ChIP-seq for identifying molecules 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 ChIP-seq analysis. Overall design: ChIP-sequencing was performed in each cell group. Cells were fixed using 1% formaldehyde, lysed and sonicated using a Bioruptor (Diagenode Inc.). Immunoprecipitation was performed with anti-H3K27ac(Millipore, 06-599) or anti-H3K4me1(Abcam, ab8895). 250-400 bp genomic libraries were generated from the input and immunoprecipitated DNA and sequenced using Illumina NextSeq500 to generate 75 bp single-end reads.