The T cell immunoglobulin and mucin domain-containing protein 3 (Tim-3) is expressed on exhausted T cells and is upregulated at the cell surface upon infection by Human Immunodeficiency Virus Type 1 (HIV-1). Recently, Tim-3 has also been described as a key inhibitor of HIV-1 egress. Previously, our studies have demonstrated that the HIV-1 accessory protein Vpu downregulates Tim-3; however, the mechanisms of Tim-3 regulation by Vpu have yet to be determined. Herein, we have identified a novel motif in the cytosolic domain of Vpu (QEELSKLM) that is required for optimal Tim-3 downregulation in HIV-1 infected primary CD4+ T cells but is dispensible for downregulation of the restriction factor tetherin. To further determine if HIV-1 infection modulates Tim-3 levels in diverse cell types, we demonstrated that Tim-3 is additionally upregulated on the surface of PMA-differentiated THP-1 macrophages. However, unlike in T cells, Vpu does not downregulate Tim-3 from the surface of macrophages. Taken together, these studies demonstrate a cell type specific modulation of Tim-3 via the accessory protein Vpu. Future studies are currently being optimized to determine how Vpu-mediated Tim-3 downregulation affects virion release, thereby contributing to the modulation of viral egress. Taken together, our studies suggest that the viral regulation of Tim-3 may be a novel therapeutic target to improve the prognosis of individuals infected with HIV-1.

HIV-1 acquires its lipid envelope as it egresses through cellular membranes of infected cells, and it can acquire selective cellular proteins present at the sites of budding. This incorporation of host cell proteins can impart new functions and phenotypes onto virions and impact viral spread and disease. Recent work in our lab has focused on the presence of the myeloid antigen CD14 in the HIV envelope. The interplay between HIV-1 and the myeloid cell compartment is a key contributor to pathogenesis, due to the inflammatory roles these cells play.

Using in vitro models, we show that HIV-1 can incorporate CD14 into the virus envelope by flow virometry, virion capture assay and western blot. Additionally, the virion-incorporated CD14 remained biologically active, as demonstrated by flow virometry and immunoprecipitation of HIV-1 pseudovirus with immobilized bacterial LPS, the ligand of CD14. Using a TLR4 reporter cell line, we also demonstrated for the first time that virions with bound LPS can activate immune cells, leading to the secretion of pro-inflammatory cytokines.

Persistent inflammation, particularly in the gut mucosae is a hallmark of chronic HIV infection, driven by a combination of activated immune cells and soluble cytokines. Contributing to this effect is the aberrant translocation of microbes across the gut mucosa, resulting from viral-induced damage to the epithelium that normally serves as an effective barrier to block microbial translocation. Our data provides proof-of-principle that virion-incorporated CD14 could be a novel mechanism through which HIV-1 can drive chronic inflammation, facilitated by HIV particles binding bacterial LPS and initiating inflammatory signaling in TLR4-expressing cells.

Background. HIV infection is associated with accelerated coronary artery disease (CAD) due to chronic inflammation. Lipid mediators from the expanded endocannabinoid system (endocannabinoidome; eCBome) and gut microbiota modulate each other and are key regulators of cardiovascular functions and inflammation. We thus investigated the plasma eCBome and gut microbiota in PWH with subclinical CAD.

Methods. ART-treated HIV+CAD+ (n=87), HIV+CAD- (n=69), HIV-CAD+ (n=22) and HIV-CAD- (n=30) individuals were enrolled. CAD was assessed using cardiac computed tomography angiography. Plasmatic levels of endocannabinoids and their congeners were quantified using liquid chromatography coupled to tandem mass spectrometry. Bacterial composition of stools from n=107 participants was assessed by 16S rDNA sequencing and amplicon sequence variants identified to determine relative abundances of bacterial taxa and community diversity.

Results. The endocannabinoid N-arachidonoylethanolamine (AEA), and its N-acylethanolamine (NAE) congeners, N-eicosapentaenoylethanolamine (EPEA), N-linoleoylethanolamine (LEA), N-docosahexaenoylethanolamine (DHEA), and N-docosapentaenoylethanolamine (DPEA (n-6)), were significantly lower in PWH compared to HIV- participants. EPEA, DHEA and N-palmitoylethanolamine (PEA) were significantly reduced in HIV+CAD+ compared to HIV+CAD- individuals, while HIV-CAD- individuals had higher plasma levels of AEA, EPEA, LEA, DHEA, and DPEA(n-6) than HIV+CAD+. Plasma levels of monoacylglycerols (MAGs), including 2-eicosapentaenoylglycerol, 2-linoleoylglycerol, 2-docosapentaenoylglycerol, and 2-oleoylglycerol (2-OG), were significantly elevated in PWH compared to HIV- controls. Moreover, the endocannabinoid 2-arachidonoylglycerol, and 2-docosahexaenoylglycerol, were increased in PWH compared to uninfected controls. While trends for increased abundance for several bacterial families in the stools of HIV-CAD+ versus controls were observed, only Marinifilacea were significantly increased, however no such changes were observed in PWH. Likewise, CAD+ associated alterations in genera abundances were observed in HIV-, but not in PWH.

