Correction: Repressive LTR Nucleosome Positioning by the BAF Complex Is Required for HIV Latency.

[This corrects the article DOI: 10.1371/journal.pbio.1001206.].

Repressive LTR nucleosome positioning by the BAF complex is required for HIV latency.

Persistence of a reservoir of latently infected memory T cells provides a barrier to HIV eradication in treated patients. Several reports have implicated the involvement of SWI/SNF chromatin remodeling complexes in restricting early steps in HIV infection, in coupling the processes of integration and remodeling, and in promoter/LTR transcription activation and repression. However, the mechanism behind the seemingly contradictory involvement of SWI/SNF in the HIV life cycle remains unclear. Here we addressed the role of SWI/SNF in regulation of the latent HIV LTR before and after transcriptional activation. We determined the predicted nucleosome affinity of the LTR sequence and found a striking reverse correlation when compared to the strictly positioned in vivo LTR nucleosomal structure; sequences encompassing the DNase hypersensitive regions displayed the highest nucleosome affinity, while the strictly positioned nucleosomes displayed lower affinity for nucleosome formation. To examine the mechanism behind this reverse correlation, we used a combinatorial approach to determine DNA accessibility, histone occupancy, and the unique recruitment and requirement of BAF and PBAF, two functionally distinct subclasses of SWI/SNF at the LTR of HIV-infected cells before and after activation. We find that establishment and maintenance of HIV latency requires BAF, which removes a preferred nucleosome from DHS1 to position the repressive nucleosome-1 over energetically sub-optimal sequences. Depletion of BAF resulted in de-repression of HIV latency concomitant with a dramatic alteration in the LTR nucleosome profile as determined by high resolution MNase nucleosomal mapping. Upon activation, BAF was lost from the HIV promoter, while PBAF was selectively recruited by acetylated Tat to facilitate LTR transcription. Thus BAF and PBAF, recruited during different stages of the HIV life cycle, display opposing function on the HIV promoter. Our data point to the ATP-dependent BRG1 component of BAF as a putative therapeutic target to deplete the latent reservoir in patients.

Real-world comparative effectiveness of acalabrutinib and ibrutinib in patients with chronic lymphocytic leukemia.

Novel agents, including Bruton tyrosine kinase inhibitors (BTKis), have become the standard of care for patients with chronic lymphocytic leukemia (CLL). We conducted a real-world retrospective analysis of patients with CLL treated with acalabrutinib vs ibrutinib using the Flatiron Health database. Patients with CLL were included if they initiated acalabrutinib or ibrutinib between 1 January 2018 and 28 February 2021. The primary outcome of interest was time to treatment discontinuation (TTD). Kaplan-Meier analysis was used to estimate unweighted and weighted median TTD. A weighted Cox proportional hazards model was used to compare the TTD between cohorts. Of the 2509 patients included in the analysis, 89.6% received ibrutinib, and 14.1% received acalabrutinib. TTD was not significantly different between cohorts in the unweighted analysis. After weighting, the cohorts were balanced on all baseline characteristics except cardiovascular risk factors and baseline medications use. The median (95% confidence interval [CI]) TTD was not reached (NR; 95% CI, 25.1 to NR) for the acalabrutinib cohort and was 23.4 months (95% CI, 18.1-28.7) for the ibrutinib cohort. The discontinuation rate at 12 months was 22% for the weighted acalabrutinib cohort vs 31% for the weighted ibrutinib cohort (P = .005). After additional adjustment for prior BTKi use, the acalabrutinib cohort had a 41% lower risk of discontinuation vs ibrutinib (hazard ratio, 0.59; 95% CI, 0.43-0.81; P = .001). In the largest available study comparing BTKis, patients with CLL receiving acalabrutinib demonstrated lower rates of discontinuation and a prolonged time to discontinuation vs those receiving ibrutinib.

The mTOR Complex Controls HIV Latency.

