The Respiratory Epithelium Expresses ACE2 Isoforms Differentially in Response to Interferons: Implications for IFN-ß As COVID-19 Therapy

Background: Angiotensin Converting Enzyme 2 (ACE2) is the host factor expressed in respiratory cells facilitating SARS-CoV-2 binding and entry. It has been reported that ACE2 is an IFN-stimulated gene raising concerns about the safety of IFN-β as COVID-19 treatment. Aims: Investigate the expression of ACE2 during the anti-viral response of the respiratory epithelium. Methods: Using RNA-seq, RT-qPCR, fluorescence microscopy and Western blotting we characterised ACE2 expression in in vitro differentiated human nasal and bronchial epithelial cells. Cells were stimulated with IFNs to activate the anti-viral response or infected with human rhinovirus (RV16). Results: Using deep-bulk RNA-seq data we identified a novel short ACE2 transcript under independent transcriptional control from long ACE2. This transcript encodes a protein, which lacks the first 357 amino acids (aa) of long ACE2 and most SARS-CoV-2 binding sites. Instead, a novel 10aa sequence at the N-terminus is present. Short ACE2 expression was highest in differentiated respiratory epithelial cells and IFN-β significantly induced expression of short ACE2, but not the long, SARS-CoV-2-binding form of ACE2. RV16 infection also preferentially induced short ACE2 expression and showed a positive correlation with IFN release. Conclusion: The conducting airways express two distinct protein-coding transcripts of ACE2. Only the novel short ACE2 transcript was induced by IFNs, not the SARS-CoV-2 binding long ACE2 isoform. Our in vitro mechanistic data provide evidence that IFN-β does not induce long ACE2 expression to promote SARS-CoV2 infectivity in the respiratory epithelium.