Consequences and Limits of Cell-Cell Communication in Airway Immune Responses

Abstract

The airways are an important barrier tissue, where successful immune responses can protect our bodies from viruses, bacteria, fungal spores, and environmental toxins. Conversely, when the immune system fails to respond or responds inappropriately in the airways, it can lead to diseases from deadly pneumonia to chronic allergies. Cell-cell communication is an important aspect of how airway immune responses are coordinated, yet it is not fully known which airway cell types send intercellular signals, under what circumstances, and what the consequences of those intercellular signals are. RNA sequencing, including single-cell RNA sequencing, has proven to be a valuable tool for answering all three of these unresolved questions.

Here, we use a combination of RNA sequencing and single-cell RNA sequencing to address these questions in three different contexts. First, we examine the airway mast cells that are overabundant in Type 2 inflammatory diseases, such as chronic rhinosinusitis. We attribute this overabundance of mast cells to a combination of in situ proliferation and immigration into the tissue. We then fully describe the subtypes of mast cells present, including which intercellular signals each subtype appears capable of sending. Second, we examine airway epithelial cells in the upper and lower airways to transcriptionally evaluate their susceptibility to SARS-CoV-2 infection. We identify the cell types with the highest expression of the SARS-CoV-2 receptor, ACE2, and provide evidence that the ACE2 mRNA gets upregulated during interferon responses. Finally, we investigated whether airway epithelial cells send secondary signals to one another after sensing immune-relevant signals like cytokines. To do this, we devised a new method for systematically detecting secondary responses in vitro and applied the method to airway epithelial cells grown in two different formats.

Collectively, our work confirms that cell-cell communication influences nearly every aspect of airway immune responses, while also illustrating the limits of our current technologies, of RNA sequencing as an analytical tool, and of cell-cell communication itself.