The role of interferon-stimulated long non-coding RNA PKR-IT1 in the regulation of Zika virus and dengue virus replication and antiviral response

ABSTRACT Interferon-stimulated genes play a critical role in the innate immune response against flaviviral infection. While recent studies have reported that interferon-stimulated lncRNAs participate in antiviral immunity, the functions of numerous lncRNAs in host-flavivirus interactions remain uncharacterized. Here, we demonstrate that the expression of lncRNA PKR-IT1 is induced by ZIKV and DENV infection. PKR-IT1 was induced by virus, poly(I:C), and IFNs in A549 cells, but this induction was largely abolished upon knockout of IPS-1 or IFNAR1 during viral infection. Additionally, PKR-IT1 overexpression inhibited viral production, whereas its suppression in A549, Huh7, and SH-SY5Y cells enhanced ZIKV replication. In PKR-IT1 knockout cells, viral replication also markedly increased compared with that in control cells. Interestingly, PKR-IT1 overexpression enhanced the activation of the JAK-STAT signaling pathway triggered by flaviviral infection and upregulated ISG expression. Conversely, PKR-IT1 deficiency decreased JAK1 and STAT1 phosphorylation levels, thereby impairing ISG expression. Mechanistically, the silencing of STAT1 in PKR-IT1-overexpressing cells partially restored ZIKV replication. Furthermore, PKR-IT1 directly bound PABPC1 and promoted its proteasome-dependent degradation. PABPC1 was found to bind to ZIKV RNA, while the inhibition of PABPC1 attenuated the levels of ZIKV protein, viral particles, and later viral RNA. Notably, the reintroduction of PABPC1 restored viral replication in PKR-IT1-overexpressing cells. Clinically, PKR-IT1 levels negatively correlate with fever duration and symptom number, and are lower in DENV-infected patients with severe leukopenia and thrombocytopenia. In summary, PKR-IT1 modulates flavivirus replication and JAK-STAT signaling, and may serve as a clinical correlate of dengue severity, offering insights for antiviral therapy development. IMPORTANCE Flaviviruses such as ZIKV and DENV pose significant public health threats, yet the roles of long non-coding RNAs (lncRNAs) in host antiviral immunity remain poorly understood. Here, we identified that PKR-IT1, as an interferon-stimulated lncRNA, not only suppresses flavivirus replication by binding PABPC1 to promote its proteasome-mediated degradation, but also enhances the activation of the JAK-STAT signaling cascade during flavivirus infection. Importantly, clinical correlations reveal that lower PKR-IT1 expression is associated with severe leukopenia and thrombocytopenia in DENV-infected patients, as well as longer fever duration and more symptoms. These findings establish that PKR-IT1 not only acts as a novel modulator of both flavivirus replication and the JAK-STAT signaling pathway, but also may serve as a correlate of dengue disease severity. By elucidating a previously uncharacterized lncRNA-mediated regulatory mechanism, this work provides a foundation for developing therapeutic strategies and prognostic tools against flaviviral infections.