Dataset Information

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

ABSTRACT: 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.

SUBMITTER: Nymark P

PROVIDER: S-EPMC1821332 | biostudies-literature | 2007

REPOSITORIES: biostudies-literature

ACCESS DATA

Publications

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

Nymark Penny P Lindholm Pamela M PM Korpela Mikko V MV Lahti Leo L Ruosaari Salla S Kaski Samuel S Hollmén Jaakko J Anttila Sisko S Kinnula Vuokko L VL Knuutila Sakari S

BMC genomics 20070301

<h4>Background</h4>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 ...[more]

PMID: 17331233

Similar Datasets

Project description:Human conjunctival cell lines are useful tools for modeling ocular surface disease and evaluation of ocular drugs and cosmetics. However, gene expression in these cells may not be comparable to primary cultured cells, raising doubts that they could be used as a substitute. We aimed to ascertain the similarities of global gene expression between commonly used cell lines and primary cells using a microarray approach. The Affymetrix U133A chip (>22,000 genes) was used to investigate conjunctival tissue (CT), primary conjunctival epithelial cells (PCEC), two conjunctival epithelial cell lines (IOBA-NHC and ChWK), and HCEC-T, a human corneal epithelial cell line (control). Using principal component analysis, the PCEC profile was clustered more closely to conjunctival tissue than either of the two cell lines. Certain extracellular matrix genes were differentially upregulated in CT compared to PCEC, suggesting presence of fibroblasts in addition to epithelial cells in CT. Overall, 67.3% (95% CI: 66.7-67.9) of transcripts in IOBA-NHC were within 1.5-fold of the corresponding transcripts in PCEC, but only 62.2% (95% CI: 61.5-62.9) in the case of ChWK. In HCEC-T, the proportion was only 58.8% (95% CI 58.1-59.4), suggesting less resemblance to PCEC than the conjunctival epithelial cell lines. The IOBA-NHC profile was more similar to PCEC than ChWK, for all genes and genes concerned with membrane association, communication, development, and regulation of metabolism, especially protein and nucleic acid metabolism. The correlation of normalized gene expression levels was high between either the IOBA-NHC or ChWK and PCEC for genes concerned with cell defense, viral life cycle, antigen presentation, antioxidation, or ubiquitin ligation. In order to evaluate the functional significance of the altered gene expression in IOBA-NHC cells, we evaluated a few proteins important for epithelial differentiation or defense, corresponding to the transcripts for S100A9, TGM2, and TLR4. Protein levels of S100A9 and TGM2 were indeed raised, and TLR4 decreased, in IOBA-NHC compared to PCEC. Gene expression in conjunctival cell lines differs from primary cells, but the profile varies according to functional gene categories. Depending on the methodology of proposed studies, if there is limited availability of PCEC, NHC-IOBA may be more suitable than ChWK, but even then, epithelial differentiation and innate immunity functions in NHC-IOBA may differ from primary cells.

Dataset Information

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

Publications

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

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

Tweets