Defining complex T-cell signatures linked to rhinovirus infection in the lower airways of children with severe asthma

Rhinovirus (RV) infection is a risk factor for the development of asthma and acute wheezing episodes. RV-specific Th1 cells are expanded in the blood of adults with asthma, even in the absence of infection. Such cells are further amplified during acute infection and resemble those CCR5 +T cells found in the lower airways of children with severe asthma. We posit that in early childhood, pathogenic T cells induced by repeated RV exposures are sustained by cues in the inflamed airways and serve to drive chronic inflammation. Little is known about the complexity and function of T cells in the lower airways of children with severe asthma, or their relation to RV, due to challenges in obtaining lung specimens and low T-cell numbers in the airway lumen. We leveraged high-dimensional single-cell phenotyping, marker enrichment modeling for designation of complex molecular signatures, and the novel machine learning algorithm, T-REX, to discriminate rare pathogenic T cells in the airways that are linked to RV infection in children aged 1–15 years who had severe asthma (RV PCR+, n=3; RV PCR-, n=8). Our novel workflow identified activated (CD38 +), proliferating (Ki-67 +) and tissue-resident (CD69 +) CCR5 +CD4 +T cells (CD45RO +ICOS +CD95 +CD27 +PD-1 +TCF-1 +) in the lower airways of all children; however, this cell population was markedly expanded in RV+ children (median of 10% vs 1% of total T cells) and was over 9-fold enriched in the airways compared with blood. Notably, these cells were inversely correlated with inhaled corticosteroid dose. Our findings suggest that the expansion and persistence of RV-induced lung-resident T cells contribute to chronic airway inflammation in children with severe asthma. Supported by grants from NIH/NIAID (RO1 AI077653, R21 AI160334)