Dynamics of HIV Latency and Reactivation in a Primary CD4+ T Cell Model

Mohammadi, Pejman; Iulio, Julia di; Muñoz, Miguel; Martínez, Raquel; Bartha, István; Cavassini, Matthias; Thorball, Christian W.; Fellay, Jacques; Beerenwinkel, Niko; Ciuffi, Angela; Telenti, Amalio

doi:10.1371/journal.ppat.1004156

Cited by 74 publications

(109 citation statements)

References 63 publications

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“…This finding is consistent with a previous population analysis of the transcriptome of infected cells using a similar model (Mohammadi et al, 2014). However, the virus used in these studies lacks expression of most viral proteins in order to limit cytopathic effect and thus may not reflect the full impact of an intact replication competent virus on the host cell.…”

Section: Discussionsupporting

confidence: 93%

“…This model is similar to models from other laboratories (Kim et al, 2014; Mohammadi et al, 2014; Sahu et al, 2006; Tyagi et al, 2010) and involves infecting activated CD4 + T cells with a GFP-expressing HIV strain (Yang et al, 2009) and sorting to obtain a pure infected population, followed by long-term (8–12 weeks) co-culture with H80 cells (Figure 1A). During this period of culture, we observed highly variegated transcriptional downregulation of HIV gene expression within the infected population.…”

Section: Resultsmentioning

confidence: 92%

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Single-Cell Analysis of Quiescent HIV Infection Reveals Host Transcriptional Profiles that Regulate Proviral Latency

et al. 2018

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SUMMARY A detailed understanding of the mechanisms that establish or maintain the latent reservoir of HIV will guide approaches to eliminate persistent infection. We used a cell line and primary cell models of HIV latency to investigate viral RNA (vRNA) expression and the role of the host transcriptome using single-cell approaches. Single-cell vRNA quantitation identified distinct populations of cells expressing various levels of vRNA, including completely silent populations. Strikingly, single-cell RNA-seq of latently infected primary cells demonstrated that HIV downregulation occurred in diverse transcriptomic environments but was significantly associated with expression of a specific set of cellular genes. In particular, latency was more frequent in cells expressing a transcriptional signature that included markers of naive and central memory T cells. These data reveal that expression of HIV proviruses within the latent reservoir are influenced by the host cell transcriptional program. Therapeutic modulation of these programs may reverse or enforce HIV latency.

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Section: Discussionsupporting

confidence: 93%

Section: Resultsmentioning

confidence: 92%

Single-Cell Analysis of Quiescent HIV Infection Reveals Host Transcriptional Profiles that Regulate Proviral Latency

et al. 2018

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“…Possible consequences of SAHA impeding T-cell activation may include decreased HIV transcription and translation, which may diminish eradication of infected cells during ART. This is consistent with a recent study in a primary CD4+ T cell latency model showing that SAHA treatment resulted in only a modest increase in HIV protein despite a 3-fold increase in HIV transcription[46]. Our data suggest that T-cell receptor activation may require particular scrutiny when evaluating dosing regimens for SAHA, or future analogues with increased bioavailability or potency.…”

Section: Discussionsupporting

confidence: 92%

“…For the majority of the genes listed in Table 1, SAHA induced changes in expression would likely favor HIV activation from latency. However, recent evidence suggests that HIV activation from latency may also require removal of an as yet unknown post-transcriptional block[46]; no obvious candidates for such an activity emerged from our results.…”

Section: Discussioncontrasting

confidence: 54%

Dose-responsive gene expression in suberoylanilide hydroxamic acid-treated resting CD4+ T cells

