Microbial and inflammatory regulation of intestinal epithelial gene transcription

摘要 我们对转录调控途径的理解存在根本性的差距， 微生物群和炎症改变了肠上皮的基因表达，以及这些途径如何促进 并可能预测肠道内稳态。我们的长期目标是了解进化保守的 肠道中宿主与微生物相互作用的潜在机制以及它们如何导致人类疾病。 该项目的总体目标是确定保守的转录调控途径， 肠上皮细胞（IEC）对微生物群和炎症的反应，并确定它们的活性是否可以 用作人类炎症性肠病（IBD）的表型指标。我们对人类的初步研究， 小鼠和斑马鱼的IEC已经发现了惊人的转录特征和调控的保守性。 机制，预测涉及人类IBD的转录因子（TF）的中心保守作用，包括 HNF4A和ELF3。我们最近发现HNF4A是一种新的IEC转录调节因子， 对斑马鱼和小鼠体内微生物群的反应。对斑马鱼和小鼠的机制研究表明，HNF4A 是微生物抑制基因正调节因子，且微生物群广泛抑制HNF4A活性， IEC。此外，我们的研究结果表明，肠道抑制HNF4A靶基因是一个普遍的特点， 人、小鼠和斑马鱼IBD模型，并表明HNF4A抑制炎症反应， 该基因可抑制微生物群并抑制保守的IBD样基因表达特征。最后，我们鉴定了DNA增强子， 小鼠IEC中受微生物群定植调节的元素，并利用这些结果来暗示 ELF3作为IEC中炎症和微生物信号的潜在整合剂。我们将检验中心假设 微生物群通过协同抑制抗炎HNF4A活性来促进肠道炎症 并激活ELF3和其他促炎转录途径。在具体目标1中，我们将确定主机 介导IEC中HNF4A活性的微生物抑制的信号传导机制。在第二阶段，我们将 定义ELF3和更广泛的转录途径在IEC对微生物群和炎症的反应中的作用， 并测试IBD表型是否与ELF 3和HNF 4A活性的不同特征相关。预期 成果将以几种方式纵向推进该领域。首先，他们将产生一个基本的机械 了解肠道微生物如何调节HNF4A和ELF3的活性，这些保守的TF具有关键作用 肠道炎症第二，它们将为转录调控提供急需的见解。 IEC用于整合微生物和炎症刺激的网络，以及这些网络是如何错乱的 在人类IBD中。这些成果预计将产生重大影响，因为它们将垂直推进 我们对IEC转录程序的理解整合了对微生物群和炎症的反应， 其可预期导致用于人IBD的新的诊断、预后和治疗方法。

ABSTRACT There exist fundamental gaps in our understanding of the transcriptional regulatory pathways through which microbiota and inflammation alter gene expression in the intestinal epithelium, and how those pathways promote and might predict intestinal homeostasis. Our long-term goal is to understand the evolutionarily-conserved mechanisms underlying host-microbe interactions in the intestine and how they contribute to human diseases. The overall objectives of this project are to identify conserved transcriptional regulatory pathways mediating intestinal epithelial cell (IEC) responses to microbiota and inflammation, and determine if their activity can be used as phenotypic indicators in human inflammatory bowel disease (IBD). Our preliminary studies in human, mouse, and zebrafish IECs have uncovered striking conservation of transcriptional signatures and regulatory mechanisms, predicting central conserved roles for transcription factors (TF) implicated in human IBD including HNF4A and ELF3. We recently made the key discovery that HNF4A is a novel mediator of IEC transcriptional responses to microbiota in zebrafish and mice. Mechanistic studies in zebrafish and mice revealed that HNF4A is a positive regulator of microbially-suppressed genes, and that microbiota broadly suppress HNF4A activity in IECs. Further, our results show that intestinal suppression of HNF4A target genes is a prevalent feature of human, mouse, and zebrafish models of IBD, and indicate that HNF4A constrains inflammatory responses to microbiota and suppresses a conserved IBD-like gene expression signature. Finally, we identified DNA enhancer elements in mouse IECs that are regulated by microbiota colonization, and leverage those results to implicate ELF3 as a potential integrator of inflammatory and microbial signals in IECs. We will test the central hypothesis that microbiota promote intestinal inflammation by coordinately suppressing anti-inflammatory HNF4A activity and activating ELF3 and other pro-inflammatory transcriptional pathways. In Specific Aim 1, we will identify host signaling mechanisms mediating microbial suppression of HNF4A activity in IECs. In Specific Aim 2, we will define the roles of ELF3 and broader transcriptional pathways in IEC responses to microbiota and inflammation, and test if IBD phenotypes are associated with distinct signatures of ELF3 and HNF4A activity. The expected outcomes will vertically advance the field in several ways. First, they will generate a foundational mechanistic understanding of how gut microbes regulate the activity of HNF4A and ELF3, conserved TFs with critical roles in intestinal inflammation. Second, they will provide much-needed insights into the transcriptional regulatory networks utilized by IECs to integrate microbial and inflammatory stimuli, and how those networks are deranged in human IBD. These outcomes are expected to have a significant impact because they will vertically advance our understanding of the IEC transcriptional programs that integrate responses to microbiota and inflammation, which can be expected to lead to new diagnostic, prognostic, and therapeutic approaches for human IBD.