title: Genome-wide identification of novel expression signatures reveal distinct patterns and prevalence of binding motifs for p53, nuclear factor-kappaB and other signal transcription factors in head and neck squamous cell carcinoma.
abstract: BACKGROUND
  Differentially expressed gene profiles have previously been observed among pathologically defined cancers by microarray technologies, including head and neck squamous cell carcinomas (HNSCCs). However, the molecular expression signatures and transcriptional regulatory controls that underlie the heterogeneity in HNSCCs are not well defined.
  
  
  RESULTS
  Genome-wide cDNA microarray profiling of ten HNSCC cell lines revealed novel gene expression signatures that distinguished cancer cell subsets associated with p53 status. Three major clusters of over-expressed genes (A to 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, nuclear factor-kappaB (NF-kappaB), activator protein (AP)-1, signal transducer and activator of transcription (STAT)3 and early growth response (EGR)1, as compared with the frequency in vertebrate promoters. Cluster A genes involved in chromatin structure and function exhibited enrichment for p53 and decreased AP-1 binding sites, whereas clusters B and C, containing cytokine and antiapoptotic genes, exhibited a significant increase in prevalence of NF-kappaB binding sites. An increase in STAT3 and EGR1 binding sites was distributed among the over-expressed clusters. Novel regulatory modules containing p53 or NF-kappaB concomitant with other transcription factor binding motifs were identified, and experimental data supported the predicted transcriptional regulation and binding activity.
  
  
  CONCLUSIONS
  The transcription factors p53, NF-kappaB, and AP-1 may be important determinants of the heterogeneous pattern of gene expression, whereas STAT3 and EGR1 may broadly enhance gene expression in HNSCCs. Defining these novel gene signatures and regulatory mechanisms will be important for establishing new molecular classifications and subtyping, which in turn will promote development of targeted therapeutics for HNSCC.
authors.affiliation: Head and Neck Surgery Branch, National Institute on Deafness and Other Communication Disorders, National Institutes of Health, Center Drive, Bethesda, Maryland 20892, USA. yanbi@nidcd.nih.gov
authors.forename: Bin
authors.initials: B
authors.lastname: Yan
authors.forename: Xinping
authors.initials: X
authors.lastname: Yang
authors.forename: Tin-Lap
authors.initials: TL
authors.lastname: Lee
authors.forename: Jay
authors.initials: J
authors.lastname: Friedman
authors.forename: Jun
authors.initials: J
authors.lastname: Tang
authors.forename: Carter
authors.initials: C
authors.lastname: Van Waes
authors.forename: Zhong
authors.initials: Z
authors.lastname: Chen
mesh_terms: D001665:Binding Sites / Q000235:genetics; D002294:Carcinoma, Squamous Cell / Q000235:genetics*; D016000:Cluster Analysis; D015972:Gene Expression Regulation, Neoplastic; D015894:Genome, Human; D006258:Head and Neck Neoplasms / Q000235:genetics*; D006801:Humans; D016328:NF-kappa B / Q000235:genetics*; D050436:Regulatory Elements, Transcriptional; D014157:Transcription Factors / Q000235:genetics*; D016159:Tumor Suppressor Protein p53 / Q000235:genetics*
chemical_list: D016328:NF-kappa B; D014157:Transcription Factors; D016159:Tumor Suppressor Protein p53