Interferon alpha inducible protein 6 is a negative regulator of innate immune responses by modulating RIG-I activation

Abstract

Interferons (IFNs), IFN-stimulated genes (ISGs), and inflammatory cytokines mediate innate immune responses, and are essential to establish an antiviral response. Within the innate immune responses, retinoic acid-inducible gene I (RIG-I) is a key sensor of virus infections, mediating the transcriptional induction of IFNs and inflammatory proteins. Nevertheless, since excessive responses could be detrimental to the host, these responses need to be tightly regulated. In this work, we describe, for the first time, how knocking-down or knocking-out the expression of IFN alpha-inducible protein 6 (IFI6) increases IFN, ISG, and pro-inflammatory cytokine expression after the infections with Influenza A Virus (IAV), Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2), and Sendai Virus (SeV), or poly(I:C) transfection. We also show how overexpression of IFI6 produces the opposite effect, in vitro and in vivo, indicating that IFI6 negatively modulates the induction of innate immune responses. Knocking-out or knocking-down the expression of IFI6 diminishes the production of infectious IAV and SARS-CoV-2, most likely because of its effect on antiviral responses. Importantly, we report a novel interaction of IFI6 with RIG-I, most likely mediated through binding to RNA, that affects RIG-I activation, providing a molecular mechanism for the effect of IFI6 on negatively regulating innate immunity. Remarkably, these new functions of IFI6 could be targeted to treat diseases associated with an exacerbated induction of innate immune responses and to combat viral infections, such as IAV and SARS-CoV-2.

Single-cell analysis reveals lasting immunological consequences of influenza infection and respiratory immunisation in the pig lung

“…In agreement with these studies, we observed reduced GFP expression in VSV∆G-GFP infected BAL cells from pH1N1 infected pigs compared to control pigs, confirming an inhibitory role of IFI6 following influenza infection. This is in contrast with a recent report showing that IFI6 can positively affect virus infection and that IFI6 overexpression results in increased influenza replication in cell cultures and in the murine model (63). Irrespective of the mechanism of action and whether this reflects species differences between mice and pigs, or between VSV and influenza infection, the sustained upregulation of IFI6 suggests that the immune system is still actively engaged in combating the virus or resolving inflammation and tissue damage at day 21 post infection.…”

The IFN-stimulated gene IFI27 counteracts innate immune responses after viral infections by interfering with RIG-I signaling

“…The effect of IFI27 facilitating viral replication is likely mediated by negative modulation of innate immune responses as suggested by experiments performed taking advantage of the fact that the response to VSV infection is affected by the previous antiviral states induced in the cells (DeDiego et al, 2016;Nogales et al, 2017). Similarly, we previously showed that IFI6, IFI44 and IFI44L counteract innate immune responses and positively affect IAV and coronavirus replication (DeDiego et al, 2019a,b;Villamayor et al, 2023), and silencing other ISGs such as IFI35 and ISG56/IFIT1 proteins, which negatively modulate IFN responses, decreases VSV replication (Li et al, 2009;Das et al, 2014). Many ISGs induced after viral infections display antiviral activities, however, other ISGs counteract innate immune responses, supporting virus replication, and providing negative feedback mechanisms, since exacerbated immune responses are deleterious to the host (Komuro et al, 2008;Richards and Macdonald, 2011).…”

“…IAV and SARS-CoV-2 are unrelated viruses but in both cases viral replication is affected by IFN responses (Iwasaki and Pillai, 2014;Vanderheiden et al, 2020). Given that several ISGs, e.g., IFI6, IFI44 and IFI44L, negatively modulate IFN responses (DeDiego et al, 2019a,b;Villamayor et al, 2023), we postulated that IFI27 could play a role downregulating IFN-mediated host antiviral responses. To test this hypothesis, parental and IFI27 KO human A549 cells WT or expressing hACE2 were infected with IAV (MOI 1) or SARS-CoV-2 (MOI 1), respectively.…”

“…Many ISGs have a clear antiviral function, but there are also ISGs that are able to prevent an excessive immune response, which can be deleterious to the host, playing a regulatory role (Komuro et al, 2008;Richards and Macdonald, 2011;Chathuranga et al, 2021). As an example, we previously described the molecular mechanisms underlying negative modulation of IFN responses mediated by the ISGs IFI6, IFI44 and IFI44L that facilitate virus replication (DeDiego et al, 2019a,b;Villamayor et al, 2023).…”

Bulk RNA sequencing for analysis of post COVID-19 condition in adolescents and young adults

“…Elevated expression was further found for IRF7 , a member of the interferon regulatory transcription factor family, and several interferon-stimulated genes (ISGs), including the IFIT family of viral replication inhibitors ( IFIT1, IFIT2, IFIT3 ) [ 40 ], the ubiquitin ligase HERC5 responsible for ISGylation of viral target proteins [ 41 ], and ubiquitin-like ISG15 [ 42 ] . Moreover, we found an upregulation of IFI6, an ISG and antiapoptotic protein, which was recently shown to enhance SARS-CoV-2 infection [ 43 ]. Other DEGs with immune-related functions include SELL , a cell surface adhesion molecule that belongs to a family of adhesion/homing receptors and is required for binding and rolling of leucocytes on endothelial cells [ 44 ], MX1 , a guanosine triphosphate (GTP)-metabolizing anti-viral enzyme [ 45 ] and PLSCR1, a phospholipid scramblase family member preventing viral entry [ 46 ].…”