Project 2: Functional Genetic Networks for Systems-Guided Precision Medicine

CCMI v2.0 项目2：系统引导的精确医学的功能遗传网络 项目负责人：普拉尚特·马里和斯蒂芬妮·弗莱利；联合调查员：艾伦·阿什沃斯，詹妮弗·格兰迪斯， 西尔维奥·古特金德、特雷·艾德克和劳拉·范特维尔。 摘要 精确医学的目标是根据患者肿瘤的遗传和分子背景量身定做治疗方法。这个 这种疗法的发展面临着许多障碍，许多障碍来自于我们对基因的无知 肿瘤发生的基础网络和可能干预的机制。为了澄清遗传逻辑 项目2将使用CRISPR/Cas9遗传扰动方法在 组合筛网、功能性筛网和机械式筛网。屏幕将聚焦于PI3K途径，即 头颈部浸润性乳腺癌(BRCA)中抑癌基因P53及其蛋白系统的突变 鳞状细胞癌(HNSCC)和肺鳞状细胞癌(LUSC)，途径和疾病 加在一起，全世界每年有100多万人死亡。这一焦点将使我们能够审问 广泛收集细胞系、实验和微环境条件。首先，我们将在重要的基础上 建立以频率为中心的合成致死和上位性遗传交互作用图谱的初步数据 上述途径和癌症亚型中的突变基因和治疗靶点(目标1)。第二，我们将 将CRISPR/CAS9筛查与一组可扩展的功能分析相结合用于癌症的大规模测量 超越细胞增殖的表型(目标2)。第三，我们将试验一项新技术STAG-CRISPR，以将 CRISPR/Cas9筛查活细胞中的实时分子事件，提供对更深层次阵列的访问 到目前为止一直对系统遗传学持顽固态度的表型(目标3)。最后，为了方便临床 已确定的基因-基因、基因-表型、基因-机制和基因-药物相互作用的翻译，我们将 应用我们丰富的BRCA、HNSCC和LUSC患者来源异种移植(PDX)模型库进行测试 体内令人信服的线索。我们还将使用BRCA的患者数据验证已识别的交互网络 I-SPY 2试验和UCSD的HNSCC患者(目标4)。总而言之，我们的综合方法建立了 广泛验证的基因、药物和多个表型终点之间相互作用的网络 推进精准肿瘤学实践。

CCMI v2.0 Project 2: Functional Genetic Networks for Systems-Guided Precision Medicine Project Leads: Prashant Mali and Stephanie Fraley; Co-Investigators: Alan Ashworth, Jennifer Grandis, Silvio Gutkind, Trey Ideker, and Laura van ’t Veer. SUMMARY Precision medicine aims to tailor therapies to the genetic and molecular background of a patient’s tumor. The development of such therapies faces numerous obstacles, many deriving from our ignorance of the genetic networks underlying tumorigenesis and the mechanisms of possible interventions. To clarify the genetic logic that governs therapeutic efficacy, Project 2 will use CRISPR/Cas9 genetic perturbation methodologies in an ensemble of combinatorial, functional, and mechanistic screens. Screens will focus on the PI3K pathway, the p53 tumor suppressor, and the protein systems mutated in invasive breast cancer (BRCA), head and neck squamous cell carcinoma (HNSCC), and lung squamous cell carcinoma (LUSC), pathways and diseases that together result in well over one million deaths each year worldwide. This focus will enable us to interrogate a broad collection of cell lines, experiments, and microenvironmental conditions. First, we will build on significant preliminary data to establish maps of synthetic lethal and epistatic genetic interactions centered on frequently mutated genes and therapeutic targets in the above pathways and cancer subtypes (Aim 1). Second, we will couple CRISPR/Cas9 screening to a panel of scalable functional assays for large-scale measurement of cancer phenotypes beyond cell proliferation (Aim 2). Third, we will pilot a new technology, STAG-CRISPR, to link CRISPR/Cas9 screening to real time molecular events in living cells, providing access to an even deeper array of phenotypes that have been recalcitrant to systems genetics thus far (Aim 3). Finally, to facilitate clinical translation of the identified gene-gene, gene-phenotype, gene-mechanism and gene-drug interactions, we will apply our extensive library of BRCA, HNSCC, and LUSC patient-derived xenograft (PDX) models to test compelling leads in vivo. We will also validate the identified interaction networks with patient data from the BRCA I-SPY 2 trial and from HNSCC patients at UCSD (Aim 4). Taken together, our integrated approach establishes a network of extensively validated interactions among genes, drugs and multiple phenotypic endpoints to advance the practice of precision oncology.