Gene expression of primary breast cancers from patients before and after neo-adjuvant Tamoxifen treatment

Tumor gene expression data (microarray from FFPE) was obtained from breast cancer patients enrolled in a pre-operative window trial (ClinicalTrials.gov Identifier: NCT00738777). Patients received an oral loading dose of 40 mg of tamoxifen twice daily for the first seven days, followed by a daily dose of 20 mg until surgery. A core needle biopsy of the tumor was taken prior to treatment (n=62) and post-treatment tumor material (n=40) was obtained during surgery 20.7 (±9.6) days later. Paired material was available for 27/74 patients. Differential analysis comparing gene expression before and after Tamoxifen treatment implicated activation of the NFκB pathway and an enrichment of EMT/stemness features upon Tamoxifen treatment. In line with these findings, exposure of ER+ breast cancer cell lines to tamoxifen, in vitro and in vivo, gives rise to a tamoxifen-tolerant population with similar NFκB activity and EMT/stemness characteristics as described in the corresponding publication. FFPE tumor material was sent to Agendia Inc. RNA was isolated from samples with sufficient tumor cell content (>30%) and analyzed on a custom Agilent array. Feature Extraction software v11.5.1.1 was used to quantify fluorescent intensities and those were normalized using DataPrint software v1.15. Downstream data processing was subsequently done at the Netherlands Cancer Institute including missing values impution with knn=10 and batch correction for date of RNA extraction using ComBat from the R package sva, using all available patient material from the trial (ClinicalTrials.gov Identifier: NCT00738777). Here we deposited samples used for the Tamoxifen focused analysis described in the cited paper.