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Transcription profiling of an orthotopic mouse model of lung cancer vs control mice and A549 cells in culture

ABSTRACT: An orthotopic model of lung cancer was established in Rag-2 null mice by injecting 1 x 106 GFP-A549 cells into the mouse lung via the trachea. After 6 weeks a primary tumor develops in the right lung. RNA was collected from tumors established in the orthotopic model after 6 weeks in three separate mice and from the right lung of three sham control mice that were injected with PBS by the same method. RNA was also collected from the A549 cells in culture. RNA was applied to an Affymetrix Customized Protease Microarray (HuMu ProtIn chip). This custom chip is able to distinguish human and mouse genes by using oligonucleotides specific for each species. The chip contains all known human and mouse proteases and protease inhibitors. A distribution of gene expression from a comparison of all human and mouse genes present in the tumor vs. the control lung was indentified as well as a distribution of gene expression from a comparison of all human and mouse genes present in the tumor vs. the cells in culture. Human and mouse genes differentially expressed in each group were identifed.

ORGANISM(S): Homo sapiens

SUBMITTER: Acuff Heath

PROVIDER: S-ECPF-MEXP-489 | biostudies-other |

REPOSITORIES: biostudies-other

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Transcription profiling of an orthotopic mouse model of lung cancer vs control mice and A549 cells in culture

Project description:An orthotopic model of lung cancer was established in Rag-2 null mice by injecting 1 x 106 GFP-A549 cells into the mouse lung via the trachea. After 6 weeks a primary tumor develops in the right lung. RNA was collected from tumors established in the orthotopic model after 6 weeks in three separate mice and from the right lung of three sham control mice that were injected with PBS by the same method. RNA was also collected from the A549 cells in culture. RNA was applied to an Affymetrix Customized Protease Microarray (HuMu ProtIn chip). This custom chip is able to distinguish human and mouse genes by using oligonucleotides specific for each species. The chip contains all known human and mouse proteases and protease inhibitors. A distribution of gene expression from a comparison of all human and mouse genes present in the tumor vs. the control lung was indentified as well as a distribution of gene expression from a comparison of all human and mouse genes present in the tumor vs. the cells in culture. Human and mouse genes differentially expressed in each group were identifed.

2006-03-01 | E-MEXP-489 | biostudies-arrayexpress

Transcription profiling of human A549 induced tumours in mice treated with PCI-5002, PCI-5003, or control vehicle

Project description:We have demonstrated that water-soluble zinc ionophores can be administered to mice at relatively high doses and inhibit the growth of A549 lung cancer cells grown in xenograft models. Gene expression profiles of tumor specimens harvested from mice four hours after treatment confirmed that the activation of stress responsive genes occurs in vivo. These findings lead us to propose that the pharmacologic delivery of zinc to tumors using water solubilized ionophores is a potential approach to cancer therapy. Experiment Overall Design: 1.25 million A549 cells were injected subcutaneously/intramuscularly into the right hind flank of 6 week old CD-1 nude mice that had been irradiated with 4 Gy of total body irradiation from a 137Cs radiation source one day prior to tumor implantation. When the average size of tumors reached approximately 100 mm3, mice were randomized by tumor size to treatment groups, typically containing 6-8 mice per group. Tumor and body weight measurements were performed three times per week. Tumor volume was calculated using the equation V (mm3) = a x b2/2, where a is the largest diameter and b is the smallest diameter. No significant body weight loss was observed. To perform gene expression profiling, mice were treated intravenously with one dose (100 μmol/kg) PCI-5002, PCI-5003, or control vehicle (4 mice per group) when the average A549 tumor size reached 500 mm3. After four hours, tumors were harvested and snap frozen immediately on dry ice. Tumor tissue was homogenized, and total RNA was isolated and subjected to analysis using Human Genome U133 Plus 2.0 Arrays as described above.

| S-ECPF-GEOD-6962 | biostudies-other

Transcription profiling of human A549 lung cancer cells treated with resveratrol (25microM) or with ethanol control for 48 h

