Substantial genomic and methylation variability between MCF-7 sublines

Cancer cell lines have long been used as in vitro models for molecular assays in diagnostic and therapeutic development due to their accessibility as a well-controlled system. MCF-7 cell lines are the most widely studied cell lines in human breast cancer research, and its sublines have been reported to exhibit clonal, cytogenetic, and transcriptomic variability. However, allele-specific methylation alterations in cancer genomes remain inadequately explored, largely due to limitations in sequencing methods. Here, we characterise the genomic and epigenomic landscapes of two MCF-7 sublines using previously published Oxford Nanopore Technology sequencing data. We identified global and local DNA methylation differences as well as ~ 5000 structural variants and ~ 26,000 single-nucleotide variants between and within the sublines. Our analysis revealed substantial divergence in methylation patterns between the sublines, with ~ 5.1% of 1909 differentially methylated regions (DMRs) overlapping known cancer driver genes. These DMRs overlap breast cancer-associated genes, including ERBB2, CDH1, SALL4, GATA2, GATA3, HMGA2, and FBLN2. We find that 31 out of 63 manually assessed DMRs are explained by differential allelic methylation, and that allele-specific DMRs often overlap points where antisense non-coding RNAs overlap protein-coding genes. Transposable elements in both sublines also showed distinct methylation profiles, with one subline having hypomethylated L1 elements compared to the other, which coincided with the amount of apparent insertional mutagenesis attributable to L1 between the sublines. Our study demonstrates the utility of nanopore sequencing in providing novel insights into genomic and methylomic differences within MCF-7 sublines, in addition to insight into the nature of differential allelic methylation.