Scientists from Hokkaido University have discovered a novel defensive response to SARS-CoV-2 that involves the viral pattern recognition receptor RIG-I. Upregulating expression of this protein could strengthen the immune response in COPD patients.
COVID-19 does not affect all infected individuals equally.
Many individuals are asymptomatic; of those who are symptomatic, the large majority have mild symptoms, and only a small number have severe cases. The reasons for this are not fully understood and are an important area of ongoing research.
A team of scientists from Hokkaido University, led by Professor Akinori Takaoka of the Institute for Genetic Medicine, has shown that RIG-I, a biological molecule that detects RNA viruses, restrains SARS-CoV-2 replication in human lung cells. Their findings, which could help predict COVID-19 patient outcomes, were published in the journal Nature Immunology.
To date, over 162 million people have been affected by COVID-19. About 40%–45% of these individuals are asymptomatic; as for the rest, around 35% – 40% experienced a mild form of the disease, while the remaining 19% were affected by symptoms that were severe enough to warrant hospitalization or were fatal, which are usually associated with comorbidities and risk factors such as chronic obstructive pulmonary disease (COPD). This range of symptoms indicates that there are vast differences between individual responses to the virus.
Microbial pathogens in our body are detected by proteins called pattern recognition receptors (PRRs), which also trigger immune responses to these pathogens. Viral infections are detected by a subset of PRRs; the scientists focused their attention on the protein RIG-I, which belongs to this subset. RIG-I is known to be critical for the detection and response to RNA viruses such as the influenza virus.
In experiments carried out in cell culture lines, the scientists found that there was little innate immune response to SARS-CoV-2 in pulmonary cells, suggesting the signaling pathway leading to immune response was aborted. Nevertheless, viral replication was suppressed.
The scientists investigated the role of RIG-I and found that its deficiency caused increased viral replication. Further experiments confirmed that the suppression of viral replication was dependent on RIG-I.
A single previous study has shown that RIG-I expression is downregulated in pulmonary cells of COPD patients. Using primary pulmonary cells from two COPD patients, the scientists showed that this downregulation of RIG-I resulted in the detection of viral replication after 5 days .
They also demonstrated that treatment of these COPD cells with all-trans retinoic acid (ATRA), which upregulates the expression of RIG-I, significantly reduced viral titres in the cells. Furthermore, using RIG-I mutants, they were able to elucidate the mechanisms by which RIG-I suppressed SARS-CoV-2 replication: The helicase domain, a structural element in RIG-I, interacts with the viral RNA, blocking a virus-derived enzyme responsible for replication.
This study has demonstrated a unique viral recognition mode of RIG-I, termed the RIG-I-mediated signaling-abortive anti-SARS-CoV-2 defense mechanism. It has also indicated that RIG-I expression levels are one of the potential parameters for the prediction of COVID-19 patient outcomes.
Further work must be done to uncover factors or conditions that modulate RIG-I expression levels, and may lead to new strategies to control SARS-CoV-2 infection.
Coronaviruses are a family of viruses with notably large single-stranded RNA genomes and broad species tropism among mammals (Graham and Baric, 2010). Recently, a coronavirus, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), was discovered to cause the severe respiratory disease known as coronavirus disease 2019 (COVID-19).
It is highly transmissible in human populations, and its spread has resulted in a global pandemic with more than a million deaths to date (Andersen et al., 2020; Zou et al., 2020). We do not fully understand the molecular basis of infection and pathogenesis of this virus in human cells. Accordingly, there is an urgent need to understand these mechanisms to guide the development of therapeutic agents.
SARS-CoV-2 encodes 27 proteins with diverse functional roles in virus replication and packaging (Bar-On et al., 2020; Wang et al., 2020). These include 4 structural proteins: the nucleocapsid (N; which binds the viral RNA) and the envelope (E), membrane (M), and spike (S) proteins, which are integral membrane proteins.
In addition, there are 16 non-structural proteins (NSP1–NSP16) that encode the RNA-directed RNA polymerase, helicase, and other components required for virus replication (da Silva et al., 2020). Finally, there are 7 accessory proteins (ORF3a–ORF8) whose function in virus replication or packaging remains largely uncharacterized (Chen and Zhong, 2020; Finkel et al., 2020).
