HIV eradication: combinatorial approaches to activate latent viruses

Nucleolar protein NOP2/NSUN1 suppresses HIV-1 transcription and promotes viral latency by competing with Tat for TAR binding and methylation

Recent efforts have been paid to identify previously unrecognized HIV-1 latency-promoting genes (LPGs) that can potentially be targeted for eradication of HIV-1 latent reservoirs. From our earlier orthologous RNAi screens of host factors regulating HIV-1 replication, we identified that the nucleolar protein NOP2/NSUN1, a m5C RNA methyltransferase (MTase), is an HIV-1 restriction factor. Loss- and gain-of-function analyses confirmed that NOP2 restricts HIV-1 replication. Depletion of NOP2 promotes the reactivation of latently infected HIV-1 proviruses in multiple cell lines as well as primary CD4+ T cells, alone or in combination with latency-reversing agents (LRAs). Mechanistically, NOP2 associates with HIV-1 5' LTR, interacts with HIV-1 TAR RNA by competing with HIV-1 Tat protein, as well as contributes to TAR m5C methylation. RNA MTase catalytic domain (MTD) of NOP2 mediates its competition with Tat and binding with TAR. Overall, these findings verified that NOP2 suppresses HIV-1 transcription and promotes viral latency.

Effects of HIV on metabolic and biological pathways of CD4+ T lymphocytes

The effects of human immunodeficiency virus (HIV) on the metabolic and biological pathways of cluster of differentiation (CD)4⁺ T lymphocytes were investigated. A total of 150 patients with acquired immune deficiency syndrome (AIDS) and 50 healthy individuals who were admitted to hospital for physical examination during the period of June 2016 to January 2017, were selected as subjects in the present study. According to the virus load, 150 AIDS patients were divided into three groups: i) Viral load >10⁶ copies/ml (group A, n=39), ii) 10⁴ copies/ml < viral load <10⁵ copies/ml (group B, n=76), and iii) viral load <10⁴ copies/ml (group C, n=35). The relationship between viral loads in the three groups and CD4⁺ T lymphocyte counts was assessed. Active lymphocytes were isolated from T lymphocytes in the subjects, and the ratio of Th1 to Th2 was measured by flow cytometry. Effects of HIV on human T-lymphocyte differentiation were observed. Differences in T-lymphocyte metabolites were detected by proton nuclear magnetic resonance and their biological pathways analyzed. The results showed that CD4⁺ T-cell counts were decreased with the increase of the viral loads of patients. The viral loads of AIDS patients differentiated T lymphocytes. In other words, high viral loads accelerated the differentiation of T lymphocytes into Th1 cells. In the high HIV viral load group, the levels of glycerol phosphodiesterase, 7-dehydrocholesterol, p-hydroxyphenylacetic acid, cholesterol and deoxyuridine were increased, but the levels of 3-methoxytyramine, cytidine deaminase, deoxycorticosterone and 3-hydroxybutyric acid were decreased. The viral loads of AIDS patients are associated with CD4⁺ T-cell counts and the ratio of CD4⁺ T to CD8⁺ T cells. At the same time, HIV viral loads can affect the lipid biosynthesis of T-lymphocyte membranes, thus affecting the differentiation and proliferation of T lymphocytes and finally intervening its mediated immune responses.

Design, synthesis, and biological evaluation of AV6 derivatives as novel dual reactivators of latent HIV-1

The “shock and kill” strategy might be a promising therapeutic approach for HIV/AIDS due to the existence of latent viral reservoirs. A major challenge of the “shock and kill” strategy arises from the general lack of clinically effective latency-reversing agents (LRAs). The 2-methylquinoline derivative, antiviral 6 (AV6) has been reported to induce latent HIV-1 expression and act synergistically with a HDAC inhibitor VA to reverse HIV latency. We report herein the design and identification of AV6 analogues which possess the zinc-binding group of HDAC inhibitors and have dual acting mechanism for the reactivation of HIV-1 from latency. Evaluation of compounds for the reactivation of HIV-1 latency identified two excellent active compounds 12c and 12d. Further bioassays revealed that these two compounds reactivated latent HIV-1 through dual mechanism, the inhibition of HDACs and NFAT-required for early HIV-1 gene expression. Additionally, it was found that 12c and 12d could reactivate HIV-1 transcription by releasing P-TEFb from the inactive complex 7SK snRNP. At last, molecular docking identified their orientation and binding interactions at the active site of HDAC2. This experimental data suggests that 12c and 12d can be served as effective HIV-1 LRAs which can be taken up for further studies.

