Host derived miRNAs can bind to HIV RNA, directly regulating pathogenesis (Trobaugh and Klimstra, 2017). For instance, recent data has shown that miR-139-5p plays a role in activating latent HIV infected cells, by regulating FOX01, as well as FOS and JUN transcription factors (Okoye et al., 2021). The expression of miR-28, miR-125b, miR-150, miR-223, and miR-382 were significantly lower in activated CD4+ T cells in comparison to its resting counterpart. The same group of miRNAs may play a role in establishing viral latency by interacting with a conserved 1.2 kb fragment found in the 3′UTR of all HIV transcripts. These miRNAs can inhibit the translation of all viral proteins with the exception of nef (Huang et al., 2007). Moreover, the study showed that infected cells with established latency could be reactivated by treatment with miRNA inhibitors, suggesting that cellular miRNAs may provide a mechanistic effect towards HIV latency (Huang et al., 2007). Besides their role in promoting HIV latency, these five miRNAs play a crucial role in preventing HIV infection of monocytes and monocyte-derived macrophages (MDM). MiR-28, miR-125b, miR-150, miR-223, and miR-382 were observed at significantly higher levels in monocytes compared to MDM. These miRNAs were found to impede HIV reverse transcriptase activity in both cell types. However, the activity of HIV reverse transcriptase was dependant on the level of these miRNAs. This may explain why monocyte differentiation into macrophages is required for effective HIV infection (Wang et al., 2009).

Nef expression can also be influenced by cellular miRNAs (Ahluwalia et al., 2008; Sun et al., 2012). Ahluwalia et al. found that miR-29a and miR-29b may target HIV nef expression, which resulted in repression of nef translation and subsequent decrease in viral load (Figure 1) (Ahluwalia et al., 2008).

Moreover, in a series of refined experiments, Sun et al. demonstrated a new regulatory circuit during HIV infection (Sun et al., 2012). The downregulation of the miR-29 family could be associated with nef up-regulation and apoptosis of CD4+ cells (Sun et al., 2012). In addition, previous studies showed that miR-29 inhibited HIV replication by approximately 60%, while miR-133b, miR-138, miR-326, miR-149, and miR-92a reduced HIV viral replication by 40% (Houzet et al., 2012). In silico screening showed that these miRNAs may possibly target the 5′LTR (miR-326), env (miR-133b, miR-138), gag (miR-149), and pol (miR-92a) leading to the repression of viral replication.

Recent work by Chen et al. showed another form of miRNA regulation of HIV viruses through the interaction of miR-146a with the viral protein gag (Figure 1) (Chen et al., 2014). This interaction resulted in a viral-RNA-mediated gag assembly blockage, thereby interfering with viral budding and infectivity (Chen et al., 2014). These findings illustrate that miRNAs can alter viral gene expression via direct targeting of HIV mRNAs, with variable mechanisms of action dictated by the cell types.

MiRNAs regulate HIV infection through indirect modulation of host factor expression. One viral-dependent factor in cells is Cyclin T1, characterised as an essential part of the PTEFb complex, responsible for facilitating viral transcription (Hoque et al., 2011). The direct modulation is facilitated through the interaction with tat, which recruits the complex to HIV TAR, thereby impacting viral latency (Hoque et al., 2011). Recent work by Sung et al. described that miR-198targets and down-regulates Cyclin T1 mRNA and protein expression, which subsequently impairs the tat-mediated transcriptional activation of HIV in infected monocytes and macrophages (Sung and Rice, 2009). Over-expression of miR-198 inhibited HIV replication in macrophages, suggesting that cell type-specific mechanisms may be an effect executed by miRNAs (Sung and Rice, 2009). Additional studies identified that Cyclin T1 inhibition is exerted by cellular miRNAs (miR-27b, miR-29b, miR-150, and miR-223) in resting CD4+ T cells (Chiang et al., 2012). However, CD4+ T cell activation followed the downregulation of the miRNAs. This result was correlated with enhanced HIV susceptibility and productive replication (Chiang et al., 2012).

The viral protein tat is an essential transcriptional activator that interacts with several cellular proteins. For efficient HIV transcriptional activation, tat must be acetylated by p300-CREB binding protein associated factor (PCAF) (D'Orso and Frankel, 2009). Remarkably, miR-17/92 family of host miRNAs impedes HIV infection by downregulating PCAF (Triboulet et al., 2007). Triboulet et al. also showed that miR-17 as well as miR-20a inhibited PCAF expression at the mRNA and protein levels. In addition, HIV can actively repress miR-17-5p and miR-20a to enhance viral translation through p300/PCAF-dependant tat activation (Triboulet et al., 2007).

