The involvement of microRNAs in HCV and HIV infection

Global MicroRNA Profiling of HSV-1 Infected Cornea Identifies miR-329 as a Novel Regulator of Virus Infection

Purpose

Although the mechanisms underlying herpes simplex virus type-1 (HSV-1) ocular infection have been extensively studied, the role of host microRNAs (miRNAs) in the pathobiology of herpetic keratitis (HK) is not well understood. The aim of this study was to identify endogenous miRNA regulators involved in the progression of HSV-1 ocular infection.

Methods

C57BL/6 mice were infected with HSV-1 strain McKrae following epithelial debridement, and corneal miRNA profiles were analyzed at various time points using miRNA sequencing (miRNA-seq). The miRNA expression was measured at 2, 4, 6, and 10 days post-infection. Ingenuity Pathway Analysis (IPA) was used to identify immune pathways potentially targeted by differentially expressed miRNAs. The role of selected miRNAs in viral entry and replication was assessed by overexpression in murine embryonic fibroblasts (MEFs) and human corneal epithelial cells (HCEs).

Results

A total of 32 miRNAs at 2 days post-infection, 21 miRNAs at 4 days post-infection, 140 miRNAs at 6 days post-infection, and 27 miRNAs at 10 days post-infection showed significant changes in expression. IPA revealed that differentially expressed miRNAs targeted several immune pathways, including TLR and interferon signaling. Notably, mmu-miR-184-3p and mmu-let-7d-5p were upregulated, whereas mmu-miR-329-3p was down-regulated during infection. Functional assays demonstrated that overexpression of miR-329, but not miR-184-3p or miR-let-7d-5p, increased HSV-1 viral entry and replication in a dose-dependent manner. In contrast, miR-329 inhibition reversed these effects, suggesting its role as a pro-viral miRNA. Increased plaque formation and viral gB expression further confirmed miR-329's pro-viral role.

Conclusions

Our findings suggest that miR-329 functions as a pro-viral miRNA by disrupting TLR9 signaling, thus facilitating HSV-1 replication. Inhibition of miR-329 enhances TLR9-mediated antiviral responses, highlighting the potential of targeting host miRNAs as a novel therapeutic strategy for managing viral keratitis.

Analysis of the Contribution of 6-mer Seed Toxicity to HIV-1-Induced Cytopathicity

HIV-1 (HIV) infects CD4+ T cells, the gradual depletion of which can lead to AIDS in the absence of antiretroviral therapy (ART). Some cells, however, survive HIV infection and persist as part of the latently infected reservoir that causes recurrent viremia after ART cessation. Improved understanding of the mechanisms of HIV-mediated cell death could lead to a way to clear the latent reservoir. Death induced by survival gene elimination (DISE), an RNA interference (RNAi)-based mechanism, kills cells through short RNAs (sRNAs) with toxic 6-mer seeds (positions 2 to 7 of sRNA). These toxic seeds target the 3' untranslated region (UTR) of mRNAs, decreasing the expression of hundreds of genes critical for cell survival. In most cells under normal conditions, highly expressed cell-encoded nontoxic microRNAs (miRNAs) block access of toxic sRNAs to the RNA-induced silencing complex (RISC) that mediates RNAi, promoting cell survival. HIV has been shown to inhibit the biogenesis of host miRNAs in multiple ways. We now report that HIV infection of cells deficient in miRNA expression or function results in enhanced RISC loading of an HIV-encoded miRNA HIV-miR-TAR-3p, which can kill cells by DISE through a noncanonical (positions 3 to 8) 6-mer seed. In addition, cellular RISC-bound sRNAs shift to lower seed viability. This also occurs after latent HIV provirus reactivation in J-Lat cells, suggesting independence of permissiveness of cells to viral infection. More precise targeting of the balance between protective and cytotoxic sRNAs could provide new avenues to explore novel cell death mechanisms that could be used to kill latent HIV. IMPORTANCE Several mechanisms by which initial HIV infection is cytotoxic to infected cells have been reported and involve various forms of cell death. Characterizing the mechanisms underlying the long-term survival of certain T cells that become persistent provirus reservoirs is critical to developing a cure. We recently discovered death induced by survival gene elimination (DISE), an RNAi-based mechanism of cell death whereby toxic short RNAs (sRNAs) containing 6-mer seed sequences (exerting 6-mer seed toxicity) targeting essential survival genes are loaded into RNA-induced silencing complex (RISC) complexes, resulting in inescapable cell death. We now report that HIV infection in cells with low miRNA expression causes a shift of mostly cellular RISC-bound sRNAs to more toxic seeds. This could prime cells to DISE and is further enhanced by the viral microRNA (miRNA) HIV-miR-TAR-3p, which carries a toxic noncanonical 6-mer seed. Our data provide multiple new avenues to explore novel cell death mechanisms that could be used to kill latent HIV.