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Mus musculus
24 Downloadable Samples
Illumina HiSeq 2000
Description
Macrophages represent an important component of the tumor microenvironment and play a complex role in cancer progression. These cells are characterized by a high degree of plasticity, and alter their phenotype in response to local environmental cues. While the M1/M2 classification of macrophages has been widely used, the complexity of macrophage phenotypes specifically in lung cancer has not been well studied. In this study we employed an orthotopic immunocompetent model of lung adenocarcinoma in which murine lung cancer cells are directly implanted into the left lobe of syngeneic mice. Using multi-marker flow cytometry we defined and recovered several distinct populations of monocytes/macrophages from tumors at different stages of progression. We used RNA-seq transcriptional profiling to define distinct features of each population and determine how they change during tumor progression. We defined an alveolar resident macrophage population that does not change in number and express multiple genes related to lipid metabolism and lipid signaling. We also defined a population of tumor-associated macrophages that increase dramatically with tumor, and selectively express a panel of chemokines genes. A third population, which resembles tumor-associated monocytes, expresses a large number of genes involved in matrix remodeling. By correlating transcriptional profiles with clinically prognostic genes, we show that specific monocyte/macrophage populations are enriched in genes that predict good or poor outcome in lung adenocarcinoma, implicating these subpopulations as critical determinants of patient survival. Our data underscore the complexity of monocytes/macrophages in the tumor microenvironment, and suggest that distinct populations play specific roles in tumor progression. Overall design: mRNA profiles of macrophage/monocyte cells isolated from murine control or tumor-bearing lung. From naive mice: MacA cells (MacA-N), MacB1 cells (MacB1-N), MacB2 cells (MacB2-N); from 2 week tumor bearing mice: MacA cells (MacA-2wk), MacB2 cells (MacB2-2wk), MacB3 cells (MacB3-3wk); from 3-week tumor bearing mice: MacB2 (MacB2-3wk), MacB3 cells (MacB3-3wk). Each population was analyzed in triplicate (cells were isolated in 3 independent experiments).
Publication Title
Expression Profiling of Macrophages Reveals Multiple Populations with Distinct Biological Roles in an Immunocompetent Orthotopic Model of Lung Cancer.
Sample Metadata Fields
Cell line, Subject
View Samples- Mus musculus
- 6 Downloadable Samples
Affymetrix Mouse Gene 1.1 ST Array (mogene11st)
Description
Mouse mammary carcinoma cell line 4TO7 was used in this experiment. Six2 overepxression experiment.The mouse Six2 cDNA taken from CMV-sport6 (Open Biosystems) was cloned into a pcDNA3.1-hygromycin vector and transfected into 4TO7 cells, after which stably transfected cells were selected. Gene expression profiles were performed in triplicate for the control and over-expressed lines.
Publication Title
Homeoprotein Six2 promotes breast cancer metastasis via transcriptional and epigenetic control of E-cadherin expression.
Sample Metadata Fields
Cell line
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GSE2514- Mus musculus, Homo sapiens
- 83 Downloadable Samples
- Affymetrix Murine Genome U74A Version 2 Array (mgu74av2)
Description
Lung tumors
Publication Title
Analysis of orthologous gene expression between human pulmonary adenocarcinoma and a carcinogen-induced murine model.
Sample Metadata Fields
No sample metadata fields
View Samples- Homo sapiens
- 62 Downloadable Samples
- Affymetrix Human Gene 1.0 ST Array (hugene10st)
Description
Persistent bronchial dysplasia (BD) is associated with increased risk of developing invasive squamous cell carcinoma (SCC) of the lung. We hypothesized that differences in gene expression profiles between persistent and regressive BD would identify cellular processes that underlie progression to SCC. RNA expression arrays (Affymetrix Hu 1.0) comparing baseline biopsies from 32 bronchial sites that persisted/progressed to 31 regressive sites showed 395 differentially expressed genes (ANOVA, FDR</=0.05). Thirty-one pathways showed statistically significant evidence of altered activity between the two groups. Multiple pathways were associated with cell cycle control/proliferation, inflammation, or epithelial differentiation/cell-cell adhesion. Polo-like kinase 1 (PLK1) was associated with multiple cell cycle pathways. Cultured persistent BD cells showed increased PLK1 expression, and following treatment with PLK1 inhibitor, showed induction of apoptosis, G2/M phase arrest and decreased proliferation compared to untreated cells. These effects were not seen in normal or regressive BD cultures. Inflammatory pathway activity was decreased in persistent BD and the presence of an inflammatory infiltrate was more common in regressive BD. Regressive BDs were also associated with trends toward overall increases in macrophages and T-lymphocytes and altered polarization of these inflammatory cell subsets. Increased desmoglein 3 and plakoglobin expression was associated with higher grade and persistence of BD. The results identify alterations in cell cycle control, inflammatory activity, and epithelial differentiation/cell-cell adhesion in the persistent subset of BDs that are associated with high risk for progression to invasive SCC. These pathways may provide strong markers of risk and effective targets for lung cancer prevention.
