EVALUATING INHIBITION OF DNA METHYLATION AND ALDH1A3 AS BREAST CANCER THERAPIES

Abstract

Breast cancer is the most common form of cancer among Canadian women. Patients with triple-negative breast cancer (TNBC) have poor prognoses, with inherently more aggressive disease and limited treatment options. New modalities for treating TNBC are required. Here, I investigate a precision medicine approach to applying DNA hypomethylating therapy and assess the potential benefits of targeting breast cancer stem cell (CSC) marker aldehyde dehydrogenase 1A3 (ALDH1A3). Dysregulation of DNA methylation is an established feature of breast cancers. DNA hypomethylating therapies like decitabine are proposed for the treatment of TNBC yet indicators of response need to be identified. I demonstrate the requirement of deoxycytidine kinase (DCK) for decitabine response in breast cancer cells; however, no predictive features or other mediators of decitabine response were identified. An shRNA-based genome-wide screen was performed to detect potent hypermethylated genes or novel mediators of decitabine. I found that loss of methylene tetrahydrofolate dehydrogenase 2 (MTHFD2) conferred decitabine resistance to TNBC cells likely by suppressing cell proliferation via limiting nucleotide biosynthesis. Therefore, while hypermethylated genes that predict hypomethylating therapy response were not obtained, the relevance of emerging drug target MTHFD2 to TNBC was confirmed. CSCs are a highly aggressive subpopulation of cells within breast tumours and are identified by their high ALDH1A3 activity. In addition to its role as an established CSC marker, ALDH1A3 plays a key role in the progression and metastasis of breast cancer. Therefore, ALDH1A3 represents a druggable anti-cancer target of interest. Nanoparticle encapsulation of ALDH1A3 inhibitor citral reduced ALDH1A3-mediated growth of MDA-MB-231 TNBC tumours. Metabolomic and gene expression analyses identified γ-aminobutyric acid (GABA) signaling/metabolism as a dysregulated pathway in ALDH1A3-hi breast tumours. In mice treated with systemic GABA there was higher rates of lung metastasis. Patient dataset analyses revealed that metastatic breast cancer has a distinct GABA metabolism profile. Together, these results suggest two new approaches for TNBC therapy: 1) use MTHFD2 to stratify patients for hypomethylating therapy or directly inhibit MTHFD2 and 2) inhibit ALDH1A3 to potentially control GABA-mediated metastasis.