Identification of DNA methylation biomarkers with potential to predict response to neoadjuvant chemotherapy in triple-negative breast cancer
Braydon Meyer, Samuel Clifton, Warwick J. Locke, Phuc‐Loi Luu, Qian Du, Dilys Lam, Nicola J. Armstrong, Beena Kumar, Niantao Deng, Kate Harvey, Alexander Swarbrick, Vinod Ganju, Susan J. Clark, Ruth Pidsley, Clare Stirzaker
Abstract
Neoadjuvant chemotherapy (NAC) is used to treat triple-negative breast cancer (TNBC) prior to resection. Biomarkers that accurately predict a patient's response to NAC are needed to individualise therapy and avoid chemotoxicity from unnecessary chemotherapy. We performed whole-genome DNA methylation profiling on diagnostic TNBC biopsy samples from the Sequential Evaluation of Tumours Undergoing Preoperative (SETUP) NAC study. We found 9 significantly differentially methylated regions (DMRs) at diagnosis which were associated with response to NAC. We show that 4 of these DMRs are associated with TNBC overall survival (P < 0.05). Our results highlight the potential of DNA methylation biomarkers for predicting NAC response in TNBC.