As dual-acting HIV LRAs, compounds 12c and 12d could activate latent HIV-1 via the NFAT-required mechanism and as histone deacetylase (HDAC) inhibitors.

The Multifaceted Contributions of Chromatin to HIV-1 Integration, Transcription, and Latency

The capacity of the human immunodeficiency virus (HIV-1) to establish latent infections constitutes a major barrier to the development of a cure for HIV-1. In latent infection, replication competent HIV-1 provirus is integrated within the host genome but remains silent, masking the infected cells from the activity of the host immune response. Despite the progress in elucidating the molecular players that regulate HIV-1 gene expression, the mechanisms driving the establishment and maintenance of latency are still not fully understood. Transcription from the HIV-1 genome occurs in the context of chromatin and is subjected to the same regulatory mechanisms that drive cellular gene expression. Much like in eukaryotic genes, the nucleosomal landscape of the HIV-1 promoter and its position within genomic chromatin are determinants of its transcriptional activity. Understanding the multilayered chromatin-mediated mechanisms that underpin HIV-1 integration and expression is of utmost importance for the development of therapeutic strategies aimed at reducing the pool of latently infected cells. In this review, we discuss the impact of chromatin structure on viral integration, transcriptional regulation and latency, and the host factors that influence HIV-1 replication by regulating chromatin organization. Finally, we describe therapeutic strategies under development to target the chromatin-HIV-1 interplay.

Systems biology applications to study mechanisms of human immunodeficiency virus latency and reactivation

Eradication of human immunodeficiency virus (HIV) in infected individuals is currently not possible because of the presence of the persistent cellular reservoir of latent infection. The identification of HIV latency biomarkers and a better understanding of the molecular mechanisms contributing to regulation of HIV expression might provide essential tools to eliminate these latently infected cells. This review aims at summarizing gene expression profiling and systems biology applications to studies of HIV latency and eradication. Studies comparing gene expression in latently infected and uninfected cells identify candidate latency biomarkers and novel mechanisms of latency control. Studies that profiled gene expression changes induced by existing latency reversing agents (LRAs) highlight uniting themes driving HIV reactivation and novel mechanisms that contribute to regulation of HIV expression by different LRAs. Among the reviewed gene expression studies, the common approaches included identification of differentially expressed genes and gene functional category assessment. Integration of transcriptomic data with other biological data types is presently scarce, and the field would benefit from increased adoption of these methods in future studies. In addition, designing prospective studies that use the same methods of data acquisition and statistical analyses will facilitate a more reliable identification of latency biomarkers using different model systems and the comparison of the effects of different LRAs on host factors with a role in HIV reactivation. The results from such studies would have the potential to significantly impact the process by which candidate drugs are selected and combined for future evaluations and advancement to clinical trials.

Comorbidities associated with HIV and antiretroviral therapy (clinical sciences): a workshop report

In the era of combination antiretroviral therapy (ART), parsing out the effects of HIV vs ART on health outcomes is challenging. Nadir CD4 count, a marker of the extent of immunosuppression, has significant long-term impact on an array of disease states in HIV+ persons; however, in the dental literature, reporting of pre-ART exposure to immunosuppression has largely been ignored and this limits the validity of previous studies. In Workshop A1, we explain fully the importance of nadir CD4, pre-ART immunosuppression, and identify a need to include specific variables in future research. The questions posed herein are challenging, typically not neatly addressed by any one study and require integration of the latest evidence from the wider medical literature. We consider topics beyond the confines of the oral cavity and examine oral health in the complex context of ART era HIV immunopathophysiology. We depict how variability in geographic setting and time period (pre- and post-ART era) can impact oral conditions - influencing when HIV infection was detected (at what CD4 count), the type and timing of ART as well as social determinants such as strong stigma and limited access to care. We hope our Workshop will stir debate and energize a rigorous focus on relevant areas of future research in HIV/AIDS.

