Comprehensive, context-aware, functional analysis of Cytochrome P450 variants

对细胞色素 P450 变体进行全面、情境感知的功能分析

基本信息

批准号：
10375437
负责人：
Maitreya J Dunham
金额：
$ 52.1万
依托单位：
UNIVERSITY OF WASHINGTON
依托单位国家：
美国
项目类别：
财政年份：
2019
资助国家：
美国
起止时间：
2019-04-01 至 2024-03-31
项目状态：
已结题

来源：
https://reporter.nih.gov/project-details/10375437
关键词：
Address Alleles Amino Acid Substitution Amino Acids Awareness Biochemical Biological Assay CYP1A1 gene CYP2C19 gene CYP2C9 gene CYP2D6 gene CYP3A4 gene Carcinogens Catalogs Cell Respiration Cells Chimera organism Clinical Complex Computational algorithm Conflict (Psychology)Copy Number Polymorphism Custom Cytochrome P450 Data Dependence Dose Engineering Environment Enzymes Family Foundations Gene Fusion Gene Library Genes Genetic Genetic Variation Genotype Goals Haplotypes Health Personnel Human Individual Large-Scale Sequencing Libraries Link Liver Malignant neoplasm of lung Measurement Measures Methods Mitotic Recombination Nicotine Patient-Focused Outcomes Patients Performance Persons Pharmaceutical Preparations Pharmacogenetics Pharmacogenomics Pharmacotherapy Physiological Population Positioning Attribute Proteins Research Personnel Scanning Sequence Analysis Site Smoking Behavior Source Substrate Specificity System Testing Therapeutic Agents Toxic Environmental Substances Toxicogenetics Uncertainty Variant Work Xenobiotics Yeasts adverse drug reaction cancer risk clinical sequencing effective therapy environmental agent enzyme activity gene discovery genetic variant genotyped patients human disease improved inter-individual variation multiplex assay mutation screening novel novel strategies personalized medicine precision drugs programs public database rare variant response variant of unknown significance

项目摘要

ABSTRACT Subject-to-subject variability in response to drugs and environmental agents creates a significant challenge for the safe and effective treatment of many human diseases. Pharmacogenomics seeks to address this challenge by linking drug response to patient genotypes at important loci, termed pharmacogenes, in order to better customize patient treatments. Cytochrome P450 (CYP) gene variation is a major contributor to adverse drug reactions resulting from alterations in a subject's ability to metabolize therapeutic agents and environmental toxins, relative to the population at large. Genetic variation in CYPs is extensive. For example, amongst 12 of the most important cytochrome P450 (CYP) genes, 10% of people carry at least one rare, potentially deleterious variant. Further complexity is introduced via complex alleles consisting of common variation plus linked rare variants, and by extensive copy number variation and gene fusions at these loci. Unfortunately, only a small number of variants have been unambiguously linked to alterations in drug/xenobiotic response. Clearly, new approaches are needed to annotate the consequences of the huge pool of variants of unknown significance, including those already identified by existing large-scale sequencing programs, and those that will be discovered as clinical sequencing becomes routine. We have developed a suite of methods to test all possible single substitutions at all amino acid residues in several CYP genes. In order to accomplish this, we use deep mutational scanning, a method we have developed that allows parallelized, quantitative measurements to be performed on libraries of genetic variants. We are in the midst of applying this approach to single site variants of CYP2C9 and CYP2D6. We propose to extend our work to include CYP2C19, the third prototypic CYP pharmacogene, CYP3A4, quantitatively the most important human liver drug metabolizing enzyme, CYP2A6, which metabolizes nicotine and modulates smoking behaviors and lung cancer risk, and CYP1A1, which bioactivates polycyclic heteroaromatic carcinogens. These efforts, which span the major xenobiotic metabolizing CYP families (CYP1-3), constitute Aim 1. In Aim 2, we will evaluate more complex alleles, including novel chimeras, and in Aim 3 we will dissect the substrate-dependency of genetic variation, both efforts focusing on the drug-metabolizing CYP2 family. The result of this project will be a comprehensive, context aware, functional analysis of CYP variants that will lead to a deeper understanding of the consequences of genetic variation in these key pharmacogenes. We will also develop new, generalizable methods for generating complex variant libraries and for directly assessing the effects of enzyme variants in a multiplex fashion.

抽象的受试者对药物和环境因素的反应存在差异，这对安全有效地治疗多种人类疾病。药物基因组学致力于应对这一挑战通过将药物反应与重要位点（称为药物基因）的患者基因型联系起来，以便更好地定制患者治疗方案。细胞色素P450（CYP）基因变异是药物不良反应的主要原因由于受试者代谢治疗药物和环境的能力的改变而导致的反应毒素，相对于广大人口。 CYP 的遗传变异非常广泛。例如，其中 12 个最重要的细胞色素 P450 (CYP) 基因，10% 的人至少携带一种罕见的、潜在的有害的变体。通过由常见变异加上的复杂等位基因引入进一步的复杂性链接罕见的变异，并通过这些位点的广泛拷贝数变异和基因融合。很遗憾，只有少数变异与药物/异生素反应的改变明确相关。显然，需要新的方法来注释大量未知变体的后果重要性，包括那些已经被现有的大规模测序计划确定的，以及那些将要确定的随着临床测序成为常规，就会被发现。我们开发了一套方法来测试所有几个 CYP 基因中所有氨基酸残基可能存在单一取代。为了实现这一目标，我们使用深度突变扫描，这是我们开发的一种方法，可以并行、定量对遗传变异文库进行测量。我们正在应用这种方法 CYP2C9 和 CYP2D6 的单位点变体。我们建议将我们的工作扩展到包括 CYP2C19，第三个原型 CYP 药物基因 CYP3A4，定量最重要的人类肝脏药物代谢 CYP2A6 酶，可代谢尼古丁并调节吸烟行为和肺癌风险，以及 CYP1A1，可生物激活多环杂芳族致癌物。这些努力涵盖了主要异生素代谢 CYP 家族 (CYP1-3)，构成目标 1。在目标 2 中，我们将评估更复杂的等位基因，包括新型嵌合体，在目标 3 中，我们将剖析遗传变异的底物依赖性，这两项工作都集中在药物代谢 CYP2 家族上。该项目的结果将是一个全面的、对 CYP 变体进行上下文感知的功能分析，这将有助于更深入地了解这些关键药物基因遗传变异的后果。我们还将开发新的、可推广的用于生成复杂变体库和直接评估酶变体在酶中的影响的方法多重时尚。