in some tumors. We found consistent high expression of Bik gene in 14/15 tumors with predominant cytoplasmic distribution. CONCLUSION: Recently, the product of the Bik gene has been associated with tumoral reversion in different neoplasic cell lines, and was proposed as therapy to induce apoptosis in cancers, including breast tumors. Even though a relationship among genes, for example those from a particular pathway, can be observed through microarrays, this relationship might not be sufficient to assign a definitive role to Bik in development and progression of the neoplasia. The findings herein reported deserve further investigation.

Adult↗

PubMed2006

Expression profiles of bovine adeno-associated virus and avian adeno-associated virus display significant similarity to that of adeno-associated virus type 5.

We present the first detailed expression profiles of nonprimate-derived adeno-associated viruses, namely, bovine adeno-associated virus (B-AAV) and avian adeno-associated virus (A-AAV), which were obtained after the infection of cell lines derived from their natural hosts. In general, the profiles of B-AAV and A-AAV were quite similar to that of AAV5; however, both exhibited features found for AAV2 as well. Like adeno-associated virus type 5 (AAV5), B-AAV and A-AAV utilized an internal polyadenylation site [(pA)p]; however, it was used to greater relative levels by B-AAV than by A-AAV. Similar to AAV5, >99% of B-AAV RNAs generated from upstream promoters were polyadenylated at (pA)p and hence not spliced. In contrast, ca. 50% of the A-AAV RNAs generated from upstream promoters read through (pA)p, as seen for AAV2. However, A-AAV generated lower levels of spliced P5 and P19 products than does AAV2, suggesting that A-AAV generates lower relative levels of Rep 68 and Rep 40. An additional difference in the expression profile of these viruses was that B-AAV generated a greater level of ITR-initiated RNAs than did A-AAV or AAV5. In addition, we demonstrate that, like AAV2, transactivation of transcription of the capsid-gene promoter of B-AAV required both adenovirus and targeting of its Rep protein to the transcription template; however, expression of the capsid-gene promoter of A-AAV was, like AAV5, largely independent of both adenovirus and its Rep proteins.

Animals↗