Gene expression profiles of head and neck squamous cell carcinoma (HNSCC) cell lines

Chromosomal comparative genomic hybridization (CGH) and oligonucleotide microarrays were used to examine 8 HNSCC cell lines and a plot of gene expression levels relative to their position on the chromosome was produced. Three highly up-regulated genes, NT5C3, ANLN and INHBA, were identified on chromosome 7p14. These genes were subjected to quantitative real-time RT-PCR on cDNA and genomic DNA derived from 8 HNSCC cell lines. ANLN and INHBA showed a strong positive correlation between mRNA expression and genomic DNA levels and a similar relationship was shown for the known oncogene, EGFR, at 7p11.2. In clinical samples, ANLN and INHBA showed a significantly higher expression in tumors than in normal tissues. Patients with high expression levels of INHBA had a shorter disease-free survival rate. Therefore, INHBA may be a promising prognostic marker of HNSCC. Keywords: Identification of molecular targets based on genome-wide gene expression profiling To identify prognostic markers of HNSCC, chromosomal CGH and oligonucleotide microarray analysis was performed on 8 HNSCC cell lines. Up-regulated genes at chromosomal gain regions detected by CGH were identified. Quantitative real-time RT-PCR on cDNA and genomic DNA from 8 HNSCC cell lines was performed for three selected genes and expression was further analyzed in clinical samples.