Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

Comparison of gene expression profiles of HT29 cells treated with Instant Caffeinated Coffee or Caffeic Acid versus control.

ABSTRACT: A summary of the work associated to these microarrays is the following: Background: Phenolic compounds present in coffee are antioxidants in vitro that might protect against cardiovascular disease and certain types of cancer in humans. Objective: Our aim was to identify differentially expressed genes upon incubation of HT-29 human colon cancer cells with instant caffeinated coffee (ICC) or caffeic acid (CA) using microarrays. Results: In HT-29 cells incubated with ICC, 77 genes were overexpressed whereas 162 were underexpressed. Upon incubation with CA, 12 genes were overexpressed whereas 33 were underexpressed. A list of five overexpressed genes and eleven underexpressed genes were found in common between the two conditions and was use to construct a biological association network. In the generated network, STAT5B and ATF-2 appeared as highly interconnected nodes. STAT5B overexpression was confirmed at the mRNA and protein levels. For ATF-2, the changes in mRNA levels were confirmed for both ICC and CA, whereas the decrease in protein levels was only observed in CA-treated cells. The levels of cyclin D1, a target gene for both STAT5B and ATF-2 transcription factors, decreased dramatically in breast cancer cells treated with CA or ICC. Conclusions: Coffee polyphenols are able to affect gene expression in cancer cells through the modulation of STA5B and ATF-2 transcription factors. The aim of our study was to evaluate, by using whole genome microarrays, the effects of one cup of coffee, either regular caffeinated coffee or a coffee polyphenol, such as caffeic acid, on HT-29 gene expression, Three experimental approaches were conducted to assess the effects of coffee on HT29 cells. I) Incubation with non cytotoxic concentrations of ICC (7 Âµg/mL) for 24h. (Group ICC); II) Incubation with non cytotoxic concentrations of CA (1.68 Âµg/mL) for 24h. (Group CA); III) non treatment of HT-29 to refered as a control (Group CNT). Triplicate samples were hybridized for each experimental condition (9 samples in total). The samples provided were analyzed using the specific software GeneSpring GX.

ORGANISM(S): Homo sapiens

SUBMITTER: carlos ciudad

PROVIDER: E-GEOD-35382 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Publications

Coffee polyphenols change the expression of STAT5B and ATF-2 modifying cyclin D1 levels in cancer cells.

Oleaga Carlota C Ciudad Carlos J CJ Noé Véronique V Izquierdo-Pulido Maria M

Oxidative medicine and cellular longevity 20120807

<h4>Background</h4>Epidemiological studies suggest that coffee consumption reduces the risk of cancer, but the molecular mechanisms of its chemopreventive effects remain unknown.<h4>Objective</h4>To identify differentially expressed genes upon incubation of HT29 colon cancer cells with instant caffeinated coffee (ICC) or caffeic acid (CA) using whole-genome microarrays.<h4>Results</h4>ICC incubation of HT29 cells caused the overexpression of 57 genes and the underexpression of 161, while CA incu ...[more]

PMID: 22919439

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Project description:A summary of the work associated to these microarrays is the following: Background: Phenolic compounds present in coffee are antioxidants in vitro that might protect against cardiovascular disease and certain types of cancer in humans. Objective: Our aim was to identify differentially expressed genes upon incubation of HT-29 human colon cancer cells with instant caffeinated coffee (ICC) or caffeic acid (CA) using microarrays. Results: In HT-29 cells incubated with ICC, 77 genes were overexpressed whereas 162 were underexpressed. Upon incubation with CA, 12 genes were overexpressed whereas 33 were underexpressed. A list of five overexpressed genes and eleven underexpressed genes were found in common between the two conditions and was use to construct a biological association network. In the generated network, STAT5B and ATF-2 appeared as highly interconnected nodes. STAT5B overexpression was confirmed at the mRNA and protein levels. For ATF-2, the changes in mRNA levels were confirmed for both ICC and CA, whereas the decrease in protein levels was only observed in CA-treated cells. The levels of cyclin D1, a target gene for both STAT5B and ATF-2 transcription factors, decreased dramatically in breast cancer cells treated with CA or ICC. Conclusions: Coffee polyphenols are able to affect gene expression in cancer cells through the modulation of STA5B and ATF-2 transcription factors. The aim of our study was to evaluate, by using whole genome microarrays, the effects of one cup of coffee, either regular caffeinated coffee or a coffee polyphenol, such as caffeic acid, on HT-29 gene expression, Three experimental approaches were conducted to assess the effects of coffee on HT29 cells. I) Incubation with non cytotoxic concentrations of ICC (7 µg/mL) for 24h. (Group ICC); II) Incubation with non cytotoxic concentrations of CA (1.68 µg/mL) for 24h. (Group CA); III) non treatment of HT-29 to refered as a control (Group CNT). Triplicate samples were hybridized for each experimental condition (9 samples in total). The samples provided were analyzed using the specific software GeneSpring GX.

