Successful antiretroviral therapy (ART) reduces mortality rates by suppressing Human Immunodeficiency Virus-1 (HIV) replication to undetectable levels in people living with HIV (PLWH). However, ART is not curative due to the establishment of the HIV reservoir that continues to persist despite prolonged ART. It has been established that long-lived memory T cells represent the most important HIV reservoir population and that a large proportion of the reservoir is composed of CD4+ T cell clones which are established early after infection and increase during ART treatment. Our studies show that cognate dendritic cell (DC):T cell interactions drive clonal expansion of latent T cell subsets in which CD28 plays a major role in regulating proliferation while IL-7 supports a pro-survival state. Low antigenic stimulation drives proliferation without viral reactivation in latent T cell subsets indicating that during interaction with antigen presenting cells, the magnitude of T cell receptor (TCR) stimulation is a key regulator of proliferation and survival mechanisms that maintain the HIV reservoir. However, it remains unknown how antigen stimulation regulates opposing biological processes of proliferation leading to clonal expansion and viral production leading to cell death. Here, we utilized a dual-fluorescent HIV latency reporter and human CD4+ T cell clones to modulate TCR signaling strengths using a panel of altered peptide ligands, and directly examined the relationship between TCR signals and proliferative responses by latent T cells. Our data argue that a critical balance between stimulatory and inhibitory pathways dictate which T cell subsets clonally expand under ART suppression. These studies have implications on stimulatory signals that can be therapeutically targeted to reduce the HIV reservoir size in PLWH.

Background: Within-host HIV populations continually diversify during untreated infection, and this diversity persists within infected cell reservoirs during antiretroviral therapy (ART). Achieving a better understanding of on-ART proviral evolutionary dynamics, and a better appreciation of how the overall persisting pool of (largely genetically defective) proviruses differs from the much smaller replication-competent HIV reservoir, is critical to HIV cure efforts.

Methods: We inferred within-host HIV evolutionary histories in blood from seven participants of the Women’s Interagency HIV Study who experienced HIV seroconversion. env-gp120 was single-genome amplified from a median 9 plasma samples/participant collected pre-ART, and a median 3 proviral samples/participant collected on-ART. To mitigate uncertainty in within-host phylogenetic reconstruction, a median 3842 phylogenies were inferred/participant using Bayesian approaches. We characterized diversity, lineage origins and ages of proviruses, where ages were estimated phylogenetically. We used the same techniques to study reservoir-origin HIV in two participants.

Results: Results suggested that proviral clonality generally increased over time on ART, with clones frequently persisting across multiple timepoints. Integration dates of proviruses persisting on ART generally spanned duration of untreated infection (though were often skewed towards years immediately pre-ART), while in contrast, reservoir-origin viremia emerging in plasma was exclusively "younger" (i.e., dated to years immediately pre-ART). The genetic and age distributions of distinct proviruses remained stable during ART in all but one participant, in whom there was evidence that younger proviruses had been preferentially eliminated after 12 years on ART. Analysis of within-host recombinant proviruses also suggested that HIV reservoirs can be superinfected with virus reactivated from an older era, yielding infectious HIV with mosaic genomes with different ages.

Conclusion: Overall, these results underscore the remarkable genetic stability of distinct proviruses that persist on ART, yet suggest that replication-competent HIV reservoir represents a genetically-restricted and overall "younger" subset of the overall persisting proviral pool in blood.

Reversal of HIV-1 latency remains a significant barrier to achieving a cure for this infection and recent studies have highlighted issues in viral RNA processing as one component of the latency barrier. Key to regulating RNA processing are the host SR (serine-arginine rich splicing factors) proteins. As part of our effort to understand the role that individual SR proteins play in regulating HIV-1 replication, we examined their interaction with HIV-1 RNA and the effect of their depletion on viral gene expression. eCLIP analysis determined that these factors had extensive overlap in their binding sites on the viral RNA. Despite similar binding profiles, of the eight SR proteins (SRSF1-7, 9) tested, depletion of only SRSF3, 5, and 9 yielded marked increases in HIV-1 protein expression and viral RNA accumulation in two T cell lines examined (JLat 10.6, CEM-T4). While SRSF3 & 5 depletion increased HIV-1 promoter function, loss of SRSF9 affected post-initiation events. In the context of CEMT4 cells, increased HIV-1 gene expression was predominately due to a >14-20 fold increase in the percentage of cells expressing Gag upon SRSF3 or SRSF9 depletion, an effect that could be further augmented by addition of various latency reversing agents. Effects on promoter function were not unique to HIV-1 as subsequent analyses determined that SRSF3 or 9 depletion also modulated promoter function of multiple host genes. Together, these observations highlight an unexpected role for SRSF3, 5, and 9 in the regulation of HIV-1 latency through affects on viral promoter function.

