Annemarthe G. van der Veen

Self-derived double-stranded RNA (self-dsRNA) acts as potent triggers of autoinflammation and damage-associated molecular patterns in cancer and infection. However, the upstream processes controlling self-dsRNA homeostasis remain unclear. We uncover a non-canonical role for human Dicer in driving cell-intrinsic immunity to self-dsRNAs that arise from editing or splicing defects, epigenetic deregulation or mitochondrial stress. Dicer loss abolishes type-I interferon induction, PKR activation, and OAS-RNase L activation in response to self – but not exogenous – dsRNA in multiple cell types, including a clinically-relevant hiPSC model of neuroinflammation. Dicer interacts with G3BP1 and LGP2 to regulate self-dsRNA availability and recognition, respectively, independently of miRNAs. As immunostimulatory self-dsRNAs fail to accumulate and activate dsRNA sensors in absence of Dicer, these findings position Dicer as a central regulator of self-dsRNA sensing. Summary figure: Self-derived dsRNAs are potent triggers of innate immune activation that accumulate due to cellular dysfunction, such as mitochondrial stress, epigenetic deregulation or editing and splicing defects. Dicer and G3BP1 are jointly required for the cytosolic accumulation of self-dsRNA, and the activation of downstream innate immune dsRNA sensors, including Dicer interactors LGP2 and PKR. Self-dsRNA driven inflammation occurs in diverse pathological contexts – including neurodegeneration, autoimmunity, and cancer – thus making Dicer and its interactors promising targets for therapeutic intervention. Created in BioRender. Ter haar, L. (2025) https://BioRender.com/40ztdl0

Introduction: The RNA sensor RIG-I performs a critical role in surveying the cytoplasm for the presence of viral nucleic acids and initiating the downstream anti-viral type I interferon pathway. Through recognition of specific features, such as the presence of a 5’ tri/diphosphate motif or highly structured base-paired regions, RIG-I effectively differentiates between RNA of viral- and self-origin. In Singleton-Merten syndrome (SMS), gain-of-function variants in RIG-I lead to a breakdown in this surveillance system and results in aberrant sensing of self-RNAs and deleterious upregulation of type I interferons. The identity of the self-RNAs binding to gain-of-function RIG-I mutants has remained elusive and their elucidation would provide a greater understanding of the aetiology of SMS. Methods: Here we used an infrared individual-nucleotide resolution UV-crosslinking and immunoprecipitation (irCLIP) approach to determine the RNA profile bound to a previously characterised ATPase-deficient SMS variant, RIG-IC268F. Results: irCLIP identified a broad array of self-RNAs, primarily those transcribed by RNA polymerase III, that were bound to RIG-I. Subsequent native RNA immunoprecipitation confirmed a prominent and specific interaction between RIG-IC268F and Y-RNAs, a family of four structurally similar non-coding RNAs. Conclusion: Manipulation of Y-RNAs alone by targeting either Y-RNA transcripts or Y-RNA stabilising proteins was insufficient to negate RIG-I induced interferon responses, hinting at a broader profile of RNA polymerase III-derived RNAs being influential in driving the sterile activation of gain-of-function RIG-I variants.

The type I Interferon (IFN-I)-induced ubiquitin-like modifier Interferon-Stimulated Gene 15 (ISG15) plays a crucial role in the innate immune response against viral infections. ISG15 is conjugated to target proteins by an enzymatic cascade, called ISGylation. While ubiquitin-specific protease 18 (USP18) serves as the major deISGylase counteracting ISG15 conjugation, ISG15 cross-reactive deubiquitylating enzymes (DUBs) have also been reported. Here, we identify USP24 as an ISG15 cross-reactive DUB through activity-based protein profiling. USP24 processes pro-ISG15 and ISG15-linked substrates in vitro, and its depletion increases ISG15 conjugates following interferon stimulation in cells without altering canonical IFN-I signaling. USP24 knockout cells show increased IFN-β and ISG expression upon activation of cytosolic RNA sensing via viral mimicry. Proteomic analysis identifies RNA helicase Moloney leukemia virus 10 (MOV10) as a specific target of USP24 for deISGylation. Our data revealed that ISGylation of MOV10 promotes MOV10 interaction with IFIT3 and enhances IFN-β production/secretion in response to viral stimuli. This process is negatively regulated by USP24, which directly deISGylates MOV10. Our data highlight USP24's role in modulating ISGylation and IFN-I production, suggesting USP24 as a potential therapeutic agent for infectious and inflammatory diseases.

RIG-I-like receptors (RLRs) are cytoplasmic RNA sensors that promote type I and type III interferon (IFN) production in response to RNA ligands of viral or endogenous origin. The RLR pathway is tightly regulated by dynamic post-translational modifications, including ubiquitination. Huwe1 is a HECT domain-containing giant ubiquitin E3 ligase that has not been implicated in the RLR or IFN pathway. Here, we investigated whether Huwe1 is required for type I IFN induction downstream of RLRs. We demonstrate that loss of Huwe1 severely attenuates the expression of IFN-β, IFN-λ1 and IFN-stimulated genes (ISGs) in ADAR1-deficient human cells and primary murine bone-marrow derived macrophages, in which unedited self RNAs that serve as RLR ligands accumulate. In addition, depletion of Huwe1 reduces the induction of type I and III IFNs upon transfection with synthetic viral RNA mimetics or infection with a picornavirus. Using proteomics, we identified several putative Huwe1 substrates, which include key components of the RLR pathway (MAVS, TRAFs). We demonstrate that these substrates interact with Huwe1 and that Huwe1 is essential for the activity of TRAF5 in type I IFN induction. Collectively, our results put Huwe1 on the map as an important ubiquitin E3 ligase in the RLR pathway and provide new insights into ubiquitin-dependent regulation of cell-intrinsic antiviral immune pathways.

Vault RNAs (vtRNAs) are a family of four small non-coding RNAs (ncRNAs) that are ubiquitously expressed in many eukaryotes and that regulate multiple cellular pathways. Their expression is increased upon infection with various DNA and RNA viruses. This suggests they are either co-opted by the virus to aid replication or function as an antiviral restriction factor. However, their precise molecular function remains unclear. Here, we show that replication of picornaviruses, alphaviruses, and beta-coronaviruses broadly enhances vtRNA expression. We find that genetic loss of vtRNAs inhibits replication of Sindbis virus (SINV) and encephalomyocarditis virus (EMCV), independent of the antiviral type I interferon (IFN) response. A proteomic screen uncovered the vtRNA interactome and revealed that vtRNAs associate with RNA binding proteins ELAVL1 and hnRNP C in uninfected and infected cells. VtRNAs facilitate the translocation of ELAVL1 and hnRNP C from the nucleus to the cytoplasm in infected cells, an event that is required for efficient viral replication. Moreover, hnRNP C and ELAVL1 fail to associate with viral RNA in the cytosol of SINV-infected cells in the absence of vtRNAs. Together, our findings reveal a novel molecular mechanism by which vtRNAs exert proviral activity during the course of SINV and EMCV infection, which opens up new avenues for therapeutic targeting to fight infectious diseases.