Phase I Amount
$1,012,272
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 expanded epigenetics toolbox that will open new avenues of immunological research and drug development.
Public Health Relevance Statement: PROJECT NARRATIVE Gene regulation is controlled in part by histone post-translational modifications (PTMs) on nucleosomes. EpiCypher® is developing fully defined semi-synthetic designer nucleosomes (dNucs) carrying specific histone PTMs for a range of high value applications from biochemical assays to epigenomic mapping. Despite our progress, dNuc technology (and related assay platforms) largely has been restricted to PTMs with previously characterized roles in gene regulation / disease. The goal of this study is to identify new or orphaned (i.e. understudied) histone PTMs with major roles in macrophage biology. This will expand EpiCypher's cutting-edge epigenetics toolbox, which will be marketed to immunology researchers and drug developers to accelerate their studies. These objectives are made possible by our team's recent advances, overcoming barriers to the unbiased functional study of histone PTMs in human cells.
Project Terms: Acetylation; Acylation; Adoption; inhibitor/antagonist; inhibitor; Antibodies; Antibody Specificity; Arginine; L-Arginine; Biological Assay; Assay; Bioassay; Biologic Assays; Biology; Bone Marrow; Bone Marrow Reticuloendothelial System; Cells; Cell Body; Chromatin; High Pressure Liquid Chromatography; HPLC; High Performance Liquid Chromatography; High Speed Liquid Chromatography; Dendritic Cells; Veiled Cells; Disease; Disorder; Pharmaceutical Preparations; Drugs; Medication; Pharmaceutic Preparations; drug/agent; Employment; Engineering; Enzymes; Enzyme Gene; Feedback; Gene Expression Regulation; Gene Action Regulation; Gene Regulation; Gene Regulation Process; Genes; Goals; Histone H3; Histones; Human; Modern Man; Inflammation; Natural Killer Cells; Cytotoxic cell; K lymphocyte; NK Cells; Lipopolysaccharides; Lysine; L-Lysine; macrophage; MÏ; Mammals; Mammalia; Methods; Methylation; Mus; Mice; Mice Mammals; Murine; Nucleosomes; Phosphorylation; Protein Phosphorylation; 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; Reagent; Research; research and development; Development and Research; R & D; R&D; Research Personnel; Investigators; Researchers; Rest; Role; social role; Running; medical schools; medical college; school of medicine; Serine; L-Serine; Mass Spectrum Analysis; Mass Photometry/Spectrum Analysis; Mass Spectrometry; Mass Spectroscopy; Mass Spectrum; Mass Spectrum Analyses; Technology; Testing; Genetic Transcription; Gene Transcription; RNA Expression; Transcription; Work; Site-Directed Mutagenesis; Site-Specific Mutagenesis; Targeted DNA Modification; Targeted Modification; Immunology; Area; Phase; Variant; Variation; Biochemical; Link; Chemicals; Orphan; Genetic; Inflammatory; tool; Immunes; Immune; Side; Animal Models and Related Studies; model of animal; model organism; Animal Model; dalton; novel; Property; response; cross reactivity; drug development; Genomics; drug discovery; Inflammatory Response; Molecular Interaction; Binding; Data; Recombinants; Collection; Epigenetic Process; Epigenetic; Epigenetic Change; Epigenetic Mechanism; Validation; Immunologics; Immunochemical Immunologic; Immunologic; Immunological; Immunologically; Development; developmental; epigenomics; innovation; innovate; innovative; human disease; tool development; commercialization; therapeutic development; therapeutic agent development; ChIP-seq; ChIP Sequencing; chromatin immunoprecipitation-sequencing; screening; Genetic study; biomarker discovery; immune system function
