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Inhibition of Virally-Induced TFEB Proteasomal Degradation as a Host-Centric Therapeutic Approach for Coronaviral Infection

ABSTRACT: The endo-lysosomal pathway plays an evolutionarily conserved role in pathogen clearance, and both bacteria and viruses have evolved complex mechanisms to evade this host defense system. Here, we describe a novel aspect of coronaviral infection, whereby the master transcriptional activator of lysosomal homeostasis – TFEB – is targeted for proteasomal-mediated degradation upon viral infection. Through mass spectrometry analysis and an unbiased siRNA screen, we identify that TFEB protein stability is coordinately regulated by the E3 ubiquitin ligase subunit DCAF7 and the PAK2 kinase. In particular, viral infection triggers marked PAK2 activation, which in turn, phosphorylates and primes TFEB for ubiquitin-mediated protein degradation. Deletion of either DCAF7 or PAK2 blocks virally-stimulated TFEB degradation and protects against virally-induced cytopathic effects. We further derive a series of novel small molecules that interfere with the DCAF7-TFEB interaction. These agents inhibit virus-induced TFEB degradation and demonstrate broad anti-viral activities including attenuating SARS-CoV-2 infection in two animal models. Together, these results delineate a virally-triggered pathway that impairs lysosomal homeostasis in the host. Small molecule E3 ubiquitin ligase DCAF7 inhibitors that restore lysosomal function represent a novel class of host-directed, anti-viral therapies useful for current and potentially future coronaviral variants.

ORGANISM(S): Homo sapiens

PROVIDER: GSE292982 | GEO | 2025/06/16

REPOSITORIES: GEO

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Project description:Upon infection, viruses remodel host cells to create an environment hospitable to viral replication. In response, host cells have evolved to sense infection and rapidly induce pathways to limit viral replication. One strategy used by both players is to regulate the host cell proteome for their benefit. To characterize these changes, we used a mass spectrometry strategy to define alterations in the viral and host proteome during infection of human cells with West Nile virus (WNV). Our studies reveal previously uncharacterized post-translational modifications (PTMs) on viral proteins, including phosphorylation sites on the WNV nonstructural proteins, NS3 and NS5, that impact viral RNA replication. Additionally, we monitored changes in host protein abundance and found that while 82 proteins had increased expression upon WNV infection, only five of these are canonical interferon stimulated genes (ISGs). Our data suggests that the majority of the upregulated non-ISGs are regulated at the translational, rather than transcriptional level, defining a new group of virus-induced proteins (VIPs). HERPUD1 is a stress-response protein that was induced at both the transcriptional and translational level. We show HERPUD1 restricts WNV replication, likely through a mechanism independent of its previously defined role in ER-associated degradation (ERAD). Our phosphoproteomics studies revealed eight phosphorylation sites on viral proteins, including a site on the WNV helicase/protease NS3 that is important for viral replication. Further, we identified XXX phosphorylation sites on host proteins with increased abundance and XXX sites with decreased abundance during WNV infection. We used bioinformatics to identify phosphosites predicted to increase host protein activity and found two antiviral host kinases that are activated by phosphorylation during WNV infection. First, we identified a phosphorylation site at S108 of AMPKβ1, a non-catalytic subunit that is thought to regulate activity of the AMPK complex. We also found that a group I p21-activated kinase, PAK2, is phosphorylated at S141. This phosphorylation event in the autoinhibitory domain activates PAK2, which restricts viral protein translation. Altogether, our work contributes to our understanding of the interplay between host and virus while providing a resource to define the changes to the proteome that regulate viral infection.

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Inhibition of Virally-Induced TFEB Proteasomal Degradation as a Host-Centric Therapeutic Approach for Coronaviral Infection

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