Single-cell analysis of the lung immune microenvironment and cell-cell interactions across healthy and diseased patients

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PROJECT SUMMARY Lung diseases, such as asthma, are believe to arise due to alterations in cell type proportion, cellular function, and tissue organization in different compartments of the respiratory system. Recent advances in high- throughput single cell RNA-sequencing (scRNA-seq) have enabled comprehensive characterization of the cellular census of the lung, which has led to a remarkable number of novel findings in new cell types and cell states at homeostasis and in disease, including our team’s recent discovery of the pulmonary ionocyte. However, our understanding of the cell type relationships and their higher order tissue organization is still lacking in the context of health and disease. In 2020, over 1 million cells of scRNA-seq data from healthy and diseased lung patients will become available, which will provide unprecedented resolution and statistical power to study the variation in the lung microenviroment across different anatomical locations in healthy and diseased individuals. Such an endeavor presents several computational challenges due to the high-dimensionality of the data and because analysis tools of cellular communication in scRNA-seq data and integration with spatial information are still at their infancy. We propose to integrate high-dimensional scRNA-seq data and correct for batch effects between laboratories in order to build a uniformly annotated single-cell atlas of more than one hundred healthy and asthma patients. Such an atlas would enable us to characterize the similarities and differences in cellular composition and cell-cell interactions at different locations along the proximal-distal axis of the healthy human lung and assess the effects of clinical correlates, such as age and smoking history, on cellular composition and organization. Location specific lung microenvironment analysis is critical to understand the context of lung disease pathogenesis, especially in the context of asthma. Furthermore, comparison between the lung microenvironment in anatomically matched regions across hundreds of normal and asthma patients will uncover commonly dysregulated cellular proportions and cell-cell interactions that can inform on shared pathways to target therapeutically. Beyond the scope of this study, we aim to validate the newly discovered cell-cell interactions using sequence- or fluoresce-based spatial data, that is available to our lab through the Human Cell Atlas network and through our ongoing collaborations at Mount Sinai.