Distinct chromatin functional states correlate with HIV latency reactivation in infected primary CD4+ T cells

Battivelli, Emilie; Dahabieh, Matthew S.; Abdel‐Mohsen, Mohamed; Svensson, J. Peter; Silva, Israel Tojal da; Cohn, Lillian B.; Gramatica, Andrea; Deeks, Steven G.; Greene, Warner C.; Pillai, Satish K.; Verdin, Eric

doi:10.7554/elife.34655

Cited by 148 publications

(224 citation statements)

References 86 publications

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“…To test the potential of FOXO1 inhibition to affect HIV-1 latency, we used the second-generation dual-color reporter virus HIVGKO (LTR-HIV-∆-env-nefATG-csGFP-EF1α-mKO2) 19 and the FOXO1 inhibitor AS1842856 (Figure 1a). In this system, latently infected K562 cells express the mKO2 fluorescent protein under the control of the EF1α promoter, while cells containing a productive and active virus express both mKO2 and GFP fluorophores, the latter controlled by the HIV-1 LTR.…”

Section: Foxo1 Is a Specific Regulator Of Hiv Latency Establishmentmentioning

confidence: 99%

FOXO1 promotes HIV Latency by suppressing ER stress in T cells

Vallejo-Gracia

Chen

Perrone

et al. 2020

Preprint

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Quiescence is a hallmark of CD4 + T cells latently infected with HIV-1. While reversing this quiescence is an effective approach to reactivate latent HIV from T cells in culture, it can cause deleterious cytokine dysregulation in patients. Here we report that FOXO1, a key regulator of T-cell quiescence, promotes latency and suppresses productive HIV infection. In resting T cells, FOXO1 inhibition induces ER stress and activates two associated transcription factors: activating transcription factor 4 (ATF4) and nuclear factor of activated T cells (NFAT). Both factors associate with HIV chromatin and are necessary for HIV reactivation. Indeed, inhibition of PKR-like endoplasmic reticulum kinase (PERK), a known link between ER stress and ATF4, and calcineurin, a calcium-dependent regulator of NFAT, synergistically suppress HIV reactivation induced by FOXO1 inhibition. Thus, our studies uncover a novel link between FOXO1, ER stress, and HIV infection that could be therapeutically exploited to selectively reverse T-cell quiescence and reduce the size of the latent viral reservoir.Luciferase Reporter Assay. For reactivation of latent HIV-1 provirus, cells were counted and collected as pellets by centrifugation at 1500 rpm for 10 min. Cells were then plated in 96-well U-bottom plates at 1×10 6 per 200 μl in the presence of 30 μM Raltegravir (Santa Cruz Biotechnology) and the indicated activator. Cells were harvested 72 h after stimulation, washed one time with PBS, and lysed in 60 μl of Passive Lysis Buffer (Promega). After 15 min of lysis, the luciferase activity in cell extracts was quantified with a SpectraMax i3x Multi-Mode plate reader (Molecular Devices, USA) after mixing 20 μl of lysate with 100 μl of substrate (Luciferase Assay System-Promega). Relative light units (RLU) were normalized to protein content determined by DC Protein assay (BIO-RAD).Synergy Bliss model. To analyze drug combinatorial effects, we used the Bliss independence model from the SynergyFinder web application (https://synergyfinder.fimm.fi) 79 . The Bliss score (∆faxy) is the difference between the calculated reactivation value if the two drugs act independently and the observed combined reactivation values. Synergy is defined as ∆faxy > 0, while ∆faxy < 0 indicates antagonism. Positive Bliss scores represent dose combinations which have greater than additive effect 25 .

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Section: Foxo1 Is a Specific Regulator Of Hiv Latency Establishmentmentioning

confidence: 99%

FOXO1 promotes HIV Latency by suppressing ER stress in T cells

Vallejo-Gracia

Chen

Perrone

et al. 2020

Preprint

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“…We next investigated whether the drug susceptibility of various clones depends on the genetic and epigenetic environments of the HIV-1 provirus 32 . The proportion of ISs in the host genes was slightly decreased in EFdA- or EFdA + PEP005-treated cells ( Fig.…”

Section: Resultsmentioning

confidence: 99%

A widely-distributed HIV-1 provirus elimination assay to evaluate latency-reversing agents in vitro

