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Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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Gene expression in organized and disorganized human breast epithelial cells

ABSTRACT: We have reported more than a dozen microenvironmental factors whose signaling must be integrated in order to effect an organized, functional tissue morphology. In order to identify underlying commonalities in gene transcription associated with the phenotype, we compared the gene expression of organized and disorganized epithelial cells of the HMT-3522 breast cancer progression series: the non-malignant S1 cells that form polarized spheres (‘acini’), the malignant T4-2 cells that form large tumor-like clusters, and the ‘phenotypically reverted’ T4-2 cells that polarize as a result of correction of the microenvironmental signaling. 24 samples were analyzed: 5 samples were non-malignant S1 cells that formed organized spherical structures ('acini'), 5 samples were the isogenic malignant counterpart of S1 cells, namely the T4-2 cells, which grow into disorganized large cell clusters; and 14 samples of T4-2 cells that had been treated with different reverting agents, these reverting agents cause the T4-2 cells to 'revert' in phenotype so that they resemble the structures formed by S1 cells.

ORGANISM(S): Homo sapiens

SUBMITTER: Sabine Becker-Weimann

PROVIDER: E-GEOD-50444 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Gene expression in organized and disorganized human breast epithelial cells

Project description:We have reported more than a dozen microenvironmental factors whose signaling must be integrated in order to effect an organized, functional tissue morphology. In order to identify underlying commonalities in gene transcription associated with the phenotype, we compared the gene expression of organized and disorganized epithelial cells of the HMT-3522 breast cancer progression series: the non-malignant S1 cells that form polarized spheres (‘acini’), the malignant T4-2 cells that form large tumor-like clusters, and the ‘phenotypically reverted’ T4-2 cells that polarize as a result of correction of the microenvironmental signaling.

2013-10-01 | GSE50444 | GEO

Transcription profiling of human mammary epithelial cell lines with finite life span and immortal non-malignant cells - time series

Project description:Nonmalignant human mammary epithelial cells (HMEC) seeded in laminin-rich extracellular matrix (lrECM) form polarized acini and, in doing so, transit from a disorganized proliferating state to an organized growth-arrested state. We hypothesized that the gene expression pattern of organized and growth-arrested HMECs would share similarities with breast tumors with good prognoses. Using Affymetrix HG-U133A microarrays, we analyzed the expression of 22,283 gene transcripts in 184 (finite life span) and HMT3522 S1 (immortal nonmalignant) HMECs on successive days after seeding in a lrECM assay. Both HMECs underwent growth arrest in G0-G1 and differentiated into polarized acini between days 5 and 7. We identified gene expression changes with the same temporal pattern in both lines and examined the expression of these genes in a previously published panel of microarray data for 295 breast cancer samples. We show that genes that are significantly lower in the organized, growth-arrested HMEC than in their proliferating counterparts can be used to classify breast cancer patients into poor and good prognosis groups with high accuracy. This study represents a novel unsupervised approach to identifying breast cancer markers that may be of use clinically. Experiment Overall Design: We analyzed gene expression in 184 (finite life span) and HMT3522 S1 (immortal non-malignant) HMECs on successive days (3, 5, and 7) post-seeding in a laminin-rich extracellular matrix assay. Both HMECs underwent growth arrest in G0/G1 and differentiated into polarized acini between days 5 and 7.

2008-06-15 | E-GEOD-8096 | biostudies-arrayexpress

Transcription profiling time series of finite life span and immortal non-malignant human mammary epithelial cell lines

2007-07-12 | GSE8096 | GEO

Transcription profiling time series of finite life span and immortal non-malignant human mammary epithelial cell lines

Project description:We analyzed gene expression in 184 (finite life span) and HMT3522 S1 (immortal non-malignant) HMECs on successive days (3, 5, and 7) post-seeding in a laminin-rich extracellular matrix assay. Both HMECs underwent growth arrest in G0/G1 and differentiated into polarized acini between days 5 and 7.

