Targeted DNA sequencing of the lung SWI/SNF complex and cancer drivers in lung adenocarcinoma cell lines. Targeted sequencing of SWI/SNF complex in LUAD cell lines

Lung adenocarcinoma (LUAD) is the main subtype of lung cancer, the most frequent and deadliest cancer worldwide. The SWI/SNF complex is a multiprotein complex that is involved in the epigenetic regulation of gene expression. SWI/SNF complex subunits, such as SMARCA4 and ARID1A, are known to be recurrently mutated in LUAD, but the biological function of the SWI/SNF complex and its alterations in LUAD are currently unknown.Here, we first performed a protein immunoprecipitation followed by tandem mass spectrometry to elucidate which SWI/SNF subunits are present at the protein level in lung cell lines. We then performed targeted DNA sequencing on the 20 lung SWI/SNF subunits detected in our proteomics assay, as well as on 5 major LUAD drivers. The gene capture was performed using a NimbleGen SeqCap EZ Choice Library kit and paired 150 bp reads were obtained in an Illumina NextSeq 500 instrument.