Translating human PPARy binding regions to gene regulation and metabolic disease

将人 PPARγ 结合区域转化为基因调控和代谢疾病

• 批准号: 8815300
• 负责人: Raymond Edward Soccio
• 金额: $ 15.48万
• 依托单位: UNIVERSITY OF PENNSYLVANIA
• 依托单位国家: 美国
• 财政年份: 2012
• 资助国家: 美国
• 起止时间: 2012-04-15 至 2016-02-29
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/8815300
• 关键词: Adipocytes; Adipose tissue; Affect; Alleles; Allelic Imbalance; Antidiabetic Drugs; Binding; Binding Sites; Bioinformatics; Biological Assay; Cell Culture Techniques; Cells; ChIP-seq; Chromatin; Clinical; Code; Complement; Computational Biology; DNA Binding; Data; Data Set; Development; Development Plans; Diabetes Mellitus; Disease; Distal; Enhancers; Environment; Epidemic; Event; Fatty acid glycerol esters; Fostering; Gene Chips; Gene Expression; Gene Expression Regulation; Gene Targeting; Genes; Genetic; Genetic Polymorphism; Genetic Transcription; Genetic Variation; Genetic study; Genome; Genomic Segment; Genomics; Genotype; Grant; Human; Human Genetics; Human Genome; Individual; Investigation; K-Series Research Career Programs; Lead; Link; Location; Massive Parallel Sequencing; Measures; Mentors; Mentorship; Metabolic; Metabolic Diseases; Metabolism; Molecular; Mus; Non-Insulin-Dependent Diabetes Mellitus; Nuclear Receptors; Nucleic Acid Regulatory Sequences; Obesity; Open Reading Frames; Other Genetics; Pathway interactions; Pennsylvania; Peroxisome Proliferator-Activated Receptors; Pharmaceutical Preparations; Phase; Phenotype; Physicians; Proteins; Recruitment Activity; Research; Resources; Scientist; Single Nucleotide Polymorphism; Site; Small Interfering RNA; Thiazolidinediones; Tissues; Training; Translating; Universities; Untranslated RNA; Variant; adipocyte differentiation; career; career development; chromatin immunoprecipitation; diabetic; disease phenotype; genome wide association study; genome-wide; global run on sequencing; histone modification; in vivo; mouse genome; new therapeutic target; novel; novel diagnostics; physiologic model; research study; tool; transcription factor; translational study

DESCRIPTION (provided by applicant): This application is for Dr. Raymond Soccio to develop his career as an academic physician-scientist focusing on the molecular mechanisms of obesity and type 2 diabetes. The career development plan includes training in genomics, bioinformatics, and computational biology, since a thorough understanding of these burgeoning fields will be essential to the cutting-edge studies proposed. There will be formal mentoring by the sponsor Dr. Mitchell Lazar and a multi-disciplinary mentorship committee of distinguished scientists. The University of Pennsylvania offers a remarkably rich environment, with access to collaborators, educational resources, and facilities that will foster Dr. Soccio's professional development. Research will focus on PPAR , a nuclear receptor transcription factor and the master regulator of fat cell development. PPAR is a target for anti-diabetic drugs and a gene associated with type 2 diabetes in genome-wide association studies (GWAS). Our initial studies used chromatin immunoprecipitation and massively parallel sequencing (ChIP-Seq) to identify the genome-wide binding sites, or cistrome, for PPAR in cultured human adipocytes. We found tens of thousands of binding sites, showing the power of cistromics to yield enormous amounts of unforeseen data, yet only ~10% were retained at corresponding locations in the mouse genome, highlighting the importance of translational investigation of human cells and tissues. Specific Aim 1 is to determine function of the PPAR cistrome, by integrating the binding sites with regulated gene expression and markers of active chromatin. We hypothesize that this may reveal general rules for regulated gene transcription by PPAR. Specific Aim 2 is to determine the PPAR cistrome in human adipose tissue, rather than in cultured adipocytes. We hypothesize that this will reveal additional relevant sites and allow clinically important comparisons. Specifi Aim 3 is to translate the PPAR cistrome to the genetics of human metabolic disease. GWAS indentify single nucleotide polymorphisms (SNPs) associated with disease, but only rarely does the SNP affect protein coding sequence, thus most are believed to affect gene regulatory regions. Since PPAR is linked to diabetes, we hypothesize that variants in PPAR binding sites affecting its target genes could likewise lead to metabolic disease. SNPs will be identified in PPAR sites where one allele has better predicted binding, then interrogated in the imputed datasets for large metabolic GWAS. Thus, cistromics could powerfully complement genetics by revealing novel associations not found in the initial GWAS and by providing the missing mechanistic link between genotype and phenotype. We will assay allelic imbalance in PPAR binding as a first step linking SNP to disease. Given the scope of the datasets, novel genes and pathways will inevitably be discovered in Aims 2 and 3, and further investigation of these will transition Dr. Soccio from the mentored to the independent phase of this 5 year career development award. These studies of the human PPAR cistrome have potentially great translational relevance to the epidemics of diabetes and obesity. .

描述（由申请人提供）：Raymond Soccio博士是一名专注于肥胖和2型糖尿病分子机制的学术医师兼科学家。职业发展计划包括基因组学、生物信息学和计算生物学方面的培训，因为对这些新兴领域的透彻理解对于提出的前沿研究至关重要。主办方Mitchell Lazar博士和一个由杰出科学家组成的多学科指导委员会将提供正式指导。宾夕法尼亚大学提供了一个非常丰富的环境，可以接触合作者，教育资源和设施，这将促进Soccio博士的专业发展。研究将集中在PPAR，一种核受体转录因子和脂肪细胞发育的主要调节因子。PPAR是抗糖尿病药物的靶标，也是全基因组关联研究（GWAS）中与2型糖尿病相关的基因。我们最初的研究使用染色质免疫沉淀和大规模平行测序（ChIP-Seq）来鉴定培养的人脂肪细胞中PPAR的全基因组结合位点或细胞。我们发现了数以万计的结合位点，这显示了细胞分裂产生大量不可预见的数据的能力，但只有约10%的结合位点保留在小鼠基因组的相应位置，这突出了人类细胞和组织的翻译研究的重要性。特异性目的1是通过整合结合位点与调控基因表达和活性染色质标记物来确定PPAR细胞的功能。我们假设这可能揭示了PPAR调控基因转录的一般规则。特异性目的2是测定人脂肪组织中的PPAR细胞，而不是体外培养的脂肪细胞。我们假设这将揭示其他相关部位，并允许临床重要的比较。具体目标3是将PPAR基因转化为人类代谢性疾病的遗传学。GWAS鉴定了与疾病相关的单核苷酸多态性（SNP），但SNP很少影响蛋白质编码序列，因此大多数被认为影响基因调控区域。由于PPAR与糖尿病有关，我们假设影响其靶基因的PPAR结合位点变异同样可能导致代谢性疾病。snp将在PPAR位点进行鉴定，其中一个等位基因可以更好地预测结合，然后在大型代谢GWAS的输入数据集中进行查询。因此，通过揭示在初始GWAS中未发现的新关联，以及提供基因型和表型之间缺失的机制联系，池化可以有力地补充遗传学。我们将检测PPAR结合中的等位基因失衡，作为将SNP与疾病联系起来的第一步。考虑到数据集的范围，新的基因和途径将不可避免地在目标2和目标3中被发现，对这些的进一步研究将使Soccio博士从这个为期5年的职业发展奖项的指导阶段过渡到独立阶段。这些人类PPAR风暴的研究对糖尿病和肥胖症的流行具有潜在的巨大转化相关性。