Comment[ArrayExpressAccession] E-GEOD-35629 MAGE-TAB Version 1.1 Public Release Date 2013-02-19 Investigation Title Vimentin DNA Methylation Predicts Survival in Breast Cancer Comment[Submitted Name] Vimentin DNA Methylation Predicts Survival in Breast Cancer Experiment Description Purpose:The Vimentin gene plays a pivotal role in epithelial-to-mesenchymal transition (EMT) and is known to be over-expressed in the prognostically poor basal-like breast cancer subtype. Recent studies have reported Vimentin DNA methylation in association with poor clinical outcomes in other solid tumors, but not in breast cancer. We therefore quantified Vimentin DNA methylation in breast tumors and matched normal pairs in association with gene expression and survival in a cohort of 83 breast cancer patients. Materials and Methods:Vimentin methylation was quantified in 14 breast cell lines, 83 breast tumors, and 57 matched normal pairs using MALDI-TOF mass spectrometry. Gene expression data via qRT-PCR in cell lines, and oligo microarray data from breast tissues was correlated with percent methylation in the Vimentin promoter. A threshold of 20 percent average methylation was set for bivariate and multivariate tests of association between methylation and tumor subtype, tumor histopathology, and survival. Results:Vimentin was differentially methylated in luminal breast cancer cell lines, and in luminal A, luminal B and HER2+ breast tumor subtypes, but was rare in basal-like cell lines and tumors. Increased methylation was strongly correlated with decreased mRNA expression in cell lines, and had a moderate inverse correlation in breast tumors. Importantly, Vimentin methylation predicted poor overall survival independent of race, subtype, stage, nodal status or estrogen receptor positivity. Conclusion:Vimentin methylation predicts overall survival in breast cancer patients and holds promise as a prognostic biomarker for guiding treatment and prophylaxis. reference x sample Term Source Name ArrayExpress EFO Term Source File http://www.ebi.ac.uk/arrayexpress/ http://www.ebi.ac.uk/efo/efo.owl Person Last Name Perou Ulirsch Perou Swift-Scanlan Person First Name Charles Jacob Charles Theresa Person Mid Initials M Person Email cperou@med.unc.edu Person Affiliation University of North Carolina at Chapel Hill Person Phone 919-843-5740 Person Fax 919-843-5718 Person Address CB#7295, University of North Carolina at Chapel Hill, 102 Mason Farm Road, Chapel Hill, NC, USA Person Roles submitter Protocol Name P-GSE35629-7 P-GSE35629-6 P-GSE35629-2 P-GSE35629-4 P-GSE35629-3 P-GSE35629-1 P-GSE35629-5 P-GSE35629-29 P-GSE35629-26 P-GSE35629-35 P-GSE35629-20 P-GSE35629-30 P-GSE35629-27 P-GSE35629-37 P-GSE35629-36 P-GSE35629-28 P-GSE35629-25 P-GSE35629-23 P-GSE35629-22 P-GSE35629-31 P-GSE35629-32 P-GSE35629-38 P-GSE35629-33 P-GSE35629-18 P-GSE35629-24 P-GSE35629-34 P-GSE35629-21 P-GSE35629-12 P-GSE35629-11 P-GSE35629-17 P-GSE35629-15 P-GSE35629-8 P-GSE35629-10 P-GSE35629-14 P-GSE35629-9 P-GSE35629-16 P-GSE35629-19 P-GSE35629-13 Protocol Description ID_REF = Spot Reference ID VALUE = same as UNF_VALUE but with flagged values removed SPOT = spot number on array CH1_MEAN = channel 1 mean intensity CH1_SD = standard deviation of channel 1 intensity CH1_BKD_MEDIAN = channel 1 background median intensity CH1_BKD_SD = standard deviation of channel 1 background median intensity CH2_MEAN = channel 2 mean intensity CH2_SD = standard deviation of channel 2 intensity CH2_BKD_MEDIAN = channel 