Epigenetic and Genetic Dissection of Drug Response

描述(由申请人提供)：阐明遗传网络的组织并确定它们如何对细胞和生物表型做出贡献在我们的基因组时代仍然是一个巨大的挑战。药物反应和基因表达是受多种遗传和非遗传因素控制的复杂表型。开发基于基因组的方法来预测药物反应，可能会被用于个体化药物，以最大限度地提高效益，将危害降至最低。因此，对决定药物反应等复杂表型的遗传和表观遗传因素进行更全面和更好的表征，可能会大大有益于我们公民的健康，并为我们的生物医药产业提供发展机会。利用国际HapMap项目样本中丰富的遗传变异数据(例如，约310万个单核苷酸多态的基因类型，SNPs)，一组来自表面健康的人淋巴母细胞系(LCL)，Dolan(本建议的共同PI)实验室通过整合这些样本上的遗传和表型数据，率先在药物基因组学发现中使用LCL模型系统。由于基因启动子区域CpG位点的DNA甲基化是基因表达调控的重要机制，因此，将现有的全基因组遗传数据(如SNP基因类型)和表型数据(如mRNA和microRNA表达)扩展到DNA甲基化，可能会为个体药物反应和表达调控的潜在机制提供新的关键见解，并反映出药物基因组和基因表达研究的一个重要新方向。因此，我们建议使用NimbleGen 2.1M豪华启动子阵列和MeDIP(甲基化DNA免疫沉淀)分析来自北欧和西欧血统的HapMap CEU(来自美国犹他州的高加索居民)样本的60个无关细胞系中所有已知启动子区域的DNA甲基化状态的自然变异。将系统地研究SNP基因型、启动子DNA甲基化状态、基因表达和药物反应之间的关系，以评估表观遗传学(特别是DNA甲基化)和遗传学(特别是SNPs)对12种抗癌药物细胞毒性的贡献。由于基因表达受到整个生物医学研究界的广泛关注，基因表达和药物反应的原始个体水平DNA甲基化数据和与甲基化相关的签名将作为一个基于网络的数据库放入公共领域，以便于使用和重新分析。完成后，这一探索性项目将显著增强基因组学和药物基因组学广泛领域的科学知识。最后，我们调查小组的多学科性质和私人投资主任的互补专业知识，增强了我们成功实施拟议项目的能力。

DESCRIPTION (provided by applicant): Elucidating the organization of genetic networks and establishing how they contribute to cellular and organismal phenotypes remain to be a grand challenge in our genomic era. Drug response and gene expression are complex phenotypes that are controlled by various genetic and non-genetic factors. Developing genome-based approaches to prediction of drug response could potentially be used in individualized medicine to maximize benefits and minimize harms. A more comprehensive and better characterization of the genetic, epigenetic factors determining complex phenotypes such as drug response, therefore, may significantly benefit the heath of our citizens and provide development opportunities for our biomedical industry. Taking advantage of the rich genetic variation data (e.g., genotypes of ~3.1 million single nucleotide polymorphisms, SNPs) on the International HapMap Project samples, a panel of human lymphoblastoid cell lines (LCLs) derived from apparently healthy individuals, the Dolan (Co-PI of this proposal) Laboratory has pioneered using the LCL model system in pharmacogenomic discovery by integrating genetic and phenotypic data on these samples. Since DNA methylation at the CpG sites of gene promoter regions is a crucial mechanism of gene expression regulation, expanding the current whole genome genetic (e.g., SNP genotypes) and phenotypic data (e.g., mRNA and microRNA expression) on these samples to include DNA methylation may provide novel and critical insights into the underlying mechanism of individual drug response and expression regulation, and reflect a significantly new direction for pharmacogenomic and gene expression studies. We therefore propose to use the NimbleGen 2.1M Deluxe Promoter Array and the MeDIP (methylated DNA immunoprecipitation) assay to profile the natural variation in DNA methylation status at all known promoter regions in 60 unrelated cell lines from the HapMap CEU (derived from Caucasian residents from Utah, USA) samples of Northern and Western European ancestry. The relationships across SNP genotypes, promoter DNA methylation status, gene expression and drug response will be investigated systematically to evaluate the contribution of epigenetics (specifically, DNA methylation) and genetics (specifically, SNPs) to the cytotoxicities of 12 anticancer drugs. Since gene expression is of broad interest to the entire biomedical research community, the primary individual-level DNA methylation data and the methylation-associated signatures for both gene expression and drug response will be put in public domain as a web-based database for easy use and re-analysis. Upon completion, this exploratory project will significantly enhance scientific knowledge in the broad fields of genomics and pharmacogenomics. Finally, the multi-disciplinary nature of our investigative team and the complementary expertise of PIs enhance our ability to conduct the proposed project successfully.