# A new epigenetic toolbox for inflammation research and drug discovery

> **NIH NIH R44** · EPICYPHER, INC. · 2022 · $1,012,272

## Abstract

PROJECT SUMMARY
 Gene regulation is controlled in part by histone post-translational modifications (PTMs) on nucleosomes.
EpiCypher® is developing fully defined recombinant designer nucleosomes (dNucs) carrying specific histone
PTMs to enable epigenetics research and drug development. The power of EpiCypher’s dNuc platform comes
from its broad chemical diversity. EpiCypher has commercialized > 100 unique dNucs, covering the most widely
studied PTM classes (e.g. lysine methylation / acylation / ubiquitylation, arginine methylation, serine
phosphorylation, etc.) and is leveraging the emergent property of this diversity for a range of high value
applications: 1) antibody specificity testing (NucleoPlex® antibody validation: e.g. chromatinantibodies.com); 2)
ultra-sensitive genomic mapping (CUTANA® CUT&RUN / CUT&Tag assays); and 3) high-throughput
biochemical approaches for drug discovery and inhibitor screening (dCypher® assays). To date, EpiCypher’s
dNuc technology (and related assay platforms) have been focused on PTMs with known associations with
chromatin states and gene regulation. Relying on the field’s largely descriptive histone PTM studies as a guide
is an inefficient way for us to expand our discovery platforms and maximize the potential of our nucleosome
generating capability to target the most functionally important PTMs. Progress on the discovery side has been
hindered by intractability of the multi-copy histone genes for functional genetics studies in mammals (vs. simpler
model organisms). Here, EpiCypher is partnering with Dr. Steven Josefowicz (Weill Cornell Medical
School) to expand epigenetic tool development for immunology research and biomarker discovery. The
innovation of this project is employment of a first-in-class mammalian histone variant H3.3 genetic replacement
method to identify orphaned / underappreciated residues (and PTMs) with roles in macrophage stimulation. We
will then develop new dNucs containing these PTMs and validate their role in macrophage function. For proof of
concept, we developed the histone replacement assay to characterize the role of some highly studied (e.g.
H3.3K4, H3.3K36) and underappreciated (H3.3S31) residues in the macrophage stimulation response, and
showed the resulting data can immediately be used to guide the delivery of new epigenetic reagents and assays
to support the study of immune system function and disease. In Phase II, we will leverage this development
pipeline to identify novel resides vital for macrophage stimulation (Aim 1). Next, we will develop a collection of
dNucs carrying PTMs on these resides, which will be used in NucleoPlex assays to identify best-in-class
antibodies to each target (Aim 2). Finally, we will validate the function of these novel PTMs in immune cell
stimulation using CUT&Tag assays as well as share our expanded reagents and capabilities with key opinion
leaders for external validation (Aim 3) Together, this work will result in the commercialization of an
exp...

## Key facts

- **NIH application ID:** 10401943
- **Project number:** 5R44AI162386-02
- **Recipient organization:** EPICYPHER, INC.
- **Principal Investigator:** Michael-Christopher Keogh
- **Activity code:** R44 (R01, R21, SBIR, etc.)
- **Funding institute:** NIH
- **Fiscal year:** 2022
- **Award amount:** $1,012,272
- **Award type:** 5
- **Project period:** 2021-05-05 → 2024-04-30

## Primary source

NIH RePORTER: https://reporter.nih.gov/project-details/10401943

## Citation

> US National Institutes of Health, RePORTER application 10401943, A new epigenetic toolbox for inflammation research and drug discovery (5R44AI162386-02). Retrieved via AI Analytics 2026-05-23 from https://api.ai-analytics.org/grant/nih/10401943. Licensed CC0.

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