2 background median intensity CH2_BKD_SD = standard deviation of channel 2 background median intensity TOT_BPIX = number of background pixels TOT_SPIX = number of spot pixels CH2BN_MEDIAN = channel 2 normalized background median intensity CH2IN_MEAN = channel 2 normalized mean intensity CH1DL_MEAN = channel 1 Lowess_normalized mean intensity CH2DL_MEAN = channel 2 Lowess_normalized mean intensity LOG_RAT2N_MEAN = log2_ratio of (CH2IN_MEAN - CH2BN_MEDIAN) over (CH1_MEAN - CH1_BKD_MEDIAN), CH2IN_MEAN and CH2BN_MEDIAN are global-normalized intensities CORR = correlation coefficient among pixels FLAG = Spot flag. 0:not flagged; negative:flagged as bad spots; positive:flagged as good spots UNF_VALUE = LOG_RAT2L_MEAN; log2_ratio of CH2DL_MEAN over CH1DL_MEAN ID_REF = Spot Reference ID VALUE = same as UNF_VALUE but with flagged values removed SPOT = spot number on array CH1_MEAN = channel 1 mean intensity CH1_SD = standard deviation of channel 1 intensity CH1_BKD_MEDIAN = channel 1 background median intensity CH1_BKD_SD = standard deviation of channel 1 background median intensity CH2_MEAN = channel 2 mean intensity CH2_SD = standard deviation of channel 2 intensity CH2_BKD_MEDIAN = channel 2 background median intensity CH2_BKD_SD = standard deviation of channel 2 background median intensity TOT_BPIX = number of background pixels TOT_SPIX = number of spot pixels CH2BN_MEDIAN = channel 2 normalized background median intensity CH2IN_MEAN = channel 2 normalized mean intensity CH1DL_MEAN = channel 1 Lowess_normalized mean intensity CH2DL_MEAN = channel 2 Lowess_normalized mean intensity LOG_RAT2N_MEAN = log2_ratio of (CH2IN_MEAN - CH2BN_MEDIAN) over (CH1_MEAN - CH1_BKD_MEDIAN), CH2IN_MEAN and CH2BN_MEDIAN are global-normalized intensities CORR = correlation coefficient among pixels FLAG = Spot flag. 0:not flagged; negative:Flagged as bad spots; positive:flagged as good spots CONTROL = Y: control gene; N: not control UNF_VALUE = LOG_RAT2L_MEAN; log2_ratio of CH2DL_MEAN over CH1DL_MEAN ID_REF = Spot Reference ID VALUE = same as UNF_VALUE but with flagged values removed SPOT = spot number on array CH1_MEAN = channel 1 mean intensity CH1_SD = standard deviation of channel 1 intensity CH1_BKD_MEDIAN = channel 1 background median intensity CH1_BKD_SD = standard deviation of channel 1 background median intensity CH2_MEAN = channel 2 mean intensity CH2_SD = standard deviation of channel 2 intensity CH2_BKD_MEDIAN = channel 2 background median intensity CH2_BKD_SD = standard deviation of channel 2 background median intensity TOT_BPIX = number of background pixels TOT_SPIX = number of spot pixels CH2BN_MEDIAN = channel 2 normalized background median intensity CH2IN_MEAN = channel 2 normalized mean intensity CH1DL_MEAN = channel 1 Lowess_normalized mean intensity CH2DL_MEAN = channel 2 Lowess_normalized mean intensity LOG_RAT2N_MEAN = log2_ratio of (CH2IN_MEAN - CH2BN_MEDIAN) over (CH1_MEAN - CH1_BKD_MEDIAN), CH2IN_MEAN and CH2BN_MEDIAN are global-normalized intensities CORR = correlation coefficient among pixels FLAG = Spot flag. 0:not flagged; negative:flagged as bad spots; positive:flagged as good spots CONTROL = Y: control gene; N: not control UNF_VALUE = LOG_RAT2L_MEAN; log2_ratio of CH2DL_MEAN over CH1DL_MEAN ID_REF = Spot Reference ID VALUE = log2_ratio of CH2DL_MEAN over CH1DL_MEAN (LOG_RAT2L_MEAN) SPOT = spot number on array CH1_MEAN = CH1_SD = standard deviation of channel 1 intensity CH1_BKD_MEDIAN = channel 1 background median intensity