Dual regulatory role of hsa-miR-122b-5p in chikungunya virus infection via interaction with CHIKV 3′-UTR and HDAC4 modulation

ABSTRACT Establishment of a viral infection in the host involves complex interactions between the virus and the host. The present study was undertaken to evaluate one such interaction between a host microRNA (miRNA) with both the virus and its cellular target. Through a comprehensive high-throughput screen of a human miRNA mimics library, we identified that hsa-miR-122b-5p bound to chikungunya virus (CHIKV) 3′-untranslated region (3′-UTR), which we abrogated upon mutating the binding sites of the miRNA and determined that this miRNA regulated CHIKV infection. In-depth scrutiny of this miRNA’s expression in CHIKV-susceptible host cells divulged that it was mainly expressed in macrophages, and temporal expression profiling analysis in these cells revealed that its expression negatively correlated to the virus infection. We further identified cellular targets of miR-122b-5p through global RNA seq analysis using antagomiRs, among which histone deacetylase 4 (HDAC4) displayed attributes that promoted CHIKV infection in macrophages. To dissect this phenomenon further, we performed loss-of-function assays using both miR-122b-5p and HDAC4 and observed regulation of pro-inflammatory cytokines, including the type I interferon system. Furthermore, miRNA mimics and antagomiR assays indicated that regulation of HDAC4 by miR-122b-5p may be associated with changes in the nuclear translocation of phosphorylated IRF3 during CHIKV infection. While this suggests a possible link, additional studies are needed to confirm this interaction and its underlying mechanism. Taken altogether, our study provides insights into the dual regulatory function of miR-122b-5p during CHIKV infection, highlighting its capacity to decrease viral titer by binding directly to the 3′UTR of the viral genome and its potential to promote nuclear translocation of phosphorylated IRF3, which may be indirectly influenced by modulation of its cellular target, HDAC4, thereby regulating host immune responses during CHIKV infection in macrophages. These findings may have significant implications for understanding the pathogenesis of CHIKV and for developing novel therapeutic strategies. IMPORTANCE Human microRNAs (miRNAs) are central regulators of viral infection, acting through direct targeting of viral genomes or by modulating host cellular pathways. In this study, we demonstrate that miR-122b-5p plays a dual antiviral role during chikungunya virus (CHIKV) infection in macrophages—critical immune cells that serve as viral reservoirs. We show that miR-122b-5p directly binds to the 3′ untranslated region of the CHIKV genome, thereby suppressing viral replication. Additionally, we uncover a previously uncharacterized mechanism in which miR-122b-5p modulates the host innate immune response by repressing HDAC4, a negative regulator of the type I interferon pathway. This repression may influence nuclear translocation of phosphorylated IRF3, potentially enhancing the antiviral transcriptional response. Our findings not only deepen our understanding of macrophage-intrinsic antiviral defenses against CHIKV but also highlight miR-122b-5p as a potential therapeutic target for enhancing host immunity and limiting viral propagation.