As obligate intracellular parasites, viruses require host cell components to translate and transport their proteins and to assemble and secrete viral particles (Maier et al., 2016). The mammalian innate immune system acts to rapidly detect and block viral infection at all stages of the virus life cycle (Chow et al., 2018; Jensen and Thomsen, 2012; Wilkins and Gale, 2010).
The primary form of intracellular virus surveillance engages the interferon pathway, which amplifies signals resulting from detection of intracellular viral components to induce a systemic type I interferon response upon infection (Stetson and Medzhitov, 2006). Specifically, cells contain various RNA sensors (such as RIG-I and MDA5) that detect the presence of viral RNAs and promote nuclear translocation of the transcription factor IRF3, leading to transcription, translation, and secretion of interferon (e.g., interferon [IFN]-α and IFN-β). Binding of IFN to cognate cell-surface receptors leads to transcription and translation of hundreds of antiviral genes.
In order to successfully replicate, viruses employ a range of strategies to counter host antiviral responses (Beachboard and Horner, 2016). In addition to their essential roles in the viral life cycle, many viral proteins also antagonize core cellular functions in human cells to evade host immune responses.
For example, human cytomegalovirus (HCMV) encodes proteins that inhibit major histocompatibility complex (MHC) class 1 display on the cell surface by retaining MHC proteins in the endoplasmic reticulum (Miller et al., 1998), polioviruses encode proteins that degrade translation initiation factors (eIF4G) to prevent translation of 5′-capped host mRNAs (Kempf and Barton, 2008; Lloyd, 2006), and influenza A encodes a protein that modulates mRNA splicing to degrade the mRNA that encodes RIG-I (Kochs et al., 2007; Zhang et al., 2018).
Suppression of the IFN response has recently emerged as a major clinical determinant of COVID-19 severity (Zhang et al., 2020), with almost complete loss of secreted IFN characterizing the most severe cases (Hadjadj et al., 2020). The extent to which SARS-CoV-2 suppresses the IFN response is a key characteristic that distinguishes COVID-19 from SARS and Middle East respiratory syndrome (MERS) (Lokugamage et al., 2020).
Several strategies have been proposed for how the related SARS- and MERS-causing viruses may hijack host cell machinery and evade immune detection, including repression of host mRNA transcription in the nucleus (Canton et al., 2018), degradation of host mRNA in the nucleus and cytoplasm (Kamitani et al., 2009; Lokugamage et al., 2015), and inhibition of host translation (Nakagawa et al., 2018). Nonetheless, the extent to which SARS-CoV-2 uses these or other strategies and how they may be executed at a molecular level remains unclear.
Understanding the interactions between viral proteins and components of human cells is essential for elucidating their pathogenic mechanisms and for development of effective therapeutic agents. Because SARS-CoV-2 is an RNA virus, and many of its encoded proteins are known to bind RNA (Sola et al., 2011), we reasoned that these viral proteins may interact with specific human mRNAs (critical intermediates in protein production) or non-coding RNAs (critical structural components of diverse cellular machines) to promote virus propagation.
Here we comprehensively define the interactions between each SARS-CoV-2 protein and human RNA. We show that 10 viral proteins form highly specific interactions with mRNAs or noncoding RNAs (ncRNAs), including those involved in progressive steps of host cell protein production.
We show that NSP16 binds to the mRNA recognition domains of the U1 and U2 RNA components of the spliceosome and acts to suppress global mRNA splicing in SARS-CoV-2-infected human cells. We find that NSP1 binds to a precise region on the 18S ribosomal RNA that resides in the mRNA entry channel of the initiating 40S ribosome.
This interaction leads to global inhibition of mRNA translation upon SARS-CoV-2 infection of human cells. Finally, we find that NSP8 and NSP9 bind to discrete regions on the 7SL RNA component of the signal recognition particle (SRP) and interfere with protein trafficking to the cell membrane upon infection.
We show that disruption of each of these essential cellular functions acts to suppress the type I IFN response to viral infection. Our results uncover a multipronged strategy utilized by SARS-CoV-2 to antagonize essential cellular processes and robustly suppress host immune defenses.
reference link: https://www.sciencedirect.com/science/article/pii/S0092867420313106
More information: Taisho Yamada et al, RIG-I triggers a signaling-abortive anti-SARS-CoV-2 defense in human lung cells, Nature Immunology (2021). DOI: 10.1038/s41590-021-00942-0
