FOXO1 promotes HIV Latency by suppressing ER stress in T cells

Vallejo-Gracia, Albert; Chen, Irene P.; Perrone, Rosalba; Besnard, Emilie; Boehm, Daniela; Battivelli, Emilie; Tezil, Tuğsan; Krey, Karsten; Raymond, Kyle A.; Hull, Philip A.; Walter, Marius; Habrylo, Ireneusz; Cruz, Andrew; Deeks, Steven G.; Pillai, Satish K.; Verdin, Eric; Ott, Mélanie

doi:10.1101/2020.04.23.058123

Cited by 6 publications

(6 citation statements)

References 78 publications

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“…This TF is associated with a quiescent central memory T cell (Tcm) phenotype, consistent with the hypothesis that cells that adopt a quiescent Tcm phenotype are more prone to latent infection (Garaud et al, 2017). Interestingly, a related Forkhead TF, FOXO1, has also recently been reported to promote HIV latency (Roux et al, 2019;Vallejo-Gracia et al, 2020). In addition to these known HIV-regulating TFs, several TFs with no known role in HIV transcription were identified by our study, and defining their role in latency will likely lead to the discovery of new mechanisms of transcriptional repression for HIV.…”

Section: Discussionsupporting

confidence: 75%

Epigenomic characterization of latent HIV infection identifies latency regulating transcription factors

Jefferys

Burgos²,

Peterson³

et al. 2020

Preprint

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SummaryTranscriptional silencing of HIV generates a reservoir of latently infected cells, but the mechanisms that lead to this outcome are not well understood. We characterized a primary cell model of HIV latency, and observed that latency is a stable, heritable viral state that is rapidly reestablished after stimulation. Using Assay of Transposon-Accessible Chromatin sequencing (ATACseq) we found that latently infected cells exhibit reduced proviral accessibility, elevated activity of Forkead and Kruppel-like factor transcription factors (TFs), and reduced activity of AP-1, RUNX and GATA TFs. Latency reversing agents caused distinct patterns of chromatin reopening across the provirus. Furthermore, depletion of a chromatin domain insulator, CTCF inhibited HIV latency, identifying this factor as playing a key role in the initiation or enforcement of latency. These data indicate that HIV latency develops preferentially in cells with a distinct pattern of TF activity that promotes a closed proviral structure and inhibits viral gene expression.

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Section: Discussionsupporting

confidence: 75%

Epigenomic characterization of latent HIV infection identifies latency regulating transcription factors

Jefferys

Burgos²,

Peterson³

et al. 2020

Preprint

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“…The DE isoform data confirms the involvement of NFKB-complex via significant 4-fold increases in relevant NFKBIA and BIRC2 isoform TPMs upon TNF-alpha treatment. Of particular note, is the highly significant (p-adj<0.1) paradoxical downregulation of a PSAT1 isoform given that previous studies have found this gene to be enriched during Tat-elicited cell proliferation in productive HIV infection (43) and during FOXO1-inhibition elicited latency reversal in HIV-infected CD4 T-cells (44). This paradoxical result can be reconciled by close inspection of its exon connectivity (Figure 4B) , which reveals that the downregulated isoform (NM_021154.4) lacks Exon 8 and results in a variant with 6-to 7-fold lower activity compared to the standard NM_058179.4 isoform that retains this exon (45).…”

Section: Resultsmentioning

confidence: 99%

Selective Ablation of 3’ RNA ends and Processive RTs Facilitate Direct cDNA Sequencing of Full-length Host Cell and Viral Transcripts

