Integrative Genomic Analyses of Macrophages in Crohns Disease

炎症性肠病（IBD）是遗传、免疫和微生物相互作用的结果， 克罗恩病和溃疡性结肠炎的亚型。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。宏程序用作 免疫系统的关键哨兵嵌入在每个组织中，提供了一个关键的开关， 和激活。浸润克罗恩病肠道组织的免疫细胞严重受 细胞因子和关键转录因子之间的相互作用;然而， 表型和调节状态目前是有限的。在目标1中，我们提出定义基因型无关 调节肠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 来自非炎症和炎症肠的人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。我们已经发表了组织特异性增强子 并提出在人类肠道中进行类似的研究。我们假设克罗恩病 关联将在肠巨噬细胞特异性增强子内特别丰富， 这些与改变的基因表达的精确关联将提供对疾病机制的重要见解， 发病机制在目标2中，我们将开发预测网络模型，充分利用自然发生的 遗传多态性（SNP作为pertubagens），以阐明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/或被鉴定为 在目标1和2的研究中进行调节。我们设计了针对34个DNA中每一个的CRISPR载体， 在肠巨噬细胞中表达的调节IBD位点基因，以确定它们对巨噬细胞的作用 等级和炎症反应。最后，我们提出了研究，以确定IBD风险变异的作用， 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/TNFSF 15和IL 1/IL 18细胞因子途径。我们的多学科小组与临床， 人类遗传学、表观遗传学、计算学、免疫学和技术开发专门知识将得到发展 了解巨噬细胞在克罗恩病中的作用，这是任何单一的 组单独。

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.