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Transcription profiling by array of human lung cell lines A549, Beas-2B and MeT5A after treatment with asbestos over a time course

ABSTRACT: Asbestos has been shown to cause chromosomal damage and DNA aberrations. The fiber is associated with many different lung diseases such as asbestosis, malignant mesothelioma, and lung cancer, but the disease-related processes are still largely unknown. Our aim was to identify specific gene expression profiles by using Affymetrix arrays, in human cell lines A549, Beas-2B, and MeT5A exposed to asbestos in a time-dependent manner. The hybridization data was analyzed using an algorithm specifically designed for clustering short time series expression data, a canonical correlation analysis (CCA) for identifying correlations between the cell lines, and a Gene Ontology (GO) analysis method for the identification of enriched differentially expressed biological processes. Samples from three cell lines were collected from asbestos exposed and non-exposed controls at 1h, 6h, 24h, 48h and 7 (168h) days (not all time-points for each cell lines). Replicates were done for one exposed sample of each cell line.

ORGANISM(S): Homo sapiens

SUBMITTER: Nymark P

PROVIDER: S-ECPF-GEOD-6013 | biostudies-other | 2007

REPOSITORIES: biostudies-other

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Transcription profiling of human lung cell lines A549, Beas-2B, and MeT5A exposed to asbestos, sampled at multiple time points

Project description:Asbestos has been shown to cause chromosomal damage and DNA aberrations. The fiber is associated with many different lung diseases such as asbestosis, malignant mesothelioma, and lung cancer, but the disease-related processes are still largely unknown. Our aim was to identify specific gene expression profiles by using Affymetrix arrays, in human cell lines A549, Beas-2B, and MeT5A exposed to asbestos in a time-dependent manner. The hybridization data was analyzed using an algorithm specifically designed for clustering short time series expression data, a canonical correlation analysis (CCA) for identifying correlations between the cell lines, and a Gene Ontology (GO) analysis method for the identification of enriched differentially expressed biological processes. Samples from three cell lines were collected from asbestos exposed and non-exposed controls at 1h, 6h, 24h, 48h and 7 (168h) days (not all time-points for each cell lines). Replicates were done for one exposed sample of each cell line.

2007-11-08 | E-GEOD-6013 | biostudies-arrayexpress

Transcription profiling of human A549 lung adenocarcinoma cell line time Course of TGF-beta treatment

Project description:Time Course of TGF-beta treatment of A549 lung adenocarcinoma cell line on Affymetrix HG_U133_plus_2 arrays; triplicate experiments. The goal of the experiment is to profile temporal gene expression changes during TGF-beta-induced epithelial-mesenchymal transition (EMT). During EMT cancer cells loose their epithelial specifc proteins and gain mesenchymal proteins to acquire migratory and invasive phenotype essential for metastasis. Human A549 lung adenocarcinoma cell line was treated with 5 ng/mL TGF-beta for 0, 0.5, 1, 2, 4, 8, 16, 24, and 72 h to induce EMT. The experiment was repeated 3 times. Samples were assayed using Affymetrix HG_U133_plus_2 arrays with 54675 probe-sets, using standard techniques. We provide the raw .CEL files and a supplementary Excel spreadsheet with log-transformed data and selected results from a statistical analysis. Experiment Overall Design: Human A549 lung adenocarcinoma cell line was treated with 5 ng/mL TGF-beta for 0, 0.5, 1, 2, 4, 8, 16, 24, and 72 h. The experiment was repeated 3 times. Samples were assayed using Affymetrix HG_U133_plus_2 arrays with 54675 probe-sets, using standard techniques. The 2 h sample of the third experiment was not run on an array due to poor RNA, so that only 26 arrays were run.

| S-ECPF-GEOD-17708 | biostudies-other

transcription profiling by array of stem cells isolated from non-small cell lung cancer cell lines (NCI-H2170 and A549) and normal lung epithelial cell line (PHBEC)

Project description:This study was designed to understand the transcriptomic composition and the biological functions of cancer stem cells isolated from non-small cell lung cancer line (NSCLC) Putative lung cancer stem cells were isolated from cancer cell lines based on expression of known stem cell surface markers: CD166, CD44 and EpCAM using the Fluorescence Activated Cell Sorter (FACS). Affymetrix microarray were performed on cancer stem cells isolated from normal lung epithelial cells and lung cancer cell lines (A549 and NCI-H2170) using GeneChip Human Gene 1.0 ST array. The normal putative stem cells isolated from normal primary human bronchial/trachial epithelial cell line (PHBEC) was serve as control. Putative cancer stem cells isolated from A549 and NCI-H2170 cell lines are the treatment group. Each sample was performed in triplicate and total number of samples are five (n=5)

| S-ECPF-GEOD-50627 | biostudies-other

Transcription profiling by array of A549 lung carcinoma cells expressing the transcription factor Nkx2-1

Project description:A transcription factor Nkx2-1 (also known as TTF-1) regulates the expression of different sets of genes. Gene expression analysis was performed using mRNAs from Nkx2-1-induced A549 cells compared to that from the control A549 cells. We used microarrays to detail the global program of gene expression controlled by Nkx2-1 and identified distinct classes of up-regulated and down-regulated genes. mRNAs were isolated from control and Nkx2-1-induced A549 cells and hybridized on Affymetrix microarrays. We sought to identify genes influenced by Nkx2-1.

| S-ECPF-GEOD-40584 | biostudies-other

Gene expression profiles in asbestos-exposed epithelial and mesothelial lung cell lines.

