TET1, TET2 and TET3 expression in breast cancer and its association with survival. Putative TET2 and TET3 methylation targets in breast cancer. Differential gene expression analysis in TCGA triple negative breast cancer patients. Putative TET1 methylation targets in ovarian cancer. 5hmC slot blot in TET1 KD cells. Drug validation assays. RNA-seq and DREAM analyses in Hs578T cells. CRISPR gRNA sequences. List of drugs correlated with TET1 expression in breast and ovarian cancer cell lines. Supplemental methods related to RNA-seq, DREAM and bioinformatics.
ARTICLE ABSTRACT
Both gains and losses of DNA methylation are common in cancer, but the factors controlling this balance of methylation remain unclear. Triple-negative breast cancer (TNBC), a subtype that does not overexpress hormone receptors or HER2/NEU, is one of the most hypomethylated cancers observed. Here, we discovered that the TET1 DNA demethylase is specifically overexpressed in about 40% of patients with TNBC, where it is associated with hypomethylation of up to 10% of queried CpG sites and a worse overall survival. Through bioinformatic analyses in both breast and ovarian cancer cell line panels, we uncovered an intricate network connecting TET1 to hypomethylation and activation of cancer-specific oncogenic pathways, including PI3K, EGFR, and PDGF. TET1 expression correlated with sensitivity to drugs targeting the PI3K–mTOR pathway, and CRISPR-mediated deletion of TET1 in two independent TNBC cell lines resulted in reduced expression of PI3K pathway genes, upregulation of immune response genes, and substantially reduced cellular proliferation, suggesting dependence of oncogenic pathways on TET1 overexpression. Our work establishes TET1 as a potential oncogene that contributes to aberrant hypomethylation in cancer and suggests that TET1 could serve as a druggable target for therapeutic intervention.Significance: This study addresses a critical gap in knowledge of how and why methylation is prognostic in breast cancer and shows how this information can be used to stratify patients with TNBC for targeted therapy. Cancer Res; 78(15); 4126–37. ©2018 AACR.
