Rhinovirus Infection Drives Complex Host Airway Molecular Responses in Children With Cystic Fibrosis

Abstract

Early-life viral infections are responsible for pulmonary exacerbations that can contribute to disease progression in young children with cystic fibrosis (CF). The most common respiratory viruses detected in the CF airway are human rhinoviruses (RV), and augmented airway inflammation in CF has been attributed to dysregulated airway epithelial responses although evidence has been conflicting. Here, we exposed airway epithelial cells from children with and without CF to RV in vitro. Using RNA-Seq, we profiled the transcriptomic differences of CF and non-CF airway epithelial cells at baseline and in response to RV. There were only modest differences between CF and non-CF cells at baseline. In response to RV, there were 1,442 and 896 differentially expressed genes in CF and non-CF airway epithelial cells, respectively. The core antiviral responses in CF and non-CF airway epithelial cells were mediated through interferon signaling although type 1 and 3 interferon signaling, when measured, were reduced in CF airway epithelial cells following viral challenge consistent with previous reports. The transcriptional responses in CF airway epithelial cells were more complex than in non-CF airway epithelial cells with diverse over-represented biological pathways, such as cytokine signaling and metabolic and biosynthetic pathways. Network analysis highlighted that the differentially expressed genes of CF airway epithelial cells' transcriptional responses were highly interconnected and formed a more complex network than observed in non-CF airway epithelial cells. We corroborate observations in fully differentiated air-liquid interface (ALI) cultures, identifying genes involved in IL-1 signaling and mucin glycosylation that are only dysregulated in the Ling et al. Rhinovirus Infection Drives Network Responses CF airway epithelial response to RV infection. These data provide novel insights into the CF airway epithelial cells' responses to RV infection and highlight potential pathways that could be targeted to improve antiviral and anti-inflammatory responses in CF.

Pseudomonas aeruginosa Affects Airway Epithelial Response and Barrier Function During Rhinovirus Infection

“…Individual infections alone, including HRV, did not significantly induce IL-1β release in our model. HRV has previously been described to increase release of IL-1β in undifferentiated airway epithelial cells ( Terajima et al., 1997 ; Piper et al., 2013 ; Ling et al., 2020 ). However, in line with our studies, other groups using air liquid interface cultures more similar to ours likewise did not observe an increase in pro-IL-1β mRNA ( Lopez-Souza et al., 2009 ) or IL-1β protein ( Hill et al., 2016 ).…”

A determination of pan-pathogen antimicrobials?

“…Recent biotechnological advancements have made possible the characterisation of signalling pathways that are conserved across infection types [45] , [46] . For example, profiling global gene expression and aligning sequences to reference genomes has enabled isolation of differentially expressed genes pre- and post-infection [47] , [48] . Selected genes are assessed against repositories and online databases to probe enrichment of functional biological pathways, and subnetworks are constructed by comparing and connecting identified genes to curated protein-protein interaction databases [49] .…”

Immunoglobulin A Mucosal Immunity and Altered Respiratory Epithelium in Cystic Fibrosis

“…The CF airway tissue responds excessively and sometimes differently to infection (viral and/or bacterial) both at the protein and at the transcriptional level than control airways. It was highlighted by recent studies for Pseudomonas aeruginosa and human rhinovirus infections through RNA sequencing of primary airway epithelial cells from children with CF and non-CF controls [ 74 , 75 ]. This can contribute to the sustained inflammatory response of the CF airways notably by increased IL-8 production at baseline [ 76 , 77 ], but also by prolonged IL-8 mRNA levels after Pseudomonas aeruginosa infection.…”

“…In broncho-alveolar lavage, concentrations of IL-6, IL1 β, Th1 (INF-γ), Th2 (IL-5, IL-13), and Th17 (IL-17A) cytokines were increased compared to non-CF controls [ 78 ]. In addition to this excessive inflammation and tampered bacterial killing and clearance, innate antiviral defense seems altered in CF against notably human parainfluenza 3 virus [ 79 ] or rhinovirus [ 75 , 80 ].…”