SARS-CoV-2 Disrupts Proximal Elements in the JAK-STAT Pathway

Abstract

SARS-CoV-2 can infect multiple organs, including lung, intestine, kidney, heart, liver, and brain. The molecular details of how the virus navigates through diverse cellular environments and establishes replication are poorly defined. Here, we generated a panel of phenotypically diverse, SARS-CoV-2-infectable human cell lines representing different body organs and performed longitudinal survey of cellular proteins and pathways broadly affected by the virus. This revealed universal inhibition of interferon signaling across cell types following SARS-CoV-2 infection. We performed systematic analyses of the JAK-STAT pathway in a broad range of cellular systems, including immortalized cells and primary-like cardiomyocytes, and found that SARS-CoV-2 targeted the proximal pathway components, including Janus kinase 1 (JAK1), tyrosine kinase 2 (Tyk2), and the interferon receptor subunit 1 (IFNAR1), resulting in cellular desensitization to type I IFN. Detailed mechanistic investigation of IFNAR1 showed that the protein underwent ubiquitination upon SARS-CoV-2 infection. Furthermore, chemical Inhibition of JAK kinases enhanced infection of stem cell-derived cultures, indicating that the virus benefits from inhibiting the JAK-STAT pathway. These findings suggest that the suppression of interferon signaling is a mechanism widely used by the virus to evade antiviral innate immunity, and that targeting the viral mediators of immune evasion may help block virus replication in patients with COVID-19. IMPORTANCE SARS-CoV-2 can infect various organs in the human body, but the molecular interface between the virus and these organs remains unexplored. In this study, we generated a panel of highly infectable human cell lines originating from various body organs and employed these cells to identify cellular processes commonly or distinctly disrupted by SARS-CoV-2 in different cell types. One among the universally impaired processes was interferon signaling. Systematic analysis of this pathway in diverse culture systems showed that SARS-CoV-2 targets the proximal JAK-STAT pathway components, destabilizes the type I interferon receptor though ubiquitination, and consequently renders the infected cells resistant to type I interferon. These findings illuminate how SARS-CoV-2 can continue to propagate in different tissues even in the presence of a disseminated innate immune response.

SARS-CoV-2 infection induces a pro-inflammatory cytokine response through cGAS-STING and NF-κB

“…This includes limiting activation of the key signaling proteins or kinases such as MAVS or TBK1, or through perturbing the function of IRF3, which is a key transcription factor in activating IFN responses 20 – 26 . SARS-CoV-2 infection has also been shown to inhibit downstream IFN signaling by attenuating JAK/STAT signaling 27 . The range of varying observations in cell-intrinsic immune response activation or repression leaves several open questions as to how SARS-CoV-2 infection modulates immune responses in infected epithelial cells and how these initial responses can lead to either viral clearance or severe disease.…”

Cellular and Molecular Effects of SARS-CoV-2 Linking Lung Infection to the Brain

“…The primary infected organ of SARS-CoV-2 is the lung causing acute respiratory distress syndrome (ARDS) and respiratory failure (39). Initially the virus infects the respiratory epithelial cells, which highly express ACE2 that provides an excellent entry for the virus (14).…”

“…The evasion of IFN-I-mediated innate immunity is likely orchestrated by the viral protein N which acts as an antagonist of IFN signaling. In this scenario, novel coronaviruses can counteract IFN expression by inhibiting the phosphorylation and nuclear translocation of transcription factors of the JAK/STAT signaling pathway (14,39,42). The suppressed expression of IFN-I can lead to an insufficient response of the host cells and inadequate clearance of viral infections (43).…”

“…The suppressed expression of IFN-I can lead to an insufficient response of the host cells and inadequate clearance of viral infections (43). Thus, the activation of early antiviral programs appears to be prohibited contributing to the evasion of innate antiviral immunity by the coronavirus (14,39). Through the suppressed expression of IFN-I, virions can regulate IFN-I signaling in infected macrophages, in which an increased level of pro-inflammatory cytokine expression (especially TNF-a and IL-6) via the NF-kB cascade is auto-amplified through positive feedback loops.…”

“…On the other hand, at a later stage, the activation of antiviral programs and the recruitment of non-infected immune cells occur. Virus particles released from the infected dead cells are recognized by endosomal RNA pattern recognition receptors (PRRs) which leads to the activation of the innate immune system and its cellular machinery (39,44). Recent studies reported that not only the main RNA sensors, including cytoplasmic retinoic acid-inducible gene I (RIG-I) and melanoma differentiation-associated gene 5 (MDA5), have a key role in the detection and identification of coronavirus derived PAMPs (45,46), but also pattern recognition toll-like receptors 3 and 7 (TLR-3 and TLR-7) are activated.…”