Integrated cistromic and expression analysis of amplified NKX2-1 in lung adenocarcinoma identifies LMO3 as a functional transcriptional target

Abstract

The NKX2-1 transcription factor, a regulator of normal lung development, is the most significantly amplified gene in human lung adenocarcinoma. To study the transcriptional impact of NKX2-1 amplification, we generated an expression signature associated with NKX2-1 amplification in human lung adenocarcinoma and analyzed DNAbinding sites of NKX2-1 by genome-wide chromatin immunoprecipitation. Integration of these expression and cistromic analyses identified LMO3, itself encoding a transcription regulator, as a candidate direct transcriptional target of NKX2-1. Further cistromic and overexpression analyses indicated that NKX2-1 can cooperate with the forkhead box transcription factor FOXA1 to regulate LMO3 gene expression. RNAi analysis of NKX2-1-amplified cells compared with nonamplified cells demonstrated that LMO3 mediates cell survival downstream from NKX2-1. Our findings provide new insight into the transcriptional regulatory network of NKX2-1 and suggest that LMO3 is a transcriptional signal transducer in NKX2-1-amplified lung adenocarcinomas.

A Surprising Cross-Species Conservation in the Genomic Landscape of Mouse and Human Oral Cancer Identifies a Transcriptional Signature Predicting Metastatic Disease

“…The NKX family of homeodomain transcription factors has been implicated in a variety of malignancies with lung adenocarcinoma serving as a prime example where Nkx2-1 has a dual role in tumor promotion and metastasis (33). Interestingly, recent work has shown that the Foxa1 pioneer factor partners with Nkx2-1 (34) and our analysis shows that Foxa1 is also upregulated in Nkx2–3 expressing aggressive tumors. Finally, with regard to MOC2–10, we identified Hoxb7 , which has been implicated in poor outcomes in OSCC (35) and Bmp4 , which promotes breast cancer metastasis (36), as candidate regulators of lung metastasis in OSCC.…”

MicroRNA-33a Mediates the Regulation of High Mobility Group AT-Hook 2 Gene (HMGA2) by Thyroid Transcription Factor 1 (TTF-1/NKX2–1)

“…In addition to being indispensable to fetal lung organogenesis and morphogenesis (17), TTF-1 also contributes to adult lung tumorigenesis based on the genetic evidence that TTF-1 is part of a recurrent multigenic amplicon in lung cancers (18 -21). Subsequent studies have identified ROR1 and LMO3 as indispensable downstream mediators of TTF-1 in lung adenocarcinomas (22,23). Seemingly at odds with the observation that TTF-1 is a lung oncogene, Ttf-1 was also found to prevent primary lung adenocarcinomas from metastasizing in a mouse model system (24).…”

SOX2 and p63 colocalize at genetic loci in squamous cell carcinomas

“…SOX2, p63 ChIP-seq, and JunD ChIPqPCR were performed as previously described with modifications (55). See Supplemental Table 8 for primers used for qPCR.…”

“…shRNA viral transfer, induction with Dox, cell growth assays, and anchorage-independent growth assays were performed as previously described (2,55).…”