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: 10401943
• 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/10401943
• 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; 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.

项目摘要 基因调节部分由组蛋白在核小体上翻译后修饰（PTM）控制。 Epicypher®正在开发携带特定组蛋白的完全定义的重组设计师核小体（DNUC） PTMS可以使表观遗传学研究和药物开发。 Epicypher DNUC平台的力量出现 来自其广泛的化学多样性。 Epicypher已商业化> 100个独特的DNUC，覆盖最广泛的DNUC 研究菌的PTM类（例如赖氨酸甲基化 /酰化 /泛素化，精氨酸甲基化，串行 磷酸化等），并利用这种多样性的新兴特性用于一系列高价值 应用：1）抗体特异性测试（nucleoplex®抗体验证：例如染色剂抗体）; 2） 超敏感的基因组映射（Cutana®剪切 / cun / cut＆TAG分析）; 3）高通量 药物发现和抑制剂筛查的生化方法（DCYPHER®分析）。迄今为止，Epicypher's DNUC技术（及相关测定平台）一直集中在PTM上，与已知的关联 染色质状态和基因调节。依靠该领域的描述性组蛋白PTM研究作为指导 对于我们扩展我们的发现平台并最大程度地发挥了我们的核能的潜力，这是一种效率低下的方式 生成目标最重要的PTM的能力。在发现方面的进步已经 受到多拷贝组蛋白基因在哺乳动物中功能遗传学研究的顽固性的阻碍（与更简单 模型生物）。在这里，Epicypher与Steven Josefowicz博士（Weill Cornell Medical）合作 学校）以扩大用于免疫学研究和生物标志物发现的表观遗传工具开发。这 该项目的创新是使用一流的哺乳动物组蛋白变体H3.3遗传替代品 识别具有巨噬细胞刺激中作用的孤儿 /不足的残留物（和PTM）的方法。我们 然后，将开发包含这些PTM的新DNUC，并验证其在巨噬细胞功能中的作用。以证明 概念，我们开发了组蛋白替换测定法，以表征某些高度研究的作用（例如 H3.3K4，H3.3K36）和不被调查（H3.3S31）导致巨噬细胞刺激反应，并且 显示所得数据可以立即用于指导新的表观遗传试剂和测定 支持免疫系统功能和疾病的研究。在第二阶段，我们将利用这一发展 识别新颖的管道对巨噬细胞刺激至关重要（AIM 1）。接下来，我们将开发一个集合 在这些住宅上携带PTM的DNUCS，该住所将用于Nucleoplex测定法以识别一流 每个目标的抗体（AIM 2）。最后，我们将验证这些新型PTM在免疫细胞中的功能 使用剪切和标签的刺激以及分享我们扩展的试剂和功能的关键意见 外部验证的领导者（目标3）一起，这项工作将导致商业化 扩展的表观遗传学工具箱将开放免疫研究和药物的新途径 发展。