People with cystic fibrosis do not show an increased interferonresponse transcriptomic signature in nasal epithelial cells

ABSTRACT

Objectives: People with CF (PwCF) are at increased risk of respiratory infections and chronic inflammation.We sought to determine whether the inflammatory response is different in nasal epithelium of PwCF compared to healthy volunteers (HV). Since Interferons can increase ACE2 expression, a protein required for SARS-CoV-2 entry,we focused our analysis on the the focusing on the interferon-response signature. Methods: We reanalysed nasal curettage sample bulk RNA-seq signatures of pilot and validation datasets for which the study methods and demographics of the recruited cohort have already been reported. For this analysis, we performed in-silico deconvolution of bulk RNA-seq data using publicly available single-cell RNA-seq data from nasal epitheliumas a reference to determine the abundance of the specific cell types in each sample. Results: Hierarchical clustering of the pilot and validation cohorts revealed 3 clusters. Analysis of the larger validation cohort revealed that Cluster A included HV (11 out of 11 subjects) and both homozygous (7 out of 13 subjects) and heterozygous (3 out of 10 subjects) PwCF. Subject cluster A was characterised by increased expression of genes related to secretory and ciliated epithelial cells, whereas Clusters B and C contained both homozygous and heterozygous PwCF only and were characterised by genes restricted to neutrophils and involved in immune responses. We then compared samples from cluster A that contained samples from HV (n = 11), PwCF homozygous (n = 7) and heterozygous (n = 3) for F508del. This analysis identified 379 genes upregulated in HV and 146 genes upregulated in PwCF homozygous for F508del and only 44 and 6 genes upregulated in HV and PwCF heterozygous for F508del, respectively (FDR q < 0.05). ACE2, TMPRS2 or other interferon-response genes were not deferentially expressed in either comparison of cluster A. Conclusion: PwCF do not have higher expression of interferon-response genes in nasal epithelial cells