Deciphering microbial-immune cell interaction using single cell approaches

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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.