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

通过构建基因组、表观基因组、mRNA和蛋白质表达变化的阵列系统，我们试图确定诊断和/或治疗靶基因，以开发食管鳞状细胞癌（ESCC）的“个性化药物”。(1)在ESCC的细胞系以及原发性肿瘤样本中，我们使用细菌人工染色体（BAC）阵列和寡核苷酸阵列进行阵列CGH分析，以探索癌症基因组中新的拷贝数变异。在一系列位于扩增和同源性缺失区域的基因中，我们确定了几个靶基因，这些基因通过这些改变与ESCC的发病机制相关。除了ESCC，我们还分析了几种类型的癌症，如卵巢癌，肝细胞癌和口腔癌，并确定了几个靶点，这可能有助于诊断/预测肿瘤。 ...更多信息 SIS和分子靶向治疗。(2)癌细胞中候选靶点的临床病理学和生物学意义的评估从扩增和同源缺失区域中鉴定出可能的癌症相关基因，我们使用定量方法，例如基于阵列的方法和实时PCR系统，在mRNA和蛋白质水平上进行表达分析。在候选肿瘤抑制基因（TSGs）中，我们还分析了表观遗传学改变的参与，例如癌细胞中DNA甲基化和组蛋白密码的改变。为了评估靶基因作为癌基因或TSGs的生物学意义，我们转染了这些基因的表达质粒或siRNA，并分析了细胞生长、细胞周期、凋亡性细胞死亡和/或侵袭性表型。(3)通过直接探索癌症中的表观遗传学改变来鉴定TSGs为了直接鉴定表观遗传学沉默的基因，我们将BAMCA（基于BAC阵列的甲基化CpG岛扩增）方法应用于癌症DNA，并探索异常甲基化区域。从确定的可能高甲基化区域的食管鳞癌细胞系，我们确定了几个候选的TSGs，并确定其在食管鳞癌的临床病理学和生物学意义。少

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