Background. The primary barrier to an HIV cure is the latent vial reservoir (LVR), a product of HIV’s integration into the host DNA of long-lived immune cells, predominantly resting CD4+ (rCD4) T cells. Continuous adherence to antiretroviral therapy (ART) is necessary as these cells can produce infectious virus if immunologically reactivated. Currently, one of the standard assays for LVR quantification is the Intact Proviral DNA Assay, designed based on HIV subtype B sequences circulating in the United States (IPDA-B). However, globally, most PWH have non-B subtypes, which the IPDA-B often fails to detect due to their high sequence diversity. As HIV subtypes can differ in viral pathogenesis, genetics, and reservoir size, subtype-specific strategies for LVR quantification are urgently needed to advance cure research for all.
Methods. We used subtype A1, D, and recombinant near-full-length proviral sequences (n=607), previously generated by our group, to adapt existing IPDA-B primers and probes for the sequence diversity observed in a Ugandan cohort (IPDA-A1D). Degenerate nucleotide bases were incorporated at locations with high sequence diversity.
Results. The IPDA-B regions could correctly identify 97.3% of proviruses with large deletions in the Ugandan cohort (n=495) in silico. The adapted IPDA-A1D returned highly comparable intact reservoir measurements to the original IPDA-B when quantifying samples whose sequences were compatible with both assays (ρ=1, p<0.0001). Furthermore, the IPDA-A1D rescued intact provirus detection in HIV non-B subtype samples for which the IPDA-B failed. Additionally, the unlabelled hypermutation discrimination probe successfully competed with the labelled probe for binding to hypermutated, but not intact, subtype A1 and D genomes.
Significance. Adaption of the IPDA to quantify non-B subtypes within the LVR will enhance HIV reservoir and cure research across Africa.

Background: In 2018, the Botswana Tsepamo study reported a concerning increased risk of neural-tube defects (NTDs) in fetuses exposed to the HIV integrase strand transfer inhibitor (INSTI) dolutegravir from the time of conception. Additionally, folate deficiency in fetal development has been associated with NTDs. Annually over 1 million people with HIV taking antiretroviral drugs become pregnant, thus it is critical to investigate the potential interactions between INSTIs such as dolutegravir and folate transport pathways in the developing fetus. We investigated the effect of in utero exposure to INSTIs on the expression of placental proteins that are critical for fetal folate delivery.

Methodology: HTR8/SVneo and BeWo human placental cell lines representative of the first and third trimester respectively, were treated with clinically relevant doses of dolutegravir, bictegravir, cabotegravir or DMSO control for a period of 3, 6, 24, or 48 hours. mRNA and protein expressions of folate receptor-α (FRα), and transporters, reduced folate carrier (RFC) and proton-coupled folate transporter (PCFT), were assessed by qPCR and immunoblotting respectively.

Results: We observed a significant downregulation of the mRNA expression of: i) FOLR1 and RFC in cabotegravir treated cells, ii) FOLR1 and PCFT in dolutegravir treated cells, and iii) FOLR1, RFC, and PCFT in bictegravir treated cells. Protein expression showed similar patterns of dysregulation in BeWo cells in which there was a significant downregulation of RFC in cabotegravir treated cells and RFC/ PCFT proteins in dolutegravir treated cells.

Conclusion: Our findings suggest that the observed dysregulation of folate transporters in the placenta caused by INSTIs treatment could potentially result in an in utero folate deficient state that could place the fetus at increased risk for adverse birth outcomes. Future studies will characterize the activity of the folate transport pathways and further examine, in vivo, fetal folate levels/toxicity. (Supported by OHTN and CIHR).

Background: Mucosal antibodies in the gut maintain homeostasis between the host and the local microbiome through the clearance of pathogenic bacteria and the development of immune tolerance to inflammatory bacteria. Bacterial vaginosis (BV) is associated with elevated HIV risk, in part by eliciting genital inflammation. However, little is known regarding the role of microbe-binding antibodies in the vagina nor whether similar bacteria-immunoglobulin interactions modulate bacteria-induced cervicovaginal inflammation and/or bacterial colonization.
Methods: We used a flow cytometry-based assay to quantify microbe-binding IgA and IgG from cervicovaginal secretions in a cross-sectional cohort of 200 HIV-uninfected women from Nairobi, Kenya that were enriched for BV and evaluated the associations of cervicovaginal IgA and IgG with the vaginal microbiome composition and local soluble immune factors.
Results: Cervicovaginal IgA and IgG are abundant and bind key vaginal bacteria ex vivo (Gardnerella vaginalis, Prevotella bivia, Lactobacillus iners, and Lactobacillus crispatus). Microbe-binding IgA and IgG were not associated with the detectability of the specific corresponding bacteria in the vaginal microbiome. The total bacteria abundance in the vaginal is inversely correlated with total and microbe-binding IgA and IgG and BV is associated with reduced total and microbe-binding IgA and IgG. Total and microbe-binding IgA and IgG were positively correlated with increased levels of multiple inflammatory cytokines (IL-6, TNF) and chemokines (IP-10, MIG, MIP-1α, MIP-1β, MIP-3α, MCP-1, IL-8) independently of total bacterial abundance.
Conclusions: Both total and microbe-binding IgA and IgG in the female genital tract are independently correlated with multiple correlates of reproductive health and HIV susceptibility. IgA and IgG inversely correlate with bacterial abundance and positively correlated with several cytokines and chemokines previously linked to HIV acquisition. This assay provides a platform to investigate the interactions between the microbiota, inflammation and cervicovaginal antibodies in human observational and interventional studies.