Regulation Of Gene Expression By Abnormal Epigenetic Modifications In Breast Cancer

Breast carcinoma is one of the most common cancers in women,accounting for³0%all cancer new diagnoses in females.In recent years,the incidence of breast cancer has become more and more young,and has seriously threatened women’life and health.It is the leading cause of cancer death in females.Breast cancer is a complex disease caused by a variety of factors,which is not only related to genomic mutations,but also closely related to the changes of epigenetic modifications.DNA methylation and histone modifications（HMs）have been shown to play an important role in the development and progression of breast cancer.Studying the effects of DNA methylation and HMs on the expression of tumor-related genes may provide new therapeutic strategies for breast cancer.Therefore,in this study,we systematically and comprehensively investigated the abnormal changes of DNA methylation and various histone modifications in breast cancer,and their effects on the breast cancer-related genes.The main conclusions include the following points:1.Based on Illumina Infinium HumanMethylation450K microarray data,we analyzed the differential DNA methylation between human breast cancer tissues and normal breast tissues,identified the hypermethylated and hypomethylated CpG sites in breast cancer tissues,and studied DNA methylation patterns in different regions of the genome in breast cancer tissues.Compared to normal breast tissues,DNA methylation of gene body region makes remarkable alterations in breast cancer tissues,while 3’UTR tended to be hypomethylated.What’s more,CpG islands（CGIs）are mainly hypermethylated in breast cancer,and shelves and shores regions flanking CGIs prefer to be hypomethylated.Most importantly,enhancers are mainly hypomethylated in breast carcinoma tissue compared to normal tissue.2.We studied the relationship between the expressions of up-/down-regulated genes（adjusted p<0.01 and|log₂（FoldChange）|>1）in breast cancer tissues and DNA methylation in different regions of genome.Results showed that hypermethylation in CpG islands was associated with the expression of down-regulated genes in breast cancer tissues,which may be an important factor leading to the decrease of expression levels of tumor suppressor genes.Hypomethylation of enhancer was related to the expression of up-regulated genes,and may promote the expression of oncogenes.It was found that some key hypomethylation sites in enhancer regions were closely related to the increase of breast oncogene expression,such as ESR1 and ERBB2.Meanwhile,some key hypermethylation sites in CpG islands were found to be associated with the decrease of tumor suppressor gene expression,such as FBLN2,CEBPA,and FAT4.The discovery of these key sites may have potential value for the clinical application of breast cancer.3.Besides DNA methylation,histone modifications play crucial roles in breast cancer.The ChIP-Seq data of 11 HMs in human breast cancer cells（MCF-7）and human normal mammary epithelial cells（HMEC）were used to analyze the signal distributions of HMs flanking transcription start sites（TSSs）of genome in two types of cells.Compared to normal breast cells,H3K79me2 levels in TSS downstream were obviously increased for breast cancer cells,and the levels of H3K27ac and H3K4me1 were significantly increased in the up-and downstream 5 kb of TSSs.Spearman correlation function was used to study the correlation between histone modifications and the expression of up/down-regulated gene in breast cancer cells.Results showed that H3K79me2 in TSS downstream has stronger positive correlation with gene expression,as well as H3K27ac and H3K4me1 near TSSs have stronger positive correlation with gene expression.In addition,based on HMs signal differences between MCF-7 and HMEC flanking TSSs,the up-and down-regulated genes in breast cancer cells were predicted by Random Forest method,and the importance of each HM was analyzed.Studies indicated that the predictive abilities of H3K79me2,H3K27ac,and H3K4me1 are robust（AUCs>0.95）.In particular,H3K79me2 in TSS downstream has a stronger effect on the expressions of up-and down-regulated genes in breast cancer cells.H3K79me2 may be a key histone modification for the occurrence of breast carcinoma.Our study will provide a better understanding of the epigenetic mechanisms of breast cancer.