Differential DNA methylation analysis of breast cancer reveals the impact of immune signaling in radiation therapy

Abstract

Radiotherapy (RT) is a central treatment modality for breast cancer patients. The purpose of our study was to investigate the DNA methylation changes in tumors following RT, and to identify epigenetic markers predicting treatment outcome. Paired biopsies from patients with inoperable breast cancer were collected both before irradiation (n = 20) and after receiving 10-24 Gray (Gy) (n = 19). DNA methylation analysis was performed by using Illumina Infinium 27K arrays. Fourteen genes were selected for technical validation by pyrosequencing. Eighty-two differentially methylated genes were identified in irradiated (n = 11) versus nonirradiated (n = 19) samples (false discovery rate, FDR = 1.1%). Methylation levels in pathways belonging to the immune system were most altered after RT. Based on methylation levels before irradiation, a panel of five genes (H2AFY, CTSA, LTC4S, IL5RA and RB1) were significantly associated with clinical response (p = 0.041). Furthermore, the degree of methylation changes for 2,516 probes correlated with the given radiation dose. Within the 2,516 probes, an enrichment for pathways involved in cellular immune response, proliferation and apoptosis was identified (FDR < 5%). Here, we observed clear differences in methylation levels induced by radiation, some associated with response to treatment. Our study adds knowledge on the molecular mechanisms behind radiation response. What's new? Radiotherapy is a central treatment modality for breast cancer patients. This study set to investigate DNA methylation changes in tumors following radiotherapy and identify epigenetic markers predicting treatment outcome. Genome-wide methylation effects were studied by comparing breast cancer biopsies before and after irradiation. 82 differentially methylated genes enriched for immune regulation pathways were identified. Based on methylation levels before irradiation, a combination of 5 genes was significantly associated with response to radiotherapy. A dose dependency was seen for 2516 probes, mainly involved in immune response and apoptosis. This study sheds light on the genes and pathways involved in radiation response. © 2014 The Authors. Published by Wiley Periodicals, Inc. on behalf of UICC.