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