Abstract 2998: BRG1 (SMARCA4) protein loss has profound effects on the transcriptome of non-small cell lung cancer (NSCLC) cell lines

Abstract

Abstract Purpose: To study the gene expression profile of NSCLC cell lines with BRG1 protein loss. Background: BRG1 is the major catalytic subunit of the SWI/SNF chromatin remodeling complex and provides ATPase activity necessary for transcriptional regulation of multiple cellular pathways. BRG1 is frequently inactivated in lung cancers and loss of BRG1 is correlated with poor prognosis. Methods: Sixty eight NSCLC cell lines were analyzed. BRG1 protein was detected by western blotting using nuclear extracts. SMARCA4 deletions or mutations were identified by NextGen sequencing and/or Sanger sequencing using genomic DNA or cDNA. Published reports and SNP analysis were also used to verify our results. Gene expression profiles were determined by Illumina human WG-6 V3 beadchip. Microarray expression data was analyzed by Significance Analysis of Microarray (SAM) and Hierarchical clustering analysis. Results: Twenty five NSCLC cell lines had lost BRG1 protein expression. Sequencing analysis found homozygous mutations (deletions, nonsense, splicing site) in twenty two of the lines. Among forty three NSCLC cell lines with BRG1 protein expression, five had homozygous missense mutations, four had heterozygous mutations. Gene expression profiling demonstrated that nearly 1500 transcripts were differentially up or down regulated (false discovery rate <5%) among the cell lines without BRG1 protein compared to the ones with WT BRG1. These transcripts are involved in many important cellular functions including proliferation, adhesion, epithelial-mesenchymal transition, signaling pathway, steroid receptor and oncogene expression. Hierarchical clustering analysis using these transcripts distinguished NSCLC cell lines without BRG1 protein as a group, different from other NSCLC cells as well as immortalized respiratory epithelial cells, while NSCLC cell lines with BRG1 missense mutations showed heterogeneity of expression patterns. Conclusions: BRG1 protein loss is frequent in lung cancer cells and has a distinct signature and profound effects on the transcriptome of NSCLC cell lines. Our findings support the concept that BRG1 functions as a “master regulator of master regulators.” Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 103rd Annual Meeting of the American Association for Cancer Research; 2012 Mar 31-Apr 4; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2012;72(8 Suppl):Abstract nr 2998. doi:1538-7445.AM2012-2998