Abstract 3127: Integrated cistromic and expression analysis of amplified NKX2-1 in lung adenocarcinoma identifies LMO3 as a functional transcriptional target.
Authors: Watanabe Hideo , Francis Joshua M. , Woo Michele S. , Etemad Banafsheh , Lin Wenchu , Fries Daniel F. , Peng Shouyong , Snyder Eric L. , Rao Tata Purushothama , Schinzel Anna C. , Cho Jeonghee , Hammerman Peter S. , Verhaak Roel G. , Hahn William C. , Rajagopal Jayaraj , Jacks Tyler , Meyerson Matthew 
Published: August 2014

Abstract
The NKX2-1 transcription factor, a regulator of normal lung development, is the most significantly amplified gene in human lung adenocarcinoma. To better understand how genomic alterations of NKX2-1 drive tumorigenesis, we generated an expression signature associated with NKX2-1 amplification in human lung adenocarcinoma, and analyzed DNA binding sites of NKX2-1 by genome-wide chromatin immunoprecipitation (ChIP-seq) from three NKX2-1-amplified human lung adenocarcinoma cell lines. Integration of these expression and cistromic analyses suggested that aberrant over-expression of NKX2-1 primarily activates the expression of transcriptional target genes whose expression is not trans-activated by NKX2-1 at physiological expression levels, and identified LMO3, itself encoding a transcription regulator, as a candidate direct transcriptional target of NKX2-1. NKX2-1 amplification is most significantly associated with over-expression of the LMO3 gene, a member of the LMO family of oncogenes that are translocated in T-ALL, the same disorder in which NKX2-1 translocation has been observed. We further show that NKX2-1 interacts physically with the LMO3 locus, and activates its expression. RNA interference analysis of NKX2-1-amplified cells compared to non-amplified cells demonstrated that LMO3 mediates cell proliferation downstream of NKX2-1. Further cistromic analyses found that consensus binding motifs including a nuclear hormone receptor signature and a Forkhead box motif, indicating that NKX2-1 might cooperate with Forkhead box FOXA1 and nuclear hormones to regulate gene expression. Genome-wide analysis of FOXA1 occupancy by ChIP-seq in the NCI-H3122 cell line revealed that FOXA1 binds not only to the LMO3 locus upstream of NKX2-1 binding site but also to many NKX2-1 occupied regions (47% of total NKX2-1-bound sites). Our findings provide new insight into the transcriptional regulatory network of NKX2-1 and suggest that LMO3 is a transducer of lineage specific cell survival of NKX2-1-amplified lung adenocarcinomas.
Citation Format: Hideo Watanabe, Joshua M. Francis, Michele S. Woo, Banafsheh Etemad, Wenchu Lin, Daniel F. Fries, Shouyong Peng, Eric L. Snyder, Purushothama Rao Tata, Anna C. Schinzel, Jeonghee Cho, Peter S. Hammerman, Roel G. Verhaak, William C. Hahn, Jayaraj Rajagopal, Tyler Jacks, Matthew Meyerson. Integrated cistromic and expression analysis of amplified NKX2-1 in lung adenocarcinoma identifies LMO3 as a functional transcriptional target. [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr 3127. doi:10.1158/1538-7445.AM2013-3127