In mammals, interferons (IFNs) mediate the primary defense mechanism against viral invasion. Until now, three types of IFN have been identified, of which include type I (IFN-I), type II (IFN-II), and type III (IFN-III).
Study: Differential interferon-α subtype induced immune signatures are associated with suppression of SARS-CoV-2 infection. Image Credit: Maryna Olyak / Shutterstock.com
Background
IFN-I activates initial antiviral responses as a result of omnipresent surface receptors IFNAR, which consist of two subunits including IFNR1 and IFNR2. Among the five types of IFN-I, IFNa expresses 12 subtypes with different antiviral and antiproliferative potencies. Although the cause of this variation remains largely elusive, varied receptor affinities and interaction interfaces have been suggested.
IFN-I therapeutics are currently proposed as an emergency treatment option against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection. Clinical trials have demonstrated the susceptibility of SARS-CoV-2 to IFN-I; however, emerging SARS-CoV-2 variants have defied host immune mechanisms, including the ability to evade the IFN-I signaling cascade.
A recent study published in Proceedings of the National Academy of Sciences analyzed IFNa subtypes for their therapeutic potential against SARS-CoV-2 and identified the underlying immune signatures and mechanisms.
Study findings
Based on the antiviral potency derived using cells from a non-human primate, IFNa subtypes were clustered into three classes including low, medium, and high. IFNa subtypes were further classified according to the antiviral activity specific to SARS-CoV-2 using human airway epithelial cells (hAEC).
The IFNa subtypes 5, 4, 14, and l3 demonstrated strong antiviral activity, whereas IFNa subtypes 17, 2, 7, and 21 showed moderate antiviral activity. Furthermore, IFNa subtypes 10, 16, 6, and 1 showed weak antiviral responses, and IFNa subtypes 2, 4, 5, and 14 exhibited superior antiviral effects as compared to those to IFNa8 and l3. Taken together, these findings demonstrate that each subtype of IFNa mediates different biological responses against SARS-CoV-2.
As compared to control-treated cells, several differences were observed in the number of up- and down-regulated genes when treated with IFNa subtypes. Higher gene expressions involving antiviral immune responses were analyzed using the Gene Ontology (GO) pathway.
IFNa17, for example, regulated genetic coding for translation, which was contrary to the other subtypes. Comparatively, IFNa5 demonstrated the strongest genetic regulation of lymphocyte activation and signaling pathways.
Upon assessment of the antiviral activities these IFNs, IFNa subtypes 1, 6, 10, and 16, all of which are considered weak antiviral subtypes, exhibited lower expression values of specific interferon-stimulated genes (ISGs) as compared to the higher expression in medium and strong IFNa subtypes.
Two clusters were differentiated between the low and intermediate to the high IFN subtypes. In the low antiviral IFN subtype, ISG15, MX1, IFI27, and others showed lower expression values, whereas IFIT1, IFIT2, and MX2, along with others, exhibited up-regulation in the intermediate- high subtypes and down-regulation in low antiviral IFN subtypes.
When identifying the immune signatures correlated with anti-SARS-CoV-2 activity, IFNa5 expressed the most exceptional genes, which was followed by the l3 subtype. Upon comparison of the high, medium and low subtypes, 19 genes including OAS2 and MX1 were found in all subtypes.
When high antiviral IFNas were compared with other subtypes, 42 differentially expressed genes (DEGs) were reported in the high antiviral group with exclusive up- or down-regulations – including genes encoding signal transduction, transcription, and metabolic processes together with noncoding RNAs and RNasel. These observations illustrate immune signatures specific to the subtypes that correlated with their differential antiviral activity.
Primary human airway epithelial cells (hAECs) pretreated with selected IFNs at different time points revealed donor and/or infection- and time-dependent clustering. Viral peptides that correlate to donor-dependent viral titers were identified.
Following treatment with IFNa5 and IFNl3, no SARS-CoV-2 peptides could be found in any of the donors. Depending on IFN stimulation, pretreated cells of IFN subtypes illustrated up- or down-regulation of a range of proteins as compared to untreated hAECs.
With the exception of IFNa16, all other IFNs revealed enriched antiviral immune responses on GO analysis of differentially abundant proteins at different time points. More specifically, IFNa16 showed induction of lymphocyte regulatory proteins.
At 72 hours post-treatment with IFNa5 and IFNl3, proteolytic, metabolic, and protein localization pathways were enriched. IFN signaling up-regulated proteins including MX1, ISG15, 1SG20, IFI35, and STAT1, all of which were considered to be on-off regulated and were found only after treatments with IFNa5, IFNa7, and IFNl3.
Various mucines and complement factors were accentuated by SARS-CoV-2 that did not depend on IFN treatment and viral titers. Conversely, treatment with IFNa5 and IFNl3 was ineffectual on antiviral immune responses like antigen presentation, lymphocyte regulation, IFN signaling, or nuclear factor-kB signaling.
Proteins included in other pathways like proteolysis or antigen exhibition by major histocompatibility complex (MHC) class I appeared to be sparsely represented under viral infection in samples treated with IFNa5. This observation was inconspicuous in samples treated with IFNl3.
Antiviral effector molecules associated with a down-regulation of viral processes, immune effector processes, and IFN-I signaling were highlighted. The researchers identified several antiviral cellular effector molecules with a potent antiviral activity that was found to be capable of controlling the SARS-CoV-2 infection.
When studying the pre- and post-treatment effects on established viral infection by combining remdesivir with IFNa5 or IFNa2, an additive antiviral activity that resulted in over 90% viral inhibition. Comparatively, post-treatment resulted in an additive and dose-dependent reduction in viral titers by 70%. The combination of low, medium, and high doses of remdesivir with IFNa5 similarly resulted in an additive effect on viral inhibition.
Further evaluation of the therapeutic effect of IFNa5 in mice with transplanted fetal lungs showed a significant reduction in viral titers. Taken together, these findings support combination treatments as an alternative therapeutic approach to impair SARS-CoV-2 viral replication.
Conclusions
The study provides data on IFN-I mediated host immune responses, which will aid in developing modified therapeutic modalities against the SARS-CoV-2 infection.
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