Epigenomic analysis of cell-free nucleosomes for cancer research

用于癌症研究的游离核小体的表观基因组分析

• 批准号: 10759168
• 负责人: Bryan J Venters
• 金额: $ 40.64万
• 依托单位: EPICYPHER, INC.
• 依托单位国家: 美国
• 财政年份: 2023
• 资助国家: 美国
• 起止时间: 2023-07-01 至 2024-06-30
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/10759168
• 关键词: Affinity; Bar Codes; Biological Assay; Biological Markers; Biomedical Research; Biopsy Specimen; Blood; Cancer Detection; Cancer Patient; Cell Differentiation process; Cells; Chromatin; Clinical; Clinical Research; DNA; DNA analysis; Data; Detection; Development; Diagnosis; Diagnostic; Diagnostics Research; Disease; Exhibits; Gene Expression Regulation; Genomics; Goals; Hematopoietic Neoplasms; Heterochromatin; Histones; Immunoprecipitation; Individual; Industry; Inflammation; Investigation; Malignant Neoplasms; Maps; Measures; Methods; Methylation; Modeling; Monitor; Nucleosomes; Patients; Phase; Plasma; Play; Population; Post-Translational Protein Processing; Proliferating; Proteins; Protocols documentation; Publishing; Reagent; Recombinant DNA; Recovery; Research; Research Methodology; Research Personnel; Role; Sampling; Sensitivity and Specificity; Services; Site-Directed Mutagenesis; Specificity; Standardization; Technology; Tissues; Titrations; Validation; Work; anticancer research; assay development; cancer cell; cell free DNA; cell type; clinical assay development; colon cancer patients; commercialization; disease diagnostic; driving force; epigenomic profiling; epigenomics; improved; innovation; interest; liquid biopsy; neoplastic cell; novel; phase 1 study; phase 2 study; promoter; tool; tumor molecular fingerprint

PROJECT SUMMARY Cell-free DNA (cfDNA) levels are elevated in the blood of individuals with cancer, leading to increased interest in liquid biopsy (LB)-based assays for disease diagnostics and monitoring. Despite this, current cfDNA assays are challenged by limited sensitivity and specificity to differentiate between cell types and disease states. cfDNA is primarily found as cell-free nucleosomes (cfNucs), which consist of histone octamers wrapped in DNA. Nuc features, such as the presence and genomic localization of histone post-translational modifications (PTMs), play important roles in gene regulation and are highly associated with tissue type and disease state. As such, the epigenomic analysis of cfNucs has the potential to deliver a transformative method of research that can provide the specificity required to diagnose and differentiate between diseases that is lacking from current assays. To meet this need, EpiCypher is developing cfNuc-seq, the first commercial platform for the epigenomic analysis of histone PTMs on cfNucs. Previous attempts to develop approaches for analysis of histone PTMs on cfNucs exhibited low sensitivity and were not truly quantitative. The innovation of this proposal is the application of ultra-affinity detection reagents to develop a novel, highly sensitive immunoprecipitation-based workflow to quantitative compare cfNucs across disease states. Our approach will leverage EpiCypher’s novel recombinant DNA-barcoded designer nucleosome spike-in controls to enable normalization and quantitative cross-sample comparison, which is essential due to the low and variable abundance of cfNucs across patients and disease states. The goal of this Phase I study is to perform foundational work towards developing and commercializing the cfNuc-seq platform. Towards this goal, we will first develop optimized assays to profile distinct chromatin compartments (Aim 1). We will then demonstrate the ability of our assay to detect distinct cancer cell signatures in clinical samples (Aim 2), demonstrating strong proof-of-concept for our approach. In subsequent Phase II studies, we will expand target validation and develop and launch high-throughput cfNuc-seq assays and services to enable exciting new biomarker and diagnostics research.

项目总结 癌症患者血液中的游离DNA(CfDNA)水平升高，导致 对用于疾病诊断和监测的基于液体活检(LB)的分析感兴趣。尽管如此，目前的cfDNA 在区分细胞类型和疾病状态方面，检测方法面临着灵敏度和特异性有限的挑战。 CfDNA主要以无细胞核小体(CfNucs)形式存在，由包裹在DNA中的组蛋白八聚体组成。 NUC特征，如组蛋白翻译后修饰(PTM)的存在和基因组定位， 在基因调控中发挥重要作用，并与组织类型和疾病状态密切相关。因此， CfNucs的表观基因组分析有可能提供一种变革性的研究方法，可以 提供诊断和区分当前缺乏的疾病所需的特异性 化验。 为了满足这一需求，EpiCypher正在开发第一个表观基因组商业平台cfNuc-seq CfNucs上组蛋白PTMS的分析。先前尝试开发分析组蛋白PTMS的方法 CfNucs的敏感性较低，且不是真正的定量。本方案的创新之处在于应用 开发一种新的、高度敏感的基于免疫沉淀的工作流程，以 定量比较不同疾病状态的cfNucs。我们的方法将利用EpiCypher的新重组 DNA条形码设计者核小体插入控件，实现标准化和定量交叉样本 比较是必要的，因为患者和疾病中cfNucs的丰度很低且变化很大。 各州。此第一阶段研究的目标是为开发和商业化进行基础性工作 CfNuc-seq平台。为了这个目标，我们将首先开发优化的分析方法来描述不同的染色质 舱室(目标1)。然后，我们将演示我们的检测方法检测不同癌细胞特征的能力。 在临床样本中(目标2)，为我们的方法展示了强大的概念验证。在随后的第二阶段 研究，我们将扩大目标验证，并开发和推出高通量cfNuc-seq检测和服务 以实现令人兴奋的新生物标记物和诊断学研究。