Deciphering microbial-immune cell interaction using single cell approaches

使用单细胞方法破译微生物与免疫细胞的相互作用

• 批准号: 10671043
• 负责人: Yuguang Liu
• 金额: $ 39.75万
• 依托单位: MAYO CLINIC ROCHESTER
• 依托单位国家: 美国
• 财政年份: 2022
• 资助国家: 美国
• 起止时间: 2022-08-01 至 2027-05-31
• 项目状态: 未结题
• 来源: https://reporter.nih.gov/project-details/10671043
• 关键词: Acceleration; Animal Model; Biological Process; Biology; Cell Communication; Cells; Coculture Techniques; Complex; Dendritic Cells; Ecosystem; Environmental Risk Factor; Gene Expression Profile; Genetic Transcription; Goals; Health; Human; Immune; Immune response; Immune system; Individual; Innate Immune System; Maintenance; Maps; Methods; Microbe; Microfluidics; Monitor; Mutation; Natural Immunity; Phenotype; Play; Population; Process; Research; Signal Pathway; Signal Transduction; Staphylococcus aureus; Symbiosis; Time; Training; Work; adaptive immunity; cell type; genome sequencing; insight; metagenomic sequencing; microbial; microbiome research; programs; rRNA Genes; response; sequencing platform; single cell sequencing; tool; transcriptome sequencing; whole genome

PROJECT SUMMARY The interaction between microbes and the immune system plays a key role in human health. Microbes can help train and develop major components of the host’s innate and adaptive immunity, while the immune system orchestrates the host-microbe symbiosis. Many studies use animal models, population level 16S rRNA gene and metagenomic sequencing to gain evidence on microbe-immune correlation, however, the underlying mechanism is relatively undefined due to the complexity of this ecosystem and the limitations of the available tools. The overarching goal of my research program is to understand how the biological functions of the microbial and cells of the innate immune system co-evolve. Dissecting the crosstalk between the microbial and immune cells is challenging and requires more sophisticated methods. My overall goal is to develop tools to understand, for example, how can microbial cells influence the innate immune system even if their number is few? How do the microbes and the immune system co-evolve according to the constantly changing strategies of the other? To probe these questions, I propose to use a bottom-up approach that starts a single microbial and immune cell and builds up complexity. Over the past 5 years, I developed a microfluidic platform and methods for single cell whole genome and transcriptome sequencing, suitable for the sequencing of both bacterial and human cells. This platform led to the discovery of preferential genetic alterations in microbes that adapted to extreme living conditions, and that the gene expression profile in individual microbial cells is distinct. During the next 5 years, I plan to modify and optimize this platform to investigate the bi-directional relationship between the microbial and immune cells. This work will be centered on dendritic cells and Staphylococcus aureus as an exemplary study, and then incorporate other cell types and environmental factors. Briefly, I plan to study how a single microbial cell can be perceived as a group to regulate the signaling pathways of a single immune cell through analyzing their transcriptional profiles. Central to this work is to integrate additional components into the platform to enable the co-culture of a single microbial and immune cell, activate and monitoring their signaling, and investigate the signaling pathways through whole transcriptome sequencing. This work will ultimately help map different immune cell phenotypes and their responses to various microbes, which will lead to the better understanding of the heterogenous and dynamic immune responses. In the long run, this research program will accelerate the study of how microbiome and the immune system are cross-regulated in more complex settings. Besides, these fundamental processes involve general biology principles at single cell transcriptional levels and are applicable to diverse host cells, lending broader significance to the proposed work.

项目摘要 微生物和免疫系统之间的相互作用在人类健康中起着关键作用。微生物可以帮助 训练和发展宿主先天免疫和适应性免疫的主要组成部分，而免疫系统 协调宿主和微生物的共生关系许多研究使用动物模型，群体水平的16S rRNA基因， 宏基因组测序以获得微生物免疫相关性的证据，然而， 由于这个生态系统的复杂性和可用工具的局限性，的 我的研究计划的首要目标是了解微生物和细胞的生物功能， 先天免疫系统的共同进化。剖析微生物和免疫细胞之间的相互干扰， 具有挑战性，需要更复杂的方法。我的总体目标是开发工具来理解， 例如，即使微生物细胞的数量很少，它们如何影响先天免疫系统？是如何 微生物和免疫系统根据对方不断变化的策略共同进化？到 为了探索这些问题，我建议使用自下而上的方法，从单个微生物和免疫细胞开始， and builds建立up complex复杂性.在过去的5年里，我开发了一个微流控平台和方法，用于单细胞 全基因组和转录组测序，适用于细菌和人类细胞的测序。 这个平台导致了在适应极端生活的微生物中发现优先遗传改变 条件下，并且单个微生物细胞中的基因表达谱是不同的。在接下来的五年里，我 计划修改和优化该平台，以研究微生物与 免疫细胞。这项工作将集中在树突状细胞和金黄色葡萄球菌作为一个示范性的研究， 然后加入其他细胞类型和环境因素。简单地说，我打算研究一个微生物 细胞可以被视为一个群体来调节单个免疫细胞的信号通路， 他们的转录谱这项工作的核心是将其他组件集成到平台中， 单一微生物和免疫细胞的共培养，激活和监测它们的信号传导，并研究 通过全转录组测序的信号通路。这项工作最终将有助于绘制不同的免疫 细胞表型及其对各种微生物的反应，这将有助于更好地了解 异质性和动态免疫应答。从长远来看，这项研究计划将加速研究 微生物组和免疫系统如何在更复杂的环境中交叉调节。再说这些 基本过程涉及单细胞转录水平的一般生物学原理， 不同的宿主细胞，为拟议的工作提供更广泛的意义。