Genetic Predictors of Human Liver CYP Expression & Activity

人类肝脏 CYP 表达的遗传预测因子

• 批准号: 8322839
• 负责人: ERIN G SCHUETZ
• 金额: $ 34.65万
• 依托单位: ST. JUDE CHILDREN'S RESEARCH HOSPITAL
• 依托单位国家: 美国
• 财政年份: 2010
• 资助国家: 美国
• 起止时间: 2010-09-15 至 2014-08-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/8322839
• 关键词: Accounting; Affect; Area; CYP2C9 gene; CYP3A4 gene; Candidate Disease Gene; Complementary DNA; Complex; Cytochrome P450; Cytochromes b5; DNA Resequencing; Data; Dose; Gene Expression; Genes; Genetic; Genetic Polymorphism; Genetic Variation; Genomics; Genotype; Goals; Grant; Hepatic; Human; Immune response; Individual; Knowledge; Liver; Measures; Mediating; Medicine; Messenger RNA; Metabolism; NADPH-Ferrihemoprotein Reductase; Nucleotides; Pathway Analysis; Patients; Pharmaceutical Preparations; Pharmacogenetics; Pharmacotherapy; Phenotype; Public Health; Research; Resources; Sampling; Systems Biology; Tail; Testing; Time; Tissues; Toxic effect; Transcription Process; Validation; Variant; base; drug clearance; drug metabolism; enzyme activity; genetic variant; genome wide association study; improved; mRNA Expression; novel; public health relevance; response; tool; trait

DESCRIPTION (provided by applicant): The long-term goal of this research is to understand how genetic variation in four candidate genes influences hepatic cytochrome P450 (CYP) activity and mRNA expression. This is necessary because, despite considerable effort to identify cis CYP nucleotide diversity, there is still unexplained variability in host response to and toxicity from drug therapies that is significantly influenced by hepatic CYP gene mediated drug clearance. We propose that expression of CYPs is really a complex trait resulting from the combined effect of multiple polymorphisms interacting to regulate gene expression and enzyme activity. We propose that recent results from human liver GWAS integrated with systems biology based network analysis has created unprecedented opportunities in the pharmacogenetic research area by identifying novel candidate genes responsible for hepatic CYP variability. Specifically a recent study with our collaborators, exploited network and pathway analysis tools to illuminate the primary CYP network and the upstream regulators whose genetic variation perturbs expression of the downstream regulated CYPs. A major goal of this proposal is to extend these novel preliminary findings to identify the functional variation in candidate genes associated with altered CYP expression/activity. Our primary approach will be our historical phenotype to genotype analysis in human livers. In this approach, our initial goal is to use liver gene expression and activity as phenotypic measures and to deep resequence the phenotyped samples, particularly the tails of the phenotypic distribution in expression/activity and identify variants that account for phenotypic variability. The need for large and diverse sets of phenotyped samples is usually a limiting factor in implementing this approach. However, we have tissue from over 700 liver samples. Hundreds of these livers were recently part of a collaborative genome wide association study (GWAS #1) that included phenotyping for nine CYP activities. This application is unique in because we also have extensively phenotyped livers for validation available through independent GWAS #2 and 3 liver resources. We use a variety of experimental approaches to identify candidate gene genetic variation starting with deep resequencing of the cDNAs (Approach 1). This is followed in Approaches 2 and 3 that identify polymorphisms leading to altered mRNA processing and transcription, and ultimately altered mRNA expression of the candidate gene. For each approach we examine the association of polymorphisms to candidate gene mRNA expression and CYP activity and expression in liver GWAS#1 livers and test for replication in GWAS #2,3 livers. Approach 4 carries out required mechanistic studies to demonstrate how any variants change candidate gene mRNA expression. In total, these aims will fill an existing knowledge gap by identifying novel genetic contributors to variable CYP mediated drug metabolism. PUBLIC HEALTH RELEVANCE: CYPs oxidatively metabolize the majority of the orally effective drugs in use today. Nevertheless, despite many years of cis CYP pharmacogenetics, knowledge is still incomplete on the genetic factors influencing CYP mediated metabolism. This study is, for the first time, pursuing novel candidate gene regulators of CYPs identified through integration of pharmacogenetics with liver system biology. Successful completion of the studies proposed herein will improve public health by advancing "personalized medicine" through understanding of how polymorphisms in the candidate genes affect CYP expression and activity, and will ultimately improve genetically tailored patient dosing.

描述(申请人提供)：这项研究的长期目标是了解四个候选基因的遗传变异如何影响肝脏细胞色素P450(CYP)活性和mRNA表达。这是必要的，因为尽管人们做出了相当大的努力来鉴定顺式CYP核苷酸的多样性，但宿主对药物治疗的反应和毒性仍然存在无法解释的变异性，这在很大程度上受到肝脏CYP基因介导的药物清除的影响。我们认为，Cyps的表达确实是一个复杂的性状，是多种基因多态相互作用调节基因表达和酶活性的综合作用的结果。我们认为，基于系统生物学的网络分析与人类肝脏GWAS的最新结果相结合，通过识别新的候选基因，为药物遗传学研究领域创造了前所未有的机会，这些候选基因负责肝脏CYP的可变性。特别是最近与我们的合作者进行的一项研究，利用网络和路径分析工具来阐明主要的CYP网络和上游调节因子，它们的遗传变异扰乱了下游调节的CYP的表达。这项建议的一个主要目标是扩展这些新的初步发现，以确定与CYP表达/活性改变相关的候选基因的功能变异。我们的主要方法将是对人类肝脏进行基因分析的历史表型。在这种方法中，我们的最初目标是使用肝脏基因的表达和活性作为表型衡量标准，并对表型样本进行深度测序，特别是表达/活性的表型分布的尾部，并识别解释表型可变性的变异。对大量和多样化的表型样本的需求通常是实施这一方法的限制因素。然而，我们有700多个肝脏样本的组织。数百个这样的肝脏最近是一项合作的全基因组关联研究(GWAS#1)的一部分，该研究包括九种CYP活动的表型。这一应用的独特之处在于，我们也有广泛的表型肝脏供验证，可通过独立的GWAS2和3肝脏资源获得。我们使用各种实验方法来识别候选基因遗传变异，首先对cDNA进行深度重新测序(方法1)。其次是方法2和方法3，这两种方法识别导致mRNA加工和转录改变的多态，并最终改变候选基因的mRNA表达。对于每种方法，我们检查了多态与候选基因mRNA表达和CYP活性的关系，以及在肝脏中的表达，并测试了在肝脏中的复制。方法4进行必要的机制研究，以证明任何变异如何改变候选基因的mRNA表达。总而言之，这些目标将通过确定可变CYP介导的药物代谢的新的基因贡献者来填补现有的知识空白。 与公共健康相关：目前使用的大多数口服有效药物中，环磷酰胺是其氧化代谢产物。然而，尽管顺式CYP药物遗传学研究已有多年，但对影响CYP介导代谢的遗传因素的认识仍不完全。本研究首次将药物遗传学与肝脏系统生物学相结合，寻找新的CYPS候选基因调控因子。本文建议的研究的成功完成将通过了解候选基因的多态如何影响CYP的表达和活性来促进“个性化药物”，从而改善公共健康，并最终改善根据基因定制的患者剂量。