Genomics: Esophageal Metaplasia-Associated Malignancy

基因组学：食管化生相关恶性肿瘤

• 批准号: 6796235
• 负责人: Stephen J Meltzer
• 金额: $ 37.13万
• 依托单位: UNIVERSITY OF MARYLAND BALTIMORE
• 依托单位国家: 美国
• 财政年份: 2002
• 资助国家: 美国
• 起止时间: 2002-09-23 至 2007-08-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/6796235
• 关键词: Barretts esophagus; DNA methylation; adenocarcinoma; biomarker; clinical research; comparative genomic hybridization; esophagus neoplasm; human tissue; microarray technology; molecular oncology; neoplasm /cancer genetics; patient oriented research; preneoplastic state

DESCRIPTION (provided by applicant): Barrett's esophagus is a highly premalignant disease of unknown prevalence, but it predisposes to the development of esophageal adenocarcinoma, which is increasing at alarming rates in Western countries. The molecular genetics of esophageal adenocarcinoma and its precursor lesion, Barrett's esophagus, has been studied intensively in recent years. However, a better knowledge of the molecular alterations occurring in this setting will yield several benefits. Firstly, the discovery of novel molecular alterations will yield clues to biological pathways underlying Barrett's-associated neoplastic transformation, and these clues may lead to better in vitro and in vivo models of this disease. Secondly, molecular alterations themselves can be used as markers of early detection, disease progression, or ultimate prognosis in patients with Barrett's or cancer. Thirdly, these molecular alterations can be pursued as possible therapeutic targets for intervention, in both the prevention and treatment of this disease. The Aims of the current proposal will be to discover novel molecular alterations in Barrett's metaplasia and neoplasia, and to concentrate on the second of these benefits, i.e., to perform translational research to determine the potential value of these alterations as markers of disease progression. By using the same cDNA microarray platform to determine changes in DNA copy number, methylation status, and gene expression level, we will facilitate the translation of molecular genetic data from the genomic, to the epigenetic, to the transcriptomic, and finally to the protein (biomarker) level. This final level will employ tissue microarrays to test and validate specific candidate genes derived from the first three levels of study. These goals will be implemented by pursuing the following Aims: Aim 1. To perform global exploration for changes in DNA copy number in the Barrett's metaplasia-dysplasia-adenocarcinoma sequence (Barrett's neoplasia), using cDNA microarray-based comparative genomic hybridization (microarray-CGH). a) Global patterns of DNA amplification and deletion will be identified by microarray-CGH and characterized at each stage of Barrett's neoplasia, using hierarchical clustering, significance analysis of microarrays (SAM), and artificial neural networks, b) Specific cDNAs showing the most consistent and/or marked alterations in DNA copy number will be identified, characterized and validated using quantitative real-time PCR, for further study in Aim 4. Aim 2. To perform global epigenetic profiling at various stages in Barrett's neoplasia, using methylation-specific oligonucleotide microarrays. The genome will be screened for novel targets of DNA hypermethylation in various stages of Barrett's neoplasia, using methylation-specific oligonucleotide microarrays. Aim 3. To Using ANNs, to perform analyses of global gene expression data in Barrett's neoplasia. Results of genomic studies in Aims 1 and 2 will be correlated with global expression data in order to identify the genes most significantly different at both the genomic and transcriptomic levels at each stage of Barrett's neoplasia, for further study in Aim 4. Aim 4. Using tissue microarrays, to evaluate and validate potential biomarkers at the protein level in Barrett's neoplasia. Potential biomarkers identified in Aims 1-3 will be studied individually for expression at the protein level in all stages of Barrett's neoplasia, using tissue microarrays.

描述（由申请人提供）：巴雷特的食道是一种高度的预先疾病，患病率是不明患病率的，但它容易发生食管腺癌的发展，而食管腺癌的发展正在以西方国家的惊人速度增加。近年来，对食道腺癌及其前体病变的分子遗传学及其前体病变，Barrett的食管。但是，更好地了解在这种情况下发生的分子改变将带来一些好处。首先，新的分子改变的发现将为Barrett相关的肿瘤转化的生物学途径提供线索，这些线索可能会导致该疾病的体外和体内模型更好。其次，分子改变本身可以用作巴雷特或癌症患者的早期发现，疾病进展或最终预后的标志。第三，在预防和治疗该疾病的情况下，可以将这些分子改变作为干预靶标的可能采用。当前提案的目的是发现巴雷特化学和肿瘤的新分子改变，并专注于这些益处的第二个好处，即进行转化研究，以确定这些改变作为疾病进展的标志物的潜在价值。通过使用相同的cDNA微阵列平台来确定DNA拷贝数，甲基化状态和基因表达水平的变化，我们将促进分子遗传数据从基因组，表观遗传学，转录组，最后向蛋白质转换为蛋白质（生物标志物）水平。该最终水平将采用组织微阵列来测试和验证从前三个研究级别得出的特定候选基因。这些目标将通过追求以下目标来实现： AIM 1。使用基于CDNA微阵列的比较基因组杂交（Microarray-CGH），使用Barrett的Metaplasia-Dysplasia-dynocinomamoma序列（Barrett的Neoplasia）进行全球DNA拷贝数（Barrett的Neoplasia）。 a）微阵列-CGH将确定全球DNA扩增和缺失的模式，并在Barrett的肿瘤阶段进行表征，使用分层聚类，微阵列（SAM）和人工神经网络的显着性分析，B）表现出最一致的cDNA将使用定量实时PCR确定，表征和验证DNA拷贝数的明显变化，以在AIM 4中进行进一步研究。 AIM 2。使用甲基化特异性寡核苷酸微阵列在Barrett肿瘤的各个阶段进行全球表观遗传分析。使用甲基化特异性寡核苷酸微阵列，将在Barrett肿瘤的各个阶段对DNA高甲基化的新靶标进行筛查。 目的3。使用ANN，在Barrett的肿瘤中对全球基因表达数据进行分析。 AIM 1和2中基因组研究的结果将与全球表达数据相关，以确定Barrett肿瘤每个阶段的基因组和转录水平上最大不同的基因，以在AIM 4中进行进一步研究。 目标4。使用组织微阵列评估和验证巴雷特肿瘤中蛋白质水平的潜在生物标志物。 AIMS 1-3中鉴定出的潜在生物标志物将在Barrett肿瘤的所有阶段单独研究以在蛋白质水平上进行表达，并使用组织微阵列进行。