A bioinformatics approach to discovery of estrogen-responsive genetic pathways in breast cancer

Breast cancers fall into two major classes depending on their estrogen receptor (ER) status. ER+ and ER- tumors have very different molecular phenotypes, and may have distinct cells of origin. ER- tumors generally fail to respond to endocrine therapy and have a poorer prognosis. To develop a comprehensive understanding of the gene networks active in ER+ compared to ER- breast cancers, we performed a meta-analysis of Grade 3 breast cancers from five published datasets. A measure of association with ER status taking into account intra- and inter-study variability was calculated for every probe set.The meta-analysis revealed that ER-/Grade 3 tumors show increased expression of proliferation-associated functional categories when compared to ER+/Grade 3 tumors. Using Gene Set Enrichment Analysis we show that transcript levels of direct transcriptional targets of ER are lower in ER- tumors, but that expression of other estrogen-induced genes is higher in ER- tumors. Transcript levels of both direct and other targets of the estrogen-regulated MYC gene and the E2F family of genes are significantly higher in ER- tumors. The increased expression of targets of MYC and E2F is particularly pronounced in the "basal" subgroup of ER- tumors. This suggests that a study assessing the association of these genes with clinical outcome in ER- patients is warranted, but is not currently feasible due to lack of suitable publicly available data. The contribution of genes regulated or bound by estrogen, MYC or E2F to increased risk of relapse in ER+ tamoxifen-treated patients was assessed in a pilot study using Cox proportional hazards models and Gene Set Enrichment Analysis. The high expression of several gene sets containing genes induced by estrogen and/or MYC and direct targets of MYC and E2F was correlated with poor outcome in these patients.We conclude that over-expression or constitutive activation of MYC, possibly in conjunction with elevated E2F activity, may lead to the induction of a set of genes characteristic of the estrogen response thereby contributing to increased proliferation in ER- breast tumors, particularly in the basal subgroup. A pilot survival study indicated that MYC- and E2F-activity may play a role in tamoxifen-resistance