In-silico immune cell deconvolution of the airway proteomes of infants with pneumonia reveals a link between reduced airway eosinophils and an increased risk of mortality

Charles J Sande; Jacqueline M Waeni; James M Njunge; Martin N Mutunga; Elijah Gicheru; Nelson K Kibinge; Agnes Gwela

Due to the paucity of mechanistic data on the immunological response to pneumonia in the airway there is broad interest in understanding the dynamics of airway-resident immune cells following pneumonia infection in infants. This effort has been hindered by the unsuitability of routine airway sampling techniques for conventional cytometric analyses. Samples from nasopharyngeal washings and naso-and oropharyngeal swabbing are the most common methods of sampling the airways of sick children, and whilst ideal for molecular diagnostics, they are less suitable for phenotyping of airway resident immune cells using conventional cytometry techniques. Sampling of the airway by these methods typically results in limited cell yields and the cells that are recovered are generally highly enriched for granulocytes, complicating detailed characterisation of less abundant phenotypes using traditional flow cytometry-based tools 8 . Recent analysis of the cellular composition of upper airway by flow cytometry showed that the typical abundances of critical effector cells like T Cells, B Cells, Mast cells, Dendritic cells and NK cells to be less than 0.5% of all airway cells, while granulocytes were present at a median frequency of >90% 9 .