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: 10384457
• 负责人: Andrea Lynn Johnstone
• 金额: $ 30.19万
• 依托单位: EPICYPHER, INC.
• 依托单位国家: 美国
• 财政年份: 2021
• 资助国家: 美国
• 起止时间: 2021-09-15 至 2022-07-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/10384457
• 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 control; disorder subtype; epigenomics; experimental study; gastrointestinal; human tissue; ileum; innovation; interest; molecular phenotype; next generation; novel; nuclease; predictive marker; 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 炎症性肠病（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。 CD可以沿着胃肠道发生，并且具有高度 异质临床表现/结果，挑战治疗。此外，预测CD的可靠标记 课程和/或治疗反应不存在。我们（和其他）表明CD子类型显示独特 与结果相关的基因表达谱；然而，潜在的监管机制仍然难以捉摸。 转录受组蛋白翻译后修饰（PTM）和 染色质蛋白（CHAP），调节染色质访问性和基因表达。我们 提议高分辨率测定对机械不同的染色质特征的注释可能会揭示 CD（和其他复杂疾病）内的异质性，揭示了新的预后生物标志物/治疗靶标。 但是，现有的染色质图测定（例如CHIP-SEQ）由于其临床研究不适合 有限的吞吐量，禁止的成本和差的可重复性以及缺乏定义的定量控制。 对于这个快速提议，Epicypher与Shehzad Sheikh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 用于下一代临床研究的映射解决方案。该项目的创新是开发96- 专门针对银行的人体组织优化的板块切割和运行平台（HT-Cutana），提供大量 使用Chip-seq不可能节省成本和敏感性和吞吐量。这些测定将是 配备了Epicypher的专有尖峰技术，用于定量跨样本比较，并且 用户友好的生物信息学工具用于流线型数据分析。 Epicypher已经生成了密钥初步 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合作伙伴。最终的端到端HT-Cutana系统将能够完全处理 在<5天内的192个样品，同时还节省了10倍的成本与芯片隔离。通过我们与Dr. 谢赫，我们将向独家策划的CD和控制患者样品进行HT-Cutana， 证明了HT-Cutana在研究CD发病机理的新型调节机制方面的实用性。在 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，目的是将单个储存样本的六个目标映射，并使用此测定 区分CD与控件。在第二阶段（AIM 2）中，我们将建立强大的自动化HT-Cutana分析和 生物信息学工具，通过提高规模和效率来降低评估成本。在AIM 3中，我们将发展HT- Cutana套件和服务，并与Sheikh博士合作，将这些工具应用于缩放，定量的临床研究 在CD患者样品中。这些实验将建立HT-Cutana作为生物医学研究的强大工具 和矛头的主要创新，以揭示新的CD机制和预后指标。