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Transcription profiling by array of human lung cancer cells after treatment with tobacco smoke condensate

ABSTRACT: Polycomb-mediated repression of Dkk-1 activates Wnt signaling and enhances tumorigenic potential of lung cancer cells following tobacco smoke exposure Experiment Overall Design: microarray techniques were used to examine proliferation and gene expression in A549 and Calu-6 lung cancer cells cultured in normal media with or without tobacco smoke condensate (TSC)

ORGANISM(S): Homo sapiens

SUBMITTER: Hussain M

PROVIDER: S-ECPF-GEOD-13309 | biostudies-other | 2009 Apr

REPOSITORIES: biostudies-other

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Transcription profiling by array of human lung cancer samples

Project description:We identified a tumor signature of 5 genes that aggregates the 156 tumor and normal samples into the expected groups. We also identified a histology signature of 75 genes, which classifies the samples in the major histological subtypes of NSCLC. A prognostic signature of 17 genes showed the best association with post-surgery survival time. The performance of the signatures was validated using a patient cohort of similar size A genome-wide gene expression analysis was performed on a cohort of 91 patients. We used 91 tumor- and 65 adjacent normal lung tissue samples. We defined sets of predictor genes (probe sets) with the expression profiles. The power of predictor genes was evaluated using an independent cohort of 96 non-small cell lung cancer- and 6 normal lung samples

| S-ECPF-GEOD-19188 | biostudies-other

Exposure of Human Lung Cells to Tobacco Smoke Condensate Inhibits the Nucleotide Excision Repair Pathway.

Project description:Exposure to tobacco smoke is the number one risk factor for lung cancer. Although the DNA damaging properties of tobacco smoke have been well documented, relatively few studies have examined its effect on DNA repair pathways. This is especially true for the nucleotide excision repair (NER) pathway which recognizes and removes many structurally diverse DNA lesions, including those introduced by chemical carcinogens present in tobacco smoke. The aim of the present study was to investigate the effect of tobacco smoke on NER in human lung cells. We studied the effect of cigarette smoke condensate (CSC), a surrogate for tobacco smoke, on the NER pathway in two different human lung cell lines; IMR-90 lung fibroblasts and BEAS-2B bronchial epithelial cells. To measure NER, we employed a slot-blot assay to quantify the introduction and removal of UV light-induced 6-4 photoproducts and cyclobutane pyrimidine dimers. We find a dose-dependent inhibition of 6-4 photoproduct repair in both cell lines treated with CSC. Additionally, the impact of CSC on the abundance of various NER proteins and their respective RNAs was investigated. The abundance of XPC protein, which is required for functional NER, is significantly reduced by treatment with CSC while the abundance of XPA protein, also required for NER, is unaffected. Both XPC and XPA RNA levels are modestly reduced by CSC treatment. Finally, treatment of cells with MG-132 abrogates the reduction in the abundance of XPC protein produced by treatment with CSC, suggesting that CSC enhances proteasome-dependent turnover of the protein that is mediated by ubiquitination. Together, these findings indicate that tobacco smoke can inhibit the same DNA repair pathway that is also essential for the removal of some of the carcinogenic DNA damage introduced by smoke itself, increasing the DNA damage burden of cells exposed to tobacco smoke.

| S-EPMC4938567 | biostudies-other

Transcription profiling by array of human lung cancer cells after treatment with dasatinib, imatinib, nilotinib or PD0325901

Project description:Cell Line: This experiment was designed to measure the transcriptional responses to four kinase inhibitors across a five-logarithm dose range. The A549 human lung cancer cell line was treated with dasatinib, imatinib or nilotinib (4 hours and 20 hours) or PD0325901 (4 hours). Treatments used a 12-point dose range (30 uM with 3-fold dilutions down to 0.17 nM; 0.5% DMSO vehicle for all treatments). Experimental design prevented row or column handling effects being confounded with dose effect.