CH1_BKD_SD = standard deviation of channel 1 background median intensity CH2_MEAN = channel 2 mean intensity CH2_SD = standard deviation of channel 2 intensity CH2_BKD_MEDIAN = channel 2 background median intensity CH2_BKD_SD = standard deviation of channel 2 background median intensity TOT_BPIX = number of background pixels TOT_SPIX = number of spot pixels CH2BN_MEDIAN = channel 2 normalized background median intensity CH2IN_MEAN = channel 2 normalized mean intensity CH1DL_MEAN = channel 1 Lowess_normalized mean intensity CH2DL_MEAN = channel 2 Lowess_normalized mean intensity LOG_RAT2N_MEAN = log2_ratio of channel 2 normalized over channel 1 (global normalization) CORR = correlation coefficient among pixels FLAG = Spot flag. 0:not flagged; negative:flagged as bad spots; positive:flagged as good spots ID_REF = Spot Reference ID VALUE = same as UNF_VALUE but with flagged values removed SPOT = spot number on array CH1_MEAN = channel 1 mean intensity CH1_SD = standard deviation of channel 1 intensity CH1_BKD_MEDIAN = channel 1 background median intensity CH1_BKD_SD = standard deviation of channel 1 background median intensity CH2_MEAN = channel 2 mean intensity CH2_SD = standard deviation of channel 2 intensity CH2_BKD_MEDIAN = channel 2 background median intensity CH2_BKD_SD = standard deviation of channel 2 background median intensity TOT_BPIX = number of background pixels TOT_SPIX = number of spot pixels CH2BN_MEDIAN = channel 2 normalized background median intensity CH2IN_MEAN = channel 2 normalized mean intensity CH1DL_MEAN = channel 1 Lowess_normalized mean intensity CH2DL_MEAN = channel 2 Lowess_normalized mean intensity LOG_RAT2N_MEAN = log2_ratio of channel 2 normalized over channel 1 CORR = correlation coefficient among pixels FLAG = Spot flag. 0:not flagged; negative:flagged as bad spots; positive:flagged as good spots CONTROL = Y: control gene; N: not control UNF_VALUE = LOG_RAT2L_MEAN; log2_ratio of CH2DL_MEAN over CH1DL_MEAN ID_REF = Agilent probe reference IDs VALUE = same as UNF_VALUE but with flagged values removed SPOT = spot number on array CH1_MEAN = channel 1 mean intensity CH1_SD = standard deviation of channel 1 intensity CH1_BKD_MEDIAN = channel 1 background median intensity CH1_BKD_SD = standard deviation of channel 1 background median intensity CH2_MEAN = channel 2 mean intensity CH2_SD = standard deviation of channel 2 intensity CH2_BKD_MEDIAN = channel 2 background median intensity CH2_BKD_SD = standard deviation of channel 2 background median intensity TOT_BPIX = number of background pixels TOT_SPIX = number of spot pixels CH2BN_MEDIAN = channel 2 normalized background median intensity CH2IN_MEAN = channel 2 normalized mean intensity CH1DL_MEAN = channel 1 Lowess_normalized mean intensity CH2DL_MEAN = channel 2 Lowess_normalized mean intensity LOG_RAT2N_MEAN = log2_ratio of (CH2IN_MEAN - CH2BN_MEDIAN) over (CH1_MEAN - CH1_BKD_MEDIAN), CH2IN_MEAN and CH2BN_MEDIAN are global-normalized intensities CORR = correlation coefficient among pixels FLAG = Spot flag. 0:not flagged; negative:flagged as bad spots; positive:flagged as good spots CONTROL = Y: control gene; N: not control UNF_VALUE = LOG_RAT2L_MEAN; log2_ratio of CH2DL_MEAN over CH1DL_MEAN ID_REF = Spot Reference ID VALUE = same as UNF_VALUE but with flagged values removed SPOT = spot number on array CH1_MEAN = CH1_SD = standard deviation of channel 1 intensity CH1_BKD_MEDIAN = channel 1 background median intensity CH1_BKD_SD = standard deviation of channel 