LncFENIX restricts influenza A virus replication by impairing PDIA3-mediated oxidative folding of hemagglutinin

Abstract

Influenza A virus (IAV) relies on host endoplasmic reticulum (ER) homeostasis machinery to support the oxidative folding and maturation of viral glycoproteins. Although long non-coding RNAs (lncRNAs) are increasingly recognized as critical regulators of host-virus interactions, whether host lncRNAs modulate ER protein-folding machinery during IAV infection remains largely unknown. In this study, we identified lncFENIX, an IAV-inducible avian lncRNA, and investigated its role and mechanism in the regulation of viral replication. Differentially expressed lncRNAs were screened by transcriptomic profiling of IAV-infected cells, followed by gain- and loss-of-function analyses to assess antiviral activity. RNA pull-down, RNA immunoprecipitation, co-immunoprecipitation, fluorescence in situ hybridization, and immunofluorescence assays were used to characterize the interaction of lncFENIX with PDIA3 and its subcellular localization. Thiol-trapping, protein stability, pharmacological inhibition, and gene silencing assays were performed to examine the effects of lncFENIX on hemagglutinin (HA) folding, PDIA3 turnover, and SEC62-dependent autophagic clearance. The antiviral effect of lncFENIX was further evaluated in a mouse model using lipid nanoparticle-mediated RNA delivery. LncFENIX was induced by IAV infection and functioned as a restriction factor against multiple IAV subtypes. Mechanistically, lncFENIX localized predominantly to the cytoplasm and bound PDIA3 through its functional C-terminal region. This interaction was associated with reduced productive association between PDIA3 and calnexin, thereby compromising PDIA3-supported oxidative folding of HA and promoting HA misfolding. In parallel, lncFENIX promoted SEC62-dependent, autophagy-associated turnover of PDIA3, which contributed to lncFENIX-associated IAV restriction. Consistent with these findings, lncFENIX delivery reduced viral burden and improved survival in IAV-infected mice. These findings identify lncFENIX as a previously unrecognized host restriction lncRNA that suppresses IAV replication by modulating a PDIA3-associated ER homeostasis pathway required for efficient viral HA maturation. Our study reveals a noncanonical lncRNA mechanism linking RNA-mediated regulation of ER protein-folding machinery to antiviral defense and provides proof-of-concept evidence that LNP-mediated lncFENIX delivery can improve disease outcome in a mouse IAV challenge model.