Matsuda

Islam²,

Takada

et al. 2019

Preprint

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22Persistence of HIV-1 latent reservoir cells during antiretroviral therapy (ART) is a major 23 obstacle for curing HIV-1. Latency-reversing agents (LRAs) are under intensive development to 24 reactivate and eradicate latently infected cells; however, there are a few useful models for 25 evaluating LRA activity in vitro. Here, we established a chronically HIV-1-infected culture 26 system harboring thousands of different HIV-1-infected cell clones with a wide distribution of 27 HIV-1 provirus similar to that observed in vivo. A combination of an LRA and an anti-HIV-1 28 drug successfully inhibited viral re-emergence after drug discontinuation, demonstrating 29 "experimental cure" in the in vitro model. We demonstrated that the epigenetic environment of 30 the integrated provirus plays a role in determining drug susceptibility. Our widely distributed 31 intact provirus elimination (WIPE) assay will be useful for optimizing therapeutics against 32HIV-1 latency and provides mechanistic insights into the selection of heterogeneous Advances in antiviral therapy have dramatically improved the therapeutic options available for 36 treating human immunodeficiency virus type 1 (HIV-1) infection. However, even with the most 37 potent combined antiretroviral therapy (cART), HIV-1-infected patients remain on medication 38 throughout their lifetime because HIV-1 persists in viral reservoirs in vivo regardless of 39 treatment 1-3 . In this regard, the "shock and kill" approach, which first activates cells latently 40 infected with HIV-1 2,3 using small molecule agents called HIV-1 latency-reversing agents 41 (LRAs), is a possible strategy for curing HIV-1 4-9 . LRAs reverse HIV-1 latency and induce viral 42 production in cells latently infected with the virus. In theory, infected cells that express viral 43 antigens are then killed by the human immune system, such as cytotoxic T lymphocytes, or viral 44 cytopathic effects 10-12 . However, LRAs that appear potent in in vitro assays are not necessarily 45 effective in vivo because the viral reservoir situation is quite different in vitro and in vivo [13][14][15][16] . 46The host factors shaping the HIV-1 reservoir in vivo include the immunological status with 47 respect to the virus, anatomical location, and a variety of host cells. From the viral perspective, 48wide heterogeneity is noted in vivo, such as the viral sequence, presence of defective proviruses, 49integration sites (ISs) in the host cellular genomic DNA, and expansion of some infected 50 clones 17-21 . These factors potentially affect the efficacy of LRA in vivo. 51As the "shock" step may trigger the production of infectious virus and thereby induce 52 de novo infection, it is essential to combine LRAs with the existing anti-HIV-1 drugs. However, 53no suitable in vitro model system to evaluate the efficacy of such combination therapies exists. 54Currently available in vitro models for HIV-1 latency, such as ACH2, J1.1, and U1 cells, carry 55 only one or two integrated proviruses with a specific genetic and epigenetic...

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“…Genomic position effects have been shown to influence HIV-1 expression and latency reversal [68][69][70] . LADs represent a repressive chromatin environment tightly associated with the nuclear periphery 68,71 . SINEs (e.g.…”

Section: Discussionmentioning

confidence: 99%

Antiretroviral APOBEC3 Cytidine Deaminases Alter HIV-1 Provirus Integration Site Profiles

Ajoge

Renner

Kohio

et al. 2019

Preprint

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APOBEC3 (A3) proteins are host-encoded deoxycytidine deaminases that provide an innate immune barrier to retroviral infection, notably against HIV-1. Low levels of deamination are believed to contribute to the rapid genetic evolution of HIV-1, while the catalytic activity of these proteins can induce catastrophic hypermutation in proviral DNA leading to near-total HIV-1 restriction. So far, little is known about how A3 cytosine deaminases might impact HIV-1 proviral DNA integrations into human chromosomal DNA. Using a deep sequencing approach, we analyzed the influence of catalytic active and inactive APOBEC3F and APOBEC3G on HIV-1 integration site selections. DNA editing was detected at the extremities of the long terminal repeat regions of the virus. Both catalytic active and non-catalytic A3 mutants decreased insertions into gene coding sequences and increased integration sites into SINE elements, oncogenes and transcriptionsilencing non-B DNA features. Our data implicates A3 as a host factor influencing HIV-1 integration site selection and promotes a more transcriptionally silent integration site profile. Ajoge et al., 2019 3 GRAPHICAL ABSTRACT Schematic depicting the influence of APOBEC3 (A3) proteins on HIV integration site targeting. Left, in the absence of A3, HIV has a strong preference for integrating into genes. Right, both catalytic active and non-catalytic A3 mutants decrease integration into genes and increase integration into SINE elements and in transcription-silencing non-B DNA features.

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Distinct chromatin functional states correlate with HIV latency reactivation in infected primary CD4+ T cells

Cited by 148 publications

References 86 publications

FOXO1 promotes HIV Latency by suppressing ER stress in T cells

FOXO1 promotes HIV Latency by suppressing ER stress in T cells

A widely-distributed HIV-1 provirus elimination assay to evaluate latency-reversing agents in vitro

Antiretroviral APOBEC3 Cytidine Deaminases Alter HIV-1 Provirus Integration Site Profiles

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