Development and Validation of a CSF Liquid Biopsy for Molecular Characterization and Monitoring of Patients with Central Nervous System Tumors

项目总结/摘要 原发性和转移性中枢神经系统肿瘤（CNS）的发病率较高 and mortality.需要新的和更有效的诊断、治疗和监测战略 原发性和转移性CNS肿瘤患者。解决分子生物学需求的方法 在CNS患者中使用精准药物和靶向治疗所需的信息 肿瘤是有限的。液体活检检测将有助于早期分子表征和监测 CNS肿瘤患者，并将彻底改变患者管理。研究表明，血液不是一种 适用于检测CNS恶性肿瘤患者肿瘤源性生物标志物的液体。与此相反， 脑脊液（CSF）由于其接近脑实质，是信息生物标志物的来源 (e.g.,循环肿瘤DNA（ctDNA）和代谢物）。我们假设有可能进行预- 通过分析ctDNA， CSF中的代谢物。此外，我们的预测是，这些生物标志物的水平将与肿瘤相关。 负担我们预计，CSF中这些生物标志物的定量将有助于监测患有以下疾病的患者： CNS癌症的肿瘤复发和对治疗的反应。我们的初步实验表明， 从小体积CSF中分离ctDNA并通过下一代测序（NGS）检测突变， 微滴数字PCR（ddPCR），突变等位基因频率分别为0.25%和0.1%。我们还 在CSF中确定了肿瘤特异性代谢特征，我们的数据显示更高水平的D-2- 在患有携带IDH 1/IDH 2突变的CNS肿瘤的患者的CSF中，我们建议 开发CSF-液体活检测定追求两个具体目标：（1）验证下一代测序 (NGS)（2）对~125例肿瘤来源的CSF进行代谢组学分析， CSF中的代谢物。这种多平台的方法将允许比较敏感性和特异性之间 各种方法和平台之间结果的相互关系。CNS病变的体积分析 在MRI中的应用将使我们能够评估每种生物标志物用于定量CNS肿瘤负荷的潜力。我们 预期这些研究将最终导致液体活检测定的临床实施， 原发性或转移性CNS成人或儿童患者的诊断和靶向治疗的使用 肿瘤的

Project Summary/Abstract Primary and metastatic central nervous system tumors (CNS) are associated with a high degree of morbidity and mortality. There is a need for new and more effective strategies for diagnosing, treating and monitoring patients with primary and metastatic CNS tumors. Methodologies that address the need for molecular information that is required for the use of precision medicine and targeted therapies, in patients with CNS tumors, are limited. A liquid biopsy assay will facilitate early molecular characterization and monitoring of patients with CNS tumors and will revolutionize patient management. Studies have shown that blood is not a suitable fluid for the detection of tumor-derived biomarkers in patients with CNS malignancies. In contrast, cerebrospinal fluid (CSF), due to its proximity to the brain parenchyma, is a source of informative biomarkers (e.g., circulating tumor DNA (ctDNA) and metabolites). We hypothesize that it is possible to perform pre- operative molecular characterization and monitoring of patients with CNS tumors by analyzing ctDNA and metabolites in the CSF. Moreover, our prediction is that the levels of these biomarkers will correlate with tumor burden. We anticipate that quantification of these biomarkers in the CSF will facilitate monitoring patients with CNS cancer for tumor recurrence and response to therapies. Our preliminary experiments show that we can isolate ctDNA from small volumes of CSF and detect mutations by next generation sequencing (NGS) and droplet digital PCR (ddPCR), at a mutant allele frequency of 0.25% and 0.1%, respectively. We have also identified tumor-specific metabolic signatures in the CSF, and our data shows higher levels of D-2- hydroglyglutarate in the CSF of patients with CNS tumors harboring an IDH1/IDH2 mutation. We propose to pursue two specific aims to develop a CSF-liquid biopsy assay: (1) Validation of a next generation sequencing (NGS) assay to quantify tumor DNA in CSF; (2) To perform metabolomic analysis of ~125 tumor-derived metabolites in CSF. This multi-platform approach will allow comparisons of sensitivity and specificity among various methodologies and cross correlation of results between platforms. Volumetric analysis of CNS lesions in MRI will allow us to evaluate the potential of each biomarker for quantifying CNS tumor burden. We anticipate that these studies will culminate in the clinical implementation of a liquid biopsy assay to facilitate diagnosis and the use of targeted therapies in adult of pediatric patients with primary or metastatic CNS tumors.