A Team Science Approach Using Bioinformatics, Chemical Genetics and Proteomics to Dissect MAP3K1 Associated Biology in Cancer - Administrative Supplement for INBRE Parent

使用生物信息学、化学遗传学和蛋白质组学的团队科学方法来剖析癌症中 MAP3K1 相关生物学 - INBRE 家长的行政补充

• 批准号: 10850459
• 负责人: PAUL L SORGEN
• 金额: $ 101.94万
• 依托单位: UNIVERSITY OF NEBRASKA MEDICAL CENTER
• 依托单位国家: 美国
• 财政年份: 2001
• 资助国家: 美国
• 起止时间: 2001-09-30 至 2025-04-30
• 项目状态: 未结题
• 来源: https://reporter.nih.gov/project-details/10850459
• 关键词: Address; Administrative Supplement; Affect; Alleles; Area; Assistantship; Award; Bioinformatics; Biology; Biomedical Research; Biophysics; CRISPR/Cas technology; Cancer Biology; Cancer cell line; Cell Differentiation process; Cell Line; Cell Proliferation; Cell physiology; Cells; Cellular biology; Chemicals; Collaborations; Communicable Diseases; Compensation; Complement; Computing Methodologies; Core Facility; Data; Databases; Defect; Development; Discipline; Disease; Doctor of Philosophy; Drug Utilization; Environment; Faculty; Failure; Funding; Gatekeeping; Genetic; Genomics; Goals; HCT116 Cells; In Vitro; Individual; Infrastructure; Institution; Knock-out; Length; Link; MAP3K1 gene; Malignant Neoplasms; Maps; Mass Spectrum Analysis; Mediating; Medical center; Methods; Mission; Mitogen-Activated Protein Kinases; Modeling; Molecular; Molecular Biology; Mutate; National Institute of General Medical Sciences; Nebraska; Neoplasm Metastasis; Network-based; Neurosciences; Operative Surgical Procedures; Outcome; Parents; Pathway interactions; Permeability; Pharmaceutical Preparations; Phosphorylation; Phosphotransferases; Positioning Attribute; Post-Translational Protein Processing; Privatization; Productivity; Proteins; Proteomics; Recombinants; Regulation; Reporting; Research; Research Personnel; Research Project Grants; Resected; Resolution; Role; Sampling; Scholars Program; Science; Signal Pathway; Signal Transduction; Specificity; Structure; Students; System; Technology; Testing; Training; Ubiquitin; Universities; Work; cancer cell; cancer type; chemical genetics; chemoproteomics; drug development; drug synthesis; drug testing; experience; faculty research; faculty support; falls; functional genomics; genetic approach; genomic tools; higher education; in vitro Assay; inhibitor; interest; knock-down; matriculation; mutant; network models; novel; overexpression; preservation; programs; protein complex; protein protein interaction; reconstitution; small molecule; small molecule inhibitor; structural biology; structural imaging; targeted treatment; therapeutic target; tool; tumor; tumor growth; ubiquitin-protein ligase; undergraduate research; undergraduate student

