Investigating Regulatory Networks that Control Cell Proliferation and Apoptosis

研究控制细胞增殖和凋亡的调控网络

• 批准号: 8348900
• 负责人: KURT KOHN
• 金额: $ 97.42万
• 依托单位: DIVISION OF BASIC SCIENCES - NCI
• 依托单位国家: 美国
• 资助国家: 美国
• 起止时间: 至
• 项目状态: 未结题
• 来源: https://reporter.nih.gov/project-details/8348900
• 关键词: Actins; Affect; Anabolism; Apoptosis; Automation; Behavior; Beryllium; Binding; Bioinformatics; Biological; Breast Cancer Cell; Categories; Cell Culture Techniques; Cell Cycle Arrest; Cell Cycle Regulation; Cell Death; Cell Death Signaling Process; Cell Line; Cell Proliferation; Cells; Cellular biology; Characteristics; Chemotherapy-Oncologic Procedure; Code; Colon; Communities; Complex; Computer software; Cytoskeleton; DNA Damage; DNA Repair; DNA biosynthesis; Data; Data Set; Databases; Development; Documentation; E-Cadherin; Electronics; Engineering; Epithelial; Epithelial Cells; Extensible Markup Language; Extracellular Matrix; Gene Expression; Gene Expression Profile; Gene Proteins; Genes; Glioblastoma; Growth Factor Receptors; Hand; Human; Indium; Individual; Infiltration; Instruction; Intervention; Investigation; Java; Laboratories; Lead; Learning; Link; Linux; Literature; Lymphoid Cell; Manuscripts; Maps; Melanins; Melanoma Cell; Melanosomes; Mesenchymal; Methods; Modeling; Molecular; Molecular Diagnosis; Neoplasm Metastasis; Normal Cell; Ontology; Pathway interactions; Patients; Pattern; Pharmaceutical Preparations; Plug-in; Post-Translational Protein Processing; Preparation; Procedures; Process; Production; Protein p53; Proteins; Proteoglycan; PubMed; Publications; Publishing; Regulation; Research; Research Project Grants; Role; Sampling; Signal Transduction; Simulate; Software Validation; Source Code; Structure; Surveys; System; Systems Biology; Tertiary Protein Structure; Testing; The Cancer Genome Atlas; Tight Junctions; Tissue Sample; Tissues; Tumor Cell Line; Tumor Tissue; Validation; Vimentin; Work; base; cancer cell; cancer therapy; cell killing; cell motility; cell type; data mining; design; grasp; improved; killings; melanocyte; melanoma; neoplastic cell; network models; novel; novel strategies; open source; overexpression; prevent; programs; research study; response; simulation; software development; syntax; tool; tumor; wiki

Using MIMs in coordination with gene expression datasets to unravel cell regulatory networks This project is based on the premise that genes that are co-regulated in a variety of cell types are likely to be functionally related. We developed that concept utilizing (1) expression data for the approximately 16,000 genes in the NCI-60 panel of human tumor cell lines; (2) data mining software, developed in our Laboratory (particularly CellMiner) for efficient access to that data; (3) NCI-60 gene expression clusters related to function categories derived by a novel procedure developed by Zeeberg et al (manuscript in preparation); (4) PathVisio-MIM diagram production software (see below); and (5) free access to the relevant scientific literature via PubMed. Utilizing those facilities, we investigated control networks involved in cell migration/invasion, functions specific to melanomas, and molecular interactions specific to cells having epithelial character, as follows. Molecular interaction network model of cell migration/invasion processes Using a set of genes derived by a new clustering procedure designed by Zeeberg et al. (manuscript in preparation) that links expression in the NCI-60 panel of human tumor cells with functions assigned by the Gene Ontology (GO) database, we assembled available information about the molecular interactions of a set of 70 expression-correlated genes. We found that about 70% of those genes could be depicted in 3 overlapping molecular interaction maps (MIMs) related to cell migration: (1) interactions with extracellular matrix; (2) interactions with the actin cytoskeleton; (3) interactions implicating proteoglycans in the extracellular matrix. Melanoma-specific Gene Expression Patterns in the NCI-60 Human Tumor Cell Lines. This project aims to elucidate the regulatory mechanisms specific to melanomas by characterizing distinct gene expression patterns and molecular interaction networks. That increased level of detail may provide new definitions of distinct melanoma subtypes that could improve the design and selection of targeted therapies. We aim to organize what is known about the molecular interactions involved in functions specific to melanoma cells and their cell type of origin, the melanocyte or a precursor thereof. It has been pointed out that melanocytes provide an excellent system for studying complex regulatory networks (Schepsky et al., 2006). Melanomas and melanocytes specifically express the pathways for melanin biosynthesis and melanosome