Project description:Resveratrol, a natural phytoestrogen found in red wine and a variety of plants, is reported to have protective effects against lung cancer, however there is very little work directed towards the understanding of the mechanism of action of resveratrol in lung cancer. In this study we used an experimental approach to understand the biological activity and molecular mechanisms of resveratrol in A549 lung cancer cells. Gene expression profiles were compiled using an oligonucleotide microarray to determine altered expression levels in resveratrol treated cells. Experiment Overall Design: A549 cells were treated with resveratrol (25microM) or with ethanol control for 48 h. 4 samples in all were hybridized to the affymetrix chip, one control sample and 3 replicates of the resveratrol treated sample. Experiment Overall Design: Gene ontology-based gene lists are supplied in a supplementary file (Genelists.txt) at the foot of this record.

| S-ECPF-GEOD-9008 | 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

Transcription profiling of human lung adenocarcinoma derived cell line A549 treated with testosterone

Project description:Effect of testosterone treatment on gene expression of lung adenocarcinoma derived cell line A549

| S-ECPF-MEXP-2003 | biostudies-other

Transcription profiling of human lung adenocarcinoma derived cell line A549 treated with dexamethasone

Project description:Effect of dexamethasone on gene expression in lung adenocarcinoma derived cell line A549

| S-ECPF-MEXP-2004 | biostudies-other

Transcription profiling of human A549 lung cancer cells and their isogenic mitochondrial DNA (mtDNA)-depleted rho zero counterparts grown in cell culture and as tumor xenografts in immune-deficient mice

Project description:Interactions between the gene products encoded by the mitochondrial and nuclear genomes play critical roles in normal eukaryotic cellular function. Here, we characterized the metabolic and transcriptional properties of A549 lung cancer cells and their isogenic mitochondrial DNA (mtDNA)-depleted rho zero counterparts grown in cell culture and as tumor xenografts in immune-deficient mice. A manuscript summarizing our conclusions is under review. Experiment Overall Design: A549 rho zero and their parental A549 cells were grown in culture and as xenografts in nude mice. All experiments conducted in culture were performed in triplicate (6 experiments total) and all experiments conducted in xenografts were performed in quadruplicate (8 experiments total). A manuscript summarizing our experimental design is under review.

| S-ECPF-GEOD-10957 | biostudies-other

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 of human LM2 cells transduced with miR-335 expression vector vs. control

Project description:the LM2 breast cancer cell line is an in vivo derived line from the MDA-MB-231 parental line. this LM2 line has been transduced either with a short hairpin control or miR-335 expression vector. Experiment Overall Design: the LM2 cell line is transduced either with a short hairpin control vector or miR-335 expression vector.

| S-ECPF-GEOD-9586 | biostudies-other

Transcription profiling of human MDAMB231 breast cancer cells by Parvin-beta in 2D vs 3D culture conditions

Project description:Parvin-beta is a focal adhesion protein downregulated in human breast cancer cells. Loss of Parvin-beta contributes to increased integrin-linked kinase activity, cell-matrix adhesion, and invasion through the extracellular matrix in vitro. The effect of ectopic Parvin-beta expression on the transcriptional profile of MDA-MB-231 breast cancer cells, which normally do not express Parvin-beta was evaluated. Particular emphasis was placed upon propagating MDA-MB-231 breast cancer cells in three-dimensional culture matrices. Gene expression profiles of vector control and Parvin-beta transfected MDA-MB-231 cells cultured on (A) monomeric type I collagen coated plastic, (B) embedded in a type I collagen gel, and (C) embedded in basement membrane (growth factor reduced Matrigel), were compared. Interestingly, Parvin-beta re-expression in MDA-MB-231 cells increased the mRNA expression, serine 82 phosphorylation (mediated by CDK9), and activity of the nuclear hormone receptor, peroxisome proliferator-activated receptor gamma (PPARgamma) and a concomitant increase in lipogenic gene expression as a downstream effector of PPARgamma. Importantly, Parvin-beta suppressed breast cancer growth in vivo with associated decreased proliferation. These data suggest that Parvin-beta might influence breast cancer progression.. Experiment Overall Design: The MDA-MB-0231 transfectants were cultured for 7 days in each growth condition and total RNA isolated using Trizol reagent (Invitrogen). Genes either upregulated or downregulated in Parvin-beta transfectants versus vector control cells were compared among the 3 different growth conditions. Venn diagrams were generated using GeneSpring software and used to produce gene lists that were unique to a particular growth condition, or shared between two or all three growth conditions. The focus was primarily on gene expression alterations observed in the 3D collagen type I and 3D Matrigel conditions.

| S-ECPF-GEOD-9747 | biostudies-other

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