Genomic approaches to guide molecular classification of glioma

 描述(申请人提供)：恶性胶质瘤占美国所有原发脑恶性肿瘤的80%以上，每年有14,000人死亡。尽管进行了积极的治疗，但恶性胶质瘤大多是致命的，因为它们的侵袭性使它们容易迅速复发。胶质瘤根据组织病理学标准进行分类，这是治疗计划的关键，因为某些亚型对特定的治疗药物表现出更高的敏感性。然而，胶质瘤往往表现出广泛的肿瘤异质性和组织学特征的模糊性，导致诊断的主观性和神经病理医生之间的低符合率。最近，一些大规模的基因组研究发现，大约80%的胶质瘤中存在TERT启动子和IDH1/2的突变。基于这些突变的发生，胶质瘤可以被分为客观的分子亚型，这些亚型比单纯根据组织学更有效地将患者划分为明确的预后亚组。然而，目前基于测序的识别这些改变的方法受到低敏感性(40%的肿瘤细胞)的限制，这是其在弥漫性浸润性胶质瘤中的临床应用的主要限制。重要的是，这项工作还揭示了20%的胶质瘤缺乏这些变化，描绘了一种被称为TERT/IDH野生型胶质瘤的肿瘤亚群。目的/假设：初步研究表明，TERT启动子和IDH突变可以有效地将患者分为基因亚型，但目前的突变检测方法缺乏敏感性(Sanger测序法)或过于耗时(下一代测序法)。我们推测，基于一步定量聚合酶链式反应的方法可以提供更灵敏和快速的这些突变的检测，并通过检测低丰度突变(例如，样本较少的肿瘤)而在胶质瘤诊断中具有实用价值。此外，我们假设尚未确定的TERT/IDH野生型胶质瘤将存在一组独特的基因改变，并表现出与其他胶质瘤不同的端粒维持机制。目的1：建立一种灵敏的检测TERT启动子和IDH1/2热点突变的诊断工具，用于胶质瘤的分子分类。目的2：鉴定TERT/IDH野生型胶质瘤的主要基因和转录改变，并探讨其端粒维持机制。这项研究的长期目标是根据患者特定的分子特征识别可以作为生物标记物的基因改变，以便更准确地诊断和治疗胶质瘤。通过开发对这些关键的TERT和IDH变化的敏感诊断，我们将促进对胶质瘤患者的准确诊断和预测。全面分析TERT/IDH野生型肿瘤的情况将有助于为这一未特定化的胶质瘤患者亚群确定新的生物标记物和治疗靶点。

 DESCRIPTION (provided by applicant): Malignant gliomas account for more than 80% of all primary brain malignancies and 14,000 deaths in the U.S. annually. Despite aggressive treatment, malignant gliomas are largely fatal, as their invasive nature renders them prone to rapid recurrence. Gliomas are classified according to histopathologic criteria which are critical t treatment planning, as certain subtypes show increased sensitivity to particular therapeutic agents. However, gliomas often exhibit extensive tumor heterogeneity and ambiguity among histologic features, leading to subjectivity in diagnosis and low concordance rates among neuropathologists. Recently, a number of large-scale genomic studies identified mutations in the TERT promoter and IDH1/2 in ~80% of all gliomas. Based on the occurrence of these mutations, gliomas can be classified into objective molecular subtypes that stratify patients into clear prognostic subgroups more effectively than by histology alone. However, current sequencing-based methods to identify these alterations are limited by low sensitivity (40% tumor cellularity), a major constraint on their clinical utility in the context of diffusely infiltrativegliomas. Importantly, this work also revealed that 20% of gliomas lack these alterations, delineating a subset of tumors known as the TERT/IDH wildtype gliomas. Objectives/Hypothesis: Preliminary studies indicate that TERT promoter and IDH mutations can effectively stratify patients into genetic subtypes, however current mutation detection methods lack sensitivity (Sanger sequencing) or are overly time-consuming (next-generation sequencing). We hypothesize that a single-step qPCR-based approach can provide more sensitive and rapid detection of these mutations and practical utility in glioma diagnosis by detecting low-abundance mutations (e.g., poorly sampled tumors). Additionally, we hypothesize that the yet undefined TERT/IDH wildtype gliomas will harbor a unique set of genetic alterations and exhibit distinct mechanisms of telomere maintenance from other gliomas. By using genetic techniques such as allele-specific qPCR and next generation sequencing, the following specific aims will be completed: Aim 1: Develop a sensitive diagnostic tool for detection of the TERT promoter and IDH1/2 hotspot mutations for molecular classification of glioma Aim 2: Characterize the major genetic and transcriptional alterations in the TERT/IDH wildtype gliomas and investigate their mechanisms of telomere maintenance. The long-term goal of this study is to identify genetic alterations that can act as biomarkers for more accurate diagnosis and treatment of glioma based on patient-specific molecular signatures. By developing a sensitive diagnostic for these critical TERT and IDH alterations, we will facilitate accurate diagnosis and prognostication of glioma patients. Comprehensively profiling the landscape of the TERT/IDH wildtype tumors will help identify novel biomarkers and therapeutic targets for this uncharacterized subset of glioma patients.