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E-GEOD-12665

ABSTRACT: Gene expression profiling of invasive breast cancer events from the tamoxifen prevention trial

OTHER RELATED OMICS DATASETS IN: PRJNA112733

PROVIDER: E-GEOD-12665 | ExpressionAtlas | 2025-01-24

REPOSITORIES: ExpressionAtlas

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Dataset's files

Source:

			Action	DRS
	E-GEOD-12665-analysis-methods.tsv	Tabular
	E-GEOD-12665-atlasExperimentSummary.Rdata	Rdata
	E-GEOD-12665-configuration.xml	Xml
	E-GEOD-12665-configuration.xml.beforeQC	Xml
	E-GEOD-12665-percentile-ranks.tsv	Tabular

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Gene expression profiling of invasive breast cancer events from the tamoxifen prevention trial

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Gene expression profiling of invasive breast cancer events from the tamoxifen prevention trial

Project description:Gene expression profiling of invasive breast cancer events from the tamoxifen prevention trial validates low estrogen receptor mRNA level as the main determinant of tamoxifen resistance in estrogen receptor positive breast cancer. In NSABP Breast Cancer Prevention Trial (BCPT), tamoxifen reduced the incidence of estrogen receptor (ER) positive tumors but not estrogen receptor negative breast cancer. More importantly, only 69% of estrogen receptor positive tumors were prevented by tamoxifen. The ER positive tumors arising in tamoxifen arm provides an ideal clinical model for acquired tamoxifen resistance. Based on data from NSABP trial B14 which showed linear prediction of the degree of benefit from adjuvant tamoxifen by the levels of ESR1 mRNA coding for ER-alpha, we hypothesized a priori that level of ESR1 mRNA would be lower in ER positive tumors arising in tamoxifen arm compared to those in placebo arm of BCPT. Keywords: Gene expression profiling analysis Formalin fixed paraffin embedded tumor blocks with enough tumor tissue for RNA extraction were available from 108 cases (69 from placebo arm and 39 from tamoxifen arm) of the 264 that experienced invasive breast cancer (175 in placebo arm and 89 in tamoxifen arm) in BCPT before unblindings . Central ER immunohistochemistry identified 84 of them as ER positive (57 from placebo arm and 27 from tamoxifen arm). A novel protocol was developed and used to obtain microarray gene expression profiling from the degraded or fragmented RNA extracted from formalin fixed paraffin blocks.Hybridization intensity data were compiled using Partek Genomic Suite. After quantile normalization, genes with mean intensity below 500 were filtred out, which left 7743 probes with informative data. Data were log2 transformed for statistical analysis.

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