Bay Area Cancer Target Discovery and Development Network

描述(由申请人提供)：目前，大量的数据是通过对一些人类肿瘤的全面分子表征而产生的。能够有效和高效地使用RNAi来评估基因靶标抑制的生物学后果对于理解基因功能和发现肿瘤特异性脆弱性至关重要。肿瘤特异性脆弱性的识别为基于生物的靶向治疗的发展提供了理论基础。RNAi筛选是一项功能强大的高通量基因功能发现技术，已被用于识别肿瘤特异性脆弱性。然而，目前可用的RNAi筛查资源有很大的局限性。由于基因组覆盖率和RNAi基因敲除效率的技术限制，迄今使用的RNAi筛选工具不能有效地针对癌症相关基因的完整纲要。这些技术限制也导致了假阳性和假阴性的屏幕点击。因此，目前可用的RNAi筛选平台对于大多数实验室的高通量筛选来说并不划算。在这里，我们介绍了克服这些限制的技术和资源，极大地提高了RNAi筛选能力。我们利用基于统计的分析和新的深度测序技术的力量，这些技术正在迅速民主化。我们的新方法将极大地促进癌症综合疗法的发展，为充分利用人类肿瘤基因组图谱的合理癌症治疗开辟了一个新的范例。为了设计有效的癌症联合疗法(综合疗法)，我们必须首先确定协同作用促进肿瘤生长或治疗耐药的信号通路。这些知识使针对这些关键的癌症“驱动”途径的治疗方法的设计成为可能。阻止或克服对靶向癌症治疗的耐药性的治疗方法的发展的一个主要障碍是，没有系统的手段来确定在功能上合作和协同推动肿瘤生长或治疗耐药性的途径。因此，寻找有效的癌症综合疗法在很大程度上是以一种特别的方式进行的，只探索了非常有限的潜在组合。合理设计最佳治疗组合的关键在于系统地识别当靶向时导致对癌细胞的特异性和协同破坏的途径。我们的新方法可以同时快速地(在1-3周内)确定大量(通常是100,000对)针对任何癌症背景下的感兴趣基因的shRNA之间的功能遗传相互作用的高精度测量。这代表着一项变革性的技术，因为我们有能力系统地发现与癌症相关的基因相互作用网络，这种网络推动了肿瘤的生长，并有可能被开发为合理的、针对肿瘤的综合疗法。 公共卫生相关性：与癌症基因组测序倡议同样重要的是，识别和编目大量变异只是努力为治疗突破提供科学基础的第一步。为了实现这一更广泛的目标，我们现在必须了解这些变异如何单独和严重地结合在一起导致人类肿瘤的恶性特性。我们的计划旨在填补这一空白。我们的团队汇集了癌症生物学、功能基因组学和系统生物学方面的一系列关键专业知识，以及独特的下一代shRNA筛选策略，该策略极大地提高了我们监控干扰基因组合的精确表型后果的能力。我们能够区分癌症司机和乘客，并使用我们尖端的新型基因相互作用方法识别与癌症相关的信号网络，这与CTD2任务高度相关，也是开发合理组合疗法的目标，可能会改善基因定义的癌症患者亚群的结果。

DESCRIPTION (provided by applicant): Currently, enormous volumes of data are being generated by the comprehensive molecular characterization of a number of human tumors. The ability to effectively and efficiently use RNAi to assess the biologic consequences of gene target inhibition is of critical importance to understanding gene function and to uncover tumor-specific vulnerabilities. The identification of tumor-specific vulnerabilities provides rationale for the development of biologically-based targeted therapies. RNAi screening is a powerful technology for high- throughput gene function discovery that has been used to identify tumor-specific vulnerabilities. However there are significant limitations to the RNAi screening resources that are currently available. The RNAi screening tools used to date do not efficiently target the full compendium of cancer relevant genes due to technological limitations in genome coverage and RNAi gene knockdown efficacy. These technological limitations also lead to false-positive and false-negative screen hits. Thus, currently available RNAi screening platforms are not cost-effective for performing high-throughput screens for most labs. Here we present technologies and resources that overcome these limitations, dramatically improving RNAi screening capabilities. We take advantage of statistically-based analyses and the power of new deep sequencing technologies that are being rapidly democratized. Our new approaches will greatly facilitate the development of cancer polytherapies, opening a new paradigm for rationally-based cancer therapeutics that fully capitalize on genomic profiling of human tumors. In order to design effective combination cancer therapies (polytherapies) we must first identify the signaling pathways that act synergistically to promote tumor growth or therapeutic resistance. This knowledge then enables the design of therapies that target these key cancer "driver" pathways. A major obstacle to the development of therapies that preclude or overcome resistance to targeted cancer therapy is that there is no systematic means by which to identify pathways that functionally cooperate and synergize to drive tumor growth or therapeutic resistance. Therefore, the search for effective cancer polytherapies has been done largely in an ad hoc manner exploring only a very limited number of potential combinations. The key to rationally designing an optimal combination of therapies lies in the systematic identification of pathways that when targeted, lead to specific and synergistic destruction of cancer cells. Our new approaches can determine simultaneously and rapidly (within 1-3 weeks) high precision measures of functional genetic interactions between large numbers (typically 100,000) pairs of shRNAs that target genes of interest in the context of any cancer. This represents a transformative technology in terms of our ability to systematically uncover cancer- relevant gene interaction networks that drive tumor growth and that potentially can be exploited as rational, tumor-specific polytherapies. PUBLIC HEALTH RELEVANCE: As important as the cancer genome sequencing initiatives are, the identification and cataloguing of large numbers of variations is only the first step in efforts to provide a scientific foundation for therapeutic breakthroughs. To achieve this broader goal, we must now understand how these variations alone and critically in combination contribute to the malignant properties of human tumors. Our program aims to fill this void. Our team brings together a critical range of expertise in cancer biology, functional genomics, and systems biology as well as a unique next generation shRNA screening strategy that greatly increases our ability to monitor the precise phenotypic consequences of perturbing combinations of genes. Our ability to distinguish cancer drivers and passengers and identify cancer-relevant signaling networks using our cutting-edge novel gene interaction approach is of high-relevance to the CTD2 mission, and the goal of developing rational combination therapies that may improve outcomes for genetically-defined subsets of cancer patients.