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

项目摘要 肠上皮不断自我更新并分化成专门的后代。这个过程 通常被认为是在宿主衍生因子控制下的硬连线遗传程序。组委会 我的主要建议是，这些上皮细胞的特化、分化和功能特化 谱系由肠道微生物群的成员及其代谢产物调节。我们小组的研究 健康和营养不良的孟加拉国儿童透露，普雷沃氏菌copri是一个关键物种， 发育中的微生物群中的丰度与重量生长正相关。我目前在 戈登实验室已经建立了一个gnotobiotic小鼠模型的母婴传播的定义集合 代表出生后肠道微生物群组装的不同阶段的人类肠道细菌菌株。我 进行了单核RNA-seq，以测试从这些定义中包括或排除P copri的影响， 社区.一个突出的上皮细胞反应的存在，P. copri是增强肠脂肪酸 氧化snRNA-seq数据集的伪时间分析揭示了脂肪酸氧化基因的表达 当肠上皮细胞从隐窝分化/迁移到绒毛上时， 受体PPAR γ似乎是这些基因的最佳候选调节因子。我假设i）暴露于 p.含有copri的群落广泛改变了表观遗传格局以及染色质可及性， 转录因子结合的肠上皮细胞执行其分化程序的绒毛，和（ii）过氧化物酶体增殖物激活物受体 作为一个关键的转录因子，介导的影响，P. copri脂肪酸氧化与额外的 其他转录因子的调控输入。我提出两个目标来检验这些假设。在目标1中，我将 以单细胞分辨率表征表观遗传景观和转录因子的变化， 包括含有P. copri的群落用来调节肠上皮细胞的信号通路 肠的分化/功能沿着肠的长度。在目标2中，我将描述如何含P. copri 确定的细菌群落调节过氧化物酶体增殖物激活受体β信号传导，以控制肠细胞脂肪酸氧化沿着 通过使用液相色谱-质谱联用，二维 类器官培养系统和无菌小鼠模型。这项研究将提供（一）机制的见解， 肠道微生物群如何调节宿主信号传导以控制上皮谱系发育、代谢功能和 功能专业化，和（ii）新的代谢物，具有治疗潜力，有利于肠道 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.