Conclusions. HIV infection results in perturbed plasma eCBome. Inverse associations between the CAD/HIV infection status with NAEs or MAGs point to these mediators as biomarkers of CAD in PWH. CAD-associated taxonomic alterations in faecal bacterial were not found in PWH.

Interleukin-32 (IL-32) consists of several isoforms (α, β, δ, ε, φ, γ). IL-32γ, but not IL-32α or IL-32β, induced HIV-1 production in latently infected CD4+ T-cells isolated from people living with HIV (PLWH). IL-32α, however, plays an anti-inflammatory role by inducing IL-10. Pre-treatment of HIV-negative PBMC with siRNA to IL-32 was shown to augmented HIV-1 replication by >4-fold. It suggests that increased non- IL-32γ in HIV-negative cells may be protective against HIV-1. We further hypothesized that HIV-exposed, sero-negative (HESN) people or delayed sero-converters have higher level of non- IL-32γ. Using qRT-PCR to investigate the RNA transcripts in the PBMC of HESN female sex workers (FSW) (n=17) or newly enrolled HIV-negative non-HESN controls (n=15), we observed no difference in the levels of IL-32 isoform transcripts between the two groups (p=0.07). However, we found reduced expression of IL6ST, which mediates inflammation and increased CCR4, CCR7, CD28, ICOS, IL4R, ITK, and MAP3K1 transcripts, which are associated with the activation of T cells in the HESN PBMC. Cervical-vaginal mucosa forms the first line of defense against heterosexual transmission of HIV-1. We hence, examined IL-32 expression in the transcriptome of cervical cells (CMC) from HESN FSW (n=6) and controls (n=4). Unexpectedly, IL-32γ transcripts were significantly elevated in the HESN group (p< 10-6) with a trending increase in IL-32α by 16% (p<0.01). This was confirmed using qRT-PCR (HESN, n=12, control, n=11). When stimulated with IFN-γ, IL-32γ response was robust but transient in the HESN CMC but the IL-32α responses were not different between the two groups. Together, the data suggest that IL-32γ’s fast but transient anti-viral response at the cervicovaginal mucosa, without inducing a prolonged inflammation may contribute to the protection against HIV-1, observed in the HESN.

Human Immunodeficiency Virus (HIV) persists as a global threat with over 38 million people infected. While much is known about HIV viral genomic RNA (vgRNA) packaging, vgRNA’s ability to evade the Nonsense Mediated mRNA Decay (NMD) pathway is poorly understood. Typically, NMD functions to degrade “faulty” transcripts that contain Premature Termination Codons (PTCs). Recent studies have demonstrated NMD protein UPF1 robustly and nonspecifically binds RNAs and translating ribosomes are capable of displacing UPF1. Despite the full-length HIV RNA genome containing multiple PTCs that should be recognized by the NMD pathway, many transcripts are instead preferentially packaged into nascent virions. The Arts laboratory has identified a critical secondary structure element termed the Genomic RNA Packaging Enhancer (GRPE) that overlaps the ribosomal frameshifting site needed for translation of the Gag-Pol polyprotein. It is hypothesized the GRPE modulates translational readthrough of the frameshift sequence allowing for downstream UPF1 displacement and subsequent NMD evasion. We hypothesize Gag-Pol translation designates these heterogeneous nuclear RNAs as genomic RNA for progeny virions. To confirm this hypothesis, an HIV backbone was modified with luciferase reporters and an inducible promoter to quantitatively measure frameshifting frequency and RNA decay rates, respectively. Frameshifting frequencies were compared to RNA decay rates of wildtype and mutant vectors. Mutants with increased frameshifting frequencies display increased RNA protection with longer RNA half-lives. Overall, these results indicate full length viral translation may serve as a mechanism of NMD evasion, but additional experiments are required to confirm this. Understanding the mechanism behind HIV NMD evasion can greatly increase lentiviral gene transduction efficiencies as all currently-used lentiviral transduction systems do not harbour a GRPE. Preliminary GRPE incorporation increased gene transduction 4-fold as a direct effect of increased packaging, increasing the plausibility of lentiviral gene transduction to help in the cure of many genetic diseases such as β-thalassaemia.

