Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

Transcription profiling by array of human mammary epithelial cells (HMEC) stimulated with TNF vs. controls reveals TNF induces distinct expression programs

ABSTRACT: HMEC cultures were left untreated or stimulated for 5h with 2 ng/ml TNF. Comparison of the gene expression profiles revealed the TNF-mediated gene expression changes.

ORGANISM(S): Homo sapiens

SUBMITTER: Dorothee Viemann

PROVIDER: E-GEOD-2638 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Publications

TNF induces distinct gene expression programs in microvascular and macrovascular human endothelial cells.

Viemann Dorothee D Goebeler Matthias M Schmid Sybille S Nordhues Ursula U Klimmek Kerstin K Sorg Clemens C Roth Johannes J

Journal of leukocyte biology 20060414 1

The relevance of the diversity of endothelial cells (ECs) for the response to inflammatory stimuli is currently not well defined. Using oligonucleotide microarray technique, we systematically analyzed the tumor necrosis factor (TNF)-induced expression profile in human microvascular ECs (HMEC) and macrovascular human umbilical vein ECs (HUVEC), analyzing 13,000 human genes by microarray analysis. Using strict inclusion and exclusion criteria, microarray analysis revealed that about half of the TN ...[more]

PMID: 16617158

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Project description:Molecular distinctions between the stasis and telomere attrition senescence barriers in cultured human mammary epithelial cells Normal human epithelial cells in culture have generally shown a limited proliferative potential of ~10-40 population doublings before encountering a stress-associated senescence barrier (stasis) associated with elevated levels of cyclin-dependent kinase inhibitors p16 and/or p21. We now show that simple changes in media composition can expand the proliferative potential of human mammary epithelial cells (HMEC) initiated as primary cultures to 50-60 population doublings, followed by p16(+), senescence-associated b-galactosidase(+) stasis. We compared the properties of growing and senescent pre-stasis HMEC with growing and senescent post-selection HMEC, i.e., cells grown in a serum-free medium that overcame stasis via silencing of p16 expression and that display senescence associated with telomere dysfunction. Cultured pre-stasis populations contained cells expressing markers associated with luminal and myoepithelial HMEC lineages in vivo, in contrast to the basal-like phenotype of the post-selection HMEC. Gene transcript and protein expression, DNA damage-associated markers, mean TRF length, and genomic stability, differed significantly between HMEC populations at the stasis vs. telomere attrition senescence barriers. Senescent isogenic fibroblasts showed greater similarity to HMEC at stasis than at telomere attrition, although their gene transcript profile was distinct from HMEC at both senescence barriers. These studies support our model of the senescence barriers encountered by cultured HMEC in which the first barrier, stasis, is Rb-mediated and independent of telomere length, while a second barrier (agonescence or crisis) results from telomere attrition leading to telomere dysfunction. Additionally, the ability to maintain long-term growth of genomically stable multi-lineage pre-stasis HMEC populations can greatly enhance experimentation with normal HMEC. 48 samples from Human Mammary Epithelial cells which includes samples from four different individuals at different passage levels which includes prestasis,intermediate,post selection and agonesence stages of cell cycle.

Project description:Dysregulation of the epigenome is a common event in malignancy. However, deciphering the earliest cancer associated epigenetic events remains a challenge. Cancer epigenome studies to date have primarily utilised cancer cell lines or clinical samples, where it is difficult to identify the initial epigenetic lesions from those that occur over time. Here, we analysed the epigenome of normal Human Mammary Epithelial Cells (HMEC) and a matched variant cell population (vHMEC) that has escaped senescence and undergone partial carcinogenic transformation. Using this model system we sought to identify the earliest epigenetic changes that potentially occur during carcinogenesis. First we show that the transcriptome of vHMEC resembles that of basal-like breast cancer. Moreover, in vHMEC there is significant deregulation of MYC, p53, EZH2/polycomb, the Aryl Hydrocarbon Receptor (AHR) and miRNAs-143, 145, 199a and 519a at the transcriptional level. Second, we find that vHMEC exhibit genome-wide changes in DNA methylation affecting key cancer-associated pathways. Hypermethylation predominately impacted gene promoters (particularly those targeted by AHR and TP53) and polycomb associated loci, whereas hypomethylation frequently affected enhancers. Next we show that long range epigenetic deregulation occurred in vHMEC involving concordant change in chromatin modification and gene expression across ~0.5-1Mb regions. Finally, we demonstrate that the DNA methylation changes we observe in vHMECs, occur in basal-like breast cancer (notably FOXA1 hypermethylation).. Overall our results suggest that the first steps of carcinogenesis are associated with a co-ordinated deregulation of DNA methylation and chromatin modification spanning a range of genomic loci potentially targeted by key transcription factors and a corresponding deregulation of transcriptional networks. We sought to compare the differences in gene expression in vHMEC when compared to isogenic HMEC cells. Two time points in the vHMEC growth phase were used to assess if continual passage of vHMEC contributed to expression differences. RNA was extracted from a total of 4 HMEC (and matched vHMEC) lines.

Dataset Information

Transcription profiling by array of human mammary epithelial cells (HMEC) stimulated with TNF vs. controls reveals TNF induces distinct expression programs

Publications

TNF induces distinct gene expression programs in microvascular and macrovascular human endothelial cells.

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