Abstract

Background: In contrast to other breast cancer subtypes, triple negative breast cancers are characterized by an absence of recurrent genetic alterations. However, alterations in the PI3K pathway are frequently observed, either through mutation or amplification of PIK3CA or the loss of the negative regulator PTEN. As a result, inhibitors of this pathway, including inhibitors of mTOR, the downstream target of the PI3K pathway, have been explored in the clinic. It has been found that mutational activation of PI3K represents an important determinant of sensitivity to mTOR inhibitors. Nevertheless, a number of PI3K wild-type cell lines also show sensitivity to these inhibitors, although the regulators of this response are still unknown. We set out to find such modulators of response to mTOR inhibitors in a panel of triple negative breast cancer cell lines initially using high throughput approaches. Material and Methods: We determined the sensitivity of a panel of triple negative breast cancer cell lines to AZD8055 (mTOR inhibitor) and BEZ235 (mTOR/PI3K dual inhibitor). This data was then used together with additional datasets generated for this panel, including RNA expression (by RNA-seq), (phospho-)protein levels (by Reverse Phase Protein Arrays) and mutational status (by post-capture DNA-seq), to carry out regression analysis to identify features correlated with response. Results: We found that the protein expression levels of 4E-BP1, a downstream target of mTOR involved in regulating cap-dependent protein synthesis, correlated with response to both inhibitors. In poorly responding cell lines expressing low levels of 4E-BP1, overexpression of the protein increased sensitivity. Conversely, in sensitive cell lines expressing high levels of 4E-BP1, knock-down of 4E-BP1 led to reduced sensitivity to mTOR inhibition. Conclusions: These results indicate that effective inhibition of protein synthesis downstream of PI3K/mTOR is an important determinant of mTOR inhibitor activity. Given that approximately 20% of breast cancer tumors annotated in The Cancer Genome Atlas show an amplification of the 4E-BP1 locus, such patients would likely benefit from mTOR inhibitor treatment. Furthermore, we hypothesize that mTOR inhibitor response can be improved even in patients expressing low 4E-BP1 by co-treating with agents that induce its expression. To this end, we are currently screening for genes and drugs that modulate 4E-BP1 levels.

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