Fig. 3.

FOXA1 is amplified and overexpressed in NSCLCs. (A) FOXA1 is frequently co-amplified with NKX2-1 in NSCLC tumors. Segmented copy number profiles of the genomic region that includes NKX2-1 and FOXA1, from SNP array datasets on primary lung adenocarcinomas from TCGA (left), and on NSCLC cell lines (right). Samples with ≥4 copies of NKX2-1 are shown in rank order of NKX2-1 amplification from left to right, with corresponding chromosome band regions indicated on the left. (B) Scatter plots comparing FOXA1 copy number with FOXA1 mRNA expression level in cell lines (top), and tumors (bottom). (C) Average FOXA1 expression levels in cell lines compared to HBEC and HSAEC cell lines (top), and in primary tumors compared to normal tissues (bottom). (D) FOXA1 mRNA levels measured by Q-RTPCR in a panel of NSCLC cell lines. RQ = relative quantification, normalized to GAPDH and calculated from three technical replicates. Error bars indicate the upper and lower limits of the RQ value. Copy number for NKX2-1 and FOXA1 are indicated on the bottom. Inset: Scatter plot comparing copy number levels in NSCLC cell lines with mRNA levels. (E) FOXA1 protein expression levels in a panel of cell lines, with copy number indicated on the bottom. (F) Representative images of lung adenocarcinomas from the PROSPECT tumor array harboring 14q-ampflication and high FOXA1 expression (top), or no amplification and low expression (bottom). (G) Scatter plot comparing FOXA1 copy number (aCGH) with quantified IHC staining for FOXA1 on PROSPECT tumor array specimens.