Unknown,Transcriptomics,Genomics,Proteomics

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The effect of ethanol on the cultured human breast cancer line MCF-7

ABSTRACT: Alcohol consumption is a known risk factor for breast cancer in humans. We used the established breast cancer cell line MCF-7 to analyze the effects of ethanol on gene expression at the RNA level. In addition, we carried out studies on protein levels and the ability of cells to grow in an anchorage independent manner. The DNA microarray results are deposited here. We also provide the results of studies on microRNA levels as a separate data set. Cells grown in culture for 1 to 4 weeks were treated with 0-25 mM ethanol. RNA was extracted using the RNeasy Plus Micro kit and subjected to analysis by DNA microarray, using the Affymetrix human Gene 1.0 ST array (platform GPL19142). RNA samples from different treatments were analysed by the UCLA DNA Core lab. Data were returned as rma values. There are control experiments in which cells were grown without added ethanol, and there are experiments in which cells were grown in the presence of 25 mM ethanol for either 1 week or 4 weeks. One column shows the gene expression values for another cell line MCF12-A, which was established using non-malignant human breast cells and which was grown in the absence of ethanol. In this particular Affymetrix array, most genes are evaluated as a single Probe Set, but there are some which are included in the array as 2 or more Probe Sets.

ORGANISM(S): Homo sapiens

SUBMITTER: Robert Gelfand

PROVIDER: E-GEOD-72010 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Project description:A sensitive assay to identify biomarkers that can accurately diagnose the onset of breast cancer using non-invasively collected clinical specimens is ideal for early detection. In this study, we have conducted a prospective sample collection and retrospective blinded validation (PRoBE design) to evaluate the performance and translational utilities of salivary transcriptomic and proteomic biomarkers for the non-invasive detection of breast cancer. The Affymetrix HG U133 Plus 2.0 Array and 2D-DIGE were used to profile transcriptomes and proteomes in saliva supernatants respectively. Significant variations of salivary transcriptomic and proteomic profiles were observed between breast cancer patients and healthy controls. Eleven transcriptomic biomarker candidates and two proteomic biomarker candidates were selected for a preclinical validation using an independent sample set. Transcriptomic biomarkers were validated by RT-qPCR and proteomic biomarkers were validated by quantitative protein immunoblot. Eight mRNA biomarkers and one protein biomarker have been validated for breast cancer detection, yielding ROC-plot AUC values between 0.665 and 0.959. This report provides proof of concept of salivary biomarkers for the non-invasive detection of breast cancer. The salivary biomarkersâ discriminatory power paves the way for a PRoBE-design definitive validation study. Keywords: Salivary biomarker, Breast cancer, Early detection, Salivary transcriptome, Salivary proteome This study, which was approved by the UCLA and Cedars-Sinai Medical Center Institutional Review Boards (#06-07-043 and #3870, respectively), started sample collection in February 2007. The sample collection followed the PRoBE principle (prospective specimen collection). The saliva bank for breast cancer project at the UCLA Dental Research Institute in collaboration with Cedars Sinai Medical Center has collected 200 saliva samples since 2007 with all subjects recruited from the Saul and Joyce Brandman Breast Cancer Center. Of these, 113 samples, including 41 breast cancer patients and 72 healthy control individuals, were selected for the discovery and validation phase of this study. Inclusion criteria of cancer patients consisted of a confirmed diagnosis of breast cancer. Exclusion criteria of cancer patients included therapy/surgery and/or a diagnosis of other malignancies within 5 years prior to saliva collection. Exclusion criteria of control patients included a diagnosis of any malignancies within 5 years prior to saliva collection. Written informed consents and questionnaire data sheets were obtained from all patients who agreed to serve as saliva donors. Unstimulated saliva samples were consistently collected, stabilized, and preserved as previously described. The sample supernatants were reserved at -80 C prior to assay. This study consisted of a discovery phase, followed by an independent preclinical validation phase. Of the 113 samples, 10 breast cancer samples and 10 healthy control samples were chosen for the discovery phase. All breast cancer cases are invasive ductal carcinoma (IDC), the most common type of breast cancer. Biomarkers identified from the discovery studies were first verified using the discovery sample set. An independent sample set, including 31 breast cancer patients and 62 healthy control subjects, was used for the biomarker validation phase.

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The effect of ethanol on the cultured human breast cancer line MCF-7

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