A highly sensitive linear amplification based DNA methylation profiling technique for clinical cancer research

用于临床癌症研究的基于高灵敏度线性扩增的 DNA 甲基化分析技术

基本信息

批准号：
10413620
负责人：
BRIAN C-H CHIU
金额：
$ 42.12万
依托单位：
UNIVERSITY OF CHICAGO
依托单位国家：
美国
项目类别：
财政年份：
2022
资助国家：
美国
起止时间：
2022-06-08 至 2025-05-31
项目状态：
未结题

来源：
https://reporter.nih.gov/project-details/10413620
关键词：
Achievement Address Aftercare Biological Assay Biological Markers Biological Process Biopsy Blood Cancer Biology Cancer Detection Cancer Diagnostics Cancer Patient Cells Clinic Clinical Clinical Oncology Colon Carcinoma CpG dinucleotide Cytosine DNA DNA Library DNA methylation profiling Detection Development Diagnosis Diagnostic Procedure Early Diagnosis Ensure Environment Epigenetic Process FDA approved Frequencies Funding Gene Expression Regulation Genetic Genomic DNA Genomics Goals Gold Guanine + Cytosine Composition Human Human Genome Individual Investigation Liquid substance Machine Learning Malignant Neoplasms Malignant neoplasm of liver Malignant neoplasm of pancreas Methylation Mission Modification Molecular Molecular Analysis Molecular Profiling Molecular Target Monitor Morbidity - disease rate Multiple Myeloma Newly Diagnosed Pathogenesis Patient Monitoring Patients Plasma Plasma Cells Population Study Prevalence Primary Neoplasm Procedures Prognosis Public Health RNA Research Residual Neoplasm Resistance Resolution Role Sampling Screening for cancer Source Specificity Specimen Systems Biology Techniques Technology Testing Tissues Tumor Bank Tumor Tissue United States National Institutes of Health Validation age group anticancer research base biobank biomarker discovery bisulfite bisulfite sequencing cancer diagnosis cancer epidemiology cancer type cell free DNA chemical stability clinical application cost efficient design epidemiology study future implementation high risk population improved innovation innovative technologies large cell Diffuse non-Hodgkin&apos s lymphoma liquid biopsy minimally invasive mortality multidisciplinary multiple omics new technology next generation sequencing noninvasive diagnosis novel prospective recruit screening sex success tool tumor tumor DNA tumor heterogeneity tumor microenvironment whole genome

项目摘要

PROJECT SUMMARY Validating highly sensitive molecular analysis approaches that can fully exploit precious clinical specimens will transform cancer research and clinical applications. Tissue biopsy is the gold standard for cancer diagnosis and has been the primary source of clinical biospecimens in cancer research. However, one of the biggest challenges in basic and clinical cancer research is the frequent lack of sufficient amount of tumor materials from biopsy for multi-omics research (e.g., parallel RNA and DNA-based profiling) after diagnostic procedures, thus limiting progress in systems biology. As such, the ability to conveniently sample bodily fluids, including circulating cell-free DNA (cfDNA) from plasma, offers great promise for enabling highly-sensitive, minimally- invasive, cost-efficient cancer diagnostic methods, and facilitating screening of high-risk populations and patient monitoring. However, cfDNA typically exists in extremely low quantity (e.g., a few nanograms from several mL of blood). Cancer-derived cfDNA is expected to constitute an even smaller portion of the already scarce cfDNA. To accelerate and enhance cancer biology and clinical applications, this R33 aims to validate a novel technology for profiling DNA methylation, i.e., 5-methylcytosines (5mC), which contributes to cancer pathobiology, is reflected in patient-derived cfDNA, and has been integrated in several FDA-approved tests. Given the prevalence of 5mC in the human genome, its roles in gene regulation, and high chemical stability, validating a novel 5mC technology in nanogram or sub-nanogram-level DNA materials offers promising opportunities for various applications in cancer research that have been limited by technology that can utilize limited clinical samples. Specifically, we developed the T7-Linear Amplification based Bisulfite Sequencing (LABS-seq) that integrates a specially-designed bisulfite conversion procedure with the next-generation sequencing (NGS) for sensitively and unbiasedly detecting 5mC in nanogram or sub-nanogram-level DNA materials (e.g., 100 pg). Our preliminary results demonstrated the technical robustness of the LABS-seq and the feasibility of using this innovative technology to identify cancer-specific 5mC changes in cfDNA. In this R33, we will rigorously validate the LABS-seq technique using banked tumor tissues/cells and plasma cfDNA samples from 250 patients with diverse cancer types and 50 frequency-matched healthy controls as well as longitudinal samples from 200 prospectively recruited cancer patients. In Aim 1, we will validate the LABS-seq in genomic DNA (gDNA) from tumor tissues/cells to detect cancer type-specific epigenetic alterations. In Aim 2, we will validate the LABS-seq in cfDNA for the detection of cancer and longitudinal changes. Upon completion of this project, we will provide a highly sensitive, cost-efficient, transformative epigenetic approach applicable to both gDNA and cfDNA, opening up opportunities for research that have been limited by technology. Our established multidisciplinary team, well-annotated human clinical specimens, and excellent environment will ensure the success of this proposed project and future implementation in the clinic.

