Project description: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 from NKX2-1-amplified human lung adenocarcinoma cell lines. Combining these expression and cistromic analyses identified LMO3, itself encoding a transcription regulator, as a candidate direct transcriptional target of NKX2-1, in addition to consensus binding motifs including a nuclear hormone receptor signature and a Forkhead box motif in NKX2-1-bound sequences. RNA interference analysis of NKX2-1-amplified cells compared to non-amplified cells demonstrated that LMO3 mediates cell proliferation downstream of NKX2-1; cistromic analysis that NKX2-1 may cooperate with FOXA1. 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. NKX2-1 ChIP-seq from three lung adenocarcinoma cell lines with amplification of NKX2-1

2013-01-22 | E-GEOD-39998 | biostudies-arrayexpress

Genomic profiling identifies TITF1 as a lineage-specific oncogene amplified in lung cancer: Expression Arrays

Project description:Lung cancer is a leading cause of cancer death, where the amplification of oncogenes contributes to tumorigenesis. Genomic profiling of 128 lung cancer cell lines and tumors revealed frequent focal DNA amplification at cytoband 14q13.3, a locus not amplified in other tumor types. The smallest region of recurrent amplification spanned the homeobox transcription factor TITF1 (also known as NKX2-1), previously linked to normal lung development and function. When amplified, TITF1 exhibited increased expression at both the RNA and protein level. siRNA-mediated knockdown of TITF1 in lung cancer cell lines with amplification led to reduced cell proliferation, manifested by both decreased cell-cycle progression and increased apoptosis. Our findings indicate that TITF1 amplification and overexpression contribute to lung cancer cell proliferation rates and survival, and implicate TITF1 as a lineage-specific oncogene in lung cancer. Set of arrays organized by shared biological context, such as organism, tumors types, processes, etc. Cell Line Keywords: Logical Set cDNA microarrays from the Stanford Functional Genomics Facility were used to perform gene expression profiling on 33 non-small cell lung cancer (NSCLC) cell lines, 1 immortalized and 2 non-immortalized lung epithelial cell lines. Mann-Whitney U-Test (p=0.046) was performed to demonstrate that TITF1 increased expression was correlated with TITF1 gene amplification (as shown by aCGH analysis). NHBEC, SAEC and BEAS-2B are Normal lung epithelial cell lines, the others are Lung cancer cell lines Using regression correlation

2010-06-25 | E-GEOD-9994 | biostudies-arrayexpress

RNAseq of two mouse lung cancer cell lines in a DSTYK-altered context

Project description:We report RNAseq data from two independent mouse syngeneic lung cancer cell lines LLC and UN-SCC679 in an altered DSTYK context Lung cancer remains the leading cause of cancer-related death worldwide. We identify DSTYK, a dual serine/threonine and tyrosine non-receptor protein kinase, as a novel actionable target altered in non-small cell lung cancer (NSCLC). We also show DSTYK´s association with a lower overall survival (OS) and poorer progression-free survival (PFS) in multiple patient cohorts. To ascertain the potential molecular carcinogenesis processes in which DSTYK was involved, we performed an RNAseq analysis of two different lung cancer cell lines with either overexpressed or inhibited DSTYK. Inhibition was achieved through shRNA technology. These cell lines were cultured in RPMI 1640 supplemented with 10% Fetalclone (Thermo Fisher Scientific) and 100 U/mL penicillin-100 µg/mL streptomycin (Thermo Fisher Scientific). All cells were grown in a humidified incubator containing 5% CO2 at 37°C. Cell lines were routinely tested for mycoplasma.

2022-09-23 | GSE212858 | GEO

Transcription profiling of human bronchial epithelial cells overexpressing the lung developmental transcription factors TTF1, NKX2-8 and PAX9

Project description:We investigated the clinical implications of lung developmental transcription factors (TTF-1, NKX2-8, and PAX9) which we recently discovered as cooperating oncogenes activated by way of gene amplification at chromosome 14q13 in lung cancer. Using stable transfectants of human bronchial epithelial cells, RNA expression profiles (signatures) representing activation of the biological pathways defined by each of the three genes were determined and used to risk stratify a non-small cell lung cancer (NSCLC) clinical dataset consisting of ninety-one early stage tumors. Co-activation of the TTF-1 and NKX2-8 pathways identified a cluster of patients with poor survival, representing approximately 20% of patients with early stage NSCLC, whereas activation of individual pathways did not reveal significant prognostic power. Importantly, the poor prognosis associated with co-activation of TTF-1 and NKX2-8 was validated in two other independent clinical datasets. Further, lung cancer cell lines showing co-activation of the TTF-1 and NKX2-8 pathways were shown to exhibit resistance to cisplatin, the standard of care for the treatment of NSCLC. Since TTF-1 and NKX2-8 lack specific inhibitors at the current time, we explored an alternative therapeutic strategy. Using signatures of signaling pathway activation, we identified deregulation of specific oncogenic pathways (Ras and Myc) in the TTF-1/NKX2-8 co-activated cohort. In vitro experiments demonstrated the ability of a Ras pathway-specific therapy to inhibit tumor cell growth in TTF-1/NKX-2 activated cells, thus, suggesting that modulation of the Ras pathway is a rational strategy to targeted therapy in high risk NSCLC patients with co-activation of specific lung developmental pathways. Experiment Overall Design: Six controls and six replicates of each transcription factor (TTF1, NKX2-8, PAX9) were prepared and analyzed.

2009-04-10 | E-GEOD-9212 | biostudies-arrayexpress

Homo sapiens

Project description:Expression data from Non small cell lung cancer cell lines

| PRJNA111915 | ENA

NKX2-1 occupancy in human lung adenocarcinoma cell lines

2013-01-22 | GSE39998 | GEO

Differential gene expression by NKX2-1 suppression in NCI-H2009 cells

2013-04-15 | GSE40270 | GEO