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

基本信息

批准号：
8867410
负责人：
Juan Ignacio Fuxman Bass
金额：
$ 9万
依托单位：
UNIV OF MASSACHUSETTS MED SCH WORCESTER
依托单位国家：
美国
项目类别：
财政年份：
2015
资助国家：
美国
起止时间：
2015-09-01 至 2016-08-31
项目状态：
已结题

来源：
https://reporter.nih.gov/project-details/8867410
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 Diamond Disease Enhancers Environment Failure Follow-Up Studies Gene Expression General Transcription Factors 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 Oranges Pathologic Pathology Pathway interactions Phase Play Point Mutation 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 Untranslated RNA Validation Work Writing Yeasts career career development cytokine experience follow-up genome editing genome wide association study in vivo innovation insight interest mutant new therapeutic target novel overexpression programs promoter public health relevance response skills therapeutic target tool transcription factor

项目摘要

DESCRIPTION (provided by applicant): My long term foal 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 Ts that can bind to the promoter 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 cytokine regulators linking them to their functional role and relevance in disease. Non coding 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 th 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 more 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.

描述（由适用提供）：我的长期小马驹是成为美国主要研究机构的独立研究者，在免疫学和系统生物学之间开发尖端研究。为了实现这一目标，我的直接目标是：（1）产生创新的高质量研究，这将导致高影响力出版物独立于我的心理研究方面，（2）获得一组新的生物信息信息技能，复杂的数据分析，免疫学，免疫学和基因组编辑方法，以完成我现有背景。获得享有声望的NIH独立奖奖将增强我的职业机会，并为我提供发展和成熟自己的研究计划的手段，并获得作为独立研究人员成功的额外培训。拟议的研究涵盖了我的主要科学利益：将免疫调节与系统生物学方法相结合以研究基因表达。细胞因子是细胞到细胞信号蛋白，在描述免疫调查中起基本作用。细胞因子的产生在转录水平上受到高度调节，并且未能适当地表达它们通常会导致多种病理，例如自身免疫性疾病，癌症和感染感染的易感性。经过三十多年的研究，细胞因子表达的许多方面仍未得到充分了解，并且在系统层面上尚未探索细胞因子基因表达的转录调节。我的研究将通过全面识别调节细胞因子基因的转录因子（TF）来描述第一个以基因为中心的细胞因子基因调节网络（GRN）。为此，我首先将通过直接使用高通量酵母单杂交（EY1H）测定法直接测试所有人类细胞因子的TS，并通过直接测试蛋白质-DNA相互作用（PDIS），该TS最近在Walhout Lab中开发。我将对检测到GRN的PDI进行建模，并将该GRN与公开可用的表达数据集成在一起，以定义哪些TF阳性或负调节细胞因子的表达。这些分析以及在基因敲除细胞系中的功能验证测定法将识别将其与它们在疾病中的功能作用和相关性联系起来的细胞因子调节剂。非编码突变是许多人类遗传疾病的核心，占全基因组关联研究中所有突变的90％。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红斑狼疮有关。这些突变会导致转录因子结合位点的损失或增益。测试PDI变化的测定是劳动密集型的，限于几十个TF。我建议使用新型的EY1H管道系统地对PDI变化进行系统询问，这是由于疾病相关的细胞因子调节区域的突变而导致的。这种实验方法的发现将在免疫核管系中得到进一步验证，并将为许多与免疫相关疾病提供机械见解和治疗靶标。我提出的跨学科计划要求我在多个研究领域获得额外的培训，这些培训将完成我的背景，并为我提供最先进的工具，以作为我作为独立研究者的未来研究。我已经将Walhout博士和Fitzgerald博士确定为理想的导师，他们将与Wolfe博士和Myers博士一起作为合作者，并具有高度互补的专业知识。与这些在刺激的环境中与这些世界著名的研究人员合作，例如UMMS的环境，以及我和我的指导委员会的培训活动，我计划为奖励的修订阶段，将使我能够（1）更精通最新的免疫学技术，并获得了最新的免疫学概念，并获得了旨在启发的构成生物学分析和必要的数据分析，并有必要的数据分析和（3），（3）3（3），（3），（3），（3）获得了（3），以及（3）的（3），（3），（3）获得了（3）的概念（3），（3）拟议工作的解释和验证。这项科学专业知识将通过职业发展的半手赛和活动来完成，以获取我作为独立调查员成功所需的修改，领导力，赠款和写作技巧。获得此奖项将使我处于理想的位置，可以利用我在Walhout实验室的经验，同时允许我定义自己的研究利基市场。该奖项将使人们更好地了解在正常和病理状况下如何监管免疫原，这将对公共卫生产生广泛的影响。