Single Cell Analysis Identifies Distinct Profiles in Pediatric Acute Respiratory Distress Syndrome

Abstract Acute respiratory distress syndrome (ARDS), termed pediatric ARDS (pARDS) in children, is a severe form of acute respiratory failure (ARF) that is associated with significant morbidity and mortality. Pathologic immune responses have been implicated in the development of pARDS. Here, we present a unique description of microbial sequencing and single cell gene expression in tracheal aspirates (TAs) obtained longitudinally from infants admitted to the pediatric intensive care unit (PICU) with ARF. Important alterations in TA epithelial cell, mononuclear phagocyte (MNP), and neutrophil transcription were associated with subjects’ illness severity, etiology (of ARF), and sampling time point. Specifically, in patients with moderate to severe pARDS compared to those with no to mild pARDS we identified reduced interferon stimulated gene (ISG) and cytokine expression in epithelial cells, reduced development over time of a regulatory IL-10 expressing macrophage population, and progressive airway neutrophilia associated with a unique transcriptional profile in aged neutrophils. In addition, we incorporated viral capture sequencing (ViroCap) with single cell transcriptomic analysis to explore interactions between respiratory syncytial virus (RSV) and host cells in infected and bystander epithelia. Our findings indicate that pARDS is defined by distinct inflammatory cell profiles that are etiology- and severity-dependent and implicate inadequate induction of ISGs, cytokines/chemokines, and repair-associated macrophage transcriptional programs in the pathogenesis of moderate to severe pARDS.