PO-367 DFNA5 methylation: a potential biomarker for breast cancer, on the basis of a large scale analysis in TCGA

Introduction Breast cancer is the most frequent cancer among women worldwide. Biomarkers for early detection and prognosis of these patients are needed. We hypothesised that DFNA5 (also know as Gasdermin E (GSDME)) may be a valuable biomarker, based upon strong indications for its role as tumour suppressor gene and its function in regulated cell death. In this study, we aimed to analyse DFNA5 methylation and expression in the largest breast cancer cohort to date using publicly available data from TCGA, in order to further unravel the role of DFNA5 as detection and/or prognostic marker in breast cancer. Material and methods We analysed Infinium HumanMethylation450k data, covering 22 different CpGs in the DFNA5 gene (668 breast adenocarcinomas and 85 normal breast samples) and DFNA5 expression (Agilent 244K Custom Gene Expression: 476 breast adenocarcinomas and 56 normal breast samples; RNA-seq: 666 breast adenocarcinomas and 71 normal breast samples). Results and discussions DFNA5 methylation and expression were significantly different between breast cancer and normal breast samples. Overall, breast cancer samples showed higher DFNA5 methylation in the putative gene promoter compared to normal breast samples, whereas in the gene body and upstream of the putative gene promoter the opposite is true. Furthermore, DFNA5 methylation, in 10 out of 22 CpGs, and expression was significantly higher in lobular compared to ductal breast cancers. An important result of this study was the identification of a combination of one CpG in the gene promoter (CpG07504598) and one CpG in the gene body (CpG12922093) of DFNA5, that was able to discriminate between breast cancer and normal breast samples (AUC=0.93). This model was externally validated in three independent datasets. Moreover, we showed that oestrogen receptor state is associated with DFNA5 methylation and expression. Finally, we were able to find a significant effect of DFNA5 gene body methylation on 5 year overall survival time. Conclusion We conclude that DFNA5 methylation shows strong potential as detection and prognostic biomarker for breast cancer.