Integrative Genomic Analyses of Macrophages in Crohns Disease

炎症性肠病(IBD)是遗传、免疫和微生物的复杂相互作用的结果 由克罗恩病和溃疡性结肠炎亚型组成。有140多个基因座与 克罗恩病牵涉到先天性免疫和巨噬细胞调节的关键作用。巨噬细胞作为 嵌入在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切换 和激活。渗入克罗恩病肠道组织的免疫细胞受 细胞因子和关键转录因子之间的相互作用；然而，对巨噬细胞基于肠道的理解 表型和调控状态目前是有限的。在目标1中，我们建议定义与基因无关 调节肠道巨噬细胞表型的机制。我们将扩大对肠道的了解 应用高维质谱(CyTOF)检测克罗恩病患者的巨噬细胞功能 非炎症性和炎症性肠巨噬细胞的表观遗传学分析。细胞飞行时间曲线分析 组织巨噬细胞将阐明巨噬细胞亚型。我们已经发表了组织特异性增强剂 并建议在人类肠道中进行类似的研究。我们假设克隆氏病 相关性将在肠道巨噬细胞特异性增强剂和映射中特别丰富 这些与基因表达变化的精确关联将为疾病机制提供关键的见解 发病机制。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(以SNPs为诱因)阐明致病的关键驱动因素和生物学机制 疾病。在目标3中，我们提出通过探索来定义巨噬细胞表型和功能的机制 转录因子和自分泌细胞因子途径与克罗恩病相关和/或被确认为 在AIMS 1和AIMS 2的研究中进行调节。我们设计了针对34个DNA的CRISPR载体 肠道巨噬细胞IBD基因表达调控基因对巨噬细胞的影响 等级和炎症反应。最后，我们建议进行研究，以确定IBD风险变量在 巨噬细胞对微生物刺激的反应，特别关注翻译后快速蛋白降解事件 影响自分泌肿瘤坏死因子/肿瘤坏死因子15和白介素1/白介素18的细胞因子途径。我们的多学科小组，临床， 人类遗传、表观遗传学、计算、免疫学和技术开发方面的专业知识将取得进展 对巨噬细胞在克罗恩病中的作用的理解是任何单一因素都不可能的 单独一组。

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.