Publication Title
Altered Cell-Cycle Control, Inflammation, and Adhesion in High-Risk Persistent Bronchial Dysplasia.
Sample Metadata Fields
Age, Specimen part
View Samples- Homo sapiens
- 53 Downloadable Samples
- Illumina HumanHT-12 V3.0 expression beadchip
Description
This SuperSeries is composed of the SubSeries listed below.
Publication Title
Frequent MYC coamplification and DNA hypomethylation of multiple genes on 8q in 8p11-p12-amplified breast carcinomas.
Sample Metadata Fields
Age, Specimen part
View Samples- Homo sapiens
- 97 Downloadable Samples
- Illumina HumanHT-12 V3.0 expression beadchip
Description
Genomic and expression profiling using 38K BAC array-CGH and Illumina HT-12 beadchips were performed on 97 diploid invasive breast tumors to assess the impact of gene dosage on gene expression patterns and the effect of other mechanisms on transcriptional levels. Patient stratification was performed according to axillary lymph node status (node-negative, pN0; node-positive, pN1) and overall survival (>8-year survivors; breast cancer-specific mortality within 8 years of diagnosis). Array-CGH results was validated by FISH using tumors showing HER2/neu gene amplification and expression profiling was confirmed using qPCR for 16 transcripts.
Publication Title
Clinical implications of gene dosage and gene expression patterns in diploid breast carcinoma.
Sample Metadata Fields
Disease, Disease stage
View Samples- Homo sapiens
- 97 Downloadable Samples
- Illumina HumanHT-12 V3.0 expression beadchip
Description
Genomic and expression profiling using 38K BAC array-CGH and Illumina HT-12 beadchips were performed on 97 diploid invasive breast tumors to assess the impact of gene dosage on gene expression patterns and the effect of other mechanisms on transcriptional levels. Patient stratification was performed according to axillary lymph node status (node-negative, pN0; node-positive, pN1) and overall survival (>8-year survivors; breast cancer-specific mortality within 8 years of diagnosis). Array-CGH results was validated by FISH using tumors showing HER2/neu gene amplification and expression profiling was confirmed using qPCR for 16 transcripts.
Publication Title
Clinical implications of gene dosage and gene expression patterns in diploid breast carcinoma.
Sample Metadata Fields
Disease, Disease stage
View Samples- Homo sapiens
- 53 Downloadable Samples
- Illumina HumanHT-12 V3.0 expression beadchip
Description
Transcriptomic profiling of human breast tumors.
Publication Title
Clinical implications of gene dosage and gene expression patterns in diploid breast carcinoma.
Sample Metadata Fields
Age, Specimen part
View Samples- Homo sapiens
- 23 Downloadable Samples
- Illumina HiSeq 2000
Description
Transcriptomic profiling of human breast tumors using RNA sequencing Overall design: Evaluation of common fusion transcripts, genetic variants, and gene expression patterns in 8p11-p12 amplified breast carcinomas
Publication Title
Genome-wide multi-omics profiling of the 8p11-p12 amplicon in breast carcinoma.
Sample Metadata Fields
Age, Specimen part, Subject
View Samples- Homo sapiens
- 18 Downloadable Samples
- IlluminaGenomeAnalyzerII
Description
gene expression profiling by RNA-seq in THP-1 cells treated with 1,25(OH)2D3 for 2.5-24 h Overall design: three independent experiments of 1,25(OH)2D3 time course in THP-1 cells
Publication Title
Epigenome-wide effects of vitamin D and their impact on the transcriptome of human monocytes involve CTCF.
Sample Metadata Fields
No sample metadata fields
View Samples