Microbiome Induced Epigenetic Changes in Intestinal Inflammation and Necrotizing Enterocolitis

项目概要 在早产儿中，过度的炎症反应与坏死性小肠结肠炎有关 （NEC），其机制尚不清楚。微生物群及其代谢物，包括短链脂肪酸 可能通过 DNA 甲基化和/或组蛋白脱乙酰化以及特定的微生物组模式来修改表观基因组 与脂质代谢、肥胖和相关基因的 DNA 甲基化改变有关 炎症。 这项研究的长期目标是确定过度炎症反应的机制 导致 NEC 并制定抗炎治疗和预防策略。具体假设为 拟议的研究是，发育中的肠道微生物群引起的表观遗传变化导致 过度的免疫和炎症反应容易导致早产儿坏死性小肠结肠炎 新生儿。我们打算首先在早产儿中建立 DNA 甲基化改变来检验这一假设 在特定目标 1 的嵌套队列临床设计中，将 NEC 与匹配对照进行比较。DNA 甲基化 将在肠上皮细胞和外周血单核细胞中描绘模式并确认 通过转录组学分析粪便肠上皮细胞中的差异基因表达并评估 全身和肠道炎症。在我们的第二个特定目标中，我们将检验特定目标的假设 微生物组和代谢组特征与表观基因组和转录组的变化相关 患有 NEC 的早产儿。在纳入的队列中，我们将通过宏基因组学和评估粪便微生物组 粪便和尿液代谢组中的微生物代谢物并记录临床元数据（例如胎龄、 喂养）进行多变量分析。我们预计不同的微生物组和代谢组特征相关 NEC 中 DNA 甲基化改变。对手术样本中肠类的后续研究将用于 通过测量暴露于特定炎症后的表观遗传变化，从机械上检验我们的假设， 从拟议的研究中确定的微生物或代谢组刺激。 拟议的研究具有创新性，因为与微生物组相关的表观基因组改变和 尚未对早产儿的炎症进行评估。我们提出了一种整体的、多组学的方法 描述早产儿过度炎症的机制。我们的研究不仅将 对新生儿领域的影响，其中主要器官发病与炎症有关，但也影响其他领域 炎症是发病机制中的诱发因素和关键因素的患者和疾病。探索 微生物群诱导的表观遗传变化与炎症反应之间的关系可能是 NEC 的病理生理学并导致早产新生儿新的预防策略。我们的研究是 意义重大，因为我们的工作将提供关于微生物组诱导的表观遗传变化的新知识，即 与癌症、感染和免疫等多种疾病相关。

PROJECT SUMMARY In preterm neonates, excessive inflammatory responses have been implicated in necrotizing enterocolitis (NEC), the mechanisms for which are unclear. Microbiota and their metabolites including short chain fatty acids may modify the epigenome by DNA methylation and/or histone deacetylation, and specific microbiome patterns have been associated with altered DNA methylation of genes linked to lipid metabolism, obesity and inflammation. The long term goal of this research is to determine the mechanism for excessive inflammatory responses that lead to NEC and devise anti-inflammatory therapeutic and preventative strategies. The specific hypothesis of the proposed research is that epigenetic changes induced by the developing intestinal microbiome result in excessive immune and inflammatory responses that predispose to necrotizing enterocolitis in the preterm neonate. We intend to test this hypothesis by first establishing DNA methylation alterations in preterm infants with NEC compared to matched controls, in a nested cohort clinical design in Specific Aim 1. DNA methylation patterns will be delineated in intestinal epithelial cells and peripheral blood mononuclear cells and confirm differential gene expressions with transcriptomics in the intestinal epithelial cells from the stools and assess systemic and intestinal inflammation. In our second Specific Aim, we will test the hypothesis that specific microbiome and metabolomic signatures are associated with changes in the epigenome and transcriptome in preterm neonates with NEC. In the cohort enrolled, we will evaluate stool microbiome by metagenomics and stool and urine metabolome for microbial metabolites and record clinical metadata (e.g. gestational age, feeding) for multi-variable analysis. We anticipate distinct microbiome and metabolome signatures associated with DNA methylation alterations in NEC. Follow up studies of enteroids from surgical samples will be used to mechanistically test our hypothesis by measuring epigenetic changes after exposure to specific inflammatory, microbial or metabolomic stimuli that are identified from the proposed research. The proposed research is innovative as the epigenome alterations in relation to the microbiome and inflammation in the preterm infant have not been evaluated. We propose a holistic, multi-omics approach to delineate the mechanisms for excessive inflammation in the preterm infant. Our research will not only make an impact in the field of neonatology where major organ morbidity is related to inflammation but in also in other patients and diseases where inflammation is an inciting and key factor in the pathogenesis. Exploring the relationship between microbiota induced epigenetic changes and inflammatory responses may underpin the pathophysiology of NEC and lead to novel preventive strategies in the preterm neonate. Our research is significant because our work will provide new knowledge on microbiome-induced epigenetic changes that is relevant to a broad-spectrum of diseases such as cancer, infection and immunity.