Gene Expression Patterns in Human Tumors Identified Using Transcript Sequencing

使用转录测序鉴定人类肿瘤中的基因表达模式

• 批准号: 7942756
• 负责人: David N Hayes
• 金额: $ 416.11万
• 依托单位: UNIV OF NORTH CAROLINA CHAPEL HILL
• 依托单位国家: 美国
• 财政年份: 2009
• 资助国家: 美国
• 起止时间: 2009-09-29 至 2014-07-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/7942756
• 关键词: Atlases; Biological Assay; Breast; Chromatin; Chromatin Structure; Clinical; Code; Coupled; DNA Methylation; DNA Microarray Chip; DNA Sequence; DNA copy number; Data; Development; Distant; Epigenetic Process; Event; Formaldehyde; Gene Expression; Gene Expression Profiling; Genes; Genomics; Glioblastoma; Head and neck structure; Human; Lead; Link; Malignant Neoplasms; Malignant neoplasm of lung; Maps; Methods; MicroRNAs; Mutation; Nucleosomes; Outcome; Output; Paint; Patients; Pattern; Phase; Portraits; Proteins; Regulation; Regulatory Element; Role; SNP genotyping; Solid; Testing; Tissues; Transcript; Tumor Subtype; Tumor Suppressor Genes; base; cancer genome; chromatin remodeling; cost; disorder subtype; experience; genome wide association study; histone modification; next generation; novel; tool; tumor

DESCRIPTION (provided by applicant): Gene expression provides a snapshot of the cellular changes that promote tumor malignancy. Quantitative gene expression analysis, especially as implemented by DNA microarrays, has proven to be an extremely valuable tool for cancer genome characterization, and has lead to the development of new genomic-based clinical tests. Our own experience with DNA microarrays to study gene expression patterns for breast, head & neck, and lung cancers has lead to the identification of novel subtypes of tumors with distinct patient outcomes and has identified new tumor suppressor genes. In the pilot phase of The Cancer Genome Atlas (TCGA) project, multiple platforms were used including tools to study gene expression (our role), tumor genomic DNA copy number alterations, SNP genotypes, DNA methylation and gene mutational analyses. Our collaborative efforts identified new tumor subtypes of glioblastoma and painted an integrated picture linking mutations to copy number changes to expression patterns, which identified biologically distinct subtypes of disease with differences in patient outcomes. For the second phase of TCGA project, we propose to continue to perform quantitative gene expression profiling of all protein-coding genes, non-protein coding mRNAs(ncRNAs) and microRNAs, on -2000 tumors per year. This approach has proven to be one of the most informative and comprehensive cancer genome characterization tools available. In addition, we propose to generate global chromatin organization profiles of cancer to identify regions of "open" chromatin domains (nucleosome-depleted regions). We will use FAIRE (Formaldehyde-Assisted isolation of Regulatory Elements), a simple, low-cost method amenable to use on small quantities of solid tissue, coupled to next-generation DNA sequencing. Since the function of most histone modifications and chromatin remodeling activities is to regulate nucleosome occupancy, FAIRE effectively summarizes the functional output of such epigenetic mechanisms in a single robust assay. Lastly, we propose to perform integrated analyses of transcript levels with chromatin structure to map important regulatory elements, which can be distant to the transcript(s) that they regulate. Our study of genome-wide transcript regulation with chromatin organization will provide a critical portrait of the cancer genome that can be integrated with (and indeed can sometimes generate) other important data, including mutations and copy number events.

描述（由申请人提供）：基因表达提供了促进肿瘤恶性的细胞变化的快照。定量基因表达分析，特别是通过DNA微阵列实现的定量基因表达分析，已被证明是用于癌症基因组表征的极其有价值的工具，并且已导致新的基于基因组的临床测试的发展。我们自己使用DNA微阵列研究乳腺癌、头颈癌和肺癌的基因表达模式的经验已经导致识别出具有不同患者结局的新型肿瘤亚型，并识别出新的肿瘤抑制基因。在癌症基因组图谱（TCGA）项目的试点阶段，使用了多个平台，包括研究基因表达（我们的角色），肿瘤基因组DNA拷贝数改变，SNP基因型，DNA甲基化和基因突变分析的工具。我们的合作努力确定了胶质母细胞瘤的新肿瘤亚型，并绘制了一幅将突变与表达模式的拷贝数变化联系起来的综合图片，从而确定了具有患者结局差异的生物学上不同的疾病亚型。对于TCGA项目的第二阶段，我们建议继续对每年约2000个肿瘤进行所有蛋白编码基因、非蛋白编码mRNA（ncRNA）和microRNA的定量基因表达谱分析。这种方法已被证明是信息量最大和最全面的癌症基因组表征工具之一。此外，我们建议生成癌症的全局染色质组织配置文件，以确定“开放”染色质结构域（核小体耗尽区域）的区域。我们将使用FAIRE（甲醛辅助分离调控元件），这是一种简单，低成本的方法，适合用于少量实体组织，并与下一代DNA测序相结合。由于大多数组蛋白修饰和染色质重塑活动的功能是调节核小体占有率，FAIRE有效地总结了这种表观遗传机制的功能输出在一个单一的强大的测定。最后，我们建议对转录水平与染色质结构进行综合分析，以绘制重要的调控元件，这些元件可能与它们调控的转录物相距甚远。我们对全基因组转录调控与染色质组织的研究将提供癌症基因组的关键画像，这些基因组可以与其他重要数据整合（有时甚至可以生成），包括突变和拷贝数事件。