1 background median intensity CH2_MEAN = channel 2 mean intensity CH2_SD = standard deviation of channel 2 intensity CH2_BKD_MEDIAN = channel 2 background median intensity CH2_BKD_SD = standard deviation of channel 2 background median intensity TOT_BPIX = number of background pixels TOT_SPIX = number of spot pixels CH2BN_MEDIAN = channel 2 normalized background median intensity CH2IN_MEAN = channel 2 normalized mean intensity CH1DL_MEAN = channel 1 Lowess_normalized mean intensity CH2DL_MEAN = channel 2 Lowess_normalized mean intensity LOG_RAT2N_MEAN = log2_ratio of channel 2 normalized over channel 1 (global normalization) CORR = correlation coefficient among pixels FLAG = Spot flag. 0:not flagged; negative:flagged as bad spots; positive:flagged as good spots UNF_VALUE = log2_ratio of CH2DL_MEAN over CH1DL_MEAN (LOG_RAT2L_MEAN) Fluorescent array images were collected for both Cy3 and Cy5 with an Agilent scanner and image intensity data were extracted and analyzed with Agilent Feature Extraction software v10.7.3.77 Fluorescent array images were collected for both Cy3 and Cy5 with an Agilent scanner and image intensity data were extracted and analyzed with Agilent Feature Extraction software v10.7.3.74 Fluorescent array images were collected for both Cy3 and Cy5 with an Agilent scanner and image intensity data were extracted and analyzed with Agilent Feature Extraction software v10.7.3.86 Fluorescent array images were collected for both Cy3 and Cy5 with an Agilent scanner and image intensity data were extracted and analyzed with Agilent Feature Extraction software v10.7.3.64 Fluorescent array images were collected for both Cy3 and Cy5 with an Agilent scanner and image intensity data were extracted and analyzed with Agilent Feature Extraction software v10.7.3.78 Fluorescent array images were collected for both Cy3 and Cy5 with an Agilent scanner and image intensity data were extracted and analyzed with Agilent Feature Extraction software v10.7.3.75 Fluorescent array images were collected for both Cy3 and Cy5 with an Agilent scanner and image intensity data were extracted and analyzed with Agilent Feature Extraction software v10.7.3.88 Fluorescent array images were collected for both Cy3 and Cy5 with an Agilent scanner and image intensity data were extracted and analyzed with Agilent Feature Extraction software v10.7.3.87 Fluorescent array images were collected for both Cy3 and Cy5 with an Agilent scanner and image intensity data were extracted and analyzed with Agilent Feature Extraction software v10.7.3.76 Fluorescent array images were collected for both Cy3 and Cy5 with an Agilent scanner and image intensity data were extracted and analyzed with Agilent Feature Extraction software v10.7.3.73 Fluorescent array images were collected for both Cy3 and Cy5 with an Agilent scanner and image intensity data were extracted and analyzed with Agilent Feature Extraction software v10.7.3.71 Fluorescent array images were collected for both Cy3 and Cy5 with an Agilent scanner and image intensity data were extracted and analyzed with Agilent Feature Extraction software v10.7.3.70 Fluorescent array images were collected for both Cy3 and Cy5 with an Agilent scanner and image intensity data were extracted and analyzed with Agilent Feature Extraction software v10.7.3.80 Fluorescent array images were collected for both Cy3 and Cy5 with an Agilent scanner and image intensity data were extracted and analyzed with Agilent Feature Extraction software v10.7.3.82 