Robust assays to define telomere maintenance mechanisms as cancer biomarkers.

将端粒维持机制定义为癌症生物标志物的稳健测定。

• 批准号: 10693944
• 负责人: CHARLES Patrick REYNOLDS
• 金额: $ 35.83万
• 依托单位: TEXAS TECH UNIVERSITY HEALTH SCIS CENTER
• 依托单位国家: 美国
• 财政年份: 2021
• 资助国家: 美国
• 起止时间: 2021-09-16 至 2026-08-31
• 项目状态: 未结题
• 来源: https://reporter.nih.gov/project-details/10693944
• 关键词: ATM activation; ATRX gene; Adult; Affect; Anticoagulants; Biological; Biological Assay; Biological Markers; Biology; Biopsy; Blood; Blood specimen; Bone Marrow; Bone Marrow Aspiration; CLIA certified; Catalytic Domain; Cells; Child; Chromosomes; Classification; Clinical; Clinical Trials; Code; Collection; DAXX gene; DNA; DNA Damage; Data; Detection; Drug Targeting; Enzymes; Fixatives; Genetic Recombination; Heparin; Human; Laboratories; Malignant Childhood Neoplasm; Malignant Neoplasms; Marrow; Messenger RNA; Modeling; Mutation; Neoplasm Metastasis; Neuroblastoma; Nucleic Acids; Nucleoproteins; Outcome; Patient risk; Patients; Pediatric Oncology Group; Phase III Clinical Trials; Phenotype; Plasma; Prevalence; Process; Prognosis; Prognostic Marker; Proliferating; Protocols documentation; Quality Control; Quantitative Reverse Transcriptase PCR; RNA; Research; Resistance; Reverse Transcriptase Polymerase Chain Reaction; Ribonucleoproteins; Sampling; Selection for Treatments; Sensitivity and Specificity; Solid Neoplasm; Source; TERC gene; TERT gene; TP53 gene; Telomerase; Telomere Maintenance; Temperature; Therapeutic Clinical Trial; Time; Tissues; Translating; Tube; Tumor Burden; Tumor Tissue; ataxia telangiectasia mutated protein; cancer biomarkers; cancer cell; cancer classification; cancer type; cell free DNA; chemotherapy; clinical application; clinical implementation; clinical risk; cohort; companion diagnostics; diagnostic assay; improved; inhibitor; mRNA Expression; molecular pathology; neoplastic cell; new therapeutic target; novel; novel strategies; novel therapeutics; participant enrollment; peripheral blood; prognostic; risk stratification; sample collection; success; targeted treatment; telomere; tumor; tumor DNA

Abstract Telomeres are nucleoproteins with TTAGGG DNA repeats at the ends of chromosomes that protect coding DNA from erosion and detection as DNA damage. Telomere maintenance is necessary for cancer cells to have unlimited proliferation capacity. Most cancers maintain their telomeres via activation of the ribonucleoprotein telomerase containing a catalytic subunit encoded by the TERT gene and an RNA template encoded by the TERC gene. Cancers with low or no telomerase activity often use another mechanism to extend their telomeres, the Alternative Lengthening of Telomeres (ALT) in which telomeres are maintained via homologous telomeric-DNA recombination, but the mechanism is still poorly understood. ALT tumors contain extra-chromosomal telomeric DNA C-circles, which (detected with a unique PCR assay) provides a specific and sensitive ALT biomarker. We have shown that quantifying TERT mRNA expression together with telomeric DNA C-circles enables classifying cancers into 3 groups based on telomere maintenance mechanism (TMM); telomerase- positive (high TERT), ALT-positive (C-circle+), and TMM-negative. Classifying the childhood cancer neuroblastoma by TMM provides prognostic information that overrides currently employed clinical and biological prognostic markers, and our preliminary data suggest this is possible for other cancer types. ALT cancers are consistently difficult to treat but have dysfunctional telomeres, creating unique vulnerabilities that can provide novel therapeutic targets. For example, we have recently demonstrated high ATM kinase activation at telomeres in ALT neuroblastoma leads to resistance to DNA damaging chemotherapy that can be reversed with a clinical-stage ATM inhibitor AZD0156. Biomarkers of TMM provide both prognostic information and the C-circle assay can potentially serve as a companion diagnostic assay to identify patients with tumors that are likely to be more responsive to novel ALT-targeted therapies. Thus, it is important to define parameters that impact accurate TMM assessment of cancers, i.e. accurate quantitation of TERT mRNA and DNA C-circles. We will define the impact of collection and storage conditions and the minimum amounts of tissue and amounts, and quality of nucleic acids needed for the assays. Identifying ALT patients from a blood sample would have clinical utility, and our preliminary data suggest that C-circles can be detected in plasma containing circulating tumor DNA. Thus, we also propose to develop and validate a plasma C-circle assay as a novel approach to identifying patients with ALT cancers. Finally, to ensure that these assays can be used for clinical risk stratification, and as companion diagnostics for selection of therapy, we propose to carry out studies necessary for CAP/CLIA certification of TERT mRNA qPCR and the telomeric DNA C- circle assay. To accomplish our aims, we are integrating sample collection from adult and pediatric cancers together with a team of experts in telomere biology and molecular pathology. This project will provide important information on analyzing cancer TMM phenotype that will be of value to both research and clinical labs and will enable completion of regulatory requirements necessary for clinical implementation of the assays.