PROJECT SUMMARY This application from the Nebraska Research Network in Functional Genomics (NE-INBRE) network responds to NIGMS call (NOT-GM-23-034) for supporting the development of team science projects. The proposal brings together four investigators with diverse training backgrounds from Nebraska to work on a team science project using bioinformatics, chemical genetics and proteomics to dissect MAP3K1 associated biology in cancer. MAP3K1, a mitogen activated protein kinase, is the only kinase that contains both a kinase domain and an E3-ubiquitin ligase domain. The presence of these two enzymatic domains uniquely positions MAP3K1 at the interface between several phosphorylation and ubiquitin-mediated signaling pathways involved in cellular signaling. This project addresses one of the main themes of the NE-INBRE which is cell signaling to understand the disease mechanisms using a diverse set of functional genomics tools that require a team science approach. Goals of the Parent Award: The mission of the Nebraska IDeA Networks of Biomedical Research Excellence (NE-INBRE) is to stimulate and develop biomedical research capacity at institutions of higher education in Nebraska. The NE-INBRE is structured around two major components: primary undergraduate institutions (PUIs) and PhD granting research institutions (RIs). Support for each PUI consists of: 1) campus research capacity development through support for faculty research and infrastructure enhancement, and 2) development of the undergraduate research pipeline of students through the NE-INBRE Scholars Program. Two features are associated with expanding research capacity at the RIs: 1) providing significant support to multi-user core facilities in order to allow investigators from PUIs and RIs access to cutting-edge technology, and 2) providing support in the form of first-year graduate assistantships for NE-INBRE scholars who matriculate into PhD programs at the RI campuses. The three participating RIs in the research network include two campuses of the University of Nebraska system and one privately supported medical center. Cutting edge multiuser core facilities include cores in genomics, bioinformatics, structural biology and imaging. The three themes reflect the scientific foci of the NE-INBRE, cell signaling and neuroscience, infectious disease, and structural biology and molecular biophysics. These themes serve to link faculty and students at the separate institutions into productive networks based on their areas of expertise and interest. Research Question to be addressed in the Supplement Proposal: The major limitation in developing drugs that block MAP3K1 is the failure of in vitro assays with recombinant MAP3K1 to recapitulate the native cellular state, where protein complexes associated with the full-length post-translationally modified MAP3K1 are preserved. The primary goal of this project is to develop genetic and chemical tools to perturb MAP3K1 in its native state. These are critical for evaluating the effect of MAP3K1 inhibition on NFκB signaling in a panel of cancer cell lines. To achieve this goal, we built a team of four accomplished investigators with expertise in molecular cell biology, chemical genetics, proteomics and bioinformatics. The overall project is divided into four sub-projects with four specific aims, each led by a co-Project Leader. In Aim 1, we will develop a panel of dox-inducible MAP3K1 wild type (WT) and MAP3K1 point mutant cell lines that will be tested by MAP3K1 inhibitors in Aim 2, and the interactomes of different mutants will be characterized by computational approaches in Aim 3 and mass-spectrometry based proteomics in Aim 4. The combined effort will not only validate the signaling defined by the reported knockdown and overexpression data but also unravel the signaling mechanisms as MAP3K1 is perturbed in its native state expressed at endogenous levels. Benefit of the Team Science Effort: Each sub-project in this proposal uses cutting-edge tools and relatively independent of each other, but the overall goal of developing orthogonal tools to dissect MAP3K1 signaling in its native state is achievable only by combining the complementary expertise of the four co-Project Leaders. For example, the MAP3K1 mutant cell lines generated by Dr. Ghosal in Aim 1, can be utilized for drug synthesis and testing by Dr. Natarajan in Aim 2 and analyzed using the proteomics approaches to determine their individual mechanistic defects by Dr. Woods in Aim 4. Dr. Woods also collaborate with Dr. Natarajan to characterize the function of the newly developed MAP3K1 inhibitors using proteomics-based methods optimized on IKAM-1. Similarly, both Drs. Woods and Guda will develop orthogonal approaches to map the MAP3K1 interactome using the mass-spectrometry proteomic and computational approaches, respectively, and use the data generated in each approach to validate their results and refine the protein-protein interaction network models. Together, the complementary aspects of our team allow for meaningful integration of approaches and data to comprehensively characterize MAP3K1 associated biology in cancer and to generate new tools and inhibitors. This project falls well within the scope of the parent NE-INBRE award, and the research questions proposed here do not duplicate any part of the work funded under the parent award.

