Interferon-Inducible MicroRNA miR-128 Modulates HIV-1 Replication by Targeting TNPO3 mRNA

Abstract

The HIV/AIDS pandemic remains an important threat to human health. We have recently demonstrated that a novel microRNA (miR), miR-128, represses retrotransposon long interspaced element 1 (L1) by a dual mechanism, namely, by directly targeting the coding region of the L1 RNA and by repressing a required nuclear import factor (TNPO1). We have further determined that miR-128 represses the expression of all three TNPO proteins (transportins TNPO1, TNPO2, and TNPO3). Here, we establish that miR-128 also influences HIV-1 replication by repressing TNPO3, a factor that regulates HIV-1 nuclear import and viral; replication of TNPO3 is well established to regulate HIV-1 nuclear import and viral replication. Here, we report that type I interferon (IFN)-inducible miR-128 directly targets two sites in the TNPO3 mRNA, significantly downregulating TNPO3 mRNA and protein expression levels. Challenging miR-modulated Jurkat cells or primary CD4+ T-cells with wild-type (WT), replication-competent HIV-1 demonstrated that miR-128 reduces viral replication and delays spreading of infection. Manipulation of miR-128 levels in HIV-1 target cell lines and in primary CD4+ T-cells by overexpression or knockdown showed that reduction of TNPO3 levels by miR-128 significantly affects HIV-1 replication but not murine leukemia virus (MLV) infection and that miR-128 modulation of HIV-1 replication is reduced with TNPO3-independent HIV-1 virus, suggesting that miR-128-indued TNPO3 repression contributes to the inhibition of HIV-1 replication. Finally, we determine that anti-miR-128 partly neutralizes the IFN-mediated block of HIV-1. Thus, we have established a novel role of miR-128 in antiviral defense in human cells, namely inhibiting HIV-1 replication by altering the cellular milieu through targeting factors that include TNPO3. IMPORTANCE HIV-1 is the causative agent of AIDS. During HIV-1 infection, type I interferons (IFNs) are induced, and their effectors limit HIV-1 replication at multiple steps in its life cycle. However, the cellular targets of INFs are still largely unknown. In this study, we identified the interferon-inducible microRNA (miR) miR-128, a novel antiviral mediator that suppresses the expression of the host gene TNPO3, which is known to modulate HIV-1 replication. Notably, we observe that anti-miR-128 partly neutralizes the IFN-mediated block of HIV-1. Elucidation of the mechanisms through which miR-128 impairs HIV-1 replication may provide novel candidates for the development of therapeutic interventions.

SIV Infection Regulates Compartmentalization of Circulating Blood Plasma miRNAs within Extracellular Vesicles (EVs) and Extracellular Condensates (ECs) and Decreases EV-Associated miRNA-128

“…In primary neurons, the HIV Tat protein up-regulates miR-128-3p with concomitant suppression of the pre-synaptic SNAP25 protein, which may perturb neuronal activity [ 81 ]. In CD4+ T cells, miR-128-3p inhibits viral replication and delays virus spread by repressing the expression of TNPO3 [ 82 ], an observation similar to miR-128-3p mediated repression of retrotransposon long interspaced element 1 by targeting TNPO1 [ 83 ]. Notably, mature miR-128 is encoded by miR-128-1 and miR-128-2 [ 84 , 85 ].…”

Decoding nonspecific interactions between human nuclear transport proteins: A computational study

“…TNPO3 also known as transportin-SR2 is a carrier and the transporter of splicing factor in humans ( Maertens et al, 2014 ). Literature study suggests that TNPO3 mediates virus entry and particularly it is involved in Human immunodeficiency virus (HIV) (Bochnakian et al, 2019; De Iaco et al, 2013; Rice et al, 2020; Valle-Casuso et al, 2012 ). Additionally, clinical study suggests that it plays a role in primary biliary cirrhosis and systemic sclerosis ( Radstake et al, 2010 ).…”

The potential use of microRNAs as a therapeutic strategy for SARS-CoV-2 infection

“…For example, type I IFN-inducible miR-128 directly targets two sites in the transportin TNPO3 mRNA, considerably downregulating TNPO3 mRNA and protein expression levels. TNPO3 is a nuclear importer that is important for HIV-1 replication, and downregulation of this protein prevents viral replication [ 11 ]. Others have shown that miR-128 can inhibit HIV replication by directly targeting the 3′-UTR of the viral genome [ 110 ].…”