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Series GSE39173 Query DataSets for GSE39173
Status Public on Aug 16, 2012
Title ECM-dependent gene expression in normal and tumor-derived mammary organoids
Organism Mus musculus
Experiment type Expression profiling by array
Summary A critical step in metastasis is cancer cell dissemination. Dissemination and metastasis are associated with specific genetic changes and changes in extracellular matrix (ECM), but how these changes interact to enable dissemination remains unclear. Here we tested the importance of ECM to dissemination in both normal and malignant mammary epithelium. By time-lapse imaging, we observed collective invasion and dissemination directly in 3D culture. Our results reveal that the pattern of epithelial migration and local dissemination are constrained by the local ECM microenvironment. To identify RNA expression changes that could regulate these changes in cell behavior, we conducted whole genome RNA expression profiling from normal and malignant mammary epithelium in 3D culture. We collected RNA from normal and malignant epithelium during active growth at 4 days in culture in either Matrigel or collagen I. We hybridized the resulting RNA to Agilent single color microarrays with a minimum of three biologically independent microarray replicates per condition. We observed significant gene expression differences between normal and malignant epithelium, even when cultured in the same ECM. In contrast, the ECM microenvironment had a relatively small impact on RNA expression, despite its large effects on migratory strategy and local dissemination.
Overall design Gene expression was measured in normal and malignant mammary epithelial fragments cultured in one of two 3D matrices (laminin-rich basement membrane gel or collagen I) and collected at day 4, which we observed to have peak invasion and dissemination. At least three independent experiments were performed at each time using different mice for each experiment.
Contributor(s) Cheung KJ, Ewald AJ, Werb Z
Citation(s) 22923691
Submission date Jul 07, 2012
Last update date Jan 12, 2017
Contact name Kevin J Cheung
Organization name Center for Cell Dynamics
Department Cell Biology
Lab Ewald Laboratory
Street address 855 N. Wolfe St, Rangos 452, Center for Cell Dynamics, Johns Hopkins School of Medicine
City Baltimore
State/province MD
ZIP/Postal code 21205
Country USA
Platforms (1)
GPL7202 Agilent-014868 Whole Mouse Genome Microarray 4x44K G4122F (Probe Name version)
Samples (13)
GSM957506 Mouse A WT (FVB) mammary epithelium organotypic culture in Matrigel 4 days with FGF2
GSM957507 Mouse B WT (FVB) mammary epithelium organotypic culture in Matrigel 4 days with FGF2
GSM957508 Mouse D WT (FVB) mammary epithelium organotypic culture in Matrigel 4 days with FGF2 (previously called D4F)
BioProject PRJNA170139

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Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE39173_RAW.tar 126.5 Mb (http)(custom) TAR (of TXT)
Processed data included within Sample table

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