Another well characterised cellular factor that interacts with HIV tat to up-regulate viral transcription is the purine-rich element binding protein α (Pur-α) (Wortman et al., 2000). A collection of six cellular miRNAs (miR-15a, miR-15b, miR-16, miR-20a, miR-93, and miR-106b) enriched in monocytes were linked with the repression of Pur-α (Shen et al., 2012). Consequently, inhibition of these miRNAs in monocytes increased the expression of Pur-α, resulting in an increase in HIV infection (Shen et al., 2012).

MiR-155 has demonstrated significant effects on HIV infection through a Toll-Like receptor (TLR)-dependant mechanism (Swaminathan et al., 2012a). Swaminathan et al. showed that miR-155 is significantly up-regulated in MDMs, stimulated by TLR3 and TLR4 (Swaminathan et al., 2012a). Furthermore, up-regulation of miR-155 through TLR stimulation leads to decreased mRNA and protein expression of ADAM10, TNPO3, NUP153, and LEDGF/p75, in MDMs (Swaminathan et al., 2012a). Gene silencing of LEDGF had the most significant effect on HIV infection (Figure 1) (Swaminathan et al., 2012a). However, co-silencing of both LEDGF and ADAM10 had a more substantial impact, impairing the transport of viral pre-integration complexes (Swaminathan et al., 2012a).

The inhibition of TRIM32 by miR-155 results in post-integration latency of HIV (Ruelas et al., 2015). TRIM32 directs NF-κB to the nucleus via a tat-independent mechanism, as described by Ruelas et al. (2015). The study characterises a novel mechanism by which TRIM32 activates NF-κB. Collectively, the inhibitory effect of miR-155 on TRIM32 highlights a new tool for HIV remaining in infected reservoirs (Ruelas et al., 2015). Despite this significant study, recent studies have identified miR-155 as a potent biomarker of activated T cells and immune dysfunction in HIV-infected individuals (Jin et al., 2017a; Jin et al., 2017b; Zhang et al., 2021a).

MiRNAs can also restrict viral entry by targeting the receptors and co-receptors exploited for HIV entry. Orecchini et al. report a tat-dependant mechanism that controls CD4 receptor by up-regulating miR-222 (Orecchini et al., 2014). In addition, Lodge et al. demonstrated that miR-221 and miR-222 are up-regulated in MDMs, targeting the 3′ UTR of CD4 (Orecchini et al., 2014). The mRNA and subsequent protein expression are reduced, ultimately impairing HIV entry into MDM (Lodge et al., 2017). Labbaye et al. showed that promyelocytic leukaemia zinc finger (PLZF) could regulate miR-146a, subsequently controlling the expression of CXCR4 in vitro (Labbaye et al., 2008). Activation of resting CD4+ T cells by phytohemagglutinin results in the downregulation of miR-146a (Quaranta et al., 2015). Downregulation of miR-146a results in the overexpression of CXCR4 co-receptor promoting viral entry in CD4+ T cells (Quaranta et al., 2015).

Vpr HIV-binding protein (vprBP) is a cellular cofactor that forms part of a ubiquitin protein ligase complex. VprBP promotes HIV infection (Ma et al., 2014). Ma et al. demonstrated that miR-1236 inhibitors increased translation of vprBP in monocytes, thus facilitating HIV infection. Contrary to monocytes, miR-1236 mimics in monocyte-derived dendritic cells had supressed vprBP, which was complemented by decreased infection (Ma et al., 2014).

High surface expression of human leukocyte antigen C (HLA-C) greatly corresponded with slower disease progression via superior control of HIV viremia. Several genetic variants have been shown to disrupt miR-148a regulation of HLA-C (Kulkarni et al., 2011; Blais et al., 2012; Kulkarni et al., 2013). Disruption of miRNA binding site allows high expressing HLA-C alleles to escape miR-148a regulation (Kulkarni et al., 2011). HLA-C alleles that do not have a disrupted miR-148a binding site are tightly regulated by miR-148a and are expressed at low levels. The polymorphisms affecting HLA-C expression through disrupted miR-148a binding are rs9264942, rs67384697, and rs735316, with the variants of rs9264942 and rs67384697 being in linkage disequilibrium (Kulkarni et al., 2011; Blais et al., 2012; Kulkarni et al., 2013). All three variants are associated with control and progression of HIV infection by miR-148a-mediated post-transcriptional regulation of HLA-C.

