Interrogating malignant gliomas using released tumor DNA in cerebrospinal fluid

使用脑脊液中释放的肿瘤 DNA 检测恶性神经胶质瘤

• 批准号: 10208816
• 负责人: CHETAN BETTEGOWDA
• 金额: $ 37.46万
• 依托单位: JOHNS HOPKINS UNIVERSITY
• 依托单位国家: 美国
• 财政年份: 2018
• 资助国家: 美国
• 起止时间: 2018-07-01 至 2023-06-30
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/10208816
• 关键词: Alleles; Anatomy; Benchmarking; Biological Assay; Biological Markers; Biopsy; Blood; Blood Circulation; Body Fluids; Brain Neoplasms; Cancer Patient; Caring; Cells; Cerebrospinal Fluid; Clinical; Clinical Trials; DNA; Data; Detection; Development; Diagnosis; Diagnostic; Diagnostic radiologic examination; Disease; Disease Progression; Dose; Evolution; Excision; Future; Genomics; Genotype; Glioma; Goals; Grant; Growth; Image; Individual; Karnofsky Performance Status; MRI Scans; Malignant Glioma; Malignant Neoplasms; Malignant neoplasm of brain; Measures; Methods; Molecular Evolution; Monitor; Mutation; Necrosis; Neurosurgical Procedures; Normal Cell; Normal tissue morphology; Operative Surgical Procedures; Outcome; Pathologic; Patients; Process; Prognosis; Radiation therapy; Recording of previous events; Recurrence; Repeat Surgery; Research; Sampling; Somatic Mutation; Specific qualifier value; Sputum; Steroids; Techniques; Testing; Time; Tissues; Treatment Protocols; Tumor Burden; Tumor Markers; Tumor Tissue; Tumor-Derived; Uncertainty; United States; Urine; X-Ray Computed Tomography; base; burden of illness; cancer biomarkers; cancer cell; candidate marker; cell free DNA; cohort; digital; driver mutation; exome sequencing; experience; high risk; imaging modality; improved; insight; minimally invasive; mutant; neoplastic cell; neuro-oncology; novel therapeutics; optimal treatments; patient subsets; personalized therapeutic; pressure; response; serial imaging; specific biomarkers; tool; treatment effect; tumor; tumor DNA; tumor progression

PROJECT SUMMARY/ABSTRACT Approximately 17,000 individuals each year are diagnosed with a malignant glioma in the United States and the vast majority of these patients will succumb to their disease. Given the lack of clinically available biomarkers for CNS malignancies, the conventional method for disease monitoring in these patients is radiographic. Unfortunately, anatomic changes detected by MRI and CT scans are often non-specific and lag behind progressing or regressing disease. Moreover, it can be difficult to discriminate between treatment effect and cancer growth with imaging alone. Patients must, therefore, have additional surgeries for definitive tissue diagnosis or inappropriately wait for radiographic findings to change as their disease progresses unabated. As a result, there is an incredible need for more sensitive and specific tumor biomarkers in neuro- oncology. We and others have shown that most cancers shed cell free molecules of tumor derived DNA into the circulation and that these molecules can be quantified as a measure of disease burden. Brain tumors are the exception to the rule and rarely shed detectable levels DNA into the bloodstream. However, we have provocative data to suggest that malignant gliomas shed cell free molecules of tumor derived DNA into the cerebrospinal fluid (CSF-tDNA). CSF-tDNA can be distinguished from DNA derived from normal cells by the presence of disease defining somatic mutations. Levels of CSF-tDNA can be quantified using sensitive digital sequencing based assays, such “Safe-SeqS”. In Aim 1, we will use Safe-SeqS to quantify CSF-tDNA levels in longitudinal spinal fluid samples derived from 20 patients with malignant gliomas. We will determine how closely CSF-tDNA levels correlate with disease status as measured by clinical, radiographic and pathological findings. If successful, this approach will accurately assess tumor response and identify those patients at highest risk for recurrence, thus enabling the clinician to alter treatment regimens. There are also burgeoning data to suggest that all cancers, including malignant gliomas, evolve over time in response to various selection pressures, including treatment. These genetic changes have important clinical implications but currently there are no minimally invasive clinical assays that are capable of providing insights into the glioma genotype. As a result, in Aim 2, we will perform whole exome sequencing directly on the CSF and compare to exomic sequencing results from matched tumor/normal samples. This will allow us to understand what fraction of tumor genotype can be detected by analyzing the CSF directly. In order to determine the background mutation rate in CSF, in Aim 3 we will perform Safe-SeqS directly on the CSF of 50 individuals without any history of cancer. At the completion of this grant, we hope to validate CSF-tDNA as a candidate biomarker for individuals with malignant glioma and set the stage for large scale clinical trials that can be conducted to demonstrate clinical utility.

项目概要/摘要 在美国，每年约有 17,000 人被诊断患有恶性神经胶质瘤 这些患者中的绝大多数将死于他们的疾病。由于缺乏临床可用 中枢神经系统恶性肿瘤的生物标志物，这些患者疾病监测的常规方法是 射线照相。不幸的是，MRI 和 CT 扫描检测到的解剖变化通常是非特异性的并且具有滞后性 疾病进展或消退的背后。此外，很难区分不同的治疗方法 单独使用成像的效果和癌症生长。因此，患者必须进行额外的手术才能确诊。 组织诊断或不适当地等待影像学结果随着疾病进展而改变 有增无减。因此，神经系统疾病领域迫切需要更灵敏、更特异的肿瘤生物标志物。 肿瘤学。 我们和其他人已经证明，大多数癌症将肿瘤来源的 DNA 的无细胞分子释放到 循环并且这些分子可以量化作为疾病负担的衡量标准。脑肿瘤是 例外情况，很少有可检测水平的 DNA 进入血液。然而，我们有 令人兴奋的数据表明，恶性神经胶质瘤将肿瘤衍生的 DNA 的无细胞分子释放到 脑脊液（CSF-tDNA）。 CSF-tDNA 可以通过以下方式与源自正常细胞的 DNA 区分开： 定义体细胞突变的疾病的存在。 CSF-tDNA 的水平可以使用敏感的数字技术进行量化 基于测序的测定，例如“Safe-SeqS”。在目标 1 中，我们将使用 Safe-SeqS 来量化 CSF-tDNA 水平 纵向脊髓液样本取自 20 名恶性神经胶质瘤患者。我们将决定如何 CSF-tDNA 水平与临床、放射学和病理学测量的疾病状态密切相关 发现。如果成功，这种方法将准确评估肿瘤反应并识别那些患者 复发风险最高，从而使临床医生能够改变治疗方案。 还有越来越多的数据表明，所有癌症，包括恶性神经胶质瘤，都会随着时间的推移而演变 应对各种选择压力，包括治疗。这些基因改变具有重要的临床意义 影响，但目前还没有能够提供见解的微创临床检测 进入神经胶质瘤基因型。因此，在目标 2 中，我们将直接在 CSF 上进行全外显子组测序 并与匹配的肿瘤/正常样本的外显子测序结果进行比较。这将使我们能够 了解通过直接分析脑脊液可以检测肿瘤基因型的哪一部分。为了 确定 CSF 中的背景突变率，在目标 3 中，我们将直接对 50 的 CSF 进行安全测序 没有任何癌症病史的人。在本次资助完成后，我们希望验证 CSF-tDNA 作为一种 恶性神经胶质瘤个体的候选生物标志物，并为大规模临床试验奠定了基础 可以进行以证明临床实用性。