2007-03-15 | E-MEXP-1006 | biostudies-arrayexpress

Homo sapiens

Project description:Gene expression in organized and disorganized human breast epithelial cells

| PRJNA217499 | ENA

Transcription profiling of human T4-2 neoplastic breast epithelial cells that overexpressed N-CoR2 in response to death induction

Project description:The series represent gene expression profiles of T4-2 neoplastic breast epithelial cells that overexpressed N-CoR2 and were treated with the death ligand TRAIL in three-dimensional reconstituted basement membrane culture. Experiment Overall Design: Four replicate cultures were established for each of the 4 experiment groups, including those using T4-2 cells that stably expressed N-CoR2 (T4-2_NCOR2), T4-2 cells expressing the empty vector (T4-2_vector), TRAIL-treated T4-2 N-CoR2 cells (T4-2_NCOR2_TRAIL), and TRAIL-treated T4-2 vector cells (T4-2_vector_TRAIL). Cells were grown on top of reconstituted basement membrane for 6 days and then treated with TRAIL (1 Î¼g/mL) or vehicles for 4 hours before the collection of RNA samples.

2008-10-25 | E-GEOD-8346 | biostudies-arrayexpress

Network Analysis of Breast Cancer Progression and Reversal with a Tree-Evolving Network Algorithm

Project description:The HMT3522 progression series of breast cells has been used to discover the roles of tissue architecture, microenvironment and signaling molecules in nonmalignant and malignant breast cell growth and behaviors, including the potential of various factors to cause phenotypic reversion of malignant cells to nonmalignant states. Despite many efforts to delineate key signaling pathways governing the malignant as well as the phenotypic reversion behaviors of T4 cells, much remains to be elucidated about the regulatory mechanisms underlying these cell states at the systems level. Here, we analyzed gene expression microarray profiles obtained from this progression series in both phenotypically malignant and reverted states using our newly developed tree-lineage-based network detection algorithm, Treegl. Our work suggests analysis of various conditions of reversion (including non-reverted) of the HMT3522 cells using Treegl can be a model system to study drug effects on breast cancer cells, and may become a tool for effective drug discovery and target identification. Gene expression microarray data was obtained using Affymetrix GeneChip Human Genome U133A arrays to analyze 15 total RNA samples prepared from the HMT3522 breast cells grown in 3D lrECM and treated with various reverting agents or vehicle control.

2014-07-24 | E-GEOD-42125 | biostudies-arrayexpress

Tumor T4 Sectors

Project description:The following CGH experiments were conducted on four sectors (S1-S4) from a single primary ductal carcinoma tumor (T4).

2009-07-10 | GSE16601 | GEO

Microarray gene expression data in liver, gonadal adipose tissue, pancreatic islets, and skeletal muscle in two lines of the Berlin Fat Mouse (BFMI861-S1 and BFMI861-S2)

Project description:The Berlin Fat Mouse Inbred line (BFMI) is a model for obesity and the metabolic syndrome. This study aimed to identify genetic variants associated with liver weight, liver triglycerides, and body weight using the obese BFMI sub-line BFMI861-S1. BFMI861-S1 mice are insulin resistant and store ectopic fat in the liver.

2022-03-27 | E-MTAB-11512 | biostudies-arrayexpress

Identification of genes responsive to change in apical polarity in the breast epithelium

Project description:Differentiation of monolayered epithelia is characterized by the formation of a basoapical polarity axis, except during the early stages of cancer development. Using mammary glandular structures (acini) produced in a three-dimensional cell culture system we have demonstrated that, in order for mammary epithelial cells to exit quiescence and enter the cell cycle, acini have to lose apical polarity. In order to identify the genes dependent on apical polarity that could control cell quiescence, and possibly other aspects of tissue homeostasis, we have used Affymetrix technology microarray analysis of the 22,277 features/genes of the Human Genome U133A 2.0 array Chip in apically polarized and non-polarized breast epithelial acinar cells in three-dimensional culture. Genes commonly down-regulated in two treatments that altered apical polarity compared to control were considered to be dependent on apical polarity status for their transcription. Apically polarized (Control) and two different populations of non-polarized human mammary epithelial cells (18-alpha-glycyrrhetinic acid =AGA, and 5-aza-2'-deoxycytidine =Aza) were used for microarray analysis containing four biological replicates (1-4) for each treatment. The two treatments that cause loss of apical polarity were compared to reference apically polarized control samples using two different statistical analysis methods (FDR and HolmM-bM-^@M-^Ys).

2012-02-29 | E-GEOD-35165 | biostudies-arrayexpress

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