Trends in Antiviral Strategies

Viral populations are true moving targets regarding the genomic sequences to be targeted in antiviral designs. Experts from different fields have expressed the need of new paradigms for antiviral interventions and viral disease control. This chapter reviews several strategies that aim at counteracting the adaptive capacity of viral quasispecies. The proposed designs are based on combinations of different antiviral drugs and immune modulators, or in the administration of virus-specific mutagenic agents, in an approach termed lethal mutagenesis of viruses. It consists of decreasing viral fitness by an excess of mutations that render viral proteins sub-optimal or non-functional. Viral extinction by lethal mutagenesis involves several sequential, overlapping steps that recapitulate the major concepts of intra-population interactions and genetic information stability discussed in preceding chapters. Despite the magnitude of the challenge, the chapter closes with some optimistic prospects for an effective control of viruses displaying error-prone replication, based on the combined targeting of replication fidelity and the induction of the innate immune response.

Small Molecule Inhibitors of BAF; A Promising Family of Compounds in HIV-1 Latency Reversal

Persistence of latently infected cells in presence of Anti-Retroviral Therapy presents the main obstacle to HIV-1 eradication. Much effort is thus placed on identification of compounds capable of HIV-1 latency reversal in order to render infected cells susceptible to viral cytopathic effects and immune clearance. We identified the BAF chromatin remodeling complex as a key player required for maintenance of HIV-1 latency, highlighting its potential as a molecular target for inhibition in latency reversal. Here, we screened a recently identified panel of small molecule inhibitors of BAF (BAFi's) for potential to activate latent HIV-1. Latency reversal was strongly induced by BAFi's Caffeic Acid Phenethyl Ester and Pyrimethamine, two molecules previously characterized for clinical application. BAFi's reversed HIV-1 latency in cell line based latency models, in two ex vivo infected primary cell models of latency, as well as in HIV-1 infected patient's CD4 + T cells, without inducing T cell proliferation or activation. BAFi-induced HIV-1 latency reversal was synergistically enhanced upon PKC pathway activation and HDAC-inhibition. Therefore BAFi's constitute a promising family of molecules for inclusion in therapeutic combinatorial HIV-1 latency reversal.

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BAF complex inhibitors (BAFi's) activate latent HIV-1 in cell line models of latency.

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BAFi's in combination with HDAC inhibitors and PKC activators synergistically activate latent HIV-1.

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The BAFi's PYR and CAPE reverse HIV-1 latency in primary cell models of latency and in cells obtained from HIV-1 patients.

Access to Combination antiretroviral therapy (cART) has made HIV-1 infection a chronic disease. However, cART is not curative, as a small number of infected cells harboring silent virus with potential to renew the infection persist despite cART. Efforts to cure HIV-1 include activation of these latent cells, making them susceptible to immune clearance. Here we describe the activity of BAF inhibitors in HIV-1 activation in in vitro models of HIV-1 latency as well as in cells obtained from HIV-1 infected patient volunteers. Our data highlight the clinical potential of BAF inhibitors for inclusion in combinatorial therapy to reverse HIV-1 latency.

A Phase I Randomized Therapeutic MVA-B Vaccination Improves the Magnitude and Quality of the T Cell Immune Responses in HIV-1-Infected Subjects on HAART

Trial Design

Previous studies suggested that poxvirus-based vaccines might be instrumental in the therapeutic HIV field. A phase I clinical trial was conducted in HIV-1-infected patients on highly active antiretroviral therapy (HAART), with CD4 T cell counts above 450 cells/mm³ and undetectable viremia. Thirty participants were randomized (2:1) to receive either 3 intramuscular injections of MVA-B vaccine (coding for clade B HIV-1 Env, Gag, Pol and Nef antigens) or placebo, followed by interruption of HAART.

Methods

The magnitude, breadth, quality and phenotype of the HIV-1-specific T cell response were assayed by intracellular cytokine staining (ICS) in 22 volunteers pre- and post-vaccination.

Results

MVA-B vaccine induced newly detected HIV-1-specific CD4 T cell responses and expanded pre-existing responses (mostly against Gag, Pol and Nef antigens) that were high in magnitude, broadly directed and showed an enhanced polyfunctionality with a T effector memory (TEM) phenotype, while maintaining the magnitude and quality of the pre-existing HIV-1-specific CD8 T cell responses. In addition, vaccination also triggered preferential CD8⁺ T cell polyfunctional responses to the MVA vector antigens that increase in magnitude after two and three booster doses.

Conclusion

MVA-B vaccination represents a feasible strategy to improve T cell responses in individuals with pre-existing HIV-1-specific immunity.

Trial Registration

ClinicalTrials.gov NCT01571466