Development of cell-free DNA assays for HCC screening and liquid biopsy

开发用于 HCC 筛查和液体活检的游离 DNA 检测方法

• 批准号: 9487193
• 负责人: Ying-Hsiu Su
• 金额: $ 39.79万
• 依托单位: BARUCH S. BLUMBERG INSTITUTE
• 依托单位国家: 美国
• 财政年份: 2016
• 资助国家: 美国
• 起止时间: 2016-06-01 至 2021-05-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/9487193
• 关键词: AFP gene; Algorithmic Analysis; Algorithms; Archives; Biological Assay; Biological Markers; Blinded; Blood; Blood Circulation; CTNNB1 gene; Cancer Etiology; Caring; Cells; Certification; Cessation of life; Clinic; Clinical; Complement; DNA; DNA Markers; DNA Modification Process; DNA Sequence Alteration; Decision Analysis; Detection; Development; Diagnosis; Diagnostic; Diagnostic tests; Disease; Disease Management; Early Diagnosis; Epigenetic Process; Evaluation; GSTP1 gene; Genome; Goals; Hepatitis; Individual; Industrialization; Industry; Intervention; Laboratories; Lead; Liver Cirrhosis; Logistic Regressions; Magnetic Resonance Imaging; Malignant Neoplasms; Malignant neoplasm of liver; Medical; Methods; Methylation; Modeling; Molecular Weight; Monitor; Mutation; Outcome; Pathway interactions; Performance; Pharmacotherapy; Physicians; Plasma; Primary carcinoma of the liver cells; Procedures; Protocols documentation; Reagent; Residual Tumors; Risk; Sampling; Science; Scientist; Serum; Source; Specificity; Specimen; Standardization; TP53 gene; Testing; Tissue Sample; Tissues; Training; Translating; Tumor-Derived; Universities; Urine; Work; X-Ray Computed Tomography; assay development; base; biomarker discovery; biomarker panel; brief intervention; cancer genetics; cancer subtypes; cell free DNA; clinical research site; comparative; design; good laboratory practice; improved; liquid biopsy; neoplastic cell; outcome forecast; personalized cancer therapy; personalized care; personalized management; prototype; public health relevance; reagent standardization; screening; tool; treatment planning; validation studies

 DESCRIPTION (provided by applicant): Development of cell-free DNA assays for HCC screening and liquid biopsy This proposal is for the development of a panel of non-invasive, cell-free (cf) DNA markers, found in the blood or urine, for clinical usage as biomarkers of hepatocellular carcinoma (HCC). This panel will be used in a Certificate for Laboratory Improvement Act (CLIA) lab setting for the early detection and liquid biopsy. The development of this panel will be accomplished by the partnership with two industrial partners, Medical Diagnostic Laboratories (MDL), a leading diagnostic company for over 130 CLIA-certified PCR diagnostic tests in-house, and JBS Science Inc., a company specialized in detecting fragmented cell-free HCC DNA modifications, and two clinical sites, Thomas Jefferson University and Johns Hopkins University. Like other cancers, HCC is a disease of the genome; identification of the DNA modifications underlying the development of HCC should provide unambiguous detection of HCC and personalized care, if HCC is detected. Although there have been numerous attempts to develop cfDNA blood-based, liquid biopsy tests for cancers, most have failed. Of the few attempts designed for HCC, there have not been any used clinically for that capacity. This proposal is for the development of assays that will overcome the obstacles of bringing biomarker discovery to clinical use in the form of liquid biopsies. We will achieve this through detection of a panel of DNA modifications that will enable screening of HCC, identifying cancer subtypes, optimizing drug treatment plans, and monitoring residual diseases to meet the unmet need in early detection and personalized treatment of the cancer. Briefly, in preliminary studies, we have shown that most cfDNA that is present in the blood or urine, and is derived from tumor cells, is low molecular weight (LMW), <300 nts, and thus requires methods specifically designed for small DNA detection and amplification. In a study of 74 HCC urine samples, we detected 77% of the HCC cases and distinguished these cases from liver cirrhosis (n=45) and hepatitis (n=42) with 95% specificity. This was accomplished by detection and quantification of DNA fragments corresponding to DNA modifications (mutations or methylation) within three cfDNA markers: TP53 mutations and methylated GSTP1 and RASSF1a. We believe that the addition of just two HCC-associated DNA modifications, Tert and CTNNB1 mutations, covering the other major HCC cancer pathways will greatly improve the performance of this panel, since almost all (98%, 60/61) HCC tissue tested contained at least one of these five DNA modifications (mutations or methylation). The assays for detecting these five DNA markers in the circulation must be standardized, and the studies must be confirmed. This proposal will therefore develop and optimize the five cfDNA assays for reduction to practice and to determine their clinical utilit in the early detection and precision management of HCC. The deliverable components will be CLIA-certified assays for which their clinical usefulness will be determined, and these assays will be ready for use in commercial CLIA labs, with which we have partnered.

 描述（通过应用提供）：用于HCC筛查和液体活检的无细胞DNA分析的开发，该建议是为了开发在血液或尿液中发现的无创，无细胞（CF）DNA标记的小组，用于临床用法，作为肝细胞癌（HCC）的临床用法。该面板将用于实验室改进证书（CLIA）实验室设置，以进行早期检测和液体活检。该小组的开发将通过与两个工业伙伴Medical Diagnostic Laboratories（MDL）的合作伙伴关系来完成，这是一家领先的诊断公司，该公司在内部拥有130多家CLIA认证的PCR诊断测试，以及JBS Science Inc.，JBS Science Inc.是一家专门研究零散的HCC DNA修饰的公司，以及零散的HCC DNA修饰，以及两个班级Johnas Johnas Johnas Johnssersons，Johnomas Jefferserson。像其他癌症一样，HCC是基因组的疾病。如果检测到HCC，则识别HCC开发基础的DNA修饰应提供明确检测HCC和个性化护理。尽管已经进行了许多尝试开发CFDNA血液基于癌症的液体活检测试，但大多数都失败了。在为HCC设计的一些尝试中，没有任何临床上使用的。该建议是为了开发将生物标志物发现以液体活检形式带到临床用途的障碍的测定法。我们将通过检测一组DNA修饰来实现这一目标，该小组将筛选HCC，鉴定癌症亚型，优化药物治疗计划以及监测残留疾病，以满足对癌症的早期发现和个性化治疗的未满足需求。简而言之，在初步研究中，我们已经表明，大多数血液或尿液中存在的CFDNA，源自肿瘤细胞，是低分子量（LMW），<300 nTS，因此需要专门为小型DNA检测和扩增而设计的方法。在一项针对74个HCC尿液样品的研究中，我们检测到77％的HCC病例，并将这些病例与肝硬化（n = 45）和肝炎（n = 42）区分开，具有95％的特异性。这是通过在三个CFDNA标记中的DNA片段修饰（突变或甲基化）对应的DNA片段的检测和定量来实现的：TP53突变和甲基化的GSTP1和RASSF1A。我们认为，仅添加两种HCC相关的DNA修饰，TERT和CTNNB1突变，涵盖了其他主要的HCC癌途径，将大大改善该小组的性能，因为几乎所有（98％，60/61）测试的HCC组织都包含至少包含这些五个DNA修饰（突变或甲基化）。必须标准化循环中检测这五个DNA标记的测定法，并且必须确认研究。因此，该提案将开发并优化五种CFDNA分析，以减少实践并确定其在HCC的早期检测和精确管理中的临床用法。可交付的组件将是确定其临床实用性的CLIA认证测定法，这些测定法可以用于我们与之合作的商业Clia Labs。