Analysis of the human monocyte-derived macrophage transcriptome and response to lipopolysaccharide provides new insights into genetic aetiology of inflammatory bowel disease.
Analysis of the human monocyte-derived macrophage transcriptome and response to lipopolysaccharide provides new insights into genetic aetiology of inflammatory bowel disease.
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DOI：
10.1371/journal.pgen.1006641
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发表时间：
2017-03
期刊：
影响因子：
4.5
通讯作者：
Hume DA
中科院分区：
文献类型：
--
作者：
Baillie JK;Arner E;Daub C;De Hoon M;Itoh M;Kawaji H;Lassmann T;Carninci P;Forrest AR;Hayashizaki Y;FANTOM Consortium;Faulkner GJ;Wells CA;Rehli M;Pavli P;Summers KM;Hume DA
FANTOM 5联盟利用基因表达帽分析（CAGE）对人类细胞和组织中的转录调控提供了前所未有的见解。在目前的研究中，我们已经使用了基于CAGE的转录谱的人单核细胞衍生的巨噬细胞生长在巨噬细胞集落刺激因子（CSF 1）的细菌脂多糖（LPS）的反应的一个延长的密集的时间过程。我们建议，该系统提供了一个模型的分化和适应单核细胞进入肠固有层。对LPS的反应显示为持续至少48小时的瞬时基因表达的连续波的级联，具有数百个正和负调节环。启动子分析使用基序活性反应分析（MARA）确定了一些转录因子可能是负责转录激活的时间分布。每个LPS诱导位点与多个诱导增强子相关，并且在每种情况下，通过CAGE检测到的多个位点的瞬时eRNA转录先于启动子相关转录物的出现。LPS诱导型长非编码RNA通常与诱导型增强子簇相关。我们使用这些数据重新检查了全基因组关联研究中与炎症性肠病（IBD）易感性相关的数百个位点。与IBD相关的基因座强烈且特异性地（相对于类风湿性关节炎和无关性状）富集了在单核细胞分化或活化中受调控的启动子。在先前鉴定的IBD易感性位点中，绝大多数包含至少一个在CSF 1依赖性单核细胞-巨噬细胞转换和/或响应于LPS中调节的启动子。在此基础上，我们得出结论，IBD基因座高度富集单核细胞特异性基因，并确定了至少134个额外的候选基因与IBD易感性相关的重新分析已发表的GWA研究。我们认为单核细胞对胃肠粘膜环境的适应失调是导致炎症性肠病的关键过程。巨噬细胞是形成抵抗病原体的第一道防线的免疫细胞，但也介导炎性疾病中的组织损伤。巨噬细胞通过识别和响应细菌细胞的成分来启动炎症。肠壁的巨噬细胞不断从血液中补充。在进入肠道后，新到达的细胞调节它们对来自肠道壁中细菌的刺激的反应。这一过程在慢性炎症性肠病（IBD）中失败。IBD的两种主要形式，克罗恩病和溃疡性结肠炎，在家庭中运行。遗传是复杂的，涉及200多个不同的基因组区域。我们假设IBD的遗传风险与控制巨噬细胞发育的基因调节改变特别相关。在这项研究中，我们使用FANTOM 5联盟产生的综合转录组数据集来确定参与巨噬细胞适应肠壁的启动子和增强子的集合，它们对细菌刺激的反应，以及它们的功能是如何整合的。对已发表的基于单核细胞中受调控基因的全基因组关联数据进行重新分析，强烈支持IBD易感性源于巨噬细胞分化的主要缺陷的观点。
The FANTOM5 consortium utilised cap analysis of gene expression (CAGE) to provide an unprecedented insight into transcriptional regulation in human cells and tissues. In the current study, we have used CAGE-based transcriptional profiling on an extended dense time course of the response of human monocyte-derived macrophages grown in macrophage colony-stimulating factor (CSF1) to bacterial lipopolysaccharide (LPS). We propose that this system provides a model for the differentiation and adaptation of monocytes entering the intestinal lamina propria. The response to LPS is shown to be a cascade of successive waves of transient gene expression extending over at least 48 hours, with hundreds of positive and negative regulatory loops. Promoter analysis using motif activity response analysis (MARA) identified some of the transcription factors likely to be responsible for the temporal profile of transcriptional activation. Each LPS-inducible locus was associated with multiple inducible enhancers, and in each case, transient eRNA transcription at multiple sites detected by CAGE preceded the appearance of promoter-associated transcripts. LPS-inducible long non-coding RNAs were commonly associated with clusters of inducible enhancers. We used these data to re-examine the hundreds of loci associated with susceptibility to inflammatory bowel disease (IBD) in genome-wide association studies. Loci associated with IBD were strongly and specifically (relative to rheumatoid arthritis and unrelated traits) enriched for promoters that were regulated in monocyte differentiation or activation. Amongst previously-identified IBD susceptibility loci, the vast majority contained at least one promoter that was regulated in CSF1-dependent monocyte-macrophage transitions and/or in response to LPS. On this basis, we concluded that IBD loci are strongly-enriched for monocyte-specific genes, and identified at least 134 additional candidate genes associated with IBD susceptibility from reanalysis of published GWA studies. We propose that dysregulation of monocyte adaptation to the environment of the gastrointestinal mucosa is the key process leading to inflammatory bowel disease. Macrophages are immune cells that form the first line of defense against pathogens, but also mediate tissue damage in inflammatory disease. Macrophages initiate inflammation by recognising and responding to components of bacterial cells. Macrophages of the wall of the gut are constantly replenished from the blood. Upon entering the intestine, newly-arrived cells modulate their response to stimuli derived from the bacteria in the wall of the gut. This process fails in chronic inflammatory bowel diseases (IBD). Both the major forms of IBD, Crohn’s disease and ulcerative colitis, run in families. The inheritance is complex, involving more than 200 different regions of the genome. We hypothesised that the genetic risk of IBD is associated specifically with altered regulation of genes that control the development of macrophages. In this study, we used the comprehensive transcriptome dataset produced by the FANTOM5 consortium to identify the sets of promoters and enhancers that are involved in adaptation of macrophages to the gut wall, their response to bacterial stimuli, and how their functions are integrated. A reanalysis of published genome-wide association data based upon regulated genes in monocytes as candidates strongly supports the view that susceptibility to IBD arises from a primary defect in macrophage differentiation.