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: 8528625
• 负责人: ERIN G SCHUETZ
• 金额: $ 33.44万
• 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/8528625
• 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，因为尽管在鉴定顺式 CYP 核苷酸多样性方面付出了相当大的努力，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，这些变异性受到肝脏 CYP 基因介导的药物清除的显着影响。我们认为 CYP 的表达实际上是一种复杂的性状，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。我们提出，人类肝脏 GWAS 的最新结果与基于系统生物学的网络分析相结合，通过识别负责肝脏 CYP 变异的新候选基因，在药物遗传学研究领域创造了前所未有的机遇。具体来说，我们的合作者最近进行的一项研究，利用网络和通路分析工具来阐明主要 CYP 网络和上游调节因子，这些调节因子的遗传变异扰乱了下游调节的 CYP 的表达。该提案的主要目标是扩展这些新颖的初步发现，以确定与 CYP 表达/活性改变相关的候选基因的功能变异。我们的主要方法是对人类肝脏的历史表型进行基因型分析。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测量，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，并识别导致表型变异的变异。对大量且多样化的表型样本的需求通常是实施这种方法的限制因素。然而，我们有来自 700 多个肝脏样本的组织。最近，数百个此类肝脏参与了全基因组协作关联研究 (GWAS #1)，其中包括九种 CYP 活性的表型分析。该应用程序的独特之处在于，我们还拥有广泛的表型肝脏，可通过独立的 GWAS #2 和 3 肝脏资源进行验证。我们使用多种实验方法来鉴定候选基因遗传变异，从 cDNA 的深度重测序开始（方法 1）。方法 2 和方法 3 遵循此方法，识别导致 mRNA 加工和转录改变的多态性，并最终改变候选基因的 mRNA 表达。对于每种方法，我们检查多态性与肝脏 GWAS#1 肝脏中候选基因 mRNA 表达和 CYP 活性和表达的关联，并测试 GWAS #2,3 肝脏中的复制。方法 4 进行所需的机制研究，以证明任何变异如何改变候选基因 mRNA 表达。总的来说，这些目标将通过识别可变 CYP 介导的药物代谢的新遗传贡献者来填补现有的知识空白。 公众健康相关性：CYP 可氧化代谢当今使用的大多数口服有效药物。然而，尽管顺式 CYP 药物遗传学研究多年，但对影响 CYP 介导代谢的遗传因素的了解仍然不完整。这项研究首次寻求通过药物遗传学与肝脏系统生物学的整合来确定 CYP 的新型候选基因调节剂。成功完成本文提出的研究将通过了解候选基因的多态性如何影响 CYP 表达和活性来推进“个性化医疗”，从而改善公共健康，并最终改善基因定制的患者剂量。

项目成果

MiRNA-Based Regulation of Hemostatic Factors through Hepatic Nuclear Factor-4 Alpha.

• DOI: 10.1371/journal.pone.0154751
• 发表时间: 2016
• 期刊: PloS one
• 影响因子: 3.7
• 作者: Salloum-Asfar S;Arroyo AB;Teruel-Montoya R;García-Barberá N;Roldán V;Vicente V;Martínez C;González-Conejero R
• 通讯作者: González-Conejero R

Regulation of coagulation factor XI expression by microRNAs in the human liver.

• DOI: 10.1371/journal.pone.0111713
• 发表时间: 2014
• 期刊: PloS one
• 影响因子: 3.7
• 作者: Salloum-Asfar S;Teruel-Montoya R;Arroyo AB;García-Barberá N;Chaudhry A;Schuetz E;Luengo-Gil G;Vicente V;González-Conejero R;Martínez C
• 通讯作者: Martínez C