Alterations in Gene Expression Associated with Head and Neck Squamous Cell Carcinoma Development

Background: Normal keratinocytes (KC) and neoplastic cells derived from a head and neck lesion (SCC-25) were grown as organotypic raft cultures to mimic in vivo architecture in the absence of contaminating cell types. Alterations in gene expression between normal keratinocytes and a head and neck squamous cell carcinoma (HNSSC) cell line (SCC-25) were analysed using gene arrays. Materials and Methods: RNA from the organotypic raft cultures were used to probe four gene arrays. Gene expression alterations between the normal and neoplastic cells were identified and analysed using both fold differences and 2-tailed t-test. Four genes from different functional groups were used for immunohistochemical staining of patient tumours to confirm the gene array data. Results: Statistical analysis of the array data revealed 124 significantly altered genes between normal and neoplastic HNSCC cells. These gene expression alterations are associated with a variety of different functional groups and indicate the complexity of gene de-regulation associated with HNSCC. Conclusion: This study identified many novel gene alterations associated with HNSCC. The significantly altered gene alterations belong in a variety functional groups including: growth control, apoptosis and detoxication and present new targets for investigating the molecular basis of HNSCC formation.