Methylation profiling study by MBD-seq for identifying genes associated with epithelial-mesenchymal transition and acquired resistance to ALK inhibitors

Treatment with ALK tyrosine kinase inhibitors often elicits profound initial antitumor responses in ALK fusion-positive patients with lung adenocarcinoma. However, patients invariably develop acquired resistance to ALK inhibitors. In this study, we aimed to identify molecular events that limit the response to ALK inhibition using genetic and epigenetic approaches. To identify novel mechanisms of acquired resistance to ALK inhibitors, we established in vitro models of acquired resistance to ceritinib using H3122 cell. For in vitro model, H3122 parental cells, ceritinib-treated resistant cells, and non-resistant cells that combinely treated with certinib and panobinostat were used for MBD-seq based methylation profiling. Overall design: MBD-seq data of 6 samples, two H3122 parental cells, two ceritinib-treated resistant cells, and two non-resistant cells that combinely treated with certinib and panobinostat, were generated. Methylated DNA was precipitated using the MethylMiner methylated DNA enrichment kit (Invitrogen). The purified methylated DNA fragments were ligated to a pair of adaptors. Sequencing was performed in single end reads (75 bp) using NextSeq 500 platform (Illumina).