Signaling pathways that converge on two different transcription factor complexes, NF? and AP-1, have been identified in estrogen receptor (ER)-positive breast cancers resistant to the antiestrogen, tamoxifen. The aim of this study was to explore the potential of linking genes upregulated by both NF?B and AP-1 with tamoxifen resistance.

The hypothesis of this study was that genes upregulated by NF?B and AP-1 in ER+, node-negative breast cancer have a prognostic association with patient outcome after adjuvant tamoxifen therapy.

This dataset contains cryobanked breast cancer specimens from the University of California San Francisco (UCSF) Comprehensive Cancer Center Breast Oncology Program Tissue Core, collected under UCSF approved protocols following patient consent. From an archive of over 1,000 liquid nitrogen frozen breast cancer specimens, 54 primary breast cancer samples (UCSF cases) had been selected, using the following criteria: early clinical stage (T1/2, N0, M0) invasive breast cancer, ER-positive status (>10% nuclear immunohistochemical staining), known primary systemic therapy (treatment era: 1989–2004, with 33/54 receiving adjuvant tamoxifen and 18/54 receiving adjuvant chemotherapy), known clinical outcome (relapse-free survival, RFS), and stratification into young (? 45 years, n = 29) or old (? 70 years, n = 25) age-at-diagnosis. The age stratification groups were balanced for standard prognostic markers (tumor size, grade, proliferation index, ERBB2 status) and adjuvant therapy, but showed differences in clinical outcome with the younger cases experiencing more frequent (7/29) and earlier metastatic relapses (median RFS = 4.84 years, range 0.13–14.14 years) than the older age-at-diagnosis cases (2/25; median RFS = 5.52 years, range 0.74–12.72 years). Sample requirements also included a minimum frozen-wet weight of 100 mg and histologic confirmation of >50% cancer cells per sample section.

Total RNA from each tissue sample was formamide extracted, purified and reconstituted in aqueous solution using RNeasy (Qiagen, CA) according to manufacturer's instructions; and the resulting RNA samples were quality verified by micro-analysis (Agilent Bioanalyzer, CA).

Total RNA (3–5 ?g per sample) was labeled and analyzed using Affymetrix (Santa Clara, CA) high-density oligonucleotide microarrays, HG-U133A (v2), in 96-well chips each with 22.2 K annotated probes representing ~13 K unique Unigenes. Gene expression analysis was performed using standard Affymetrix procedures within the Lawrence Berkeley National Lab and Life Science Division's Molecular Profiling Laboratory (MPL). Probe set measurements were generated from quantified Affymetrix image files (.CEL files) using the RMA algorithm from BioConductor R. The resulting data matrix consisted of normalized log abundance values for each probe set and sample; these data files and associated clinical parameters for each sample have been entered into the NCBI Gene Expression Omnibus (GEO) repository (GSE7378).

Zhou, Yamei, Christina Yau, Joe W. Gray, Karen Chew, Shanaz H. Dairkee, Dan H. Moore, Urs Eppenberger, Serenella Eppenberger-Castori, and Christopher C. Benz. “Enhanced NF Kappa B and AP-1 Transcriptional Activity Associated with Antiestrogen Resistant Breast Cancer.” BMC Cancer 7 (2007): 59. doi:10.1186/1471-2407-7-59.