Abstract
BackgroundBreast cancer is the malignant tumor with the highest incidence in women. DNA methylation has an important effect on breast cancer, but the effect of abnormal DNA methylation on gene expression in breast cancer is still unclear. Therefore, it is very important to find therapeutic targets related to DNA methylation.ResultsIn this work, we calculated the DNA methylation distribution and gene expression level in cancer and para-cancerous tissues for breast cancer samples. We found that DNA methylation in key regions is closely related to gene expression by analyzing the relationship between the distribution characteristics of DNA methylation in different regions and the change of gene expression level. Finally, the 18 key genes (17 tumor suppressor genes and 1 oncogene) related to prognosis were confirmed by the survival analysis of clinical data. Some important DNA methylation regions in these genes that result in breast cancer were found.ConclusionsWe believe that 17 TSGs and 1 oncogene may be breast cancer biomarkers regulated by DNA methylation in key regions. These results will help to explore DNA methylation biomarkers as potential therapeutic targets for breast cancer.
Highlights
Breast cancer is the malignant tumor with the highest incidence in women
By analyzing gene expression data, we found that 3741 genes were significantly up-regulated, and 2369 genes were significantly down-regulated in breast cancer tissues
By computing the DNA methylation data in the promoter regions of genes, it was found that 2991 genes were hypermethylated and 832 genes were hypomethylated in breast cancer tissues
Summary
DNA methylation has an important effect on breast cancer, but the effect of abnormal DNA methylation on gene expression in breast cancer is still unclear. It is very important to find therapeutic targets related to DNA methylation. Many studies have reported that DNA methylation can affect gene expression, which is an important factor in the development and progression of cancer [11]. Hypermethylation of tumor suppressor genes (TSGs) can lead to cancer development [13,14,15]. The hypermethylation in promoters of APC, SFRP1, SFRP2, SFRP5, WIF1, DKK3, ITIH5, and RASSF1A [17] are associated with the development of breast cancer, and studies have found that APC and RASSF1A are common epigenetic
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