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.
Public Health Relevance Statement: NARRATIVE Gene expression studies indicate a crucial role for epigenetic mechanisms in Crohn's disease (CD). However, current tools used to map distinct chromatin features, such as chromatin immunoprecipitation (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. Here, EpiCypher will develop a high-throughput, quantitative chromatin mapping technology (HT-CUTANA), specifically optimized for human tissue samples, and apply this breakthrough approach for next-generation CD clinical research.
Project Terms: Automation; Automobile Driving; driving; Biological Assay; Assay; Bioassay; Biologic Assays; Biology; Biomedical Research; Biopsy; Cells; Cell Body; Chromatin; Clinical Research; Clinical Study; Ulcerative Colitis; Ulcerated Colitis; Colon; Crohn's disease; Crohn disease; Crohn's; Crohn's disorder; Granulomatous Enteritis; eleocolitis; regional enteritis; Data Analyses; Data Analysis; data interpretation; Disease; Disorder; Gastrointestinal tract structure; Alimentary Canal; Digestive Tract; GI Tract; Gastrointestinal Tract; alimentary tract; digestive canal; Gene Expression; Goals; Heterogeneity; Histones; Human; Modern Man; ileum; Industry; Inflammatory Bowel Diseases; Inflammatory Bowel Disorder; Libraries; Manuals; Maps; Methods; Noise; Patients; Phenotype; Physicians; Post-Translational Protein Processing; Post-Translational Modification Protein/Amino Acid Biochemistry; Post-Translational Modifications; Post-Translational Protein Modification; Posttranslational Modifications; Posttranslational Protein Processing; Protein Modification; Proteins; Research; Research Personnel; Investigators; Researchers; RNA; Non-Polyadenylated RNA; RNA Gene Products; Ribonucleic Acid; Role; social role; Savings; Signal Transduction; Cell Communication and Signaling; Cell Signaling; Intracellular Communication and Signaling; Signal Transduction Systems; Signaling; biological signal transduction; Standardization; Technology; Tissue Banks; Tissue Collection; Tissue repository; Tissues; Body Tissues; Genetic Transcription; Gene Transcription; RNA Expression; Transcription; Work; Price; pricing; Cost Savings; Chronic; Clinical; Phase; Letters; Companions; tool; Complex; human tissue; Reaction; System; gastrointestinal; interest; Services; nuclease; novel; research study; Pathogenesis; Cell Fraction; Sampling; disease subgroups; disease subtype; disorder subtype; Genomics; disease control; disorder control; Bio-Informatics; Bioinformatics; Tissue Sample; ChIP assay; chromatin immunoprecipitation; tissue processing; Data; International; Molecular Marker of Prognosis; Prognosis Marker; prognostic biomarker; prognostic indicator; Prognostic Marker; Reproducibility; Resolution; Clinical Data; Epigenetic Process; Epigenetic; Epigenetic Change; Epigenetic Mechanism; Process; Development; developmental; epigenomics; cost; next generation; Outcome; innovation; innovate; innovative; user-friendly; therapeutic target; treatment response; response to treatment; therapeutic response; molecular phenotype; ChIP-seq; ChIP Sequencing; chromatin immunoprecipitation-sequencing; predictive marker; predictive biomarkers; predictive molecular biomarker; ATAC-seq; ATACseq; experimental study; experiment; experimental research; Genetic Diseases; genetic condition; genetic disorder; bioinformatics tool; bio-informatics tool