项目概要 来自内布拉斯加州功能基因组学研究网络 (NE-INBRE) 网络的此应用程序响应 拨打 NIGMS 电话 (NOT-GM-23-034)，支持团队科学项目的开发。该提案带来 来自内布拉斯加州的四名具有不同培训背景的研究人员一起开展团队科学研究 使用生物信息学、化学遗传学和蛋白质组学来剖析 MAP3K1 相关生物学的项目 在癌症中。 MAP3K1 是一种丝裂原激活蛋白激酶，是唯一同时包含激酶结构域的激酶 和E3-泛素连接酶结构域。这两个酶结构域的存在独特地定位了 MAP3K1 位于细胞中涉及的几种磷酸化和泛素介导的信号通路之间的界面 发信号。该项目解决了 NE-INBRE 的主题之一，即细胞信号传导 使用多种功能基因组学工具了解疾病机制，这些工具需要 团队科学方法。 家长奖的目标：内布拉斯加州 IDeA 生物医学研究卓越网络的使命 （NE-INBRE）旨在刺激和发展高等教育机构的生物医学研究能力 内布拉斯加州。 NE-INBRE 围绕两个主要组成部分构建：初级本科院校 （PUI）和博士学位授予研究机构（RI）。对每个 PUI 的支持包括：1) 校园研究 通过支持教师研究和基础设施增强来发展能力，以及 2) 发展 通过 NE-INBRE 学者计划，扩大学生的本科研究渠道。两个特点是 与扩大 RI 的研究能力相关：1) 为多用户核心提供重要支持 设施，以便 PUI 和 RI 的研究人员能够获得尖端技术，以及 2) 提供 以第一年研究生助学金的形式为攻读博士学位的 NE-INBRE 学者提供支持 RI 校区的项目。研究网络中的三个参与研究机构包括该研究中心的两个校区 内布拉斯加大学系统和一所私人支持的医疗中心。尖端的多用户核心设施 包括基因组学、生物信息学、结构生物学和成像的核心。三大主题体现科学性 NE-INBRE、细胞信号传导和神经科学、传染病、结构生物学和分子生物学的焦点 生物物理学。这些主题有助于将不同机构的教师和学生连接到富有成效的网络中 基于他们的专业知识和兴趣领域。 补充提案中要解决的研究问题：药物开发的主要限制 阻断 MAP3K1 的原因是重组 MAP3K1 的体外测定未能重现天然细胞 状态，其中与全长翻译后修饰的 MAP3K1 相关的蛋白质复合物是 保存下来。该项目的主要目标是开发干扰 MAP3K1 的遗传和化学工具 处于其原始状态。这些对于评估 MAP3K1 抑制对 NFκB 信号传导的影响至关重要 一组癌细胞系。为了实现这一目标，我们建立了一个由四名出色的研究人员组成的团队 分子细胞生物学、化学遗传学、蛋白质组学和生物信息学方面的专业知识。总体工程是 分为四个子项目，每个子项目有四个具体目标，每个子项目由一名联合项目负责人领导。在目标 1 中，我们将开发 一组 dox 诱导的 MAP3K1 野生型 (WT) 和 MAP3K1 点突变细胞系，将由 Aim 2 中的 MAP3K1 抑制剂以及不同突变体的相互作用组将通过计算来表征 目标 3 中的方法和目标 4 中基于质谱的蛋白质组学。综合努力不仅将 验证由报告的敲低和过度表达数据定义的信号传导，同时也阐明信号传导 MAP3K1 在内源水平表达的天然状态受到干扰。 团队科学努力的好处：本提案中的每个子项目都使用尖端工具和相对 彼此独立，但开发正交工具来剖析 MAP3K1 信号传导的总体目标 它的原始状态只有通过结合四位联合项目负责人的互补专业知识才能实现。为了 例如，Ghosal 博士在 Aim 1 中生成的 MAP3K1 突变细胞系可用于药物合成和 Natarajan 博士在目标 2 中进行测试，并使用蛋白质组学方法进行分析以确定其个体 Woods 博士在目标 4 中提出了机械缺陷。Woods 博士还与 Natarajan 博士合作，描述了 使用在 IKAM-1 上优化的基于蛋白质组学的方法研究新开发的 MAP3K1 抑制剂的功能。 同样，两位博士。 Woods 和 Guda 将开发正交方法来绘制 MAP3K1 相互作用组图，使用 分别使用质谱蛋白质组学和计算方法，并使用中生成的数据 每种方法都验证其结果并完善蛋白质-蛋白质相互作用网络模型。在一起， 我们团队的互补方面允许对方法和数据进行有意义的整合，以全面 表征癌症中 MAP3K1 相关生物学并产生新的工具和抑制剂。 该项目完全属于 NE-INBRE 奖项的范围，并且研究问题 这里提出的建议不要与父奖资助的工作的任何部分重复。

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