Key gut microbes shape intestinal epithelial lineage development, differentiation and metabolic function

项目总结 肠道上皮不断自我更新，并分化成专门的后代。这一过程 通常被视为在宿主衍生因子的控制下的硬连线遗传程序。组织工作 我建议的原则是这些上皮细胞的规范、分化和功能特化 谱系受肠道微生物区系成员及其代谢产物的调节。我们小组对 健康和营养不良的孟加拉国儿童透露，普雷沃特拉菌是一个关键物种，其 发育中的微生物区系中的丰度与体重的增长呈正相关。我目前在美国的工作 戈登实验室已经建立了一种特定收集物的母婴传播的灵知菌小鼠模型 代表肠道微生物区系出生后组装的不同阶段的人类肠道细菌菌株。我 进行单核RNA-SEQ，以测试包括或排除这些已定义的 社区。对铜绿假单胞菌存在的一个显著的上皮反应是肠细胞性脂肪酸的增加。 氧化。对SnRNA-seq数据集的伪时间分析揭示了脂肪酸氧化基因的表达 在肠细胞从隐窝向上绒毛和细胞核分化/迁移过程中受到P.Copri的空间调控 受体PPAR似乎是这些基因的首选调节因子。我假设我)暴露在 含铜绿假单胞菌的群落广泛地改变了表观遗传景观以及染色质的可及性 转录因子结合时，肠细胞执行其分化程序向上绒毛，和(Ii)PPAR 作为一个关键的转录因子，介导P.Copri对脂肪酸氧化的影响，通过额外的 来自其他转录因子的调节输入。我提出了两个目的来检验这些假设。在《目标1》中，我将 在单细胞分辨率下，表征表观遗传格局和转录因子的变化 包括含有铜绿假单胞菌的群落用来调节肠道细胞的信号通路 沿着肠道的长度分化/起作用。在目标2中，我将描述含有铜绿假单胞菌的 确定的细菌群落调节PPAR信号来控制沿着肠道细胞的脂肪酸氧化 隐窝到绒毛轴，采用液-质联用，二维 有机培养系统，灵知生菌小鼠模型。这项研究将提供(I)机械的见解 肠道微生物区系如何调节宿主信号以控制上皮细胞系的发育、代谢功能和 功能专业化，以及(Ii)具有治疗潜力的有益于肠道的新代谢物 生理和功能。

PROJECT SUMMARY The intestinal epithelium perpetually self-renews and differentiates into specialized progenies. This process is often viewed as a hard-wired genetic program under the control of host-derived factors. The organizing principal of my proposal is that specification, differentiation and functional specialization of these epithelial lineages are modulated by members of the gut microbiota and their metabolic products. Our groups' studies of healthy and undernourished Bangladeshi children revealed that Prevotella copri is a key species whose abundance in the developing microbiota is positively associated with ponderal growth. My current work in the Gordon lab has established a gnotobiotic mouse model of mother-to-infant transmission of defined collections of human gut bacterial strains that represent different stages in the postnatal assembly of gut microbiota. I performed single-nucleus RNA-seq to test the effects of including or excluding P copri from these defined communities. A prominent epithelial response to the presence of P. copri is enhanced enterocytic fatty acid oxidation. Pseudotime analysis of snRNA-seq datasets disclosed that expression of fatty acid oxidation genes was spatially regulated by P. copri as enterocytes differentiate/migrate from crypts up villi and that nuclear receptor PPAR appears to be a top candidate regulator of these genes. I hypothesize that i) exposure to the P. copri-containing community broadly alters the epigenetic landscape as well as chromatin accessibility to transcription factor binding as enterocytes execute their differentiation program up the villus, and (ii) PPAR functions as a key transcription factor that mediates the effects of P. copri on fatty acid oxidation with additional regulatory inputs from other transcription factors. I propose two aims to test these hypotheses. In Aim 1, I will characterize, at single-cell resolution, changes in the epigenetic landscape and the transcription factors that comprise the signaling pathways that P. copri-containing community uses to regulate enterocyte differentiation/function along the length of the intestine. In Aim 2, I will characterize how the P. copri-containing defined bacterial community modulates PPAR signaling to control enterocytic fatty acid oxidation along the crypt-to-villus axis, by using a combination of liquid-chromatography mass spectrometry, 2-dimensional organoid culture system, and gnotobiotic mouse models. This research will provide (i) mechanistic insights on how gut microbiota modulates host signaling to control epithelial lineage development, metabolic function, and functional specialization, and (ii) novel metabolites that have therapeutic potential to benefit intestinal physiology and function.