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体表型做出贡献仍然是我们基因组时代的重大挑战。药物应答和基因表达是受各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用于个体化医疗，以最大限度地提高效益，减少危害。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，可能会大大有利于我们公民的健康，并为我们的生物医学产业提供发展机会。利用丰富的遗传变异数据（例如，在国际人类基因组单体型图项目样本（一组来自明显健康个体的人类淋巴母细胞样细胞系（LCL））上，Dolan（该提案的共同PI）实验室率先通过整合这些样本的遗传和表型数据，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的CpG位点处的DNA甲基化是基因表达调控的关键机制，因此扩展了当前的全基因组遗传（例如，SNP基因型）和表型数据（例如，mRNA和microRNA表达），包括DNA甲基化，可能会提供新的和关键的见解，个体药物反应和表达调控的潜在机制，并反映了药物基因组学和基因表达研究的新方向。因此，我们建议使用NimbleGen 2.1 M Deluxe Promoter Array和MeDIP（甲基化DNA免疫沉淀）检测来分析来自北方和西欧血统的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。将系统研究SNP基因型、启动子DNA甲基化状态、基因表达和药物应答之间的关系，以评价表观遗传学（特别是DNA甲基化）和遗传学（特别是SNP）对12种抗癌药物细胞毒性的贡献。由于基因表达对整个生物医学研究界具有广泛的意义，因此基因表达和药物反应的主要个体水平DNA甲基化数据和甲基化相关签名将作为基于网络的数据库置于公共领域，以便于使用和重新分析。完成后，这一探索性项目将大大提高基因组学和药物基因组学广泛领域的科学知识。最后，我们的调查团队的多学科性质和PI的互补专业知识增强了我们成功开展拟议项目的能力。

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.