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.

Comparison of the performance of two targeted metagenomic virus capture probe-based methods using synthetic viral sequences and clinical samples

“…Moreover, these earlier data showed that this hybridisation panel of approximately two million capture probes designed in 2015 was suited for the detection of novel coronaviruses by reactivity with other vertebrate betacoronavirus probes 10 . During the past years, this specific hybridisation panel distributed by Roche has been adopted in a broad range of different clinical 15,[22][23][24][25][26][27][28][29] and zoonotic settings 22,29,30 is the author/funder, who has granted medRxiv a license to display the preprint in (which was not certified by peer review)…”

Developing a mechanistic understanding of pediatric acute respiratory distress syndrome one cell at a time

“…One recent study using bulk mRNAseq to evaluate the nasal epithelial transcriptome of PARDS patients found that one subgroup of patients had loss of epithelial stem cells genes and those patients had a longer course of PARDS 9 . Another analysed tracheal aspirates of intubated PARDS patients using single‐cell RNAseq and found a subset of monocytes that expressed repair related transcripts 10 . These monocytes were more common in patients with a lower level of illness severity and were hypothesised to be critical for the clearance of pro‐inflammatory cells thus paving the way for repair and regeneration 10 .…”

“…9 Another analysed tracheal aspirates of intubated PARDS patients using single-cell RNAseq and found a subset of monocytes that expressed repair related transcripts. 10 These monocytes were more common in patients with a lower level of illness severity and were hypothesised to be critical for the clearance of pro-inflammatory cells thus paving the way for repair and regeneration. 10 Additionally, there is evidence that cross talk between multiple different reparative macrophage phenotypes may help promote repair and regeneration in pediatric patients with severe lung injury.…”

“…10 These monocytes were more common in patients with a lower level of illness severity and were hypothesised to be critical for the clearance of pro-inflammatory cells thus paving the way for repair and regeneration. 10 Additionally, there is evidence that cross talk between multiple different reparative macrophage phenotypes may help promote repair and regeneration in pediatric patients with severe lung injury. 11 Taken together, these studies have begun to delve into the cell populations, pathways, and cell-cell crosstalk involved in repair and regeneration in pediatric patients recovering from PARDS.…”