IL-10 is a multifunctional anti-inflammatory cytokine produced by various immune cells. With regards to miRNA regulation of IL-10, the let-7 family can directly target IL10. In vitro infection with HIV elevated IL10 levels through the reduction of let-7. In addition, CD4+ T cells of chronically infected HIV-positive individuals had significantly lower let-7 levels than uninfected individuals and long-term non-progressors. (Swaminathan et al., 2012b). A single miRNA is able to regulate multiple target genes. In addition to IL10, let-7c is involved in the regulation of p21. let-7c overexpression in Jurkat cells resulted in a 1.38-fold change in p21 expression (Figure 1) (Farberov et al., 2015).

B lymphocyte-induced maturation protein-1 (Blimp-1) is a transcriptional repressor of IL-2 (an important cytokine required for T cell growth and survival). In HIV-infected individuals, BLIMP-1 may contribute to T cell dysregulation through alterations in IL-2 levels. MiR-9 inhibited BLIMP1 expression in CD4+ T cells. Chronically infected HIV-positive patients had lower miR-9 and higher BLIMP1 expression in comparison to uninfected healthy individuals and long-term non-progressors (Seddiki et al., 2013).

It is estimated that 1,254 human genes are involved in viral replication. Genome-wide RNA interference has enabled researchers to identify multiple host factors that are involved in HIV life cycle. This large array of host gene targets may be essential in the development of new therapeutic strategies against HIV. By identifying and understanding the mechanisms behind the associations of specific miRNAs and their targets, we can exploit these factors for HIV viral control. Several HIV-associated genes are shown to be under the regulation of miRNAs in other diseases.

Blocking the access of HIV into host cells is the first step in preventing the HIV proviral genome from integrating into the host’s genome. The human chemokine receptor 5 (CCR5) plays an important role in the internalization of HIV into the host cell (Lederman et al., 2006). Individuals with the 32 base pair deletion in their CCR5 gene are known to be resistant to HIV as they have lower levels of CCR5 on the surface of their CD4+ T cells. Thus, the regulation of CCR5 expression may be essential in inhibiting HIV replication. Che et al. found that miR-107 binds to the 3′UTR of CCR5 (Che et al., 2016). CCR5 proteins and gene expression were found to be significantly lower in the presence of miR-107 (Che et al., 2016). Since CCR5 is important in the HIV context, miR-107 may be of potential therapeutic value in preventing HIV infection.

Intercellular adhesion molecule 1 (ICAM-1) also plays a significant role in HIV entry. The binding of ICAM-1 with LFA-1 on the cell surface facilitates viral infectivity. ICAM-1 increases viral infectivity by directly inserting into mature HIV virions (Fortin et al., 1997; Bounou et al., 2002). Lui et al. demonstrated that ICAM1 is negatively regulated by miR-296-3p in the malignant highly metastatic M12 cell line (Liu et al., 2013). Furthermore, in prostate cancer cells there is a negative correlation between miR-296-3p and ICAM1 (Liu et al., 2013). In the context of HIV, the downregulation of ICAM1 by miR-296-3p would reduce the rate of infectivity (Liu et al., 2013).

The tripartite motif (TRIM) proteins are a family of E3 ubiquitin ligases with diverse anti-viral functions (van Gent et al., 2018). TRIM22, TRIM11, and KAP1 (TRIM28) were previously shown to have anti-HIV activity (Barr et al., 2008; Allouch et al., 2009; Yuan et al., 2016). TRIM22 inhibits the processing of viral particles and viral budding through the ubiquitylation in HIV. TRIM22 also has anti-Hepatitis C virus (HCV) activity. Tian et al. confirmed that TRIM22 was regulated by miR-215 (Tian and He, 2018). In Con1b cells, the overexpression of miR-215 facilitated HCV replication by downregulating TRIM22. Knockdown of miR-215 suppressed HCV replication through the increased expression of TRIM22 in Huh7.5.1 cells (Tian and He, 2018). In colon cancer, TRIM11 is negatively regulated by miR-24-3p, promoting cellular proliferation and inhibiting apoptosis (Yin et al., 2016). Likewise, Qi et al. demonstrated that miR-491 levels inversely corresponded with TRIM28 expression in glioblastoma multiforme (GBM) (Qi et al., 2016). Their data showed that miR-491 was reduced in GBM and indicated that the low levels of miR-491 are associated with poor prognosis (Qi et al., 2016). miR-491 inhibited TRIM28 translation in GBM cells (Qi et al., 2016).

