Identification of molecular target for diagnosis and therapy of esophageal squamous-cell carcinoma based on microarray technology.

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We have constructed array-based system to analyze genomic DNA copy-number, mRNA expression, and protein expression quantitatively and qualitatively. In order to identify a set of genes useful for the molecular-targeted diagnosis and therapy of esophageal squamous-cell carcinoma (ESCC), we applied our system to screen putative ESCC-associate genes in a genome-wide manner.1) Analysis of genomic copy-number aberration using array-comparative genomic hybridization (array-CGH) and identification of target geneWe analyzed genomic DNA from ESCC cell lines as well as primary tumor cells specifically isolated by microdissection using in-house array-based CGH (array-CGH). 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. In addition, we explored molecular markers associated with specific phenotypes, such as lymph node metastasis and prognosis, by comparing pattern of genomic copy-number changes and clinicopathological parameters. The same approach with mRNA and protein expression analyses was applied to other cancers, resulting in the identification of many cancer-related genes, including genes correlated with prognosis.2) Identification of tumor-suppressor genes silenced by DNA methylation using BAC-array-based methylated CpG-island amplification (BAMCA)We combined MCA method to amplify methylated sequences with array-CGH (BAMCA), and screened aberrantly methylated sequences in cancers. Using BAMCA with following database search and expression analyses with and without pharmacological modifications, we successfully identified several genes silenced by methylation in ESC and other tumors. Among them, one gene was frequently silenced by CpG island methylation in ESC and showed growth suppressive effect on ESC cells, suggesting that this gene is a candidate tumor-suppressor for ESC (unpublished data)