Development of a high-throughput epigenomic mapping platform to molecularly phenotype Crohn's disease

开发克罗恩病分子表型的高通量表观基因组作图平台

• 批准号: 10683287
• 负责人: Andrea Lynn Johnstone
• 金额: $ 100.21万
• 依托单位: EPICYPHER, INC.
• 依托单位国家: 美国
• 财政年份: 2022
• 资助国家: 美国
• 起止时间: 2022-09-01 至 2024-08-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/10683287
• 关键词: ATAC-seq; Automation; Automobile Driving; Bioinformatics; Biological Assay; Biology; Biomedical Research; Biopsy; Cell Fraction; Cells; ChIP-seq; Chromatin; Chronic; Clinical; Clinical Data; Clinical Research; Colon; Companions; Complex; Cost Savings; Crohn' s disease; Data; Data Analyses; Development; Disease; Epigenetic Process; Gastrointestinal tract structure; Gene Expression; Genetic Diseases; Genetic Transcription; Genomics; Goals; Heterogeneity; Histones; Human; Industry; Inflammatory Bowel Diseases; International; Letters; Libraries; Manuals; Maps; Methods; Noise; Outcome; Pathogenesis; Patients; Phase; Phenotype; Physicians; Post-Translational Protein Processing; Price; Process; Prognostic Marker; Proteins; RNA; Reaction; Reproducibility; Research; Research Personnel; Resolution; Role; Sampling; Savings; Services; Signal Transduction; Standardization; System; Technology; Tissue Banks; Tissue Sample; Tissues; Ulcerative Colitis; Work; bioinformatics tool; chromatin immunoprecipitation; cost; disorder subtype; epigenomics; experimental study; gastrointestinal; human tissue; ileum; innovation; interest; molecular phenotype; next generation; novel; nuclease; predictive marker; prognostic indicator; research study; therapeutic target; tissue processing; tool; treatment response; user-friendly

SUMMARY The inflammatory bowel diseases (IBDs), Crohn’s disease (CD) and ulcerative colitis (UC), are chronic conditions of the gastrointestinal (GI) tract. CD can occur anywhere along the GI tract and has highly heterogeneous clinical presentation/outcomes, challenging treatment. Further, reliable markers that predict CD course and/or treatment response do not exist. We (and others) have shown that CD subtypes display unique gene expression profiles associated with outcomes; yet, underlying regulatory mechanisms remain elusive. Transcription is controlled by the combined effects of histone post-translational modifications (PTMs) and chromatin associated proteins (ChAPs), which modulate chromatin accessibility and gene expression. We propose that high-resolution assays annotating mechanistically distinct chromatin features may unravel the heterogeneity within CD (and other complex diseases), revealing new prognostic biomarkers/therapeutic targets. However, existing chromatin mapping assays (e.g. ChIP-seq) are unsuitable for clinical studies due to their limited throughput, prohibitive costs, and poor reproducibility, as well as a lack of defined quantitative controls. For this Fast-Track proposal, EpiCypher is partnering with Dr. Shehzad Sheikh and the UNC’s Center for Gastrointestinal Biology and Disease (CGIBD) to develop HT-CUTANA™, a high-throughput, low-cost genomic mapping solution for next-generation clinical research. The innovation of this project is the development of a 96- well plate CUT&RUN platform (HT-CUTANA) specifically optimized for banked human tissues, providing massive cost savings and gains in sensitivity and throughput that are impossible using ChIP-seq. These assays will be equipped with EpiCypher’s proprietary spike-in technologies for quantitative cross-sample comparisons, and user-friendly bioinformatic tools for streamlined data analysis. EpiCypher has already generated key preliminary data for CUT&RUN assay automation, supporting feasibility of this proposal and drawing significant early interest from our partners in industry and pharma. The final end-to-end HT-CUTANA system will be able to fully process 192 samples in <5 days while also delivering >10-fold cost savings vs. ChIP-seq. Via our partnership with Dr. Sheikh, we will apply HT-CUTANA to an exquisite physician-curated bank of CD and control patient samples, demonstrating the utility of HT-CUTANA to study novel regulatory mechanisms underlying CD pathogenesis. In Phase I (Aim 1), we will develop standardized 96-well plate HT-CUTANA methods for analysis of banked human colon tissue, with the goal of mapping six targets from a single banked sample and using this assay to discriminate CD vs. controls. In Phase II (Aim 2), we will establish robust automated HT-CUTANA assays and bioinformatics tools, driving down assay costs by increasing scale and efficiency. In Aim 3, we will develop HT- CUTANA kits and services, and work with Dr. Sheikh to apply these tools for scaled, quantitative clinical research in CD patient samples. These experiments will establish HT-CUTANA as a powerful tool for biomedical research and spearhead major innovations to reveal novel CD mechanisms and prognostic indicators.

概括 炎性肠道疾病（IBD），克罗恩病（CD）和溃疡性结肠炎（UC）是慢性的 胃肠道（GI）的条件可以沿着该区域的任何地方发生，并且具有高度 异质临床表现/结果，更具挑战性的可靠标记。 课程和/或治疗反应不存在。 与结果相关的基因表达谱；基本的调节机制仍然难以捉摸。 转录受组蛋白翻译后修饰（PTM）和 染色质蛋白（CHAPS），这些蛋白质可及性和基因表达 提出高分辨率测定的注释机械上明显的特征可能会揭示 CD（和其他复杂疾病）内的异质性，陶醉于新的程序生物标志物/治疗靶标。 但是，现有的染色质映射测定（例如CHIP-SEQ）不适合临床研究 有限的吞吐量，不良成本和便便繁殖以及缺乏定义的定量控制。 对于这个快速提议，Epicypher与博士博士和UNC的中心合作 胃肠道生物学和疾病（CGIBD）开发HT-Cutana™，一种高通量，低成本的基因组 下一代临床研究的映射解决方案。 专门针对野马组织优化的井盘切割和运行平台（HT-Cutana），提供大量 使用CHIP-seq不可能的敏感性和提升的成本节省。 配备了Epicypher的专有尖峰技术，用于定量跨样本比较， 用户友好的生物信息学工具用于流线型数据分析。 剪切和运行测定自动化的数据，支持该提案的可行性并引起重大的早期兴趣 来自我们的工业和制药的合作伙伴。 192个样本在<5天内也通过与Dr. Dr. 谢赫，我们将向精美的医师策划的CD和控制患者样本应用HT-Cutana， 证明了HT-Cutana的实用性，研究了CD发病机理的新型调节机制 第一阶段（AIM 1），我们将开发标准化的96孔板HT-Cutana方法用于分析人类 结肠组织，目的是使用Asay绘制单个银行样本的六个目标 INEVIPE CD与II阶段的控制（AIM 2），我们将建立强大的自动化HT-Cutana分析 生物信息学工具，通过提高AIM 3的规模和功效来降低测定成本。 Cutana套件和服务，并与Sheikh博士合作，以应用定量临床研究的工具 在CD患者样品中。 和矛头的主要创新，以启用新颖的新颖CD机制和预后指标。