Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

Listeria infection of Caco-2 cells

ABSTRACT: This experiment set contains all of the arrays described in Baldwin et al., Genome Biology, 2002. All experiments are time courses, with the exception of multiple measurements for the zero time point in the parallel time course for the purpose of zero transformation. The parallel four hour time course was performed on a single day and three independent measurements were taken prior to infection. The eight hour time courses were each performed on different days, with single time zero measurements. Each array represents a measurement of human mRNA from cultured intestinal epithelial cells (red channel), relative to the control reference pool of mRNA (green channel), at different time points during the course of an infection by Listeria monocytogenes, or the mutants actA (defective in actin-based motility) and prfA (defective in virulence factor gene expression). Set of arrays organized by shared biological context, such as organism, tumors types, processes, etc. Computed

ORGANISM(S): Homo sapiens

SUBMITTER: David Baldwin

PROVIDER: E-GEOD-3567 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Publications

A gene-expression program reflecting the innate immune response of cultured intestinal epithelial cells to infection by Listeria monocytogenes.

Baldwin David N DN Vanchinathan Veena V Brown Patrick O PO Theriot Julie A JA

Genome biology 20021223 1

<h4>Background</h4>Listeria monocytogenes is a Gram-positive, facultative, intracellular bacterial pathogen found in soil, which occasionally causes serious food-borne disease in humans. The outcome of an infection is dependent on the state of the infected individual's immune system, neutrophils being key players in clearing the microorganism from the body. The first line of host defense, however, is the intestinal epithelium.<h4>Results</h4>We have examined the transcriptional response of cultu ...[more]

PMID: 12537547

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Project description:Summary: Breast cancer cell lines have been used widely to investigate breast cancer pathobiology and new therapies. Breast cancer is a molecularly heterogeneous disease, and it is important to understand how well and which cell lines best model that diversity. In particular, microarray studies have identified molecular subtypes (luminal A, luminal B, ERBB2-associated, basal-like and normal-like) with characteristic gene-expression patterns and underlying DNA copy number alterations (CNAs). Here, we studied a collection of breast cancer cell lines to catalog molecular profiles and to assess their relation to breast cancer subtypes. Whole-genome DNA microarrays were used to profile gene expression and CNAs in a collection of 52 widely-used breast cancer cell lines, and comparisons were made to existing profiles of primary breast tumors. Hierarchical clustering was used to identify gene-expression subtypes, and Gene Set Enrichment Analysis (GSEA) to discover biological features of those subtypes. Genomic and transcriptional profiles were integrated to discover within high-amplitude CNAs candidate cancer genes with coordinately altered gene copy number and expression. Transcriptional profiling of breast cancer cell lines identified one luminal and two basal-like (A and B) subtypes. Luminal lines displayed an estrogen receptor (ER) signature and resembled luminal-A/B tumors, basal-A lines were associated with ETS-pathway and BRCA1 signatures and resembled basal-like tumors, and basal-B lines displayed mesenchymal and stem-cell characteristics. Compared to tumors, cell lines exhibited similar patterns of CNA, but an overall higher complexity of CNA (genetically simple luminal-A tumors were not represented), and only partial conservation of subtype-specific CNAs. We identified 80 high-level DNA amplifications and 13 presumptive homozygous deletions, and the resident genes with concomitantly altered gene-expression, highlighting known and novel candidate breast cancer genes. Overall, breast cancer cell lines were genetically more complex than tumors, but retained expression patterns with relevance to the luminal-basal subtype distinction. The compendium of molecular profiles defines cell lines suitable for investigations of subtype-specific pathobiology, biomarkers and therapies, and provides a resource for discovery of new breast cancer genes. HEEBO oligonucleotide microarrays from the Stanford Functional Genomics Facility were used to perform gene expression profiling of 50 human breast epithelial cell lines, in comparison to a universal RNA reference. Expression data were analyzed by hierarchical clustering to identify subgroups, and gene set enrichment analysis to identify subgroup-specific gene pathways.

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Dataset Information

Listeria infection of Caco-2 cells

Publications

A gene-expression program reflecting the innate immune response of cultured intestinal epithelial cells to infection by Listeria monocytogenes.

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