Scalable and quantitative chromatin profiling from formalin-fixed paraffin-embedded samples

对福尔马林固定石蜡包埋样品进行可扩展和定量的染色质分析

基本信息

批准号：
10696343
负责人：
Michael-Christopher Keogh
金额：
$ 40.63万
依托单位：
EPICYPHER, INC.
依托单位国家：
美国
项目类别：
财政年份：
2023
资助国家：
美国
起止时间：
2023-05-01 至 2025-04-30
项目状态：
未结题

来源：
https://reporter.nih.gov/project-details/10696343
关键词：
Acceleration Antibodies Antibody Activation Benchmarking Biological Assay Biological Markers Cell Nucleus Cells ChIP-seq Chimeric Proteins Chromatin Clinical Clinical Research Collection Cultured Cells DNA DNA Damage Data Development Disease Enhancers Ensure Epigenetic Process Formalin Freezing G-substrate Genes Genetic Transcription Genomics Goals Histones Hyperactivity In Vitro Ligation Location Maps Measurement Methods Molecular Nucleosomes Paraffin Embedding Pathology Performance Pharmaceutical Preparations Phase Polymerase Post-Translational Protein Processing Process Protein Fragment Proteins Protocols documentation Regulation Research Research Personnel Resolution Running Sampling Site Site-Directed Mutagenesis Technology Tissue Embedding Tissue Sample Tissues Tn5 transposase Translational Research Validation biomarker discovery bisulfite sequencing clinical application commercialization cross reactivity data quality epigenomics genome-wide innovation interest new therapeutic target next generation novel novel marker novel therapeutic intervention phase 1 study preservation promoter sample fixation therapeutic target tool tool development

Acceleration Antibodies Antibody Activation Benchmarking Biological Assay Biological Markers Cell Nucleus Cells ChIP-seq Chimeric Proteins Chromatin Clinical Clinical Research Collection Cultured Cells DNA DNA Damage Data Development Disease Enhancers Ensure Epigenetic Process Formalin Freezing G-substrate Genes Genetic Transcription Genomics Goals Histones Hyperactivity In Vitro Ligation Location Maps Measurement Methods Molecular Nucleosomes Paraffin Embedding Pathology Performance Pharmaceutical Preparations Phase Polymerase Post-Translational Protein Processing Process Protein Fragment Proteins Protocols documentation Regulation Research Research Personnel Resolution Running Sampling Site Site-Directed Mutagenesis Technology Tissue Embedding Tissue Sample Tissues Tn5 transposase Translational Research Validation biomarker discovery bisulfite sequencing clinical application commercialization cross reactivity data quality epigenomics genome-wide innovation interest new therapeutic target next generation novel novel marker novel therapeutic intervention phase 1 study preservation promoter sample fixation therapeutic target tool tool development

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项目摘要

PROJECT SUMMARY The development of tools to map the location of histone post-translational modifications (PTMs) genome- wide has ushered in a new era of epigenetic research, placing histone PTMs and associated mechanisms in the spotlight as novel biomarkers and therapeutic targets. Despite this progress, leveraging epigenomics for clinical research has been hindered by a lack of high-performance genomic mapping assays that are compatible with formalin-fixed paraffin-embedded (FFPE) tissue, due to DNA damage that is incurred during the FFPE process. Indeed, existing FFPE sample-compatible genomic mapping assays are either low-throughput and insensitive (requiring large sample inputs), or do not resolve specific chromatin features (e.g., promoters, enhancers, etc.). Therefore, next-generation chromatin profiling assays that are able to resolve specific chromatin features using banked FFPE samples are key to unlock access to the massive collection of banked clinical samples and enable novel biomarker discovery / validation for disease-relevant histone PTM targets. To meet this need, EpiCypher is developing CUTANA-FFPETM, a first-in-class low input genomic mapping solution for the study of FFPE clinical samples. This technology is inspired by EpiCypher’s commercial CUTANA® CUT&Tag (Cleavage Under Targets & Tagmentation) assays, and leverages an innovative in vitro transcription-based workflow to mitigate the limitations imposed by FFPE sample processing-induced DNA damage. The goal of this Phase I study is to demonstrate the ability of CUTANA-FFPE assays to reliably map histone PTMs in FFPE tissue samples. In Aim 1, we will develop the CUTANA-FFPE workflow to map histone PTMs in fixed cultured cells. Then, in Aim 2, we will employ CUTANA-FFPE assays in clinical FFPE tissue samples and benchmark our results with genomic maps derived from donor-matched fresh frozen tissue. This study will demonstrate feasibility for CUTANA-FFPE to become a powerful new tool to perform high-value epigenomic research in previously inaccessible banked clinical samples. This technology will be of broad interest to basic researchers and drug developers, unlocking the full potential of epigenomics for clinical applications. In Phase II, we will develop robust CUTANA-FFPE kits and automated assay protocols that are optimized for FFPE tissue using ultra-low sample inputs, which will be key for commercializing CUTANA-FFPE to enable epigenomic studies of FFPE clinical samples.

项目摘要开发用于绘制组蛋白翻译后修饰（PTMS）基因组位置的工具的开发广泛迎来了表观遗传研究的新时代，将组蛋白PTM和相关机制放在聚焦为新颖的生物标志物和治疗靶标。尽管取得了这种进展，但利用表观基因组学进行临床缺乏与之兼容的高性能基因组映射测定法所阻碍了研究由于FFPE过程中引起的DNA损伤，福尔马林固定的石蜡包裹（FFPE）组织。实际上，现有的FFPE样品兼容基因组映射测定要么是低通量和不敏感的（需要大型样品输入），或者不解析特定的染色质特征（例如启动子，增强剂等）。因此，能够使用特定染色质特征的下一代染色质分析测定法存储的FFPE样品是解锁大量融合临床样本的关键，并启用新型生物标志物发现 /与疾病相关的组蛋白PTM靶标的验证。为了满足这种需求，Epicypher 正在开发Cutana-FFPETM，这是一种研究FFPE临床研究的第一类低输入基因组映射解决方案样品。这项技术的灵感来自Epicypher的商业Cutana®剪切和标签（目标下的裂解）＆标记）测定，并利用创新的基于转录的工作流程来减轻 FFPE样品加工引起的DNA损伤施加的局限性。我研究的这一阶段的目标是证明了Cutana-FFPE Assas在FFPE组织样品中可靠地绘制组蛋白PTM的能力。目标 1，我们将开发Cutana-FFPE工作流程以绘制固定培养细胞中的组蛋白PTM。然后，在AIM 2中，我们将在临床FFPE组织样品中采用cutana-ffpe分析，并用基因组基准我们的结果源自供体匹配的新鲜冷冻组织的地图。这项研究将证明Cutana-ffpe的可行性成为一种有力的新工具，可以在以前无法访问的库存中进行高价值表观基因组研究临床样品。这项技术将引起基础研究人员和药物开发人员的广泛关注，解锁表观基因组学在临床应用中的全部潜力。在第二阶段，我们将开发强大的Cutana-FFPE套件以及使用超低样品输入为FFPE组织优化的自动测定方案，这将是将Cutana-FFPE商业化的关键，以实现FFPE临床样品的表观基因组学研究。