Multiomic phenotyping of the airways in health and disease at single-cell resolution to discover molecular mechanisms of asthma

Asthma is a heterogenous disease of the airways showing phenotypic diversity across patients, requiring varied approaches to treatment. However, the underlying pathophysiological processes which drive the differences have not been comprehensively studied. To profile the varied molecular pathways involved in its pathogenesis, I present a collection of single cell and spatial transcriptomic datasets, together spanning over 400,000 cells captured from upper and lower airway tissue sites from 62 individuals (asthma patients and healthy controls) across multiple molecular modalities (transcriptome, immune repertoire, protein expression). In addition to profiling the cell surface proteome, I developed a technique to interrogate antigen binding in allergic asthma with house dust-mite sensitisation. This rich omics data resource is accompanied by detailed clinical phenotyping, thereby providing the largest single-cell atlas of asthma and its key phenotypes. Analysis of this resource reveals that in patients with allergic sensitisation, contrary to past concepts of allergic asthma pathogenesis, IgE-producing plasma cells were not found in the lung. However, IgE-binding cells were detected (e.g. basophils and mast cells), suggesting that IgE may be entering from the periphery. Notably, the allergens thought to cause IgE secretion were found to bind to immune cells, including antigen-presenting cells, suggesting the IgE secretion may be localised to lymphoid tissues. Profiling the differences between asthmatic and healthy individuals in the spatial context reveals probable mast cell - plasma cell and CD4+ - B cell niches, which may contribute to disease mechanism. Differential abundance and gene expression analyses between the whole asthma cohort and healthy individuals showed features predominantly related to type 2 eosinophilic inflammation. Those changes correlated with clinical variables describing lung function, such as FEV1 and FVC. In contrast, comparisons between the asthma phenotypes allowed identification of features associated with neutrophilic inflammation. These features included IL-1 signalling, antibacterial defence, and inflammasome activation. My findings underscore critical importance of careful phenotyping to uncover underlying molecular changes in asthma, as well as providing a rich resource to study it further.