Delineation of a cytokine gene regulatory network and rewiring in disease

细胞因子基因调控网络的描绘和疾病中的重新布线

• 批准号: 9323076
• 负责人: Juan Ignacio Fuxman Bass
• 金额: $ 24.9万
• 依托单位: BOSTON UNIVERSITY (CHARLES RIVER CAMPUS)
• 依托单位国家: 美国
• 财政年份: 2015
• 资助国家: 美国
• 起止时间: 2015-09-01 至 2019-07-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/9323076
• 关键词: Address; Affect; Alleles; American; Area; Arthritis; Autoimmune Diseases; Autoimmunity; Award; Binding; Binding Sites; Bioinformatics; Biological Assay; Biological Response Modifiers; Cell Line; Cells; Chronic; Collaborations; Complement; Complex; Cues; Cytokine Gene; Cytokine Signaling; DNA-Protein Interaction; Data; Data Analyses; Disease; Enhancers; Environment; Failure; Follow-Up Studies; Gene Expression; Genes; Genetic Transcription; Goals; Health; Hereditary Disease; Human; Human Genetics; Hybrids; Immune; Immune System Diseases; Immune response; Immunology; Infection; Inflammatory Response; Institution; Knock-out; Laboratories; Lead; Leadership; Learning; Link; Malignant Neoplasms; Mentors; Modeling; Mutation; Nucleic Acid Regulatory Sequences; Pathologic; Pathology; Pathway interactions; Phase; Play; Positioning Attribute; Predisposition; Preparation; Process; Production; Public Health; Publications; Regulation; Regulator Genes; Research; Research Personnel; Resources; Role; Secure; Signal Transduction; Signaling Protein; System; Systemic Lupus Erythematosus; Systems Biology; Techniques; Testing; Training; Training Activity; Transcriptional Regulation; United States National Institutes of Health; Validation; Work; Writing; Yeasts; career; career development; cross disciplinary program; cytokine; experience; follow-up; genome editing; genome wide association study; in vivo; innovation; insight; interest; mutant; new therapeutic target; novel; overexpression; programs; promoter; response; skills; therapeutic target; tool; transcription factor

My long-term goal is to become an independent investigator at a major American research institution, developing cutting-edge research at the interface between immunology and systems biology. To achieve this goal my immediate objectives are: (1) to produce innovative, high quality research that will result in high impact publications that are independent of my mentor’s lines of research, (2) to acquire a new set of skills in bioinformatics, complex data analyses, immunology, and genome editing approaches to complement my existing background. Obtaining the prestigious NIH pathway to independence award would bolster my career opportunities and provide me with the means to develop and mature my own research program, plus acquire the additional training I need to succeed as an independent researcher. The proposed research encompasses my major scientific interests: integrating immune regulation with systems biology approaches to study gene expression. Cytokines are cell-to-cell signaling proteins that play fundamental roles in delineating immune responses. Cytokine production is highly regulated at the transcriptional level, and failure to express them appropriately often results in several pathologies such as autoimmune diseases, cancer and susceptibility to infections. After more than three decades of research, many aspects of cytokine expression are still not well understood, and transcriptional regulation of cytokine gene expression has not been explored on a systems level. My research will delineate the first gene-centered cytokine gene regulatory network (GRN) by comprehensively identifying the transcription factors (TFs) that regulate cytokine genes. To do so, I will first identify the TFs that can bind to the promoters and other known regulatory regions for all human cytokines by directly testing for protein-DNA interactions (PDIs) using high-throughput yeast one-hybrid (eY1H) assays, recently developed in the Walhout lab. I will model the PDIs detected into a GRN and will integrate this GRN with publicly available expression data to define which TFs positively or negatively regulate cytokine expression. These analyses, together with functional validation assays in knockout cell lines, will identify novel cytokine regulators linking them to their functional role and relevance in disease. Noncoding mutations are at the core of many human genetic diseases, and constitute 90% of all mutations identified in genome-wide association studies. For instance, mutations in cytokine regulatory regions have been associated with cancer, higher susceptibility to infections, chronic arthritis and systemic lupus erythematosus. These mutations can result in loss or gain of transcription factor binding sites. Assays to test for PDI changes are labor intensive and limited to a few dozen TFs. Thus, I propose to use a novel eY1H pipeline to systematically interrogate for PDI changes that result as a consequence of disease-associated mutations in cytokine regulatory regions. Findings from this experimental approach will be further validated in immune cell lines and will provide mechanistic insights and therapeutic targets for many immune related diseases. The cross-disciplinary program I propose requires that I obtain additional training in multiple areas of research that will complement my background, and will provide me with state-of-the-art tools for my future research as an independent investigator. I have identified Dr. Walhout and Dr. Fitzgerald as ideal mentors to carry out my proposed work, together with Dr. Wolfe and Dr. Myers as collaborators, with highly complementary expertise. Working in collaboration with these world-renowned researchers in a stimulating environment such as that of UMMS, together with the training activities my mentoring committee and I have planned for the mentored phase of the award, will enable me to: (1) become proficient in state-of-the-art immunology techniques and learn up-to-date immunology concepts, (2) acquire bioinformatics and complex data analysis skills, and (3) learn genome editing approaches, all necessary for the interpretation and validation of the proposed work. This scientific expertise will be complemented with career development seminars and activities to acquire the mentoring, leadership, grantsmanship and writing skills I will need to succeed as an independent investigator. Securing this award would place me in an ideal position to capitalize on my experience to date in the Walhout laboratory, while allowing me to define my own research niche. This award will lead to a better understanding of how immune genes are regulated in normal and pathologic conditions, which will have a broad impact on public health.