production. Studies of gene actions involved specifically in these processes therefore spotlight the mechanisms involved in those cell types and sharply focuses investigations of a particular set of interrelated molecular control systems. Epithelial gene expression signatures from the NCI-60 human tumor cell lines. In a new approach to the characterization of cells having epithelial character, we focused on the expression of genes for the proteins involved in tight-junctions, structures that are required to maintain polarity of epithelial cells. We found that gene expression of tight-junction proteins in the NCI-60 cell lines is consistent with and more specific than previous epithelial cell characterizations based on expression ratios of E-cadherin and vimentin. Enhancing the utility of our Molecular Interaction Map (MIM) notation In order to make the MIM notation readily accessible to the scientific community and make it easier to learn, as well as to provide tools for developers of MIM applications, we have developed the following software: PathVisio-MIM PathVisio is a tool for creating and editing pathway diagrams (www.pathvisio.org). We developed and published a plug-in to PathVisio for creating and editing MIMs: Luna, A., Sunshine, M.L., van Iersel, M.P., Aladjem, M.I., and Kohn, K.W. (2011). PathVisio-MIM: PathVisio plugin for creating and editing Molecular Interaction Maps (MIMs). Bioinformatics 27, 2165-2166. We now use PathVisio-MIM to create all of our MIM diagrams and find it much easier and faster than the graphics programs we previously used. It greatly facilitates editing or modifying the diagrams, particularly when sections of a diagram have to be moved to provide space for additions. It will make it much easier for new MIM users, because the proper MIM graphics elements are at hand and identified either in pull-down menus or as icons. Also of help for both new and proficient users will be the coordinated use of the Validator plugin described below. Tools for MIM developers In order to provide tools for MIM software development based on our MIM notation rules (Kohn et al., Mol. Biol. Cell 17: 1-13, 2006), we published the following Research Article: Luna, A., Karac, E.I., Sunshine, M., Chang, L., Nussinov, R., Aladjem, M.I., and Kohn, K.W. (2011). A formal MIM specification and tools for the common exchange of MIM diagrams: an XML-Based format, an API, and a validation method. BMC Bioinformatics 12:167. This publication makes available a Java-based application programming interface (API) that can be used by developers to help incorporate support for our new MIMML format. In addition, we have created and included validation software for MIMML datasets that allows MIM users to know if their diagrams conform to syntactic rules outlined by the new MIM specification. We provided documentation and examples for the use of the MIM API and for the validation of the MIMML, as well as a set of MIM diagram examples. PathVisio Validator We collaborated with developers of PathVisio and SBGN (Systems Biology Graphics Notation) to develop a validation framework in PathVisio that can be used with rule sets for MIM or other diagram notations, and we have submitted the following Systems Biology note: Kumar Chandan, Martijn P. van Iersel, Mirit I. Aladjem, Kurt W. Kohn and Augustin Luna (2011). PathVisio Validator: A Rule-based Validation Plugin for Pathway Graphical Notations in PathVisio. The Validator will help users check whether their diagrams conform to a standard rule set, such as for MIM, so as to make the diagrams unambiguous and coded in a manner suitable for exchange with other users. That will be important also for development of automation. The Validator plugin is free and open source. It works with versions of PathVisio 2.0.11 and later on Windows, Mac OS X, and Linux. The plugin along with instructions, example rulesets, and Java source code can be downloaded at http://pathvisio.org/wiki/PathwayValidatorHelp. Functions of MdmX in Fine-Tuning the Response of p53 to DNA Damage Based on a molecular interaction map (MIM) of the p53-Mdm2-MdmX control network, we simulated simplified models and surveyed parameter space to disclose regions where oscillatory behavior did or did not occur: Kim S, Aladjem MI, McFadden GB, Kohn KW. Predicted functions of MdmX in fine-tuning the response of p53 to DNA damage. PLoS Comput Biol. 6(2):e1000665, 2010. A major finding was that MdmX can dampen the p53 oscillations that occur after DNA damage. That action may prevent high transient p53 activity at could lead to unnecessary cell death. MdmX thus may protect against p53 excess. We are currently testing this novel hypothesis in cell culture. We have engineered the needed cell lines and have preliminary data supporting our hypothesis.

