TRANSCRIPTION FACTOR EB REGULATES APOPTOSIS, DNA REPAIR, AND CELL PROLIFERATION IN TRIPLE-NEGATIVE BREAST CANCER CELLS

Abstract

Breast cancer is the leading cause of cancer-related death among women in Canada. Molecular heterogeneity among breast cancer patients dictates survival outcomes and treatment selection, with triple-negative breast cancer (TNBC) being the molecular subtype with the worst survival rates. TNBC is defined by the absence of the estrogen receptor, human epidermal growth factor receptor 2, and progesterone receptor. TNBC patients have a higher rate of recurrence, partially due to the lack of targeted therapies thus a greater understanding of the molecular pathways which promote TNBC survival is required. Transcription factor EB (TFEB) is a master regulator of lysosomal biogenesis, autophagy, and metabolism with critical roles in several cancers. Lysosomal autophagy promotes cancer survival through the degradation of toxic molecules and the maintenance of adequate nutrient supply. We hypothesized that TFEB mediated lysosomal biogenesis was critical for TNBC cell proliferation and treatment resistance. In this thesis, I find that TFEB is highly expressed in TNBC, and treatment of TNBC cells with the chemotherapeutic doxorubicin (DOX) results in TFEB dephosphorylation, nuclear translocation, and transcriptional activation. Loss of TFEB expression reduced TNBC cell viability, which was associated with elevated caspase-3 dependent apoptosis, and increased sensitivity to DOX in a mechanism independent of changes in lysosomal function. Transcriptomics identified that TFEB regulates homologous recombination repair, which correlated with increased sensitivity to DNA damage induced by DOX. Other pathways dysregulated by loss of TFEB expression in TNBC cells included death receptor signaling and nucleotide metabolism, while metabolomics identified that abundance of the pyrimidine nucleobase cytosine was decreased by TFEB silencing. Bioinformatics found that transcriptional networks controlled by MYC, FOXM1, and the E2F were downregulated by TFEB knockdown. TFEB was found to have a direct role in TNBC cell cycle regulation, with loss of TFEB function causing G1/S cell cycle arrest. Lastly, TFEB silencing induces synthetic lethality with inhibitors of the mitotic regulator Aurora Kinase A. Overall, this research describes the molecular mechanisms through which TFEB promotes the survival and growth of TNBC cells and identifies novel therapeutic targets for the treatment of triple-negative breast cancer.