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E-GEOD-8096 - Transcription profiling of human mammary epithelial cell lines with finite life span and immortal non-malignant cells - time series

Status
Submitted on 12 June 2007, released on 15 June 2008, last updated on 2 May 2014
Organism
Homo sapiens
Samples (12)
Array (1)
Protocols (8)
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.
Experiment types
transcription profiling by array, unknown experiment type
Contact
Citation
Gene Expression Signature in Organized and Growth-Arrested Mammary Acini Predicts Good Outcome in Breast Cancer. Marcia V. Fournier, Katherine J. Martin, Paraic A. Kenny, Kris Xhaja, Irene Bosch, Paul Yaswen and Mina J. Bissell. Cancer Res 66:7095-7102 (2006)
MIAME
PlatformsProtocolsVariablesProcessedRaw
Files
Investigation descriptionE-GEOD-8096.idf.txt
Sample and data relationshipE-GEOD-8096.sdrf.txt
Raw data (1)E-GEOD-8096.raw.1.zip
Processed data (1)E-GEOD-8096.processed.1.zip
Array designA-AFFY-33.adf.txt
R ExpressionSetE-GEOD-8096.eSet.r
Links