Differential host responses by the type I and III interferons in primary differentiated human nasal epithelial cells are a determinant of antiviral activity.

Background: The interferon (IFN) response is a crucial innate antiviral defence mechanism at the airway epithelium. The epithelial IFN response is predominantly mediated by the type I (IFN-β1) and III (IFN-λ) IFNs, which activate a transcriptional program expressing antiviral and inflammatory genes. Type III IFNs have been purported to be less inflammatory than type I IFN, but exhibit reduced potency. As both type I and III IFNs exert broad antiviral functions, there has been considerable interest in harnessing them as antiviral therapeutics. A better understanding of the effects of exogenous IFN on the host may enable its safer utilisation and prevent unwanted effects in clinical settings. Few studies have compared their potency using a standardised concentration or on primary human cells. Methods: Here, using differentiated primary human nasal epithelial cell (hNEC) cultures grown at the air-liquid interface, we compared the transcriptional profiles upon exogenous treatment (25 ng/mL) with IFN-β1 and IFN-λ1, -λ2, -λ3, and -λ4 across three time points (6 h, 24 h, and 72 h) by RNA-sequencing. Additionally, we investigated how the apicobasal polarity of the differentiated nasal epithelial influences IFN response by compartmentalised (apical vs. basal) treatment. Results: Our results revealed that the IFN response is weakly stimulated upon apical IFN treatment and requires additional basal treatment to mount an efficient antiviral response. Upon supplemental basal IFN treatment, IFN-β1 activates a robust transcriptional program of thousands of genes, of which the top differentially expressed genes are involved in the antiviral response and inflammatory pathways. The type III IFNs resulted in fewer genes (hundreds); amongst the type III IFNs, IFN-λ1 and -λ3 had comparable transcriptional profiles, followed by IFN-λ2. IFN-λ4 did not activate the IFN response at the tested concentration. Prophylactic treatment of hNECs with IFN-β1 or IFN-λ1 during influenza A infection demonstrated dose dependent antiviral properties, with IFN-β1 showing superior potency. Conclusion: Taken together, our study highlights the potency of type I IFN in antiviral control and provides a global IFN transcriptional profile in a physiologically relevant model that could serve as a fundamental framework of the type I and III IFN host response.