Exploration of diagnostic and therapeutic targets through array-based analyses for genomic and epigenomic alterations in esophageal squamous-cell carcinoma

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By constructing the array-based system for genomic, epigenomic, and mRNA and protein expression changes, we tried to identify diagnostic and/or therapeutic target genes necessary and sufficient to develop "personalized medicine" for esophageal squamous-cell carcinoma (ESCC).(1) Investigation of genomic copy-number aberrations using CGH-array in ESCC In cell lines as well as primary tumor samples of ESCC, we performed array-CGH analyses using bacterial artificial chromosome (BAC)-arrays and oligo-arrays to explore novel copy-number alterations in cancer genome. Among series of genes locating within the identified amplified and homozygously deleted regions, we determined several target genes, which are associated with the pathogenesis of ESCC through these alterations. In addition to the ESCC, we also analyzed several types of cancers, such as ovarian cancer, hepatocellular carcinoma, and oral cancers, and identified several targets, which may be useful for diagnosis/prediction of progno … More sis and molecular targeting therapy.(2) Evaluation of clinicopathological and biological significance of candidate targets in cancer cells Possible cancer-associated genes identified from amplified and homozygously deleted regions, we performed expression analyses in mRNA and protein levels using quantitative methods, such as array-based methods and real-time PCR system. In candidate tumor-suppressor genes (TSGs), we also analyzed the involvement of epigenetic alterations, such as alterations in DNA methylation and histone codes, in cancer cells. To evaluate biological significance of target genes as oncogenes or TSGs, we transfected expression plasmids or siRNAs for those genes, and analyzed cell growth, cell cycle, apoptotic cell death, and/or invasive phenotype.(3) Identification of TSGs through direct exploration of epigenetic alterations in cancer In order to identify epigenetically silenced genes directly, we applied BAMCA (BAC-array based methylated CpG island amplification) method to cancer DNA, and explored abnormally methylated region. From identified possibly hypermethylated regions in ESCC cell lines, we identified several candidate TSGs and determined their clinicopathological and biological significance in ESCC. Less