Gallardo

Nguyen

Routh

et al. 2022

Preprint

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Alternative splicing (AS) is necessary for viral proliferation in host cells and a critical regulatory component of viral gene expression. Conventional RNA-seq approaches provide incomplete coverage of AS due to their short read-lengths and are susceptible to biases and artifacts introduced in prevailing library preparation methodologies. Moreover, viral splicing studies are often conducted separately from host cell transcriptome analysis, precluding an assessment of the viral manipulation of host splicing machinery. To address current limitations, we developed a quantitative full-length direct cDNA sequencing strategy to simultaneously profile viral and host cell transcripts. This nanopore-based approach couples processive reverse transcriptases with a novel one-step chemical ablation of 3' RNA ends (termed CASPR) which decreases ribosomal RNA reads and enriches for poly-adenylated coding sequences. We extensively validate our approach using synthetic reference transcripts and show CASPR doubles the breadth of coverage per transcript and increases detection of long transcripts (>4kb), while being functionally equivalent to PolyA+ selection for transcript quantification. We used our approach to interrogate host cell and HIV-1 transcript dynamics during viral reactivation and identified novel putative HIV-1 host factors containing exon skipping or novel intron retentions and delineated the HIV-1 transcriptional state associated with these differentially regulated host factors.

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“…The reversal of double-positive cells after sorting may reflect the intrinsically stochastic transcription of HIV-1 (86)(87)(88). Latent cell lines are notoriously sensitive to cellular stresses, which cause reactivation (89)(90)(91). It is, therefore, possible that the less stable GFPpositive cells represent cells that are temporarily activated, and which slowly revert back to a latent state.…”

Section: Discussionmentioning

confidence: 99%

A two-color haploid genetic screen identifies novel host factors involved in HIV latency

Röling

Sisakht

et al. 2021

Preprint

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To identify novel host factors as putative targets to reverse HIV latency, we performed an insertional mutagenesis genetic screen in a latently HIV-1-infected pseudo-haploid KBM7 cell line (Hap-Lat). Following mutagenesis, insertions were mapped to the genome and bioinformatic analysis resulted in the identification of 69 candidate host genes involved in maintaining HIV-1 latency. A select set of candidate genes was functionally validated using shRNA mediated depletion in latent HIV-1 infected J-Lat A2 and 11.1 T cell lines. We confirmed ADK, CHD9, CMSS1, EVI2B, EXOSC8, FAM19A, GRIK5, IRF2BP2, NF1, and USP15 as novel host factors involved in the maintenance of HIV latency. Chromatin immunoprecipitation assays indicated that CHD9, a Chromodomain Helicase DNA-binding protein, maintains HIV latency via direct association with the HIV 5’LTR, and its depletion results in increased histone acetylation at the HIV-1 promoter, concomitant with HIV-1 latency reversal. FDA-approved inhibitors 5-Iodotubercidin, Trametinib, and Topiramate, targeting ADK, NF1, and GRIK5, respectively were characterized for their latency reversal potential. While 5-Iodotubercidin exhibited significant cytotoxicity in both J-Lat and primary CD4+ T cells, Trametinib reversed latency in J-Lat cells but not in latently HIV-1-infected primary CD4+ T cells. Crucially, Topiramate reversed latency in cell-line models and latently infected primary CD4+ T cells, without inducing T cell activation or significant toxicity. Thus, using an adaptation of a haploid forward genetic screen, we identified novel and druggable host factors contributing to HIV-1 latency.ImportanceA reservoir of latent HIV-1-infected cells persists in the presence of combination antiretroviral therapy (cART), representing a major obstacle for viral eradication. Reactivation of the latent HIV-1 provirus is part of curative strategies which aim to promote clearance of the infected cells. Using a two-color haploid screen, we identified 69 candidate genes as latency maintaining host factors and functionally validated a subset of 10 of those in additional T-cell based cell line models of HIV-1 latency. We further demonstrated that CHD9 is associated with HIV-1’s promoter, the 5’LTR while this association is lost upon reactivation. Additionally, we characterized the latency reversal potential of FDA compounds targeting ADK, NF1, and GRIK5 and identify the GRIK5 inhibitor Topiramate as a viable latency reversal agent with clinical potential.

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FOXO1 promotes HIV Latency by suppressing ER stress in T cells

Cited by 6 publications

References 78 publications

Epigenomic characterization of latent HIV infection identifies latency regulating transcription factors

Epigenomic characterization of latent HIV infection identifies latency regulating transcription factors

Selective Ablation of 3’ RNA ends and Processive RTs Facilitate Direct cDNA Sequencing of Full-length Host Cell and Viral Transcripts

A two-color haploid genetic screen identifies novel host factors involved in HIV latency

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