Differential methylation analysis in normal breast tissue contralateral to tumour reveals PROM1 as a potential prognostic biomarker

While the DNA methylation landscape is significantly altered in breast cancer, little is known about whether histologically normal breast tissue (HNBT) adjacent to tumor is truly connected to normal breast epithelium at the epigenetic and molecular level due to the cancer field effect. Here, we analyzed publicly available DNA methylation dataset, GSE133985, to examine whether field cancerization effect is present in the HNBT adjacent to the tumor (ipsilateral-normal) and to identify a potential prognostic marker for breast cancer. Differential methylation analysis on matched tumor, ipsilateral-normal, and contralateral-normal tissue (histologically normal breast tissue nonadjacent to the tumor) identified more differentially methylated (DM) CpG loci between contralateral-normal and tumor (163,621 CpG sites, q < 0.05), than ipsilateral-normal and tumor (101,207 CpG sites, q < 0.05). We identified a distinct set of genes that were DM in tumor compared to contralateral-normal tissue but not in tumor compared to ipsilateral-normal tissue, and vice versa. Differential methylation analysis also identified PROM1 gene as the most DM (hypermethylated) gene in tumor compared to contralateral-normal tissue. Pairing our differential methylation results of the PROM1 gene with its expression data from the gene expression atlas database, we highlighted the potential prognostic value of PROM1 in breast cancer and provided evidence supporting its involvement in this disease. Our study highlights the significance of studying differences in DNA methylation in tumor relative to contralateral-normal tissue to avoid field effect observed in ipsilateral-normal tissue and increase the list of potential epigenetic biomarkers for this disease. Our study also highlights the potential role of PROM1 in breast cancer development and progression, suggesting that further investigation is warranted in the future to evaluate its prognostic value in a clinical setting.