Integrative Genomic Analyses of Macrophages in Crohns Disease

克罗恩病巨噬细胞的综合基因组分析

• 批准号: 9767134
• 负责人: JUDY H. CHO
• 金额: $ 75.94万
• 依托单位: ICAHN SCHOOL OF MEDICINE AT MOUNT SINAI
• 依托单位国家: 美国
• 财政年份: 2016
• 资助国家: 美国
• 起止时间: 2016-09-01 至 2021-07-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/9767134
• 关键词: Adult; Affect; Biological; Cells; Chromatin; Chronic; Clinical; Clustered Regularly Interspaced Short Palindromic Repeats; Complex; Crohn' s disease; Cytometry; DNA; Data; Data Set; Data Sources; Disease; Dissection; Distal part of ileum; Enhancers; Environment; Epigenetic Process; Event; Excision; Flow Cytometry; Gene Expression; Genes; Genetic; Genetic Polymorphism; Genetic Transcription; Genomics; Genotype; Granulocyte-Macrophage Colony-Stimulating Factor; Hematopoietic stem cells; Human; Human Genetics; IL18 gene; Immune; Immune system; Immunologics; Inflammatory; Inflammatory Bowel Diseases; Inflammatory Response; Inflammatory disease of the intestine; Interleukin-1; Intestines; Macrophage Colony-Stimulating Factor; Mediating; Mus; Natural Immunity; Nucleic Acid Regulatory Sequences; Operative Surgical Procedures; Pathogenesis; Pathway Analysis; Pathway interactions; Phenotype; Publishing; Regulation; Regulator Genes; Regulatory Element; Role; Sampling; Sentinel; Signal Pathway; Signal Transduction; Stimulus; System; TNF gene; TNFSF15 gene; Techniques; Tissues; Ulcerative Colitis; Variant; autocrine; base; comparative; cytokine; design; genome wide association study; high dimensionality; human tissue; insight; mRNA Expression; macrophage; microbial; monocyte; multidisciplinary; network models; paracrine; response; risk variant; technology development; transcription factor; vector

Inflammatory bowel disease (IBD) results from a complex interplay of genetic, immunologic and microbial factors and is comprised of Crohn's disease and ulcerative colitis subtypes. The over 140 loci associated to Crohn's disease implicate key roles for innate immunity and macrophage regulation. Macrophages serve as critical sentinels of the immune system embedded in each tissue, providing a key switch between tolerance and activation. The immune cells that infiltrate Crohn's disease gut tissue are heavily influenced by the interplay between cytokines and key transcription factors; however, understanding of macrophage gut-based phenotype and regulatory state is presently limited. In Aim 1, we propose defining genotype-independent mechanisms modulating intestinal macrophage phenotypes. We will expand understanding of intestinal macrophage function in Crohn's disease through high dimensional mass cytometry (CyTOF) and through epigenetic analyses of human macrophages from non-inflamed and inflamed intestine. CyTOF profiling of tissue macrophages will elucidate macrophage subtypes. We have published the tissue-specific enhancer landscape in mice and propose similar studies in human intestine. We hypothesize that Crohn's disease associations will be particularly enriched within intestinal macrophage-specific enhancers and that mapping these precise correlations with altered gene expression will provide critical insights into mechanisms of disease pathogenesis. In Aim 2, we will develop of predictive network models that fully leverage naturally-occurring genetic polymorphisms (SNPs as pertubagens) to elucidate the key drivers and biological mechanisms of disease. In Aim 3, we propose defining mechanisms of macrophage phenotype and function by exploring transcription factor and autocrine cytokine pathways associated to Crohn's disease and/or identified to be regulated in studies from Aims 1 and 2. We have designed CRISPR vectors targeted to each of the 34 DNA regulatory IBD loci genes expressed in intestinal macrophages to determine their effects on macrophage hierarchies and inflammatory responses. Finally, we propose studies to define the role of IBD risk variants in macrophage responses to microbial stimuli with a particular focus on rapid post-translational proteolytic events affecting the autocrine TNF/TNFSF15 and IL1/IL18 cytokine pathways. Our multidisciplinary group with clinical, human genetic, epigenetic, computational, immunological and technology development expertise will advance understanding of the role of macrophages in Crohn's disease in a way that would not be possible by any single group alone.

炎症性肠病（IBD）是遗传、免疫和微生物复杂相互作用的结果 因素，包括克罗恩病和溃疡性结肠炎亚型。超过 140 个位点与 克罗恩病涉及先天免疫和巨噬细胞调节的关键作用。巨噬细胞充当 嵌入每个组织中的免疫系统的关键哨兵，提供耐受性之间的关键转换 和激活。浸润克罗恩病肠道组织的免疫细胞受到以下因素的严重影响： 细胞因子和关键转录因子之间的相互作用；然而，对巨噬细胞的了解基于肠道 表型和监管状态目前有限。在目标 1 中，我们建议定义基因型无关的 调节肠道巨噬细胞表型的机制。我们将扩大对肠道的了解 通过高维质谱细胞术 (CyTOF) 和通过 来自非炎症和炎症肠道的人类巨噬细胞的表观遗传学分析。 CyTOF 分析 组织巨噬细胞将阐明巨噬细胞亚型。我们已经发布了组织特异性增强剂 在小鼠中观察并提出在人类肠道中进行类似的研究。我们推测克罗恩病 肠道巨噬细胞特异性增强剂中的关联将特别丰富，并且映射 这些与基因表达改变的精确相关性将为疾病机制提供重要的见解 发病。在目标 2 中，我们将开发充分利用自然发生的预测网络模型 遗传多态性（SNP 作为 pertubagens）来阐明关键驱动因素和生物机制 疾病。在目标 3 中，我们通过探索巨噬细胞表型和功能的定义机制 与克罗恩病相关和/或被鉴定为的转录因子和自分泌细胞因子途径 在目标 1 和 2 的研究中受到监管。我们设计了针对 34 个 DNA 中每一个的 CRISPR 载体 在肠道巨噬细胞中表达的调节性 IBD 位点基因以确定其对巨噬细胞的影响 层次结构和炎症反应。最后，我们提出研究来定义 IBD 风险变异在 巨噬细胞对微生物刺激的反应，特别关注快速翻译后蛋白水解事件 影响自分泌 TNF/TNFSF15 和 IL1/IL18 细胞因子途径。我们的多学科团队拥有临床、 人类遗传、表观遗传、计算、免疫学和技术开发专业知识将取得进步 以任何单一方法都无法实现的方式了解巨噬细胞在克罗恩病中的作用 单独组。