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Transcription profiling by array of human non-small cell lung cancer tissue

Project description:PURPOSE The development of reliable gene expression profiling technology is having an increasing impact on our understanding of lung cancer biology. The present study aims to determine whether the phenotypic heterogeneity and genetic diversity of lung cancer are correlated. PATIENTS AND METHODS In this study, microarray analysis was performed in a set of 91 non-small cell lung cancer (NSCLC) samples in order to: establish gene signatures in primary adenocarcinomas and squamous-cell carcinomas; determine differentially expressed gene sequences at different stages of the disease; and identify sequences with biological significance for tumor progression. After microarray analysis, the expression level of 92 selected genes was validated by qPCR in an independent set of 70 samples. RESULTS Gene sequences were differentially expressed as a function of tumor type, stage, and differentiation grade. High upregulation was observed for KRT15 and PKP1, which may be good markers to distinguish squamous cell carcinoma samples. High downregulation was observed for DSG3 in stage IA adenocarcinomas. CONCLUSION Expression signatures in NSCLC distinguish tumor type, stage, and differentiation grade. Keywords: Tumor vs control comparative genomics study 91 samples studied, 46 tumors and 45 controls. All samples are paired except three.

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Transcription profiling by array of human lung cancer cells after treatment with various inhibitors of LIMK1 and LIMK2

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Transcription profiling by array of human primary lung adenocarcinomas

Project description:"Gene transcription in a set of 49 human primary lung adenocarcinomas and 9 normal lung tissue samples was examined using Affymetrix GeneChip technology. We aimed to investigate differential gene expression between the two tissue types. A total of 3,442 genes, called the set MAD, were found to be either up- or down-regulated by at least two fold between the two phenotypes. Genes assigned to a particular gene ontology term were found, in many cases, to be significantly unevenly distributed between the genes in and outside MAD. Terms that were overrepresented in MAD included functions directly implicated in cancer cell metabolism. Based on their functional roles and expression profiles, genes in MAD were grouped into likely co-regulated gene sets."

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Transcription profiling by array of human breast cancer cell lines after treatment with lapatinib

Project description:Dose and time course response of lapatinib in breast cancer cell lines.

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Acute and Chronic Environmental Tobacco Smoke Condensate Exposure to Primary Human Bronchial Epithelial Cells

Project description:The goal was to assess global gene expression changes in primary human bronchial epithelial cells exposed to environmental tobacco smoke (ETS) condensate. ETS-C was standardized by HPLC analysis and two timepoints of exposure in two different donor bronchial epithelial cell populations were assessed. These findings demonstrate that even short exposure (4.5 h) to ETS is sufficient to induce a stress response, as reflected by decreased antioxidant levels, induced HSP family members, and modulation of the family of glutathione metabolism enzymes in primary human lung cells. Upon longer exposures (48 h) with ETS-condensate, bronchial epithelial cells arrest at the G2/M phase of the cell cycle. Taken together, these data support a stress-induced state in primary human bronchial epithelial cells that culminates in cell cycle arrest. Keywords: time course, comparative, stress response

2006-12-25 | GSE4234 | GEO

Transcription profiling by array of human breast cancer metastases

Project description:Comparisons among breast cancer metastases at different organs revealed distinct microenvironments as characterized by cytokine content. Such microenvironment distinction might be important to dictate how the cancer cells adapt to survival before they successfully colonize. Experiment Overall Design: 58 breast cancer metastases from different organs were profiled and compared by the expression level of over 400 cytokines. 29 samples were incuded in this series. 29 others as well as 7 in the present series were profiled on U133A platforms and included in series GSE14018.

| S-ECPF-GEOD-14017 | biostudies-other

Transcription profiling by array of human non-small cell lung cancer and normal adjacent lung tissue matched pairs

Project description:Affymetrix exon array data set (HuEx-1.0_st) derived from matched pairs of non-small cell lung cancer (NSCLC) and normal adjacent lung tissue (NAT). This data set includes both the adenocarcinoma (AdCa) as well as the squamous cell carcinoma (SCC) subtype of NSCLC.

| S-ECPF-MEXP-2644 | biostudies-other

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