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

基本信息

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
项目类别：
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&apos 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

项目摘要

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) 是慢性疾病胃肠道 (GI) 疾病可发生在胃肠道的任何部位，并且发病率很高。异质的临床表现/结果，具有挑战性的治疗以及预测 CD 的可靠标志物。我们（和其他人）已经证明 CD 亚型表现出独特的病程和/或治疗反应。与结果相关的基因表达谱；然而，潜在的调控机制仍然难以捉摸。转录受组蛋白翻译后修饰 (PTM) 和染色质相关蛋白 (ChAP)，调节染色质可及性和基因表达。提出注释机械上不同的染色质特征的高分辨率测定可能会揭示 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/治疗靶点。然而，现有的染色质作图分析（例如 ChIP-seq）由于其不适合临床研究。有限的通量、高昂的成本、较差的再现性以及缺乏明确的定量控制。对于这项快速通道提案，EpiCypher 正在与 Shehzad Sheikh 博士和北卡罗来纳大学研究中心合作胃肠生物学和疾病 (CGIBD) 开发 HT-CUTANA™，一种高通量、低成本基因组该项目的创新之处在于开发了 96- 下一代临床研究的绘图解决方案。孔板 CUT&RUN 平台 (HT-CUTANA) 专门针对储存的人体组织进行了优化，提供大量使用 ChIP-seq 无法实现的成本节省以及灵敏度和通量的提高。配备 EpiCypher 专有的掺入技术，用于定量跨样本比较，以及用于简化数据分析的用户友好的生物信息学工具已经生成了关键的初步结果。 CUT&RUN 检测自动化的数据，支持该提案的可行性并引起了人们的早期兴趣最终的端到端 HT-CUTANA 系统将能够完全处理。通过我们与 ChIP-seq 的合作，在不到 5 天内即可获得 192 个样本，同时还可以节省 10 倍以上的成本。 Sheikh，我们将把 HT-CUTANA 应用于由医生精心策划的 CD 库和对照患者样本，展示 HT-CUTANA 在研究 CD 发病机制的新调控机制方面的实用性。第一阶段（目标 1），我们将开发标准化 96 孔板 HT-CUTANA 方法，用于分析库存人类结肠组织，目的是从单个存储样本中绘制六个目标，并使用此测定法区分 CD 与对照。在第二阶段（目标 2），我们将建立强大的自动化 HT-CUTANA 检测和生物信息学工具，通过提高规模和效率来降低检测成本在目标 3 中，我们将开发 HT-。 CUTANA 套件和服务，并与 Sheikh 博士合作，将这些工具应用于规模化、定量的临床研究这些实验将使 HT-CUTANA 成为生物医学研究的强大工具。并带头进行重大创新，揭示新的 CD 机制和预后指标。