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Detecting diverse nucleic acid biomarkers of cancer with solid-state nanopores

利用固态纳米孔检测癌症的多种核酸生物标志物

基本信息

批准号：
10025696
负责人：
Adam Roger Hall
金额：
$ 108.97万
依托单位：
WAKE FOREST UNIVERSITY HEALTH SCIENCES
依托单位国家：
美国
项目类别：
财政年份：
2020
资助国家：
美国
起止时间：
2020-08-01 至 2024-07-31
项目状态：
已结题

来源：
https://reporter.nih.gov/project-details/10025696
关键词：
Affect Base Sequence Biological Assay Biological Markers Blood specimen Cancer Diagnostics Cancer Family Cancer cell line Cell Survival Cell physiology Cells Characteristics Charge Clinical Complex DNA DNA lesion Data Detection Devices Diagnostic Disease Elements Epigenetic Process Family Genes Goals Health Human Human Cell Line Individual Infrastructure Ionizing radiation Label Lesion Link Location Malignant Neoplasms Malignant neoplasm of lung Measurement Measures Methods MicroRNAs Modification Molecular Molecular Chaperones Nature Nucleic Acid Probes Nucleic Acids Outcome Output Patients Performance Physiological Plasma Positioning Attribute Proteins Protocols documentation Radiation Radiation exposure Role Sampling Scheme Signal Transduction Source Specificity Speed Structure System Technology Testing Yang base cancer biomarkers cost epigenetic marker experience human model improved individual patient insight microRNA biomarkers nano nanopore nanoscale novel strategies radiation response screening solid state tool translational diagnostics

项目摘要

Project Summary Nucleic acid biomarkers have tremendous potential value to patient health, but by their nature are often difficult to probe. Solid-state (SS-) nanopores are uniquely positioned to contribute to a solution for this challenge. The platform enables individual molecules to be probed as they translocate electrically through a synthetic, nanometer-scale aperture. The intrinsic sensitivity, compact nature, and electronic output make the system an attractive candidate for use as a translational diagnostic device. The central goal of this R33 project is to use SS-nanopore technology to assess nucleic acid biomarkers with applications to cancer through a highly selective assay developed in our lab. With our novel approach, target nucleic acid fragments can be detected and quantified only when bound to a protein chaperone, yielding a binary output. The measurement is rapid, sensitive, and yields an unambiguous electrical signal for analysis. We propose to apply this general measurement scheme in ways that enable the assessment of two broadly significant families of nucleic acid biomarkers. In Aim 1, we will assess epigenetic modifications and single base lesions. Modified bases regulate a variety of cellular functions but are challenging to probe with conventional technology. We will first use our approach to study global abundance of radiation-induced base modifications in model human cancer cell lines and then develop a strategy for determining the gene-specific location of modifications. In Aim 2, we will probe nucleic acid sequence motifs, focusing on microRNA. The link between microRNAs and cell function/malfunction is well established, but such short motifs can be challenging to study. We will first optimize our measurement for probing specific sequences, and then apply it to the assessment of lung cancer-relevant microRNA in de-identified patient blood samples.

项目概要核酸生物标志物对患者健康具有巨大的潜在价值，但本质上往往很难去探查。固态（SS-）纳米孔具有独特的优势，有助于解决这一挑战。这平台使得能够在单个分子通过合成的电移位时对其进行探测，纳米级孔径。固有的灵敏度、紧凑的性质和电子输出使该系统成为用作转化诊断设备的有吸引力的候选者。这个 R33 项目的中心目标是使用 SS-纳米孔技术通过高度评估核酸生物标志物在癌症中的应用我们实验室开发的选择性测定。通过我们的新方法，可以检测目标核酸片段仅当与蛋白质伴侣结合时才进行定量，产生二进制输出。测量速度快，灵敏，并产生明确的电信号以供分析。我们建议应用这一一般性规定测量方案能够评估两个广泛重要的核酸家族生物标志物。在目标 1 中，我们将评估表观遗传修饰和单碱基损伤。修饰碱基调节多种细胞功能，但用传统技术探测具有挑战性。我们将首先使用我们的研究人类癌细胞系模型中辐射诱导碱基修饰的整体丰度的方法然后制定确定基因特异性修饰位置的策略。在目标 2 中，我们将探究核酸序列基序，重点关注 microRNA。 microRNA与细胞之间的联系功能/故障已得到很好的证实，但如此短的基序研究起来可能具有挑战性。我们首先会优化我们用于探测特定序列的测量，然后将其应用于肺癌相关的评估未识别的患者血液样本中的 microRNA。