Objective: Odontogenic tumors are rare and their classification is controversial. Granular cell odontogenic tumor (GCOT) is extremely rare and it has usually a benign clinical behavior but sometimes it can exhibit clinico-pathological features of malignancy. Methods: RNA was extracted from the biopsies and cDNA was synthesized by using Superscript II (Life Technologies) and amino-allyl dUTP (Sigma). Mono-reactive Cy3 and Cy5 esters (Amersham Pharmacia) were used for indirect cDNA labeling. A pool of normal gingiva mucosa RNAs was used as control. Human 19.2 K DNA microarrays were used and hybridization was at 37 degrees Celsius overnight. Washing was performed 3 times with 1x SSC, 0.1% SDS at 42 degrees Celsius, and 3 times with 0.1 x SSC at room temperature. Slides were dried by centrifugation for 2 minutes at 2000 rpm. A GenePix 4000a DNA microarrays scanner (Axon) was used to scan the slides, and data were extracted with GenePix Pro. Genes with expression levels of less than 1000 were not included in the analysis. Results: Hybridization of mRNA-derived probes to cDNA microarrays allows us to perform systemic analysis of expression profiles for thousands of genes simultaneously and provide primary information on trascriptional changes in GCOT. We identified several genes whose expression was definitely up- or down-regulated. The differentially expressed genes cover a broad range of functional activities: (a) transcription, (b) signaling transduction, (c) cell-cycle regulation, (d) apoptotic stimulation, and (e) differentiation. Among the genes expressed in GCOT not all have a well defined function. Conclusion: The analysis of cDNA microarrays can be a useful approach to improve the understanding of the biology of tumors, a possible tool for a better classification of the odontogenic tumors, and can be of help in identifying some biological behaviors.

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