Base-Editing the Cancer Kinome to Enable Drug Discovery

对癌症激酶组进行碱基编辑以实现药物发现

• 批准号: 10687392
• 负责人: Neil Vasan
• 金额: $ 148.05万
• 依托单位: COLUMBIA UNIVERSITY HEALTH SCIENCES
• 依托单位国家: 美国
• 财政年份: 2023
• 资助国家: 美国
• 起止时间: 2023-09-19 至 2026-08-31
• 项目状态: 未结题
• 来源: https://reporter.nih.gov/project-details/10687392
• 关键词: Acceleration; Award; Breast; Cancer Cell Growth; Case Study; Catalysis; Cell Proliferation; Cell physiology; Cells; Clinical; Combined Modality Therapy; Data; Drug Combinations; Drug Design; Environment; Enzymes; Family; Gene Expression; Genes; Human; Human Genome; Institution; Investigation; Knock-in; Knock-out; Lead; Malignant Neoplasms; Mammals; Medical center; Methods; Mutagenesis; Mutate; Mutation; Oncologist; Operative Surgical Procedures; Pharmaceutical Preparations; Phosphotransferases; Physiological; Physiological Processes; Protein Biochemistry; Protein Kinase; Research; Signal Transduction; Translating; Universities; Validation; base editing; cancer cell; cancer type; cell growth; drug development; drug discovery; enzyme activity; experience; experimental study; innovation; kinase inhibitor; knock-down; malignant breast neoplasm; new technology; novel; precision oncology; prevent; response; small molecule; small molecule inhibitor; structural biology; targeted treatment; therapeutic target; tool

The human genome contains 556 kinase genes, commonly called the kinome. Kinases are enzymes that regulate nearly all aspects of cell signaling and their dysregulation leads to excess cell proliferation, a hallmark of cancer. Kinases are one of the most important targets in precision oncology, but the ideal kinase targets or kinase drug combinations for most cancers have not been established. Determining the cellular consequences of turning off kinase enzymes has immense potential to transform our understanding of kinases and kinase inhibitors. In this New Innovator Award application, I seek to decipher how kinase catalysis regulates cancer cell function by using cutting-edge base editing tools to turn off the enzyme activity in every human kinase across the kinome. This approach will identify novel kinases for therapeutic targeting and will act as a surrogate for small-molecule inhibition to enable drug discovery. Prior methods to perturb the kinome in cells use knock-out or knock-down, which are crude tools that remove the entire gene and do not necessarily translate to the effects of a small-molecule inhibitor. My base editing approach to inactivate kinase catalysis will solve two major issues that prevent existing mutagenesis and knock-in methods to both scale across the kinome and perform mutations at physiologic levels. Base editing can mutate hundreds of genes at physiologic levels in a pooled experiment due to its high editing efficiency. Here, I propose a base editing platform to turn off catalysis in in 556 kinases in cancer cells for pooled functional studies. As a case study, I will investigate breast cancer, where multiple kinase inhibitors are standard therapies but where new treatments are urgently needed. I have developed a suite of new technologies enabling whole kinome base editing in cells, supported by preliminary data. I will use this platform to interrogate how kinase activity regulates 1) cancer cell growth, 2) sensitivity to targeted therapies, and 3) druggable gene expression. This platform will compress the interval between kinome hit and lead discovery from decades to years by identifying the optimal mechanisms to inhibit kinases, transforming drug development and design of combination therapies. This proposal focuses on human kinases in cancer but once we establish this framework it will be applicable to studying any enzyme class in any physiologic process in mammals. This proposal is innovative conceptually, technically, and materially as the first experiment for precise, surgical inhibition of a large and diverse family of enzymes in a comprehensive fashion. My background studying structural biology, protein biochemistry, and kinase signaling; my clinical experience as a breast oncologist; and the strong institutional environment at Columbia University Irving Medical Center make me uniquely well-equipped to perform these investigations.

人基因组包含556个激酶基因，通常称为Kinome。激酶是调节细胞信号传导几乎所有方面的酶，其失调导致细胞增殖过多，这是癌症的标志。激酶是精确肿瘤学中最重要的靶标之一，但是尚未确定大多数癌症的理想激酶靶标或激酶药物组合。确定关闭激酶酶的细胞后果具有巨大的潜力，可以改变我们对激酶和激酶抑制剂的理解。在这个新的创新奖应用程序中，我试图通过使用尖端的基础编辑工具来关闭整个激酶的每个人类激酶中的酶活性来解密激酶催化如何调节癌细胞功能。这种方法将确定用于治疗靶向的新型激酶，并将作为小分子抑制以实现药物发现的替代物。先前使用敲除或淘汰的细胞中的Kinome的方法，这些方法是去除整个基因的粗糙工具，不一定会转化为小分子抑制剂的作用。我的基础编辑方法灭活激酶催化将解决两个主要问题，以防止现有的诱变和敲入方法在整个Kinome范围内扩展并在生理水平上进行突变。由于其高编辑效率，基础编辑可以在合并实验的生理水平上突变数百个基因。在这里，我提出了一个基础编辑平台，以在癌细胞中关闭556种激酶中的催化，以进行合并的功能研究。作为案例研究，我将研究乳腺癌，其中多种激酶抑制剂是标准疗法，但迫切需要新的治疗方法。我已经开发了一套新技术，从而在细胞中提供了整个Kinome基础编辑，并得到了初步数据的支持。我将使用此平台来询问激酶活性如何调节1）癌细胞生长，2）对靶向疗法的敏感性，以及3）可药物基因表达。该平台将通过确定抑制激酶的最佳机制，改变药物开发和组合疗法设计的最佳机制，从而压缩从数十年到几年之间的Kinome HIT和LED发现之间的间隔。该提案的重点是癌症中的人类激酶，但是一旦我们确定了该框架，它将适用于在哺乳动物的任何生理过程中研究任何酶类别。该提案在概念，技术上和物质上都是创新的，作为第一个实验，以全面的方式对大型多样的酶家族进行精确的外科手术抑制。我的背景研究结构生物学，蛋白质生物化学和激酶信号传导；我作为乳房肿瘤学家的临床经验；哥伦比亚大学欧文医学中心的强大机构环境使我能够独特地进行这些调查。