Exploration of molecular targets for diagnosis and therapy of oral cancer through array-CGH based analysis of cancer genome.

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1) Banking of primary samples of oral cancer and its premalignant lesions with clinicopathological dataWe made collections of cell lines as well as primary samples of oral cancer and its premalignant lesions with clinicopathological data for analyses of cancer genome of this disease.2) Analysis of genomic copy-number aberration using array-comparative genomic hybridization (array-CGH) and identification of target geneWe analyzed genomic DNA from oral and esophageal cell lines using in-house array-based CGH (MCG Whole Genome Array-4500 and MCG Cancer Array-800). From the regions showing cryptic but remarkable genomic copy-number changes, such as high-level amplification and homozygous deletion, we tried to identify target genes for those aberrations. Together with further analyses using primary tumor samples, we successfully identified many cancer-related genes, including genes correlated with clinicopathological as well as biological significances.3) Identification of tumor-suppressor genes silenced by DNA methylation using BAC-array-based methylated CpG-island amplification (BAMCA) and Chromatin immunoprecipitation (ChIP) -on-chip methodWe combined MCA method to amplify methylated sequences with array-CGH (BAMCA), and screened aberrantly methylated sequences in cancer genome. We also combined ChIP with array-CGH (ChIP-on-chip) for screening of methylated sequences. Using those screening methods with following database search and expression analyses with and without pharmacological modifications, we successfully identified several genes silenced by methylation in esophageal and oral cancers. Among them, candidate tumor-suppressors frequently methylated in oral and esophageal cancers have been successfully identified (unpublished data)