Development of a low-cost epigenetic screening assay for Pap specimen-based detection of early-stage ovarian cancer in high-risk women

开发一种低成本表观遗传筛查方法，用于基于巴氏标本的高危女性早期卵巢癌检测

• 批准号: 10678833
• 负责人: Thomas Russell Pisanic II
• 金额: $ 42.36万
• 依托单位: JOHNS HOPKINS UNIVERSITY
• 依托单位国家: 美国
• 财政年份: 2021
• 资助国家: 美国
• 起止时间: 2021-06-15 至 2026-05-31
• 项目状态: 未结题
• 来源: https://reporter.nih.gov/project-details/10678833
• 关键词: Aberrant DNA Methylation; Achievement; Address; Algorithms; BRCA mutations; Benign; Bioinformatics; Biological Assay; Biological Markers; Biometry; Cancer Biology; Carcinoma; Carcinoma in Situ; Case/Control Studies; Cervix Uteri; Clinical; Clinical Research; Clinical Sensitivity; Clinical assessments; Collaborations; Complex; Curative Surgery; Cytology; DNA; DNA Methylation; Detection; Development; Diagnosis; Discrimination; Disease; Early Diagnosis; Engineering; Epigenetic Process; Excision; Exhibits; Feces; Female Genital Diseases; Fluorescence; Germ-Line Mutation; Goals; Gynecologic; Gynecologic Pathology; High Risk Woman; Hypermethylation; Intercept; Laboratories; Lesion; Liquid substance; Malignant Epithelial Cell; Malignant Female Reproductive System Neoplasm; Malignant Neoplasms; Malignant neoplasm of ovary; Mammalian Oviducts; Mammography; Methods; Methylation; Microfluidic Microchips; Microfluidics; Morbidity - disease rate; Operative Surgical Procedures; Ovary; Pap smear; Pathology; Patients; Performance; Recording of previous events; Research; Research Personnel; Resolution; Sampling; Scheme; Sensitivity and Specificity; Serous; Side; Specificity; Specimen; Statistical Models; Survival Rate; Symptoms; Techniques; Technology; Testing; Time; Tissues; Training; Translating; Travel; Tumor stage; Ultrasonography; Vagina; Woman; Work; assay development; cancer type; cohort; cost; cost effective; detection assay; diagnostic technologies; digital; early detection biomarkers; epigenetic marker; genome wide methylation; high risk; imaging modality; improved; instrumentation; liquid biopsy; melting; methylation biomarker; mortality; multidisciplinary; multiplex assay; neoplastic cell; novel; parallelization; performance tests; ratiometric; screening; success; tumor; tumor progression; user-friendly; variant detection

PROJECT SUMMARY With a 5-year survival rate of only 47%, high-grade serous carcinoma (HGSC) remains the most lethal of all types of ovarian cancer. This is a particular concern for women with familial histories or BRCA mutations, who exhibit 20 to 35-fold higher risk of developing HGSC in their lifetime. The high mortality of the disease is largely attributable to the fact that HGSC almost always remains undiagnosed until advanced stages when curative surgery is no longer feasible. Recently, numerous studies have demonstrated that most HGSCs likely originate in the fallopian tubes as precursor lesions called serous tubal intraepithelial carcinomas (STICs) that progress over a period of 6-7 years before rapidly metastasizing to the ovary and surrounding tissues. This suggests there exists a critical window of time in which STIC lesions and early-stage tumors might be detected so that tumor progression can be effectively intercepted before reaching an incurable stage. Recent studies have held out hope by showing that STIC and tumor cells are able to freely travel from the fallopian tubes to the cervix where they can be readily-detected in routinely-collected Pap specimens. Nonetheless, two notable challenges to this approach remain: (1) issues associated with the sensitivity and specificity of current biomarkers that undermine test performance and (2) a cost-effective diagnostic technology with sufficient sensitivity to detect exceedingly-rare copies of biomarkers from early-stage HGSC in complex samples such as Pap specimens. In the present proposal, we seek to address both of these challenges by developing a new type of HGSC screening assay called PapDREAM that is based on the sensitive, cost-effective detection of a novel set of epigenetic biomarkers that we have recently shown to be prevalently and specifically hypermethylated in both early, precursor (STIC) lesions and later-stage HGSC tumors. The PapDREAM assay will employ a unique, digital methylation analysis technique called µ-DREAMing (microfluidic Discrimination of Rare EpiAlleles by Melt) that provides a simple, but highly-effective means of detecting and quantifying rare, aberrantly- methylated DNA, even in challenging samples such as stool, liquid biopsies and Pap specimens. A user- friendly workflow based on common laboratory instrumentation will be developed to enable PapDREAM to be readily translated and performed in various research and clinical settings at a cost of only a few dollars per assay. Ultimately, the PapDREAM assay can be used alone or in combination with other assays to provide an ideal screening method for women at high risk for developing HGSC. We have assembled a multi-disciplinary team with complementary expertise in gynecologic pathology, assay development and DNA methylation bioinformatics to accomplish this goal by achieving the following aims: (1) Evaluate and prioritize methylation biomarkers to be included in the PapDREAM assay, (2) Incorporate µ- DREAMing assays into PapDREAM: a simple, multiplexed digital methylation assay for the detection of early- stage HGSC, and (3) Assess the clinical performance of the PapDREAM assay in Pap specimens.

