RIG-I triggers a signaling-abortive anti-SARS-CoV-2 defense in human lung cells

Abstract

Efficient immune responses against viral infection are determined by sufficient activation of nucleic acid sensor-mediated innate immunity 1,2 . Coronavirus disease 2019, caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), remains an ongoing global pandemic. It is an urgent challenge to clarify the innate recognition mechanism to control this virus. Here we show that retinoic acid-inducible gene-I (RIG-I) sufficiently restrains SARS-CoV-2 replication in human lung cells in a type I/III interferon (IFN)-independent manner. RIG-I recognizes the 3′ untranslated region of the SARS-CoV-2 RNA genome via the helicase domains, but not the C-terminal domain. This new mode of RIG-I recognition does not stimulate its ATPase, thereby aborting the activation of the conventional mitochondrial antiviral-signaling protein-dependent pathways, which is in accordance with lack of cytokine induction. Nevertheless, the interaction of RIG-I with the viral genome directly abrogates viral RNA-dependent RNA polymerase mediation of the first step of replication. Consistently, genetic ablation of RIG-I allows lung cells to produce viral particles that expressed the viral spike protein. By contrast, the anti-SARS-CoV-2 activity was restored by all-trans retinoic acid treatment through upregulation of RIG-I protein expression in primary lung cells derived from patients with chronic obstructive pulmonary disease. Thus, our findings demonstrate the distinctive role of RIG-I as a restraining factor in the early phase of SARS-CoV-2 infection in human lung cells.More than 140 million people around the world have been affected by coronavirus disease 2019 (COVID-19) caused by SARS-CoV-2. COVID-19 varies from mild to severe, life-threatening respiratory infection with coagulopathy. Most (81%) people infected with SARS-CoV-2 show a mild and self-limited course 3 , while severe cases of disease are more likely to be present in older patients with underlying comorbidities, such as chronic obstructive pulmonary disease (COPD) 4-6 , compared to patients with mild disease. But even young healthy adults sometimes experience severe illness. Conversely, it has been reported that nearly 40-45% of patients with SARS-CoV-2 infections are asymptomatic 7 . The wide spectrum of clinical manifestations of COVID-19 suggests that individual immune responses to the underlying pathogen may play some crucial role in determining the clinical course. Currently, no efficient therapies and preventive measures exist for COVID-19, thus studies about host immune response against SARS-CoV-2 infection are required for a better understanding of the pathological processes for the rational development of countermeasures to control SARS-CoV-2 infection. There is also an urgent need to identify biomarkers that can predict which patients will deteriorate.Microbial invasion in our body is sensed by pattern-recognition receptors (PRRs) that are present in most types of cells, which initiate the activation of cell-intrinsic defense and innate immune responses. During ...

The RNA sensor MDA5 detects SARS-CoV-2 infection

“…In Calu-3 cells, RIG-I was largely dispensable for the antiviral cytokine response to infection. While our study was in preparation, other manuscripts reported that MDA5 and its adaptor MAVS recognise SARS-CoV-2 infection 19 , 20 , 24 , 34 . Three of these reports 19 , 20 , 24 included siRNA-mediated knockdown and/or genetic ablation in Calu-3 cells.…”

“…While our study was in preparation, other manuscripts reported that MDA5 and its adaptor MAVS recognise SARS-CoV-2 infection 19 , 20 , 24 , 34 . Three of these reports 19 , 20 , 24 included siRNA-mediated knockdown and/or genetic ablation in Calu-3 cells. In contrast to these three studies and to our work, another study found that both MDA5 and RIG-I sense SARS-CoV-2 infection in Calu-3 cells, and that upregulation of the pro-inflammatory cytokine IL6 was uncoupled from MDA5, but dependent on RIG-I and MAVS 21 .…”

“…Other reports have established that A549 and THP1 cells do not support viral entry and/or replication, likely due to insufficient expression of the viral entry receptor ACE2 22 , 23 . In addition, it has recently been suggested that high baseline levels of RIG-I present in cells such as A549 prevent SARS-CoV-2 replication 24 . Mechanistically, this may be independent of IFN induction but instead involve reduced binding of the viral polymerase to viral RNA occupied by RIG-I 24 .…”

“…In addition, it has recently been suggested that high baseline levels of RIG-I present in cells such as A549 prevent SARS-CoV-2 replication 24 . Mechanistically, this may be independent of IFN induction but instead involve reduced binding of the viral polymerase to viral RNA occupied by RIG-I 24 . Intriguingly, we could detect high levels of viral RNA but no induction of an IFN or cytokine response in HEK293 and Huh7 cells.…”

A stem-loop RNA RIG-I agonist confers prophylactic and therapeutic protection against acute and chronic SARS-CoV-2 infection in mice

“…The innate immune system utilizes host-encoded nucleic acid sensors, known as the pattern recognition receptors (PRRs), to surveil viral pathogens by detecting their pathogen-associated molecular patterns (PAMPs) 7 . Following SARS-CoV-2 infection, multiple cytosolic PRRs, including RIG-I, MDA-5, and LGP2, mediate viral RNA recognition in infected lung epithelial cells and initiate front-line antiviral defense through the production of IFN-I 8,9 . Upon secretion, IFN-I engages with its universally expressed receptor in autocrine and paracrine fashions, stimulating the expression of a large network of interferon stimulated genes (ISGs) to inhibit viral replication, and cytokines and chemokines to recruit specialized immune cells to sites of infection.…”