Genomic and expression profiling of neuroblastoma

尽管最近肿瘤治疗取得了进展，但晚期神经母细胞瘤患者的总体存活率仍然很低。此外，目前使用的预后标志物有时不足以预测中等危险型肿瘤患者的预后。本研究的主要目的是通过对神经母细胞瘤标本的基因组异常和表达谱的分析，构建神经母细胞瘤的早期分类系统，并帮助选择合适的治疗策略。在这项研究中，我们获得了以下结果：1)神经母细胞瘤的表达谱我们先前制作了一个内部的、适用于肿瘤的基因芯片，该芯片包含了从原发神经母细胞瘤中收集的11,000个基因。该芯片被应用于不同预后的神经母细胞瘤的表达谱分析。同时，通过与加州大学旧金山分校肿瘤中心的合作，我们应用基于BAC阵列的阵列计算全息方法来检测肿瘤DNA中拷贝数的变化。To c…为了更好地比较基因表达水平与基因在11,000个基因芯片上的丢失和/或获得，利用UCSC基因组浏览器数据库搜索了11000个cDNA的核苷酸序列，进行了染色体定位。2)神经母细胞瘤基因组和分子特征的综合分析我们完成了268个来自原发神经母细胞瘤和细胞系的样本的阵列CGH分析，并比较了基因表达特征和基因组异常(如染色体丢失和获得)。我们可以将染色体1lq上缺失的最小重叠区域定义为大约10Mb，在该区域中发现了一个在神经母细胞瘤有利和不利之间存在差异表达的基因。因此，我们进一步利用多个神经母细胞瘤RNA样本对该基因进行了实时定量RT-PCR分析，并通过亚硫酸氢盐测序检测了其启动子区域的表观遗传修饰。对染色体1p36区域也进行了类似的分析。我们的下一个计划是确认目前的结果，并对我们已经确定的候选基因进行功能分析。较少

In spite of recent progress in cancer therapy, the overall survival rate of the patients with neuroblastoma in advanced stages is still quite low. Furthermore, prognostic markers currently used are sometimes not enough to predict prognosis of the patients with intermediate risk type of tumors. The main purpose of this study is to construct a system for early classification of such tumors and to help choose appropriate therapeutic strategy, through the analyses of genomic aberrations and expression profiling of neuroblastoma samples. In this study, following results were obtained :1) Expression profiling of neuroblastomaWe previously made an in-house, tumor-proper cDNA chip harboring the 11,000 genes collected from primary neuroblastomas. The chip was applied to the expression profiling of neuroblastomas with various prognoses. In parallel, by collaborating with UCSF Cancer Center, we applied BAC array-based array CGH method to survey the copy number changes occurred in tumor DNAs. To c … More ompare the gene expression level with genomic loss and/or gain of each gene on the 11,000 cDNA chip, chromosome mapping of 11000 cDNAs was conducted by searching their nucleotide sequences against the UCSC genome browser databases. The data obtained were submitted to the public microarray databases NCBI GEO.2) Integrated analyses of genomic and molecular signatures of neuroblastomaWe have finished array CGH analysis of 268 samples prepared from primary neuroblastomas and cell lines and compared the gene expression signatures and genomic aberrations such as chromosomal losses and gains. We could define the smallest region of overlaps of deletions at chromosome 1lq to be approximately 10 Mb, in which one gene exhibiting the differential expression between favorable and unfavorable neuroblastomas was identified. Therefore, we further performed quantitative real-time RT-PCR analysis of the gene by using multiple neuroblastoma RNA samples and also examined epigenetic modifications of its promoter region by bisulfite sequencing. Similar analysis was conducted for chromosome 1p36 region. Our next plan is to confirm the present results and do the functional analyses of the candidate genes that we have identified. Less