Promoter Methylation Modulates Indoleamine 2,3-Dioxygenase 1 Induction by Activated T Cells in Human Breast Cancers

Triple-negative breast cancer (TNBC) cells are modulated in reaction to tumor-infiltrating lymphocytes. However, their specific responses to this immune pressure are unknown. In order to address this question, we first used mRNA sequencing to compare the immunophenotype of the TNBC cell line MDA-MB-231 and the luminal breast cancer cell line MCF7 after both were cocultured with activated human T cells. Despite similarities in the cytokine-induced immune signatures of the two cell lines, MDA-MD-231 cells were able to transcribe more than MCF7 cells. The two cell lines had similar upstream JAK/STAT1 signaling and mRNA stability. However, using a series of breast cancer cell lines, IFNγ stimulated IDO1 protein expression and enzymatic activity only in ER, not ER, cell lines. Treatment with 5-aza-deoxycytidine reversed the suppression of expression in MCF7 cells, suggesting that DNA methylation was potentially involved in induction. By analyzing several breast cancer datasets, we discovered subtype-specific mRNA and promoter methylation differences in , with TNBC/basal subtypes exhibiting lower methylation/higher expression and ER/luminal subtypes exhibiting higher methylation/lower expression. We confirmed this trend of methylation by bisulfite pyrosequencing breast cancer cell lines and an independent cohort of primary breast tumors. Taken together, these findings suggest that promoter methylation regulates anti-immune responses in breast cancer subtypes and could be used as a predictive biomarker for IDO1 inhibitor-based immunotherapy. .