我的长期目标是成为美国主要研究机构的独立研究员， 在免疫学和系统生物学之间的界面上开发尖端研究。实现这一目标 目标我的直接目标是：（1）产生创新的高质量研究，这将导致高影响力 独立于我导师的研究方面的出版物，（2）获得一套新的技能 生物信息学，复杂的数据分析，免疫学和基因组编辑方法的完成方法 现有背景。获得享有声望的NIH独立奖将使我的职业发展 机会并为我提供发展和成熟的手段，并获取 作为独立研究人员，我需要取得成功的额外培训。 拟议的研究涵盖了我的主要科学利益：将免疫学与 系统生物学研究基因表达的方法。细胞因子是细胞到细胞信号传导蛋白的发挥作用 在描述免疫反应中的基本作用。细胞因子的产生受到高度调节 转录级别和未能适当表达它们的情况常常导致几种病理 自身免疫性疾病，癌症和感染的易感性。经过三十多年的研究， 细胞因子表达的许多方面仍然不太了解，并且细胞因子的转录调节 基因表达尚未在系统级别探索。我的研究将描述以基因为中心的第一个以基因为中心 通过全面识别转录因子（TF），细胞因子基因调节网络（GRN） 调节细胞因子基因。为此，我将首先确定可以绑定到启动子和其他已知的TF 使用高通量直接测试蛋白-DNA相互作用（PDI）的所有人类细胞因子的调节区域 最近在Walhout实验室开发的酵母单杂交（EY1H）测定法。我将建模PDI 检测到GRN，并将此GRN与公开可用的表达数据集成在一起，以定义哪个TFS 积极或负调节细胞因子的表达。这些分析以及功能验证 敲除细胞系中的测定，将识别新型的细胞因子调节剂将其链接到其功能作用和 与疾病相关。 非编码突变是许多人类遗传疾病的核心，占所有人的90％ 在全基因组关联研究中发现的突变。例如，细胞因子调节区域的突变 与癌症，感染较高的敏感性，慢性关节炎和全身性狼疮有关 红斑。这些突变会导致转录因子结合位点的损失或增益。测试测定 因为PDI的变化是劳动密集型的，并且仅限于几十个TF。那我建议使用新颖的EY1H 管道系统地对PDI变化进行系统询问，这是由于疾病相关而导致的 细胞因子调节区域的突变。这种实验方法的发现将在 免疫细胞系，将为许多免疫相关的机械见解和治疗靶标提供 疾病。 我提出的跨学科计划要求我在多个领域获得额外的培训 可以完成我的背景的研究，并为我提供最先进的工具 作为独立研究者的研究。我已经确定Walhout博士和Fitzgerald博士是理想的导师 与Wolfe博士和Myers博士一起担任合作者，从事我建议的工作，高度 完全专业知识。与这些世界知名的研究人员合作进行刺激 诸如UMMS之类的环境，以及我和我的心理委员会的培训活动 计划在奖励的问题阶段，将使我能够：（1）精通最先进的 免疫学技术和学习最新的免疫学概念，（2）获取生物信息学和复杂 数据分析技能以及（3）学习基因组编辑方法，这是解释和 验证拟议的工作。这种科学专业知识将随着职业发展而完成 我将需要的精神，领导力，授予技巧和写作技巧的半手和活动 作为独立调查员成功。获得此奖项将使我处于理想的位置 根据我在Walhout实验室的经验，同时允许我定义自己的研究利基市场。这 奖励将使人们更好地了解如何在正常和病理中调节免疫基因 条件将对公共卫生产生广泛影响。