Antiviral restriction factors are the initial line of defense against many viruses including HIV-1. Interferons induce the expression of anti-viral restriction factors that can interfere with multiple steps of the viral replication cycle. Interferon-alpha (IFN-α) induces many restriction factors that have the potential to restrict HIV-1. Humans have 13 IFN-α genes which encode 12 different functional IFN-α subtypes. Our previous studies with IFN-α14 showed a greater reduction of viral load than the clinically approved IFN-α2 subtype in HIV-1 infected humanized mice. However, the mechanisms behind the more potent control of HIV-1 by IFN-α14 are unknown. Analysis of cells harvested from IFN-α14 treated humanized mice using RNA-seq indicated upregulation of restriction factors like MX2, ISG15, APOBEC3A compared to IFN-α2. We have also previously observed that IFN-α14 increases the deamination activity of APOBEC3G compared to IFN-α2. To study the importance of each IFN-α14 modulated restriction factor in the more potent control of HIV-1 and to investigate if they are independent or interdependent, we used a CRISPR-Cas9 lentivirus system to create stable restriction factor knockouts in the MT4C5 cell line. MT4C5 cells are a CD4+ T cell line that is susceptible to both X4- and R5-tropic HIV-1 strains and do not produce measurable amounts of endogenous IFN-α. Wildtype MT4C5 cells treated with IFN-α14 HIV-1 produced higher levels of Mx2 and had a significantly lower viral load and produced fewer infectious particles compared to IFN-α2 and untreated cells. We have successfully produced Mx2 knockout MT4C5 cells and are currently assessing the effect of IFN-α14 on viral load compared to IFN-α2. The generation of ISG15 and APOBEC3G knockouts will also be tested for their effect on HIV-1 viral replication and infectivity, respectively. We further plan to knockout IFN-α14 modulated restriction factors simultaneously to study potential synergistic effects on the potent control of HIV-1 by IFN-α14.

HIV-risk groups include heterosexual individuals (HET), men-who-have-sex-with-men (MSM), people who inject drugs (PWID) and people who received contaminated blood transfusions (CBT). When HIV-1 is transmitted, typically only a single clone establishes the new infection, creating a transmission bottleneck for the virus. The viral clone that establishes infection is called the transmitted/founder (T/F) virus. This phenomenon is especially prevalent in HET and MSM transmission while less stringent in transmission from blood contact (PWID and CBT). Specific traits that permit successful transmission have not been well characterized.

This project aims to assess transmission fitness between T/F viruses from different transmission routes by ex vivo competition assays. Subsequently, phenotypic assays were employed to investigate the roles of selected factors in transmission fitness. In the competitions on cervical tissues, we found that T/F viruses from the PWID group exhibit limited replication capacity, thus diminishing their chances of transmission to T helper type 1 (Th1) and Th17 cells. This reduced transmission fitness effect of the PWID group is not observed when infecting Th1 and Th17 cells directly, bypassing cervical tissues. Additionally, T/F viruses display distinct phenotypic characteristics in comparison to chronic viruses. The PWID group required the least stringent cellular co-receptor conformations to enter susceptible cells compared to other T/F viruses. Furthermore, T/F viruses across all transmission modes exhibited lower envelope expression levels than chronic viruses. However, there is no significant difference in cellular entry speed or receptor/co-receptor usage efficiency both within the T/F viruses and between T/F and chronic viruses. These suggest the disparity of transmission fitness in cervical tissue competitions is more likely caused by the envelope structure or glycosylation patterns/levels. This project will establish the key viral phenotypes contributing to successful virus transmission to inform the design of a robust anti-HIV vaccine and will help the improvement of the antiretroviral therapy strategy.

Epidemiological links between the vaginal microbiome and risk of HIV infection are well established, but the underlying mechanisms remain poorly understood. In reproductive age women, a healthy vaginal microbiome is dominated by a single Lactobacillus species that protects the niche through the production of lactic acid and other antimicrobial compounds. However, Lactobacillus dominance commonly gives way to an alternate state characterized by the overgrowth of anaerobic bacteria. Known clinically as bacterial vaginosis (BV), anaerobic vaginal dysbiosis exhibits a population point prevalence of 10–30% worldwide and makes a woman 2–3x more susceptible to HIV infection. Proteolytic activity is elevated during BV and has been attributed to increased human matrix metalloproteinase (MMP) expression and activity, which is in turn linked with HIV acquisition. We recently discovered that select vaginal anaerobes, including several prevalent Prevotella species, secrete proteases that cleave reporter substrates commonly used to detect MMP activity in human samples and infection models, suggesting the contributions of microbiome proteases could have been mistakenly ascribed to MMPs in published experiments. Culture-based studies and proteomic analyses of human vaginal fluid demonstrated Prevotella proteases degrade cervical barrier proteins, including collagens and elastin. Collagen zymography and proteomics studies revealed that Prevotella proteases also target MMPs, including the HIV-associated enzymes MMP-8 and MMP-9, for activation and degradation. In a polarized endocervical cell culture model, MMP-reporter activity was significantly higher with exposure to proteolytic Prevotella species than with exposure to non-proteolytic anaerobic bacteria that similarly induced MMP expression. Our experiments further revealed that P. bivia exhibits a unique signature of barrier protein cleavage and was able to traverse across the endocervical epithelium. In summary, our findings suggest a new mechanism whereby proteolytic Prevotella species directly degrade structural cervical barrier proteins, while amplifying their effects via MMP activation and mimicry to potentially increase endocervical susceptibility to HIV.