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: 8144439
• 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/8144439
• 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（由申请人提供）：本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细胞色素P450（CYP）活性和mRNA表达。这是必要的，因为，尽管相当大的努力，以确定顺式核苷酸的多样性，仍然有无法解释的变异性，在宿主的反应和毒性的药物治疗，这是显着影响肝β基因介导的药物清除。我们认为CYP的表达实际上是多种多态性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，最近的结果，从人类肝脏GWAS集成系统生物学为基础的网络分析，创造了前所未有的机会，在药物遗传学研究领域，通过确定新的候选基因负责肝脏的变异性。特别是最近与我们的合作者的一项研究，利用网络和途径分析工具来阐明主要的CYP网络和上游调控因子，其遗传变异干扰下游调控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，以确定候选基因的功能变化与改变的表达/活动。我们的主要方法将是我们的历史表型基因型分析在人类肝脏。在这种方法中，我们的最初目标是使用肝脏基因表达和活性作为表型指标，并对表型样本进行深度重测序，特别是表达/活性中表型分布的尾部，并鉴定导致表型变异的变体。需要大量不同的表型样本通常是实施这种方法的限制因素。不过，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协作性全基因组关联研究（GWAS #1）的一部分，该研究包括9种肝脏活性的表型分析。该应用是独一无二的，因为我们还通过独立的GWAS #2和3肝脏资源获得了广泛的表型肝脏进行验证。我们使用多种实验方法来鉴定候选基因的遗传变异，从cDNA的深度重测序开始（方法1）。这在方法2和3中遵循，其鉴定导致改变的mRNA加工和转录以及最终改变的候选基因的mRNA表达的多态性。对于每种方法，我们检查了多态性与候选基因mRNA表达和GWAS#1肝脏中的mRNA活性和表达的关联，并测试了GWAS#2、3肝脏中的复制。方法4进行所需的机制研究以证明任何变体如何改变候选基因mRNA表达。总之，这些目标将填补现有的知识空白，通过确定新的遗传贡献可变的药物代谢介导的药物。 公共卫生相关性：CYP氧化代谢目前使用的大多数口服有效药物。然而，尽管顺式代谢药物遗传学研究多年，但对影响顺式代谢介导的代谢的遗传因素的了解仍然不完整。这项研究首次探索通过药物遗传学与肝脏系统生物学的整合而确定的新型CYP候选基因调节剂。本文提出的研究的成功完成将通过理解候选基因中的多态性如何影响mRNA表达和活性来推进“个性化医学”，从而改善公共健康，并最终改善基因定制的患者给药。