Difference of DNA methylation and Chromatin accessibility of J82 SP cell and J82 NSP cell

Subpopulations of highly tumorigenic, drug resistant cancer stem-like cells play a key role in cancer recurrence and progression. Surprisingly, these aggressive cells can arise repeatedly de novo from bulk tumor cells independently of mutational events. We investigated whether transition to and from a cancer stem-like state is associated with epigenetic alterations, such as DNA methylation and chromatin accessibility. By Hoechst dye staining and FACS analysis, side population (SP) and non-side population cells were sorted from J82 cells. AcceSssIble assay by Infinium EPIC BeadArray platform was used to identify potential epigenetic driver genes in the process of SP /NSP phenotype plasticity. Genes with differential accessible promoter regions were overlapped with genes differentially expressed by HuEx array analysis. Oncomine and Basespace were adopted to explore the clinical relevance of the target genes. Intact nuclei are harvested from J82 SP and NSP cells and treated with M.SssI at 37 ˚C for 15 minutes supplied with S-Adenosyl methionine (SAM). The no-enzyme (NE) controls are also included for each cell. DNA is then extracted, bisulfite converted and run on an Infinium methylationEPIC array. The Beta values of the no-enzyme controls show the original DNA methylation level. The subtracted beta values (M.SssI treated - NE) are used to determine regions that have gained by the in vitro M.SssI treatment, and these are used to infer chromatin state.