Reardon¹,

Beliakova-Bethell²,

Spina

et al. 2015

Aids

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Design Persistent latently infected CD4+ T cells represent a major obstacle to HIV eradication. Histone deacetylase inhibitors (HDACis) are a proposed activation therapy. However, off-target effects on expression in host immune cells are poorly understood. We hypothesized that HDACi-modulated genes would be best identified with dose-response analysis. Methods Resting primary CD4+ T cells were treated with 0.34, 1, 3, or 10 μM of the HDACi, SAHA, for 24 hours and subjected to microarray gene expression analysis. Genes with dose-correlated expression were filtered to identify a subset with consistent up or downregulation at each SAHA dose. Histone modifications were characterized in 6 SAHA dose-responsive genes by chromatin immunoprecipitation (ChIP-RT-qPCR). Results A large number of genes were shown to be up (N=657) or downregulated (N=725) by SAHA in a dose-responsive manner (FDR p-value < 0.05, fold change ≥ |2|). Several genes (CTNNAL1, DPEP2, H1F0, IRGM, PHF15, and SELL) are potential in vivo biomarkers of SAHA activity. SAHA dose-responsive genes included transcription factors, HIV restriction factors, histone methyltransferases, and host proteins that interact with HIV. Pathway analysis suggested net downregulation of T cell activation with increasing SAHA dose. Histone acetylation was not correlated with host gene expression, but plausible alternative mechanisms for SAHA-modulated gene expression were identified. Conclusions Numerous genes in CD4+ T cells are modulated by SAHA in a dose-responsive manner, including genes that may negatively influence HIV activation from latency. Our study suggests that SAHA influences gene expression through a confluence of several mechanisms, including histone modification, and altered expression and activity of transcription factors.

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“…Viral RNA accumulation in culture supernatants increased further by day 6 with 1 M SAHA treatment for only one of the two animals. As expected, cell activation with anti-CD2/CD3/CD28 beads also induced an upregulation of virion production, which exceeded the amount of virus produced following either of the SAHA treatments, consistent with findings for ex vivo treatment of cells from cART-suppressed HIV-1-infected people (30,66,67).…”

supporting

confidence: 87%

Effect of Suberoylanilide Hydroxamic Acid (SAHA) Administration on the Residual Virus Pool in a Model of Combination Antiretroviral Therapy-Mediated Suppression in SIVmac239-Infected Indian Rhesus Macaques

Prete

Shoemaker

Oswald

et al. 2014

Antimicrob Agents Chemother

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Nonhuman primate models are needed for evaluations of proposed strategies targeting residual virus that persists in HIV-1-infected individuals receiving suppressive combination antiretroviral therapy (cART). However, relevant nonhuman primate (NHP) models of cART-mediated suppression have proven challenging to develop. We used a novel three-class, six-drug cART regimen to achieve durable 4.0-to 5.5-log reductions in plasma viremia levels and declines in cell-associated viral RNA and DNA in blood and tissues of simian immunodeficiency virus SIVmac239-infected Indian-origin rhesus macaques, then evaluated the impact of treatment with the histone deacetylase inhibitor (HDACi) suberoylanilide hydroxamic acid (SAHA; Vorinostat) on the residual virus pool. Ex vivo SAHA treatment of CD4 ؉ T cells obtained from cART-suppressed animals increased histone acetylation and viral RNA levels in culture supernatants. cART-suppressed animals each received 84 total doses of oral SAHA. We observed SAHA dose-dependent increases in acetylated histones with evidence for sustained modulation as well as refractoriness following prolonged administration. In vivo virologic activity was demonstrated based on the ratio of viral RNA to viral DNA in peripheral blood mononuclear cells, a presumptive measure of viral transcription, which significantly increased in SAHAtreated animals. However, residual virus was readily detected at the end of treatment, suggesting that SAHA alone may be insufficient for viral eradication in the setting of suppressive cART. The effects observed were similar to emerging data for repeat-dose SAHA treatment of HIV-infected individuals on cART, demonstrating the feasibility, utility, and relevance of NHP models of cART-mediated suppression for in vivo assessments of AIDS virus functional cure/eradication approaches.

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Dynamics of HIV Latency and Reactivation in a Primary CD4+ T Cell Model

Cited by 74 publications

References 63 publications

Single-Cell Analysis of Quiescent HIV Infection Reveals Host Transcriptional Profiles that Regulate Proviral Latency

Single-Cell Analysis of Quiescent HIV Infection Reveals Host Transcriptional Profiles that Regulate Proviral Latency

Dose-responsive gene expression in suberoylanilide hydroxamic acid-treated resting CD4+ T cells

Effect of Suberoylanilide Hydroxamic Acid (SAHA) Administration on the Residual Virus Pool in a Model of Combination Antiretroviral Therapy-Mediated Suppression in SIVmac239-Infected Indian Rhesus Macaques

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