使用 MIM 与基因表达数据集配合来解开细胞调控网络 该项目的前提是，在多种细胞类型中共同调控的基因可能在功能上相关。我们利用 (1) NCI-60 人类肿瘤细胞系组中约 16,000 个基因的表达数据开发了这一概念； (2) 我们实验室开发的数据挖掘软件（特别是 CellMiner），用于有效访问该数据； (3)由Zeeberg等人开发的新程序衍生的与功能类别相关的NCI-60基因表达簇（手稿正在准备中）； （4）PathVisio-MIM图制作软件（见下文）； (5) 通过 PubMed 免费获取相关科学文献。 利用这些设施，我们研究了涉及细胞迁移/侵袭的控制网络、黑色素瘤特有的功能以及具有上皮特征的细胞特有的分子相互作用，如下。细胞迁移/侵袭过程的分子相互作用网络模型使用由 Zeeberg 等人设计的新聚类程序衍生的一组基因。 （准备中的手稿）将人类肿瘤细胞 NCI-60 组中的表达与基因本体论 (GO) 数据库指定的功能联系起来，我们收集了有关一组 70 个表达相关基因的分子相互作用的可用信息。我们发现这些基因中约 70% 可以在与细胞迁移相关的 3 个重叠的分子相互作用图谱 (MIM) 中描述：(1) 与细胞外基质的相互作用； (2)与肌动蛋白细胞骨架的相互作用； (3)涉及细胞外基质中蛋白聚糖的相互作用。 NCI-60 人类肿瘤细胞系中黑色素瘤特异性基因表达模式。该项目旨在通过表征不同的基因表达模式和分子相互作用网络来阐明黑色素瘤特有的调节机制。细节水平的提高可能会提供不同黑色素瘤亚型的新定义，从而改善靶向治疗的设计和选择。我们的目标是整理关于黑色素瘤细胞及其细胞来源类型（黑色素细胞或其前体）特异功能的分子相互作用的已知信息。有人指出，黑素细胞为研究复杂的调节网络提供了一个优秀的系统（Schepsky et al., 2006）。黑色素瘤和黑色素细胞特异性表达黑色素生物合成和黑色素体产生的途径。因此，对这些过程中具体涉及的基因作用的研究重点关注这些细胞类型中涉及的机制，并重点研究一组特定的相互关联的分子控制系统。 NCI-60 人类肿瘤细胞系的上皮基因表达特征。在一种表征具有上皮特征的细胞的新方法中，我们重点关注参与紧密连接的蛋白质的基因表达，紧密连接是维持上皮细胞极性所需的结构。我们发现 NCI-60 细胞系中紧密连接蛋白的基因表达与之前基于 E-钙粘蛋白和波形蛋白表达比率的上皮细胞特征一致，并且比之前的上皮细胞特征更特异。增强分子相互作用图 (MIM) 表示法的实用性 为了使 MIM 表示法易于科学界使用并使其更易于学习，并为 MIM 应用程序开发人员提供工具，我们开发了以下软件： PathVisio-MIM PathVisio 是用于创建和编辑路径图的工具 (www.pathvisio.org)。我们开发并发布了 PathVisio 插件，用于创建和编辑 MIM：Luna, A.、Sunshine, M.L.、van Iersel, M.P.、Aladjem, M.I. 和 Kohn, K.W. （2011）。 PathVisio-MIM：用于创建和编辑分子相互作用图 (MIM) 的 PathVisio 插件。生物信息学 27, 2165-2166。 我们现在使用 PathVisio-MIM 来创建所有 MIM 图表，并发现它比我们以前使用的图形程序更容易、更快。