Breast cancer is a heterogeneous disease that will affect 1 in 8 women throughout their lifetime. It can be divided into clinically relevant subtypes that can be therapeutically targeted with drugs inhibiting the actions of estrogen receptors, progesterone receptors and human epidermal growth factor receptor 2. Triple negative breast cancer (TNBC) comprises 14-20% of all breast cancers and is the subtype with the worst prognosis due to the lack of the aforementioned therapeutic targets. According to gene expression data, TNBC can be further divided into two major subtypes: basal-like and a more stem-like/mesenchymal subtype known as claudin-low. While they are molecularly distinct, neither of the primary TNBC subtypes have been effectively therapeutically targeted in the clinic. Hence, discerning the mechanisms driving TNBC progression is necessary to develop therapies for these diseases. I propose elucidating the epigenetic modifications that convey altered transcriptomes in TNBCs as a means to identify drivers of malignancy. One such epigenetic mechanism is a specialized type of enhancer called a super-enhancer (SE). These are large continuous clusters of typical enhancer sequences within DNA that have the ability to activate and sustain the expression of cell identity genes and oncogenes via interactions with transcription factors, co-factors, and epigenetic histone modifiers. While changes in the global transcriptomes of TNBC have previously been reported, these studies have been unable to directly reveal true drivers versus genes whose expression is changed as a result of the transformation process. I propose that discovering the SEs, and their cognate genes, within the breast cancer subtypes would reveal essential genes whose expression must be maintained to sustain TNBC aggressiveness. Using TNBC cell lines, I have already defined SE landscapes for the basal and claudin-low subtypes.
In Aim 1, I will determine if the SEs identified in vitro are recapitulated in patient derived xenografts (PDX). SEs that are conserved in vitro and in vivo will provide a core set of SEs for TNBC.
In Aim 2, following the PDX analysis, I will disrupt candidate SEs from this core set in cell lines to test their impact on the cancer phenotypes of migration and invasion in vitro.
In Aim 3, I will test the in vivo function of selected SEs by evaluating the ability of the SE-disrupted cell lines to form tumors and metastasize in mice. This approach should reveal key genes essential for the maintenance and progression of TNBC. In addition, it should uncover the genes/proteins that would be prime targets for future therapeutic intervention in this disease.
Breast cancer is a collection of diseases that are defined by the activity of their genes. This proposal focuses on identifying the regulatory switches that control genes driving the aggressive features of tumors known as triple negative breast cancers. This approach should reveal key genes and their regulatory processes that could serve as new therapeutic targets in breast cancer.