nc886 noncoding RNA regulates hepatitis B virus replication via PKR-dependent eIF2α phosphorylation

Objective(s) Hepatitis B virus (HBV) replication is tightly controlled by host stress and innate immune pathways. The small noncoding RNA nc886 (vtRNA2-1) is a known endogenous inhibitor of protein kinase R (PKR), but its role in HBV biology remains unclear. This study aimed to define the function of the nc886–PKR–eIF2α axis in HBV-replicating hepatoma cells and to determine whether nc886 depletion suppresses HBV replication via PKR-dependent translational control. Materials and methods Huh7 cells and Huh7 cells stably harboring a 1.3-mer HBV replicon were used. Endogenous nc886 and PKR expression was assessed by RT-qPCR and Western blot. Loss-of-function experiments employed two independent siRNAs against nc886 and one siRNA against PKR, alone or in combination, with scramble siRNA as control. PKR activation was induced by Poly(I:C); PKR and integrated stress response (ISR) were pharmacologically modulated using C16 (PKR inhibitor) and ISRIB (eIF2B activator), at non-toxic doses defined by MTT assay. Intracellular HBV DNA was measured by Southern blot, HBV pgRNA and subgenomic RNAs by Northern blot and RT-qPCR, and secreted HBsAg/HBeAg by ELISA. PKR–eIF2α–ATF4 signaling was evaluated by Western blot. Results nc886 and PKR were efficiently and specifically knocked down without affecting cell viability. nc886 silencing in Huh7–HBV cells increased PKR-dependent eIF2α phosphorylation and ATF4, reduced HBV pgRNA and subgenomic RNAs, and decreased intracellular HBV DNA and secreted HBsAg/HBeAg. PKR knockdown alone slightly enhanced HBV readouts and completely rescued nc886-mediated inhibition of HBV replication and ISR activation in dual-knockdown cells. C16 or ISRIB restored HBV DNA, RNA and antigen production in nc886-silenced or Poly(I:C)-treated cells, while having no effect in control cells, indicating that rescue depended on ISR modulation. Conclusion nc886 acts as a critical negative regulator of PKR-dependent ISR signaling during HBV replication in Huh7 cells. Its depletion activates PKR and eIF2α, imposing a translational block that suppresses HBV gene expression. The nc886–PKR–eIF2α module represents a novel host regulatory axis with potential relevance for host-directed HBV therapies.