Bay Area Cancer Target Discovery and Development Network

描述（由申请人提供）：目前，对许多人类肿瘤的综合分子表征正在产生大量的数据。有效和高效地使用RNAi来评估基因靶标抑制的生物学后果的能力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学的靶向治疗的发展提供了理论依据。RNAi筛选是一种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筛选资源有很大的局限性。由于基因组覆盖率和RNAi基因敲除效果的技术限制，迄今为止使用的RNAi筛选工具并不能有效地针对癌症相关基因的全部纲要。这些技术限制也会导致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进行高通量筛选并不具有成本效益。在这里，我们提出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，这些技术正在迅速普及。我们的新方法将极大地促进癌症多疗法的发展，为充分利用人类肿瘤基因组图谱的合理癌症治疗开辟新的范例。为了设计有效的联合癌症治疗（多疗法），我们必须首先确定协同作用以促进肿瘤生长或治疗耐药性的信号通路。这些知识使得设计针对这些关键癌症“驱动”途径的疗法成为可能。开发排除或克服对靶向癌症治疗的耐药性的治疗方法的一个主要障碍是，没有系统的方法来确定在功能上合作和协同驱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殊的方式进行的，只探索了非常有限数量的潜在组合。合理设计最佳治疗组合的关键在于系统地识别靶向时导致癌细胞特异性和协同破坏的途径。我们的新方法可以同时快速（在1-3周内）高精度地测定任何癌症背景下大量（通常为100,000对）靶向感兴趣基因的shrna对之间的功能遗传相互作用。这代表了一项变革性的技术，我们有能力系统地揭示驱动肿瘤生长的癌症相关基因相互作用网络，并有可能被利用为合理的、肿瘤特异性的综合疗法。

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.