Deciphering microbial-immune cell interaction using single cell approaches

项目总结 微生物与免疫系统之间的相互作用对人类健康起着关键作用。微生物可以提供帮助 培养和发展宿主先天免疫和获得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。许多研究使用动物模型、种群水平的16S rRNA基因和 元基因组测序以获得微生物-免疫相关性的证据，然而，潜在的机制 由于这一生态系统的复杂性和可用工具的限制，其定义相对不明确。这个 我的研究计划的首要目标是了解微生物和细胞的生物学功能 先天免疫系统的共同进化。剖析微生物和免疫细胞之间的串扰是 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？你是如何 微生物和免疫系统根据对方不断变化的策略共同进化？至 为了探讨这些问题，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 并增加了复杂性。在过去的5年里，我开发了一个用于单细胞的微流控平台和方法 全基因组和转录组测序，适用于细菌和人类细胞的测序。 这一平台导致在适应极端生活的微生物中发现了优先基因变化 条件，并且在单个微生物细胞中的基因表达谱是不同的。在接下来的5年，我 计划修改和优化此平台，以调查微生物和 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示范研究， 然后结合其他类型的细胞和环境因素。简而言之，我计划研究一种单一的微生物 通过分析，细胞可以被认为是一个调节单个免疫细胞的信号通路的群体 他们的转录档案。这项工作的核心是将其他组件集成到平台中，以实现 单个微生物和免疫细胞的共培养，激活和监测它们的信号，并研究 通过整个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，这将有助于更好地理解 异源和动态免疫反应。从长远来看，这项研究计划将加速这项研究 微生物组和免疫系统如何在更复杂的环境中交叉调节。此外，这些 基本过程涉及单细胞转录水平的一般生物学原理，并适用于 不同的宿主细胞，为拟议的工作赋予了更广泛的意义。

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.