Identification of drug targets for the treatment of Basal-like tumors

Genomic studies have identified at least five distinct subtypes of breast tumors [1]. These subtypes are believed to develop from different epithelial cell types and show different overall survival outcomes. Of particular interest is the estrogen receptor (ER)-negative Basal-like subtype, which accounts for 10–15% of all breast tumors and shows poor outcomes. In the breast cancer clinic, there are currently two biologically directed therapies that target either the ER or HER2 proteins. The Basal-like tumors lack both of these proteins [2], and hence the only treatment options for these patients are cytotoxic chemotherapies. A goal of ours was therefore to use primary breast tumor gene expression data and cell line models to identify and validate candidate biologically-based therapies for Basal-like tumors.

To identify potential targets, the gene expression data for approximately 1500 drug targets were examined across a breast tumor data set of 150 samples. Squalene epoxidase (SQLE) was expressed in most Basal-like tumors, as well as in the Basal-like tumor-derived cell lines SUM102 and SUM149. SQLE is an attractive target because it is highly expressed, it is a rate-limiting step in the cholesterol biosynthetic pathway, and there is an available inhibitor (NB598) [3]. Recent studies using inhibitors of HMGCoA reductase (the first rate-limiting step) in epithelial cell lines suggest that inhibition of this pathway may be a potential target for therapeutic intervention [4].

Using the SUM102 and SUM149 cell lines and two more widely used luminal/ER+ lines (MCF-7 and ZR-75-1), we treated cells with NB598 and separately with lovastatin (an HMGCoA reductase inhibitor) and determined their sensitivity by identifying their 72-hour IC₅₀ dose. Sensitivity was similar across three of the four cell lines for NB598, with the exception of SUM102, which was approximately 300 times more sensitive. Conversely, sensitivity to lovastatin was similar across three of the four cell lines except MCF-7, which was approximately five times more resistant. Since many drugs are rarely used as single agents, we also looked at the interactions between these two inhibitors and commonly used chemotherapeutics. Drug-combination sensitivities again varied across the four cell lines; however, it appears that combinations of NB598 and 5-fluorouracil were typically synergistic, while combinations with carboplatin or paclitaxel were typically antagonistic. Similar analyses are being performed for lovastatin/chemotherapy combinations. Gene expression responses of these cell lines were also assayed using DNA microarrays. The effect on the cholesterol pathway showed that, for MCF-7 and SUM102, adding either inhibitor greatly induced most genes in the cholesterol biosynthetic pathway, while SUM149 treated with lovastatin showed induction of the pathway but treatment with NB598 did not. ZR-75-1 treated with either drug showed a slight reduction in expression of the pathway. These in vitro data suggest that inhibition of SQLE activity can reduce cell line proliferation rates and, in some instances, was synergistic with chemotherapy. These data also suggest that inhibition of the cholesterol pathway by addition of HMGCoA reductase inhibitors is different from inhibition of the pathway with SQLE inhibitors.