A new epigenetic toolbox for inflammation research and drug discovery

用于炎症研究和药物发现的新表观遗传学工具箱

• 批准号: 10257054
• 负责人: Michael-Christopher Keogh
• 金额: $ 101.23万
• 依托单位: EPICYPHER, INC.
• 依托单位国家: 美国
• 财政年份: 2021
• 资助国家: 美国
• 起止时间: 2021-05-05 至 2024-04-30
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/10257054
• 关键词: Acetylation; Acylation; Adoption; Animal Model; Antibodies; Antibody Specificity; Area; Arginine; Binding; Biochemical; Biological Assay; Biology; Bone Marrow; Cells; ChIP-seq; Chemicals; Chromatin; Collection; Data; Dendritic Cells; Development; Disease; Employment; Engineering; Enzymes; Epigenetic Process; Feedback; Gene Expression Regulation; Genes; Genetic; Genetic Transcription; Genetic study; Genomics; Goals; High Pressure Liquid Chromatography; Histone H3; Histones; Human; Immune; Immunologics; Immunology; Inflammation; Inflammatory; Inflammatory Response; Link; Lipopolysaccharides; Lysine; Mammals; Mass Spectrum Analysis; Methods; Methylation; Mus; Natural Killer Cells; Nucleosomes; Orphan; Pharmaceutical Preparations; Phase; Phosphorylation; Post-Translational Protein Processing; Property; Reagent; Recombinants; Research; Research Personnel; Rest; Role; Running; Serine; Side; Site-Directed Mutagenesis; Technology; Testing; Validation; Variant; Work; biomarker discovery; commercialization; cross reactivity; dalton; drug development; drug discovery; epigenomics; human disease; immune system function; inhibitor/antagonist; innovation; macrophage; medical schools; novel; research and development; response; screening; therapeutic development; tool; tool development

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 expanded epigenetics toolbox that will open new avenues of immunological research and drug development.

项目概要 基因调控部分由核小体上的组蛋白翻译后修饰 (PTM) 控制。 EpiCypher® 正在开发携带特定组蛋白的明确完全重组设计核小体 (dNucs) EpiCypher 的 dNuc 平台的强大功能使 PTM 能够实现表观遗传学研究和药物开发。 由于其广泛的化学多样性，EpiCypher 已将超过 100 种独特的 dNuc 商业化，涵盖最广泛的领域。 研究 PTM 类别（例如赖氨酸甲基化/酰化/泛素化、精氨酸甲基化、丝氨酸 磷酸化等），并利用这种多样性的新兴特性来实现一系列高价值 应用：1) 抗体特异性测试（NucleoPlex® 抗体验证：例如 chromatinantibodies.com）；2) 超灵敏基因组作图（CUTANA® CUT&RUN / CUT&Tag 检测）；以及 3) 高通量 用于药物发现和抑制剂筛选的生化方法 (dCypher®s) 迄今为止，EpiC Assayypher 的。 dNuc 技术（和相关检测平台）一直专注于与已知相关的 PTM。 依靠该领域的大量描述性组蛋白 PTM 研究作为指导。 对于我们来说，这是一种低效的方式来扩展我们的发现平台并最大限度地发挥核小体的潜力 生成针对功能最重要的 PTM 的能力在发现方面取得了进展。 哺乳动物功能遗传学研究中的多拷贝组蛋白基因的难处理性阻碍了这一点（与更简单的研究相比） EpiCypher 与 Steven Josefowicz 博士（威尔康奈尔医学中心）合作。 School）扩大用于免疫学研究和生物标志物发现的表观遗传学工具开发。 该项目的创新之处在于采用了一流的哺乳动物组蛋白变体 H3.3 基因替代 识别在巨噬细胞刺激中起作用的孤儿/未被充分重视的残基（和 PTM）的方法。 然后将开发包含这些 PTM 的新 dNuc，并验证它们在巨噬细胞功能中的作用。 概念，我们开发了组蛋白替代测定来表征一些经过深入研究的组蛋白的作用（例如 H3.3K4、H3.3K36）和巨噬细胞刺激反应中未被充分重视的（H3.3S31）残基，以及 显示所得数据可立即用于指导新的表观遗传试剂和测定的交付 在第二阶段，我们将利用这一进展来支持免疫系统功能和疾病的研究。 确定对巨噬细胞刺激至关重要的新残基的管道（目标 1）。 dNucs 在这些残基上携带 PTM，将用于 NucleoPlex 检测以确定同类最佳 最后，我们将验证这些新型 PTM 在免疫细胞中的功能。 使用 CUT&Tag 检测进行刺激，并与关键意见分享我们扩展的试剂和功能 外部验证的领导者（目标 3） 总之，这项工作将导致 扩展的表观遗传学工具箱将为免疫学研究和药物开辟新途径 发展。