Development of an automated, point of care DNA methylation cartridge blood test for colorectal cancer detection in LMICs- an academic-industrial partnership

开发用于中低收入国家结直肠癌检测的自动化护理点 DNA 甲基化盒血液检测 - 学术与工业合作伙伴关系

• 批准号: 10635412
• 负责人: SARASWATI SUKUMAR
• 金额: $ 61.88万
• 依托单位: JOHNS HOPKINS UNIVERSITY
• 依托单位国家: 美国
• 财政年份: 2023
• 资助国家: 美国
• 起止时间: 2023-06-06 至 2028-05-31
• 项目状态: 未结题
• 来源: https://reporter.nih.gov/project-details/10635412
• 关键词: 2019-nCoV; Actins; Affect; Africa; African; Age; Aliquot; Asia; Attention; Benign; Biological Assay; Blood Tests; Body mass index; Breast Cancer Detection; Cells; Cessation of life; Characteristics; Classification; Clinical; Clinical Research; Collaborations; Colonoscopy; Colorectal Cancer; Communicable Diseases; Community Health; Cost Savings; DNA; DNA Methylation; DNA Modification Process; Data; Detection; Development; Diagnosis; Diagnostic; Disease; Early Diagnosis; Ensure; Equilibrium; Future; Genes; Goals; Hour; Hypermethylation; Industrialization; Infrastructure; Intervention; Knowledge; Laboratories; Lead; Lesion; Malignant - descriptor; Malignant Neoplasms; Manuals; Measures; Memorial Sloan-Kettering Cancer Center; Methods; Methylation; Modification; Molecular; Nigeria; Oncology Group; Outcome; Pathology; Patient Care; Patient Selection; Patients; Performance; Persons; Plasma; Predictive Value; Prospective Studies; Publishing; Reproducibility; Research; Resource-limited setting; Resources; Sampling; Sensitivity and Specificity; Signs and Symptoms; Specificity; System; Technology; Testing; Tissues; Training; Triage; Tumor Subtype; Validation; biomarker panel; bisulfite; cancer biomarkers; cell free DNA; clinical practice; colon cancer patients; colorectal cancer screening; colorectal cancer treatment; commercialization; cost; detection assay; diagnostic tool; financial toxicity; flu; improved; industry partner; innovation; liquid biopsy; low and middle-income countries; methylation biomarker; mortality; patient subsets; point of care; point of care testing; product development; programs; prospective; prototype; rapid detection; rapid diagnosis; sex; success; tumor; underserved area

ABSTRACT Colorectal cancer (CRC) is diagnosed at advanced stages in many low- and middle-income countries (LMICs). The lack of knowledge of CRC signs and symptoms by patients and community health practitioners frequently leads to delayed presentation with Stage 3-4 disease. This initial delay, paired with limited colonoscopy facilities, leads to prolonged diagnostic delays. The result is a 5-year mortality rate in LMIC up to 5 times higher than that in USA. An innovative solution to this problem could be an affordable, easily deployable, “point of care” molecular test to identify and prioritize patients likely to have a malignancy for expedited colonoscopy and pathology review leading to better outcomes. Continuing our established collaboration with our industrial partner, Cepheid, we propose to build on our strong published data on hypermethylated markers in CRC to develop an affordable, <3- hour, automated CRC-methylation detection blood test that analyzes a panel of five hypermethylated genes in cell free DNA from 1 ml of plasma. The proposed innovations could lead to a single-cartridge assay for quick CRC detection with a 3-fold reduction in cost. In Aim 1a, we will optimize a cartridge-less bisulfite DNA conversion method for plasma and test its efficiency in Patient Set 1 plasma (N= 20 malignant, 20 normal). In Aim 1b we will select one optimal 5-marker panel out of 20 CRC markers using DNA from FFPE samples from the U.S and Nigeria (N= 30 malignant, 30 benign), and one optimal “pan” set will be confirmed in plasma using U.S Patient Set 2 and Nigeria Set 3 (N=35 malignant, 35 benign). In Aim 1c, we will evaluate analytical performance of the CRC-MD assay. Intra-assay reproducibility will be assessed on multiple aliquots of U.S Patient Set 4 plasma (N=35 malignant, 35 benign). Inter-operator reproducibility will be determined using replicate aliquots of plasma from Patient Set 4 (N= 35 malignant, 35 benign). The goal of Aim 2a is to technically validate the CRC-MD assay using prospectively collected samples in Nigeria. We will first select a threshold in a Training set of plasma from Patient Set 4 (N=90 malignant, 90 benign) to optimally balance sensitivity and specificity, and validate performance of the selected threshold in a Test set of plasma from Patient Set 5 (N= 90 malignant, 90 benign). Accuracy (sensitivity, specificity, and positive- and negative-predictive value) of CRC- MD-based diagnosis to distinguish benign versus malignant disease will be measured using histopathological diagnosis of the lesion as the gold standard. Lastly, in Aim 2b, to determine whether the performance of the CRC-MD assay is altered by select patient characteristics, we will test its clinical accuracy among specific patient subgroups classified by age, sex, BMI, and tumor characteristics. Our prior success in developing automated cell-based/liquid biopsy assays with Cepheid has established the path ensuring an accurate and reliable test. This intervention could be cost saving by hastening colonoscopy for those who need it urgently, thus expediting detection and treatment of CRC in LMICs. This will save thousands of lives yearly. This study will also facilitate further development of the CRC-MD assay moving toward future commercialization and access globally.

