Genome-wide promoter methylation profiling of glioma

描述(由申请人提供)：拟议的为期五年的培训计划旨在为首席研究员提供基于微阵列的全基因组表观基因组图谱的背景知识，用于转化性脑癌研究。作为一名助理教授，PI是一名临床活跃的神经肿瘤学家，拥有指定的实验室空间。这一培训计划将使他能够进入一个与他的临床工作直接协同的新的研究领域，他作为加州大学洛杉矶分校/基因泰克公司最近开放的临床试验(目标登记70名患者)的联合首席调查员，评估贝伐单抗(阿瓦斯丁)与替莫唑胺和放射治疗新诊断的胶质母细胞瘤患者的联合使用。他的培训计划中的关键决定因素是导师斯坦·纳尔逊博士，对加州大学洛杉矶分校神经肿瘤学数据库的访问，以及对加州大学洛杉矶分校脑瘤研究环境的积极支持。Nelson博士是全基因组阵列分析领域公认的领导者，一直活跃于加州大学洛杉矶分校神经肿瘤学数据库中对患者胶质母细胞瘤组织的大规模遗传表征，该数据库是患者组织、细胞系和放射图像的大型临床注释集合。加州大学洛杉矶分校小组最近的大量研究已经实现了利用这个数据库进行强大的相关研究的潜力。该研究计划的总体目标是基于最近的一项发现，即肿瘤具有O(6)-甲基鸟嘌呤DNA甲基转移酶(MGMT)启动子甲基化的胶质母细胞瘤患者表现出更好的存活率和对替莫唑胺(TMZ)的反应。这一发现强调了异常甲基化在脑癌中的重要性。我们假设胶质瘤全基因组甲基化分析将导致发现新的甲基化基因和协调甲基化基因的签名，并证明了使用差异甲基化杂交(DMH)来实现这些目标的可行性。其具体目的是：1)通过比较低级别星形细胞瘤、间变性星形细胞瘤、原发和继发性胶质母细胞瘤以及正常脑标本的基因组甲基化谱，了解启动子甲基化在星形细胞瘤转化中的作用；2)确定与贝伐单抗与放射治疗和TMZ相结合的新型前期疗法的反应相关的全基因组甲基化、基因表达和杂合性丢失(LOH)谱；3)通过描绘药物或基因调控DNMT1活性引起的胶质母细胞瘤细胞系基因组甲基化变化，研究DNA甲基转移酶1(DNMT1)在胶质母细胞瘤甲基化中的作用。这项建议的总体目标是通过基于肿瘤样本的前瞻性分子特征开发个性化方法来改善胶质瘤患者的治疗结果。

DESCRIPTION (provided by applicant): The proposed five-year training program is designed to provide the principal investigator with the background in microarray-based genome-wide epigenomic profiling directed towards translational brain cancer research. As an Assistant Professor, the PI is a clinically active neuro-oncologist with designated laboratory space. This training program will enable him to enter a new area of research that is directly synergistic with his clinical efforts as a co-principal investigator on a recently opened UCLA/Genentech clinical trial (target enrollment of 70 patients) evaluating the use of bevacizumab (Avastin) in combination with temozolomide and radiation for patients with newly-diagnosed glioblastoma. Critical determinants in his training program are the mentor, Dr. Stan Nelson, access to the UCLA Neuro-oncology database, and active support of the UCLA brain tumor research environment. Dr. Nelson is a recognized leader in the field of genome-wide array based analysis and has been active in large-scale genetic characterization of patient glioblastoma tissue in the UCLA Neuro-oncology database, a large clinically annotated collection of patient tissue, cell lines, and radiographic images. The potential for powerful correlative studies harnessing this database have been realized by a large number of recent studies from the UCLA group. The overall goal of the research plan is based on the recent discovery that glioblastoma patients whose tumors have O(6)-Methylguanine DNA methyltransferase (MGMT) promoter methylation demonstrate better survival and response to temozolomide (TMZ). This finding emphasizes the importance of aberrant methylation in brain cancer. We hypothesize that genome-wide methylation profiling of glioma will lead to the discovery of novel methylated genes and signatures of coordinately methylated genes, and we demonstrate the feasibility of using differential methylation hybridization (DMH) to achieve these goals. The specific aims are: 1) to understand the role of promoter methylation in astrocytoma transformation by comparing genome-wide methylation profiles of low grade astrocytomas, anaplastic astrocytomas, primary and secondary glioblastomas, and normal brain samples, 2) to determine genome-wide methylation, gene expression, and loss of heterozygosity (LOH) profiles associated with response to a novel upfront therapy combining bevacizumab with radiation therapy and TMZ, 3) to examine the role of DNA methyltransferase 1 (DNMT1) in glioblastoma methylation by profiling genome-wide methylation changes in glioblastoma cell lines resulting from pharmacologic or genetic modulation of DNMT1 activity. The overall goal of this proposal is to improve therapeutic outcomes for glioma patients by developing personalized approaches based on prospective molecular characterization of tumor samples.