Genome-wide identification of novel expression signatures reveal distinct patterns and prevalence of binding motifs of p53, NF-kappaB and other signal transcription factors in head and neck squamous cell carcinoma

Background : Differentially expressed gene profiles have previously been observed among pathologically defined cancers by microarray technologies, including head and neck squamous cell carcinomas ( HNSCC). However, the molecular expression signatures and transcriptional regulatory controls underlying the heterogeneity in HNSCC have not been well defined. Results : Genome-wide cDNA microarray profiling of ten HNSCC cell lines revealed novel gene expression signatures which distinguished cancer cell subsets associated with their p53 status. Three major clusters of overexpressed genes ( A-C) were defined through hierarchical clustering, gene ontology and statistical modeling. The promoters of genes in these clusters exhibited different patterns and prevalence of transcription factor binding sites for p53, NF-kappa B, AP-1, STAT3 and EGR1, when compared with the frequency in vertebrate promoters. Cluster A genes involved in chromatin structure and function showed enrichment for p53 and decreased AP-1 binding sites, while cluster B-C, containing cytokine and anti-apoptotic genes, showed a significant increase in prevalence of NF-kappa B binding sites. An increase in STAT3 and EGR1 binding sites was distributed among the over-expressed clusters. Novel regulatory modules containing p53 or NF-kappa B concomitant with other transcription factor binding motifs were identified, and experimental data supported the predicted transcriptional regulation and binding activity. Conclusion : Transcription factors p53, NF-kappa B, and AP-1 may be important determinants of the heterogeneous pattern of gene expression, while STAT3 and EGR1 may broadly enhance gene expression. Defining these novel gene signatures and regulatory mechanisms will be important for establishing new molecular classifications and sub-typing for development of targeted therapeutics for HNSCC.