Studies have also demonstrated a link between RAD51 expression and HIV disease (Chipitsyna et al., 2004; Cosnefroy et al., 2012; Kaminski et al., 2014; Thierry et al., 2015). Elevated expression of RAD51 promotes HIV-1 transcription (Kaminski et al., 2014). Evidence demonstrates that RAD51 may have stimulatory or inhibitory effects on specific steps of retroviral replication cycles (Thierry et al., 2015). These effects depend on RAD51 being able to recruit both transcription machinery and proteins implicated in chromatin remodelling and formulation of RAD51 stimulatory compound (Thierry et al., 2015). Findings from Gasparini et al. indicate that DNA repair is indirectly regulated by miR-155 through its interaction with RAD51 in breast cancer (Gasparini et al., 2014).

The regulation of several other HIV-associated host factors such as TRAF6, CCL4, CCL3, IRF7, RSAD2, ISG15, TLR3, SETDB1, and Rab27a by miRNAs could potentially play a role in HIV infection. Table 2 provides a list of HIV-associated host genes which should be investigated in future miRNA studies. The host’s genes and associated miRNAs described in Table 2 may provide novel therapeutic targets against HIV.

Extensive research has paved the way for developing multiple antiretroviral drugs targeting specific phases of the viral life cycle, leading to a combination of antiretroviral therapy (cART). Currently, this treatment results in controlled viral replication in many treated individuals (Cohen et al., 2016). Despite the progress with lifesaving HAART, infection with HIV remains pathogenic and incurable. In addition, these drugs lead to the development of toxicities and adverse side effects which may only be combated by changing the drug regimen. Furthermore, the increasing emergence of HIV drug resistance poses a threat to the success of the current regimens (Bertagnolio et al., 2012; Le Douce et al., 2012; Stadeli and Richman, 2013). These compounding factors highlight the importance of identifying novel and complementary treatment regimens.

RNA-based therapeutics appear ready to deliver on their promise. Significant success has been observed in several clinical trials using potential miRNA drugs in multiple infectious and non-infectious diseases, including cancer (Hatley et al., 2010; Li et al., 2010; Steele et al., 2011; Wong et al., 2012; Yamanaka et al., 2012), hepatitis C (Jopling et al., 2005; Sarasin-Filipowicz et al., 2009; Lanford et al., 2010), heart abnormalities (Thum et al., 2008; Liu et al., 2010), kidney disease, pathologic fibrosis, and even keloid formation. Interestingly, studies have also shown that dysregulated miRNA profiles play a role in HIV replication (Barr et al., 2008; Pincetic et al., 2010; Liu et al., 2011; Sirois et al., 2011; Tyagi and Kashanchi, 2012; Raposo et al., 2013; Doyle et al., 2015). The vaccine, iHIVARNA is a combination of mRNA sequences that serve as an HIV immunogen. In the first round of clinical trials, iHIVARNA is tolerated in HIV-infected patients on chronic cART (De Jong et al., 2019). Despite this progress, the application of miRNAs as diagnostic and interventional medicine remains an underexplored area of research. The clinical trial was merely a proof-of-concept trial; the stability and delivery of the mRNA are still being tested (De Jong et al., 2019).

The Achilles heel of miRNA-based viral therapy is the lack of targeted miRNA delivery systems, off-target effects, and unidentified targets of miRNAs. In addition, miRNAs are relatively unstable, which may result in insufficient circulation and poor half-life of the miRNA-based therapy. Future research should be directed towards constructing optimal miRNA delivery systems and identifying methods to prevent off-target effects. As the use of miRNAs as treatment strategies is a growing field, only a few drugs have been FDA approved (Nature Biotechnology, 2020; Zhang et al., 2021b), which highlights the potential of RNAs for therapeutic intervention. MiRNAs provide a unique, reversible approach to treating human diseases and may be our secret weapon in our fight against HIV.