A platform for genome-wide discovery of synthetic lethal interactions in cancer

癌症中合成致死相互作用的全基因组发现平台

• 批准号: 7847686
• 负责人: Kris C. Wood
• 金额: $ 5.22万
• 依托单位: WHITEHEAD INSTITUTE FOR BIOMEDICAL RES
• 依托单位国家: 美国
• 财政年份: 2008
• 资助国家: 美国
• 起止时间: 2008-07-01 至 2011-06-30
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/7847686
• 关键词: Antineoplastic Agents; Area; Biocompatible; Biocompatible Materials; Biological Assay; Biomedical Research; Cancer cell line; Candidate Disease Gene; Cell Death; Cell Survival; Cells; Collection; Communities; Deposition; Development; Drug Delivery Systems; Engineering; Financial cost; Gene Targeting; Genes; Genetic; Genome; Goals; Growth; Human; Human Cell Line; Human Genome; Hydrogels; Institutes; Institution; Interphase Cell; Laboratories; Lead; Letters; Libraries; Malignant Neoplasms; Methods; Mutation; PTEN gene; Physiological; Plant Roots; Printing; Property; RNA Interference; Reagent; Research; Research Project Grants; Screening procedure; Signal Pathway; Signal Transduction; Speed; Subfamily lentivirinae; Surface; Synthetic Genes; System; Technology; Testing; Tetracyclines; Training; Tumor Suppressor Genes; Tumor Suppressor Proteins; Virus; Work; cell type; density; drug development; functional genomics; functional group; gene function; genome wide association study; genome-wide; high throughput analysis; high throughput screening; improved; loss of function; method development; miniaturize; nanostructured; research study; tool

DESCRIPTION (provided by applicant): We propose the development of a platform to accelerate the discovery of synthetic lethal interactions in human cancers. This work makes use of a human genome-wide library of lentiviral RNAi constructs recently developed by our lab and others (collectively termed "The RNAi Consortium" (TRC)) that targets over 18,000 human genes using over 90,000 lentiviral clones, yields stable suppression of target genes, and is compatible with both dividing and non-dividing cells. To enable miniaturized, high-throughput, arrayed loss- of-function screens with this library, our first aim will be to optimize the properties of lentivirus-infected cell microarrays (LICMs), a technology currently under development in our laboratory. Specifically, this aim will focus on optimizing the number of viruses deposited on each microarray feature by increasing the density of functional groups on the array surface using nanostructured surface features and/or biocompatible hydrogel coatings. In our second aim, we will fabricate whole-genome LICMs and demonstrate their feasibility toward large-scale loss-of-function screens. In our final aim, we will apply these systems to a screen that will be used to identify synthetic lethal interactions in cancers harboring deficiencies in PTEN, a tumor suppressor gene that is frequently implicated in human cancers. Specifically, in this aim we will use an engineered U-87 human cell line with tetracycline inducible PTEN expression to first identify genes that are synthetic lethal with PTEN, then test these candidate genes on a panel of human cancer cell lines with impaired PTEN function to identify those genes which are synthetic lethal in a range of diverse genetic and physiological contexts. The long-term objectives of this project are: (1) to identify genes which are synthetic lethal with PTEN, and thus targets for cancer drug development, and (2) to establish a robust, broadly useful arrayed screening platform to accelerate progress in functional genomics. Lay description: We propose to develop a high-throughput screening platform which will allow for the rapid and systematic identification of new, selective drug targets for human cancers. This project involves three components: the optimization of the proposed screening platform; the application of this platform to genome-wide screening experiments; and the use of this platform to systematically identify new cancer drug targets. The screening platform developed in this study has the potential to become an enabling tool for high-throughput screening experiments throughout the biomedical research community, and the particular application of these systems to cancer may significantly accelerate the discovery of new cancer drugs.

描述（由申请人提供）：我们建议开发一个平台，以加速发现人类癌症中的合成致死相互作用。这项工作利用了我们实验室和其他人（统称为“RNAi联盟”（TRC））最近开发的慢病毒RNAi构建体的人类全基因组文库，该文库使用超过90，000个慢病毒克隆靶向超过18，000个人类基因，产生对靶基因的稳定抑制，并且与分裂和非分裂细胞相容。为了使小型化，高通量，阵列功能丧失的屏幕与这个库，我们的第一个目标将是优化的慢病毒感染的细胞微阵列（LICMs），目前正在开发中的技术在我们的实验室的属性。具体而言，该目标将集中于通过使用纳米结构化表面特征和/或生物相容性水凝胶涂层增加阵列表面上的官能团密度来优化沉积在每个微阵列特征上的病毒数量。在我们的第二个目标中，我们将制造全基因组LICMs，并证明它们对大规模功能丧失筛选的可行性。在我们的最终目标中，我们将把这些系统应用于筛选，该筛选将用于识别携带PTEN缺陷的癌症中的合成致死相互作用，PTEN是一种经常与人类癌症有关的肿瘤抑制基因。具体地，在这个目标中，我们将使用具有四环素诱导的PTEN表达的工程化U-87人细胞系来首先鉴定与PTEN合成致死的基因，然后在具有受损的PTEN功能的一组人癌细胞系上测试这些候选基因，以鉴定在一系列不同的遗传和生理背景下合成致死的那些基因。该项目的长期目标是：（1）鉴定与PTEN合成致死的基因，从而为癌症药物开发提供靶点，以及（2）建立一个强大的，广泛有用的阵列筛选平台，以加速功能基因组学的进展。铺设说明：我们建议开发一个高通量筛选平台，该平台将允许快速和系统地识别新的、选择性的人类癌症药物靶点。该项目包括三个组成部分：优化拟议的筛选平台;将该平台应用于全基因组筛选实验;以及使用该平台系统地识别新的癌症药物靶点。本研究开发的筛选平台有可能成为整个生物医学研究界高通量筛选实验的有利工具，这些系统在癌症中的特殊应用可能会显着加速新癌症药物的发现。