Gene Expression in Cancer by Microarray Hybridization

通过微阵列杂交在癌症中进行基因表达

基本信息

批准号：
7787114
负责人：
PATRICK O. BROWN
金额：
$ 51.3万
依托单位：
STANFORD UNIVERSITY
依托单位国家：
美国
项目类别：
财政年份：
1997
资助国家：
美国
起止时间：
1997-09-30 至 2012-03-31
项目状态：
已结题

来源：
https://reporter.nih.gov/project-details/7787114
关键词：
4-thiouracil Adopted Affect Affinity Chromatography Arabidopsis Architecture Area Basal cell carcinoma Biological Biological Models Cancer Model Cell Culture Techniques Cell Proliferation Cells Characteristics Colon Carcinoma DNA DNA Microarray Chip Databases Development Diagnosis Elements Funding Gene Expression Gene Expression Profiling Genes Genome Goals Grant Human Human Cell Line Individual Investigation Kinetics Knowledge Malignant Epithelial Cell Malignant Neoplasms Maps Measurement Messenger RNA Methodology Methods Modeling Molecular Molecular Biology Nature Nuclear Export Pathogenesis Patient Care Patient Care Planning Pattern Phase Physiologic pulse Physiological Play Postdoctoral Fellow Proteins RNA RNA Splicing RNA chemical synthesis RNA-Binding Proteins Regulation Reproducibility Research Research Personnel Risk Role Saccharomyces cerevisiae Signal Transduction Source Specificity Surveys Testing Time Tissues Tracer Transcript Translational Regulation Translations Variant Work Yeasts analytical tool autocrine base cancer cell cancer microarray cancer stem cell cell type design frontier genome wide association study genome-wide genome-wide analysis graduate student infancy inhibitor/antagonist innovation insight mRNA Decay mRNA Transcript Degradation malignant breast neoplasm new technology outcome forecast paracrine programs research study self-renewal system architecture tool

项目摘要

From the start, the goal of this program has been the development and application of genome-wide approaches to systematic and quantitative analysis of gene expression patterns in cancer. In the eight years since we began this project, the experimental and analytical tools for systematic studies of global gene expression patterns at the level of transcript abundance have developed dramatically and they have become widely available and widely used for the study of cancer. The resulting studies have produced a wealth of new insight into cancer and they are even beginning to influence patient care. Profiling mRNA transcript levels, however, provides only a partial picture of the global gene expression program. While there is abundant evidence that regulation of the translation, subcellular localization and decay of mRNA are critical elements of biological regulation, practical and robust genome-wide approaches to studying these levels of regulation remain to be developed. As a result, our knowledge of the systems architecture, molecular mechanisms and biological roles of these regulatory mechanisms, including the roles they play in human cancer, is barely in its infancy. We therefore propose to develop practical, robust, high-throughput methods using DNA microarraysto profile three critical aspects of global regulation at the post-transcriptional level: translational regulation, regulation of mRNA degradation, and the specific interactions of RNA binding proteins with their targets. These studies will build on preliminary studies we've already begun in the Saccharomyces cerevisiae model system, but will focus on human cells. As the essential methodologies are developed, we will apply them to developing a foundational framework of knowledge, investigating the patterns in which these regulatory mechanisms are used in basic physiological and developmental programs, how they vary from one cell type to another and between individuals, and beginning to investigate the underlying molecular mechanisms. The goal is to develop both the experimental methodology and an interpretive framework to the point that these post-transcriptional levels of gene expression can be systematically profiled and studied on a genome-wide scale almost as routinely as transcript levels are today.

从一开始，该计划的目标就一直是全基因组的开发和应用对癌症基因表达模式进行系统和定量分析的方法。在八年自从我们开始这个项目以来，用于全球基因系统研究的实验和分析工具成绩单丰度水平上的表达模式已经显着发展，它们已经变成广泛可用的，广泛用于癌症研究。由此产生的研究产生了很多对癌症的新见解，甚至开始影响患者护理。分析mRNA转录本但是，级别仅提供了全球基因表达程序的部分图片。而有大量证据表明，翻译，亚细胞定位和mRNA的衰减是关键的证据生物调节的要素，实用和强大的全基因组方法研究这些水平法规仍有待制定。结果，我们对系统体系结构的了解，分子这些调节机制的机制和生物学作用，包括它们在人类中的作用癌症几乎没有起步。因此，我们建议开发实用，健壮，高通量方法在转录后级别使用DNA Microaraysto轮廓全球调节的三个关键方面：翻译调节，mRNA降解的调节和RNA结合的特定相互作用蛋白质及其靶标。这些研究将基于我们已经开始的初步研究酿酒酵母模型系统，但将集中在人类细胞上。作为基本方法论已开发，我们将它们应用于开发知识的基本框架，调查这些调节机制用于基本生理和发育的模式程序，它们如何从一种单元格到另一种细胞类型，并开始调查潜在的分子机制。目标是开发实验方法和解释性框架，即这些转录后基因表达水平可以是在基因组范围内进行系统的分析和研究，几乎与转录水平一样常规今天。

项目成果

期刊论文数量（27）

专著数量（0）

科研奖励数量（0）

会议论文数量（0）

专利数量（0）

The Stanford Microarray Database accommodates additional microarray platforms and data formats.

DOI：
10.1093/nar/gki006
发表时间：
2005-01-01
期刊：
Nucleic acids research
影响因子：
14.9
作者：
Ball CA;Awad IA;Demeter J;Gollub J;Hebert JM;Hernandez-Boussard T;Jin H;Matese JC;Nitzberg M;Wymore F;Zachariah ZK;Brown PO;Sherlock G
通讯作者：
Sherlock G

Gene expression programs of human smooth muscle cells: tissue-specific differentiation and prognostic significance in breast cancers.

DOI：
10.1371/journal.pgen.0030164
发表时间：
2007-09
期刊：
PLoS genetics
影响因子：
4.5
作者：
通讯作者：

ESRRA-C11orf20 is a recurrent gene fusion in serous ovarian carcinoma.

DOI：
10.1371/journal.pbio.1001156
发表时间：
2011-09
期刊：
PLoS biology
影响因子：
9.8
作者：
Salzman J;Marinelli RJ;Wang PL;Green AE;Nielsen JS;Nelson BH;Drescher CW;Brown PO
通讯作者：
Brown PO

Transcriptional program induced by Wnt protein in human fibroblasts suggests mechanisms for cell cooperativity in defining tissue microenvironments.

DOI：
10.1371/journal.pone.0000945
发表时间：
2007-09-26
期刊：
PLOS ONE
影响因子：
3.7
作者：
Klapholz-Brown, Zach;Walmsley, Graham G.;Nusse, Ysbrand M.;Nusse, Roel;Brown, Patrick O.
通讯作者：
Brown, Patrick O.

Anatomic demarcation by positional variation in fibroblast gene expression programs.