Project description:Metastasis and drug-resistance are major problems in cancer chemotherapy. The purpose of this work was to analyze the molecular mechanisms underlying the invasive potential of drug-resistant colon carcinoma cells. Cellular models included the parental HT-29 cell line and its drug-resistant derivatives selected after chronic treatment with either 5-fluorouracil (5-FU), methotrexate (MTX), doxorubicin (DOX) or oxaliplatin (OXA). Drug-resistant invasive cells were compared to non invasive cells using cDNA microarray, qRT-PCR, flow cytometry, immunoblots and ELISA. Functional and cellular signaling analyses were undertaken using pharmacological inhibitors, function-blocking antibodies, and silencing by retrovirus-mediated RNA interference. 5-FU- and MTX-resistant HT-29 cells expressing an invasive phenotype in collagen type I and a metastatic behaviour in immunodeficient mice exhibited high expression of the chemokine receptor CXCR4. Macrophage migration inhibitory factor (MIF) was identified as the critical autocrine CXCR4 ligand promoting invasion in drug-resistant colon carcinoma HT-29 cells. Silencing of CXCR4 and impairing the MIF-CXCR4 signaling pathways by ISO-1, pAb FL-115, AMD-3100, mAb 12G5, and BIM-46187 abolished this aggressive phenotype. Induction of CXCR4 is associated with up-regulation of two genes encoding transcription factors previously shown to control CXCR4 expression (HIF-2a and ASCL2) and maintenance of intestinal stem cells (ASCL2). Enhanced CXCR4 expression was detected in liver metastases resected from colon cancer patients treated by the standard FOLFOX regimen. Combination therapies targeting the CXCR4-MIF axis can potentially counteract the emergence of the invasive metastatic behaviour in clonal derivatives of drug-resistant colon cancer cells. Samples: HT-29 cell clones were obtained by limiting dilution from HT-29 subpopulations resistant to methothrexate (HT-29 5M21 cell clone) and or to 5-Fluoro-uracil (HT-29 5F7 and HT-29 5F31). Samples were provided by Dr. T Lesuffleur. Xenografts: HT-29 5M21, HT-29 5F7, and HT-29 5F31 xenografts were obtained by a first subcutaneous inoculation of cells in Nude mice and then fragments of subcutaneous tumors were reimplantated in SCID mice. First experiment of microarrays: HT-29 5M21 and HT-29 5F7 cells (that are invasive in in vitro assays on type I collagen) were compared to HT-29 5F31 cells (that are not invasive in vitro on type I collagen). Samples were co-hybridized on Agilent Human 44K GEP arrays (respectively 5F31 vs 5M21, 5F31 vs 5F7, 5M21 vs 5F31 and 5F7 vs 5F31). Second experiment of microarrays: HT-29 5M21 and HT-29 5F7 xenografts (that develop metastases in immuno-deficient mice lungs) were compared to HT-29 5F31 xenografts (that do not develop metastases in immuno-deficient mice lungs). Samples were consequently co-hybridized on human and mouse 4x44K GEP arrays (respectively AG41_5F31-5M21-138869, AG39_5F31-5F7-138867, AG42_5M21-5F31-138870 and AG40_5F7-5F31-138868 for human microarrays; 5M21_5F31_27033_4, 5F31_5M21_27033_3, 5F7_5F31_27033_2 and 5F31_5F7_27033_1_1 for mouse microarrays).

Dataset Information

Comparison of gene expression profiles of HT29 cells treated with Instant Caffeinated Coffee or Caffeic Acid versus control.

Publications

Coffee polyphenols change the expression of STAT5B and ATF-2 modifying cyclin D1 levels in cancer cells.

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