Fluorescent array images were collected for both Cy3 and Cy5 with a GenePix 4000B fluorescent scanner and image intensity data were extracted and analyzed with GenePix Pro 5.1 analysis software. Fluorescent array images were collected for both Cy3 and Cy5 with an Agilent scanner and image intensity data were extracted and analyzed with Agilent Feature Extraction software v10.7.3.83 Fluorescent array images were collected for both Cy3 and Cy5 with an Agilent scanner and image intensity data were extracted and analyzed with Agilent Feature Extraction software v10.7.3.63 Fluorescent array images were collected for both Cy3 and Cy5 with an Agilent scanner and image intensity data were extracted and analyzed with Agilent Feature Extraction software v10.7.3.72 Fluorescent array images were collected for both Cy3 and Cy5 with an Agilent scanner and image intensity data were extracted and analyzed with Agilent Feature Extraction software v10.7.3.84 Fluorescent array images were collected for both Cy3 and Cy5 with an Agilent scanner and image intensity data were extracted and analyzed with Agilent Feature Extraction software v10.7.3.69 Fluorescent array images were collected for both Cy3 and Cy5 with a GenePix 4000B fluorescent scanner and image intensity data were extracted and analyzed with GenePix Pro 4.1 analysis software. described in Hu et al., 2005, BioTechniques, 38:121-124 Agilent quick amplification kit protocol Total RNA isolated using Qiagen RNeasy mini Kit Total RNA isolated by Stratagene. Qiagen Rneasy Kit Total RNA isolated by stratagene described in Hu et al., 2005, BioTechniques, 38:121-124 Agilent quick amplification kit protocol Data for both channels were Lowess-normalized and then the log(2) ratio was taken Data for both channels were Lowess-normalized and then log(2) ratio was taken Protocol Type bioassay_data_transformation bioassay_data_transformation bioassay_data_transformation bioassay_data_transformation bioassay_data_transformation bioassay_data_transformation bioassay_data_transformation image_aquisition image_aquisition image_aquisition image_aquisition image_aquisition image_aquisition image_aquisition image_aquisition image_aquisition image_aquisition image_aquisition image_aquisition image_aquisition image_aquisition image_aquisition image_aquisition image_aquisition image_aquisition image_aquisition image_aquisition image_aquisition hybridization hybridization nucleic_acid_extraction nucleic_acid_extraction nucleic_acid_extraction nucleic_acid_extraction labeling labeling feature_extraction feature_extraction Experimental Factor Name STAGE AT CLASS LEVEL SLIDENAME RACE CALL ID AT BREAST CANCER DX BIOSOURCEPROVIDER OSM OS IN MONTHS RFSM RFS IN MONTHS SEX ANY SIZE WITH DIRECT EXTENSION TO CHEST WALL OR SKIN GEO ARRAY NAME Experimental Factor Type stage at class level slidename race call id at breast cancer dx BioSourceProvider osm os in months rfsm rfs in months sex any size with direct extension to chest wall or skin geo array name Publication Title Vimentin DNA methylation predicts survival in breast cancer. Publication Author List Ulirsch J, Fan C, Knafl G, Wu MJ, Coleman B, Perou CM, Swift-Scanlan T PubMed ID 23239149 Publication DOI 10.1007/s10549-012-2353-5 Comment[SecondaryAccession] GSE35629 Comment[GEOReleaseDate] 2013-02-19 Comment[ArrayExpressSubmissionDate] 2012-02-08 Comment[GEOLastUpdateDate] 2013-02-19 Comment[AEExperimentType] transcription profiling by array SDRF File E-GEOD-35629.sdrf.txt