High EGFR gene copy number by FISH is frequent in HNSCC and is a poor prognostic indicator. Additional investigation is indicated to determine the biologic significance and implications for EGFR inhibitor therapies in HNSCC.

Human papillomavirus (HPV) is associated with a subset of head and neck squamous cell carcinoma (HNSCC). Between 15% and 35% of HNSCCs harbor HPV DNA. Demographic and exposure differences between HPV-positive (HPV + ) and negative (HPV À ) HNSCCs suggest that HPV + tumors may constitute a subclass with different biology, whereas clinical differences have also been observed. Gene expression profiles of HPV + and HPV À tumors were compared with further exploration of the biological effect of HPV in HNSCC. Thirty-six HNSCC tumors were analyzed using Affymetrix Human 133U Plus 2.0 GeneChip and for HPV by PCR and real-time PCR. Eight of 36 (22%) tumors were positive for HPV subtype 16. Statistical analysis using Significance Analysis of Microarrays based on HPV status as a supervising variable resulted in a list of 91genes that were differentially expressed with statistical significance. Results for a subset of these genes were verified by real-time PCR. Genes highly expressed in HPV + samples included cell cycle regulators (p16 INK4A , p18, and CDC7) and transcription factors (TAF7L, RFC4, RPA2, andTFDP2).The microarray data were also investigated by mapping genes by chromosomal location (DIGMAP). A large number of genes on chromosome 3q24-qter had high levels of expression in HPV + tumors. Further investigation of differentially expressed genes may reveal the unique pathways in HPV + tumors that may explain the different natural history and biological properties of these tumors. These properties may be exploited as a target of novel therapeutic agents in HNSCC treatment.Head and neck cancer remains one of the most devastating cancers in the United States. Development of the vast majority of these tumors has been attributed to use of tobacco and ethanol products, but a significant portion of these tumors are associated with human papillomavirus (HPV; refs. 1, 2). Infection with HPV is associated with malignant and premalignant lesions of the uterine, cervix, vulva, penis, conjunctiva, and upper aerodigestive tract (for review, see ref.3). Over 100 subtypes of HPV have been described in humans, with HPV type 8, 11, 16, and 18 being associated with the majority of human disease. In the cervix, a distinction is made between ''low-risk'' (types 8 and 11) and ''high-risk'' (types 16 and 18) HPV, depending on their association with premalignant and malignant lesions, respectively. Reports of the prevalence of HPV infection in head and neck squamous cell carcinoma (HNSCC) indicate that 15% to 35% of HNSCC may harbor HPV sequences, depending on the detection method used (4). DNA amplification by PCR remains the most sensitive technique to detect HPV, with almost 35% of HNSCCs yielding HPV-specific amplification products, although this result may be biased because of contamination problems associated with PCR. HPV is most commonly found in tonsillar tumors (45-100%; ref. 5) with HPV type 16 (HPV16) being found in the vast majority and HPV18 associated with most others (6).There INK4A alterations are common (50% and ...

Gene expression signatures generated from DNA microarray analyses have shown promise as predictive biomarkers of clinical outcome. In this study, we determined a high-risk signature for disease recurrence using formalin-fixed head and neck squamous cell carcinoma (HNSCC) tumors and compared the results with an independent data set obtained from fresh frozen tumors. We also showed that genes involved in epithelial-to-mesenchymal transition (EMT) and nuclear factor-KB (NF-KB) signaling deregulation are the most prominent molecular characteristics of the high-risk tumors. Gene expression was determined in 40 samples, including 34 formalin-fixed tissues and 6 matched frozen tissues, from 29 HNSCC patients. A 75-gene list predictive of disease recurrence was determined by training on the formalin-fixed tumor data set and tested on data from the independent frozen tumor set from 60 HNSCC patients. The difference in recurrence-free survival (RFS) between the high-risk versus low-risk groups in the training and test sets was statistically significant (P = 0.002 and 0.03, respectively, log-rank test). In addition, the gene expression data was interrogated using Gene Set Enrichment Analysis to determine biological significance. The most significant sets of genes enriched in the high-risk tumors were genes involving EMT, NF-KB activation, and cell adhesion. In conclusion, global gene expression analysis is feasible using formalin-fixed tissue. The 75-gene list can be used as a prognostic biomarker of recurrence, and our data suggest that the molecular determinants of EMT and NF-KB activation can be targeted as the novel therapy in the identified high-risk patients. (Cancer Res 2006; 66(16): 8210-8)