Chromosome X genomic and epigenomic aberrations and clinical implications in breast cancer by base resolution profiling

Aim: Abnormal inactivation or loss of inactivated X chromosome (Xi) is implicated in women's cancer. However, the underlying mechanisms and clinical relevance are little known. Materials & methods: High-throughput sequencing was conducted on breast cancer cell lines for copy number, RNA expression and 5′-methylcytosine in ChrX. The results were examined in primary breast tumors. Results & conclusion: Breast cancer cells demonstrated reduced or total loss of hemimethylation. Most cell lines lost part or one of X chromosomes. Cell lines without ChrX loss were more active in gene expression. DNA methylation was corroborated with Xi control lincRNA XIST. Similar transcriptome and DNA methylation changes were observed in primary breast cancer datasets with clinical phenotype associations. Dramatic genomic and epigenomic changes in ChrX may be used for potential diagnostic or prognostic markers in breast cancer.