摘要 结直肠癌（CRC）在许多低收入和中等收入国家（LMIC）中被诊断为晚期。 患者和社区卫生工作者对CRC体征和症状缺乏了解， 导致3-4期疾病的延迟表现。最初的延误，加上有限的结肠镜检查设施， 导致诊断延迟时间延长。其结果是，低收入国家的5年死亡率高达5倍， 在美国.这个问题的一个创新解决方案可能是一种负担得起的，易于部署的“护理点”分子， 一项检查，用于识别和优先考虑可能患有恶性肿瘤的患者，以进行快速结肠镜检查和病理学检查 带来更好的结果。继续与我们的工业合作伙伴Cepheid建立合作关系， 我建议建立在我们关于CRC中高甲基化标志物的强有力的已发表数据的基础上，以开发一种负担得起的，<3- 小时，自动化CRC甲基化检测血液测试，分析一组五个高甲基化基因， 来自1 ml血浆的无细胞DNA。所提出的创新可能会导致一个单一的盒测定快速 CRC检测，成本降低3倍。在目标1a中，我们将优化一个无酶解的亚硫酸氢盐DNA 血浆的转换方法，并测试其在患者组1血浆（N= 20例恶性，20例正常）中的效率。在 目的1b：我们将使用来自来自以下的FFPE样品的DNA从20个CRC标记物中选择一个最佳的5标记物组： 美国和尼日利亚（N= 30例恶性，30例良性），并使用 美国患者集2和尼日利亚患者集3（N=35例恶性，35例良性）。在目标1c中，我们将评估分析 CRC-MD测定的性能。将对多等份美国 患者组4血浆（N=35例恶性，35例良性）。将使用以下方法确定操作员间重现性 来自患者组4（N= 35例恶性，35例良性）的重复等分血浆。目标2a的目标是在技术上 使用在尼日利亚前瞻性采集的样本验证CRC-MD检测。我们将首先在 a来自患者组4（N=90恶性，90良性）的血浆的训练组，以最佳地平衡灵敏度，以及 特异性，并在来自患者组5的血浆测试组中验证所选阈值的性能（N= 90 恶性，90例良性）。CRC的准确性（灵敏度、特异性、阳性和阴性预测值）- 将使用组织病理学方法测量基于MD的诊断以区分良性与恶性疾病。 以病变诊断为金标准。最后，在目标2b中，为了确定 CRC-MD检测因选择患者特征而改变，我们将在特定患者中测试其临床准确性 根据年龄、性别、BMI和肿瘤特征分类的亚组。我们之前在开发自动化 Cepheid基于细胞的/液体活检检测已经建立了确保检测准确可靠的途径。 这种干预可以通过为那些迫切需要结肠镜检查的人加速结肠镜检查来节省成本，从而加快 LMIC中CRC的检测和治疗。这将每年拯救成千上万的生命。这项研究还将促进 CRC-MD检测的进一步发展，走向未来的商业化和全球访问。