Analysis of human neutrophils from nasal polyps by single-cell RNA sequencing reveals roles of neutrophils in chronic rhinosinusitis

Abstract

BackgroundChronic rhinosinusitis with nasal polyps (CRSwNP) is characterized by type 2 (T2) inflammation. Recent studies, including our own, suggest that neutrophils are also elevated in T2 nasal polyps (NPs) and that elevated neutrophils display an activated phenotype. However, the actual roles of neutrophils in NP pathogenesis in T2 CRSwNP are still largely unclear. ObjectiveTo reveal the roles and heterogeneity of neutrophils in NP tissue by single cell RNA-Sequencing (scRNA-Seq) analysis. MethodsWe developed a novel microwell-based scRNA-Seq assay (BD Rhapsody platform) using granulocyte enriched samples from 5 control sinus tissues (CTs), 5 NP tissues and patient matched peripheral blood (PB) samples. This approach allowed for the examination of differential expression of genes in NP neutrophils by the Benjamini-Hochberg algorithm and predicted the overall function of NP neutrophils by pathway and gene ontology (GO) enrichment analyses. ResultsAfter all QC steps, we successfully detected neutrophils. We identified 333 down-regulated and 128 up-regulated genes in NP neutrophils (1,151 cells) compared to all PB neutrophils (13,591 cells) (>1.5-fold, q<0.05), and found commonly dysregulated genes in NP neutrophils compared to both all PB and CT neutrophils (3,136 cells). Commonly down-regulated genes in NP neutrophils were associated with the innate immune system, and up-regulated genes were associated with NF-κB signaling, cytokine activity and cellular response to oxygen-containing compounds. NP neutrophils displayed 4 clusters revealing potential heterogeneity of neutrophils in NP tissue. ConclusionsElevated neutrophils in NP tissue appear to exist in several subphenotypes that may play important pathogenic roles in CRSwNP.