Systematic cell-based functional screening for LDL and triglyceride genes

基于细胞的系统性低密度脂蛋白和甘油三酯基因功能筛查

基本信息

批准号：
9322539
负责人：
Chad Albert Cowan
金额：
$ 52.51万
依托单位：
MASSACHUSETTS GENERAL HOSPITAL
依托单位国家：
美国
项目类别：
财政年份：
2014
资助国家：
美国
起止时间：
2014-08-07 至 2019-06-30
项目状态：
已结题

来源：
https://reporter.nih.gov/project-details/9322539
关键词：
Address Affect Alleles Apolipoproteins B Biological Assay Biology Blood Catalogs Cause of Death Cells Cellular Assay Code Collection Complement Complementary DNA Cultured Cells DNA DNA Sequence Data Disease Face Genes Genetic Genetic Complementation Test Genetic Variation Genetic study Genome Genomic approach Genotype Goals Health Heritability Human Human Genetics Image Analysis Individual Inherited Institutes Institution LDL Cholesterol Lipoproteins Lead Lipids Lipoproteins Measures Modernization Monitor Mutate Mutation Myocardial Infarction Noise Phase Phenotype Plasma Play Principal Investigator Proteins Resolution Risk Risk Factors Role Signal Transduction Technology Testing Triglycerides Variant Weight assay development base blood lipid case control combinatorial exome exome sequencing expectation functional genomics gene discovery genetic resource genetic variant high throughput screening improved induced pluripotent stem cell insight knock-down lipoprotein triglyceride low density lipoprotein triglyceride microscopic imaging new technology new therapeutic target novel overexpression phenotypic data population based protein function public health relevance quantitative imaging rare variant scale up screening small hairpin RNA therapeutic target

项目摘要

DESCRIPTION (provided by applicant): Apolipoprotein-B (apoB) containing lipoproteins, as marked by plasma low-density lipoprotein cholesterol (LDL-C) and triglycerides (TG), are causal, heritable risk factors for myocardial infarction (MI), the leading cause of death worldwide. New strategies to lower apoB- containing lipoproteins and MI risk are needed and studying inherited human genetic variation can lead to therapeutic targets that reduce MI risk. Through population-based sequencing and genotyping studies we and others are deriving systematic catalogues of all protein-coding DNA variants present in tens of thousands of individuals characterized for plasma LDL-C, TG, and MI status. However, most protein-coding variants discovered through these approaches are "neutral", i.e., they have little or no effect on the function of the protein encoded by the gene. As such, attempts to associate protein-coding variants with LDL-C, TG, or MI face a tremendous signal to noise problem where the signal from functional alleles is overwhelmed by the noise from neutral alleles. Therefore, the critical barrie facing human genetic studies is distinguishing alleles causal for disease from nonpathogenic variants. To overcome this challenge, we propose a systematic cell-based functional genomics approach that: 1) establishes cell-based assays to measure apoB biology; 2) tests the effect of specific genes and variants on cellular assays; and 3) analyzes association with either lipids or MI risk after weighting alleles based on their functional significance in these cellular assays. We hypothesize that the combination of genetics with systematically- acquired functional data in cells can pinpoint new genes responsible for not only altered LDL- C or TG but also MI risk. To test this hypothesis, we propose the following aims: Aim 1 - To robustly establish systematic overexpression, knockdown and complementation for testing multiple genes and variants in parallel for apoB-relevant functions in cells; Aim 2 - To scale up the application of our technology to test 120 genes with the goal of identifying additional novel LDL-C and TG genes; and Aim 3 - To exploit our technology to decipher which LDL-C and TG genes also confer risk for MI. This proposal addresses a fundamental challenge to modern genetics (to distinguish functionally-relevant from neutral variants in an individual's genome) by applying novel technology (systematic cell-based functional characterization of genes and genetic variants) to a significant unmet health need (improved treatments for MI).

描述（由申请人提供）：载脂蛋白-B（APOB）含有脂蛋白，由血浆低密度脂蛋白胆固醇（LDL-C）和甘油三酸酯（TG）标记，是因果关系的因果，是遗传性的，可遗传的危险因素（MI）。需要新的策略来降低含有脂蛋白的脂蛋白和MI风险，并且研究遗传的人类遗传变异可能会导致降低MI风险的治疗靶标。通过基于人群的测序和基因分型研究，我们和其他人是在数以万计的成千上万个以等离子体LDL-C，TG和MI状态的个体中的蛋白质编码DNA变异的系统目录。但是，通过这些方法发现的大多数蛋白质编码变体都是“中性”的，即它们对基因编码的蛋白质功能几乎没有影响。因此，尝试将蛋白质编码变体与LDL-C，TG或MI相关联的尝试面对噪声问题的巨大信号，在这些信号中，功能等位基因的信号被中性等位基因的噪声所淹没。因此，面对人类遗传学研究的关键巴里是将疾病的因果关系与非人为变异区分开。为了克服这一挑战，我们提出了一种基于系统的基于细胞的功能基因组学方法：1）建立基于细胞的测定方法以测量APOB生物学； 2）测试特定基因和变体对细胞测定的影响； 3）分析基于这些细胞测定中的功能意义加权后与脂质或MI风险的关联。我们假设遗传学与细胞中系统获得的功能数据的组合可以查明新基因不仅改变了LDL-C或TG，还可以改变MI风险。为了检验这一假设，我们提出了以下目的：目标1-以鲁棒性建立系统的过表达，敲低和互补，以测试多个基因和变体的APOB相关功能在细胞中的功能；目标2-扩大我们技术在测试120个基因的应用，以识别其他新型LDL -C和TG基因；目标3-利用我们的技术破译哪些LDL -C和TG基因也赋予MI的风险。该提案通过应用新技术（基于系统的细胞基因和遗传变异的基于系统的功能表征）来解决现代遗传学的根本挑战（以将功能相关的与个人基因组中的中性变异区分开来），以对健康需求（改善MI的治疗方法）。