Project description:BACKGROUND: Asbestos has been shown to cause chromosomal damage and DNA aberrations. Exposure to asbestos causes many lung diseases e.g. asbestosis, malignant mesothelioma, and lung cancer, but the disease-related processes are still largely unknown. We exposed the human cell lines A549, Beas-2B and Met5A to crocidolite asbestos and determined time-dependent gene expression profiles by using Affymetrix arrays. The hybridization data was analyzed by using an algorithm specifically designed for clustering of short time series expression data. A canonical correlation analysis was applied to identify correlations between the cell lines, and a Gene Ontology analysis method for the identification of enriched, differentially expressed biological processes. RESULTS: We recognized a large number of previously known as well as new potential asbestos-associated genes and biological processes, and identified chromosomal regions enriched with genes potentially contributing to common responses to asbestos in these cell lines. These include genes such as the thioredoxin domain containing gene (TXNDC) and the potential tumor suppressor, BCL2/adenovirus E1B 19kD-interacting protein gene (BNIP3L), GO-terms such as "positive regulation of I-kappaB kinase/NF-kappaB cascade" and "positive regulation of transcription, DNA-dependent", and chromosomal regions such as 2p22, 9p13, and 14q21. We present the complete data sets as Additional files. CONCLUSION: This study identifies several interesting targets for further investigation in relation to asbestos-associated diseases.

| S-EPMC1821332 | biostudies-literature

Gene expression profiling of asbestos-related lung squamous cell carcinoma

Project description:To identify gene expression biomarkers associate with asbestos-related lung squamous cell carcinoma, we analyzed gene expression profiles for a total of 56 lung squamous cell carcinomas using 44K Illumina Gene Expression microarrays. Twenty-six cases had lung asbestos body counts above levels associated with urban dwelling (ARLC-SCC: asbestos-related lung cancer-squamous cell carcinoma) and 30 cases had no lung asbestos bodies (NARLC-SCC: non-asbestos related lung cancer- squamous cell carcinoma). Genes differentially expressed between ARLC-SCC and NARLC-SCC were identified on fold change and P-value, and then prioritised using gene ontology. Total RNA was obtained from fresh frozen lung tumour tissue and stratified by asbestos phenotype. Gene expression profiling was performed to identify differences in the gene profiles of asbestos-related and non-asbestos related lung squamous cell carcinomas.

| S-ECPF-GEOD-23822 | biostudies-other

Time Course of TGF-beta treatment of A549 lung adenocarcinoma cell line

2009-08-20 | GSE17708 | GEO

Global profiling of platinum drugs resistant genes in A549 cell lines

Project description:Non Small Cell Lung Cancer (NSCLC) causes the premature death of over 1 million people worldwide each year, but remains inadequately understood at the molecular level. To provide new insights for NSCLC treatment we performed a molecular characterisation of wild type and platinum drugs resistance in A549 cells. Transcriptome profiling revealed contrasting patterns of gene expression in sensitive and resistant cells and identified genes whose expression was highly correlated with the platinum drugs. Our results revealed a gene set of 15 transcripts whose expression was highly correlated with platinum-resistance in NSCLC A549 cell lines.

| S-ECPF-MEXP-3123 | biostudies-other

Time course transcriptional profiling of senescing barley leaves.

Project description:Cell senescence occurs as a part of developmental or stress-induced process. It is tightly regulated and involves a sequence of metabolic and structural alterations, eventually leading to cell death. Dark-induced leaf senescence is a useful model for studying senescence-related events. To facilitate the integration of physiological and molecular studies utilizing this model, we generated the microarray data set providing time course gene expression profiles in senescing barley leaves. Here, we describe the detailed procedures and data analysis scheme of our experiment. The entire data set (available at NCBI/GEO database under GSE62539) has been successively explored to find the genes differentially expressed during the senescence process as well as to identify genes with the invariant expression as reliable references for qPCR or ddPCR experiments.

| S-EPMC4535845 | biostudies-literature

Conditioned medium from asbestos-exposed fibroblasts affects proliferation and invasion of lung cancer cell lines.

Project description:The importance of the role of fibroblasts in cancer microenvironment is well-recognized. However, the relationship between fibroblasts and asbestos-induced lung cancer remains underexplored. To investigate the effect of the asbestos-related microenvironment on lung cancer progression, lung cancer cells (NCI-H358, Calu-3, and A549) were cultured in media derived from IMR-90 lung fibroblasts exposed to 50 mg/L asbestos (chrysotile, amosite, and crocidolite) for 24 h. The kinetics and migration of lung cancer cells in the presence of asbestos-exposed lung fibroblast media were monitored using a real-time cell analysis system. Proliferation and migration of A549 cells increased in the presence of media derived from asbestos-exposed lung fibroblasts than in the presence of media derived from normal lung fibroblasts. We observed no increase in proliferation and migration in lung cancer cells cultured in asbestos-exposed lung cancer cell medium. In contrast, increased proliferation and migration in lung cancer cells exposed to media from asbestos-exposed lung fibroblasts was observed for all types of asbestos. Media derived from lung fibroblasts exposed to other stressors, such as hydrogen peroxide and UV radiation didn't show as similar effect as asbestos exposure. An enzyme-linked immunosorbent assay (ELISA)-based cytokine array identified interleukin (IL)-6 and IL-8, which show pleiotropic regulatory effects on lung cancer cells, to be specifically produced in higher amounts by the three types of asbestos-exposed lung fibroblasts than normal lung fibroblasts. Thus, the present study demonstrated that interaction of lung fibroblasts with asbestos may support the growth and metastasis of lung cancer cells and that chrysotile exposure can lead to lung cancer similar to that caused by amphibole asbestos (amosite and crocidolite).

| S-EPMC6730856 | biostudies-literature

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