项目概要验证可以充分利用珍贵临床标本的高度灵敏的分子分析方法将改变癌症研究和临床应用。组织活检是癌症诊断的金标准并一直是癌症研究中临床生物样本的主要来源。然而，最大的之一癌症基础和临床研究面临的挑战是经常缺乏足够的肿瘤材料诊断程序后进行多组学研究（例如基于平行 RNA 和 DNA 分析）的活检，从而限制了系统生物学的进展。因此，能够方便地采集体液样本，包括来自血浆的循环游离 DNA (cfDNA) 为实现高度敏感、最低限度的侵入性、具有成本效益的癌症诊断方法，并促进高危人群的筛查和患者监测。然而，cfDNA 的存在量通常极低（例如，几纳克）几毫升血液）。癌症衍生的 cfDNA 预计仅占已存在的 cfDNA 的一小部分。稀缺的cfDNA。为了加速和增强癌症生物学和临床应用，该 R33 旨在验证用于分析 DNA 甲基化（即 5-甲基胞嘧啶 (5mC)）的新技术，这种甲基化会导致癌症病理生物学，反映在患者来源的 cfDNA 中，并已整合到 FDA 批准的多项测试中。鉴于 5mC 在人类基因组中的普遍性、其在基因调控中的作用以及高化学稳定性，在纳克或亚纳克级 DNA 材料中验证新型 5mC 技术提供了前景广阔的前景癌症研究中各种应用的机会受到可利用技术的限制临床样本有限。具体来说，我们开发了基于 T7 线性扩增的亚硫酸氢盐测序 (LABS-seq) 将专门设计的亚硫酸氢盐转化程序与下一代技术相结合测序 (NGS) 用于灵敏且公正地检测纳克或亚纳克级 DNA 中的 5mC 材料（例如，100 pg）。我们的初步结果证明了 LABS-seq 的技术稳健性和使用这种创新技术来识别 cfDNA 中癌症特异性 5mC 变化的可行性。在这款R33中，我们将使用库存的肿瘤组织/细胞和血浆 cfDNA 严格验证 LABS-seq 技术来自 250 名患有不同癌症类型的患者和 50 名频率匹配的健康对照者的样本以及来自 200 名前瞻性招募的癌症患者的纵向样本。在目标 1 中，我们将验证 LABS-seq 检测肿瘤组织/细胞的基因组 DNA (gDNA)，以检测癌症类型特异性表观遗传改变。在目标 2 中，我们将验证 cfDNA 中的 LABS-seq 用于检测癌症和纵向变化。完成后在这个项目中，我们将提供一种高度敏感、具有成本效益、适用的变革性表观遗传方法 gDNA 和 cfDNA 的结合，为受技术限制的研究提供了机会。我们的建立的多学科团队、注释完善的人体临床标本以及优良的环境将确保该拟议项目的成功以及未来在诊所的实施。