抽象的 端粒是在染色体末端具有 TTAGGG DNA 重复序列的核蛋白，可保护编码 DNA 免受 侵蚀和检测为 DNA 损伤。端粒的维持是癌细胞无限增殖所必需的 容量。大多数癌症通过激活含有催化活性的核糖核蛋白端粒酶来维持其端粒。 由TERT基因编码的亚基和由TERC基因编码的RNA模板。端粒酶水平低或无端粒酶的癌症 活动经常使用另一种机制来延长端粒，即端粒替代延长法 (ALT)，其中 端粒是通过同源端粒 DNA 重组来维持的，但其机制仍知之甚少。 ALT 肿瘤含有染色体外端粒 DNA C 环，（通过独特的 PCR 测定检测）提供了 特异性且敏感的 ALT 生物标志物。我们已经证明，将 TERT mRNA 表达与端粒一起定量 DNA C 环能够根据端粒维持机制 (TMM) 将癌症分为 3 组；端粒酶- 阳性（高 TERT）、ALT 阳性（C 环+）和 TMM 阴性。儿童癌症神经母细胞瘤的分类 TMM 提供的预后信息超越了当前使用的临床和生物预后标志物，并且 我们的初步数据表明这对于其他癌症类型也是可能的。 ALT 癌症一直难以治疗，但 功能失调的端粒，产生独特的脆弱性，可以提供新的治疗靶点。例如，我们有 最近证明 ALT 神经母细胞瘤中端粒处的 ATM 激酶高激活可导致对 DNA 损伤的抵抗 可以用临床阶段 ATM 抑制剂 AZD0156 逆转化疗。 TMM 的生物标志物同时提供 预后信息和 C 环检测有可能作为伴随诊断检测来识别患有以下疾病的患者 可能对新型 ALT 靶向疗法更敏感的肿瘤。因此，定义参数很重要 影响癌症的准确 TMM 评估，即 TERT mRNA 和 DNA C 环的准确定量。我们将 定义收集和储存条件的影响以及组织的最小数量和数量以及质量 检测所需的核酸。从血液样本中识别 ALT 患者将具有临床实用性，我们的 初步数据表明，可以在含有循环肿瘤 DNA 的血浆中检测到 C 环。因此，我们也建议 开发并验证血浆 C 环测定作为识别 ALT 癌症患者的新方法。最后，为了 确保这些测定可用于临床风险分层，并作为治疗选择的伴随诊断， 我们建议开展 TERT mRNA qPCR 和端粒 DNA C 的 CAP/CLIA 认证所需的研究 圆测定。为了实现我们的目标，我们正在将成人和儿童癌症的样本收集与 端粒生物学和分子病理学专家团队。该项目将提供有关分析的重要信息 癌症 TMM 表型对研究和临床实验室都有价值，并将有助于完成监管 临床实施测定所需的要求。