项目概要 高级别浆液性癌 (HGSC) 的 5 年生存率仅为 47%，仍然是所有癌症中最致命的 对于有家族史或 BRCA 突变的女性来说，这是一个特别值得关注的问题。 一生中患 HGSC 的风险高出 20 至 35 倍。该疾病的高死亡率主要是由于。 这是因为 HGSC 几乎总是未被诊断出来，直到晚期才进行治疗 最近，大量研究表明大多数 HGSC 可能源自手术。 输卵管中的前驱病变称为浆液性输卵管上皮内癌 (STIC)，并且会进展 这表明在快速转移到卵巢和周围组织之前需要 6-7 年的时间。 存在一个可以检测到 STIC 病变和早期肿瘤的关键时间窗口，以便 最近的研究表明，在达到无法治愈的阶段之前，可以有效地阻止肿瘤的进展。 通过证明 STIC 和肿瘤细胞能够自由地从输卵管移动到子宫颈，我们看到了希望 然而，在常规采集的巴氏标本中可以很容易地检测到它们，但存在两个显着的挑战。 这种方法仍然存在：（1）与当前生物标志物的敏感性和特异性相关的问题 破坏测试性能以及 (2) 具有足够灵敏度来检测的经济有效的诊断技术 来自早期 HGSC 的复杂样本（例如巴氏标本）中极其罕见的生物标志物副本。 在本提案中，我们寻求通过开发新型 HGSC 来应对这两个挑战 称为 PapDREAM 的筛选试验基于对一组新颖的、具有成本效益的灵敏检测 我们最近发现表观遗传生物标志物在两种疾病中普遍且特异性地高度甲基化 PapDREAM 检测将采用独特的、早期前驱 (STIC) 病变和晚期 HGSC 肿瘤。 称为 µ-DREAMing 的数字甲基化分析技术（通过微流控技术对稀有表观等位基因进行鉴别） Melt）提供了一种简单但高效的方法来检测和量化罕见的异常现象 甲基化 DNA，即使是在粪便、液体活检和巴氏涂片标本等具有挑战性的样本中。 将开发基于通用实验室仪器的友好工作流程，以使 PapDREAM 能够 易于翻译并在各种研究和临床环境中进行，每个成本仅为几美元 最终，PapDREAM 测定可以单独使用或与其他测定结合使用，以提供 对于患有 HGSC 高风险女性的理想筛查方法。 我们组建了一支多学科团队，在妇科病理学、化验方面具有互补的专业知识 开发和 DNA 甲基化生物信息学通过实现以下目标来实现这一目标：(1) 评估并优先考虑要包含在 PapDREAM 检测中的甲基化生物标志物，(2) 合并 µ- PapDREAM 中的 DREAMing 检测：一种简单的多重数字甲基化检测，用于检测早期- HGSC 阶段，以及 (3) 评估 PapDREAM 检测在巴氏标本中的临床表现。

项目成果

Multiplex Digital Methylation-Specific PCR for Noninvasive Screening of Lung Cancer.

• DOI: 10.1002/advs.202206518
• 发表时间: 2023-06
• 期刊: ADVANCED SCIENCE
• 影响因子: 15.1
• 作者: Zhao, Yang;O'Keefe, Christine M.;Hsieh, Kuangwen;Cope, Leslie;Joyce, Sonali C.;Pisanic, Thomas R.;Herman, James G.;Wang, Tza-Huei
• 通讯作者: Wang, Tza-Huei

Current and Emerging Methods for Ovarian Cancer Screening and Diagnostics: A Comprehensive Review.

• DOI: 10.3390/cancers14122885
• 发表时间: 2022-06-11
• 期刊: CANCERS
• 影响因子: 5.2
• 作者: Liberto, Juliane M.;Chen, Sheng-Yin;Shih, Ie-Ming;Wang, Tza-Huei;Wang, Tian-Li;Pisanic, Thomas R., II
• 通讯作者: Pisanic, Thomas R., II