它极大地方便了编辑或修改图表，特别是当必须移动图表的某些部分以提供添加空间时。这将使新的 MIM 用户变得更加容易，因为正确的 MIM 图形元素就在手边，并且可以在下拉菜单中或作为图标进行识别。对于新用户和熟练用户来说，协调使用下面描述的验证器插件也将有所帮助。 MIM 开发人员工具 为了提供基于我们的 MIM 符号规则的 MIM 软件开发工具（Kohn 等人，Mol. Biol. Cell 17: 1-13, 2006），我们发表了以下研究文章：Luna, A.、Karac, E.I.、Sunshine, M.、Chang, L.、Nussinov, R.、Aladjem, M.I. 和 Kohn, K.W. （2011）。用于 MIM 图公共交换的正式 MIM 规范和工具：基于 XML 的格式、API 和验证方法。 BMC 生物信息学 12：167。 该出版物提供了一个基于 Java 的应用程序编程接口 (API)，开发人员可以使用它来帮助整合对我们新的 MIMML 格式的支持。此外，我们还创建并包含了 MIMML 数据集的验证软件，使 MIM 用户能够知道他们的图表是否符合新 MIM 规范概述的语法规则。我们提供了有关使用 MIM API 和验证 MIMML 的文档和示例，以及一组 MIM 图示例。 PathVisio 验证器 我们与 PathVisio 和 SBGN（系统生物学图形符号）的开发人员合作，在 PathVisio 中开发了一个验证框架，该框架可与 MIM 或其他图表符号的规则集一起使用，并且我们已提交以下系统生物学注释：Kumar Chandan、Martijn P. van Iersel、Mirit I. Aladjem、Kurt W. Kohn 和 Augustin Luna (2011)。 PathVisio Validator：PathVisio 中路径图形符号的基于规则的验证插件。 验证器将帮助用户检查他们的图表是否符合标准规则集（例如MIM），以便使图表明确并以适合与其他用户交换的方式进行编码。这对于自动化的发展也很重要。 验证器插件是免费且开源的。它适用于 Windows、Mac OS X 和 Linux 上的 PathVisio 2.0.11 及更高版本。该插件以及说明、示例规则集和 Java 源代码可以从 http://pathvisio.org/wiki/PathwayValidatorHelp 下载。 MdmX 在微调 p53 对 DNA 损伤的响应中的功能基于 p53-Mdm2-MdmX 控制网络的分子相互作用图 (MIM)，我们模拟了简化模型并调查了参数空间，以揭示发生或未发生振荡行为的区域：Kim S、Aladjem MI、McFadden GB、Kohn KW。 MdmX 在微调 p53 对 DNA 损伤的反应中的预测功能。 PLoS 计算生物学。 6(2):e1000665, 2010。一个主要发现是 MdmX 可以抑制 DNA 损伤后发生的 p53 振荡。这种作用可能会阻止 p53 的短暂高活性，从而导致不必要的细胞死亡。因此，MdmX 可以防止 p53 过量。我们目前正在细胞培养中测试这一新假设。我们已经设计了所需的细胞系，并有初步数据支持我们的假设。