A population of CD4 T lymphocytes harboring latent HIV genomes can persist in patients on antiretroviral therapy, posing a barrier to HIV eradication. To examine cellular complexes controlling HIV latency, we conducted a genome-wide screen with a pooled ultracomplex shRNA library and in vitro system modeling HIV latency and identified the mTOR complex as a modulator of HIV latency. Knockdown of mTOR complex subunits or pharmacological inhibition of mTOR activity suppresses reversal of latency in various HIV-1 latency models and HIV-infected patient cells. mTOR inhibitors suppress HIV transcription both through the viral transactivator Tat and via Tat-independent mechanisms. This inhibition occurs at least in part via blocking the phosphorylation of CDK9, a p-TEFb complex member that serves as a cofactor for Tat-mediated transcription. The control of HIV latency by mTOR signaling identifies a pathway that may have significant therapeutic opportunities.

Therapy for latent HIV-1 infection: the role of histone deacetylase inhibitors.

Persistence of HIV-1 in latently infected CD4(+) T-cells prevents eradication in HIV-infected treated patients. Latency is characterized by a reversible silencing of transcription of integrated HIV-1. Several molecular mechanisms have been described which contribute to latency, including the establishment and maintenance of repressive chromatin on the HIV-1 promoter. Histone deacetylation is a landmark modification associated with transcriptional repression of the HIV-1 promoter and inhibition of histone deacetylase enzymes (HDACs) reactivates latent HIV-1. Here, we review the different HDAC inhibitors that have been studied in HIV-1 latency and their therapeutic potential in reactivating latent HIV-1.

Reactivation of latent HIV by histone deacetylase inhibitors.

Latent HIV persists in CD4(+) T cells in infected patients under antiretroviral therapy (ART). Latency is associated with transcriptional silencing of the integrated provirus and driven, at least in part, by histone deacetylases (HDACs), a family of chromatin-associated proteins that regulate histone acetylation and the accessibility of DNA to transcription factors. Remarkably, inhibition of HDACs is sufficient to reactivate a fraction of latent HIV in a variety of experimental systems. This basic observation led to the shock and kill idea that forcing the transcriptional activation of HIV might lead to virus expression, to virus- or host-induced cell death of the reactivated cells, and to the eradication of the pool of latently infected cells. Such intervention might possibly lead to a cure for HIV-infected patients. Here, we review the basic biology of HDACs and their inhibitors, the role of HDACs in HIV latency, and recent efforts to use HDAC inhibitors to reactivate latent HIV in vitro and in vivo.

HIV latency: experimental systems and molecular models.

Highly active antiretroviral therapy (HAART) has shown great efficacy in increasing the survival of HIV infected individuals. However, HAART does not lead to the full eradication of infection and therefore has to be continued for life. HIV persists in a transcriptionally inactive form in resting T cells in HAART-treated patients and can be reactivated following T-cell activation. These latently infected cells allow the virus to persist in the presence of HAART. Here, we review recent advances in the study of the molecular mechanisms of HIV latency. We also review experimental models in which latency is currently studied. We focus on the epigenetic mechanisms controlling HIV transcription and on the role of chromatin and its post-translational modifications. We discuss how small molecule inhibitors that target epigenetic regulators, such as HDAC (histone deacetylase) inhibitors, are being tested for their ability to reactivate latent HIV. Finally, we discuss the clinical potential of these drugs to flush out latently infected cells from HIV-infected patients and to eradicate the virus.

Epigenetic regulation of HIV latency.

PURPOSE OF REVIEW: A reservoir of latently infected cells remains in HIV-infected patients treated with highly active antiretroviral therapy treatment. Persistence of HIV in this latent reservoir has prevented full viral eradication. In order to understand and develop rational therapeutics to flush out HIV latency, the molecular mechanisms governing the phenomena of HIV latency need to be understood. Several mechanisms have been proposed to explain HIV latency. RECENT FINDINGS: Epigenetic regulation of the HIV promoter in the 5' long terminal repeat of HIV-1 via histone protein modifications and the presence of inhibitory nucleosomes play a critical role in the establishment, maintenance, and reactivation of HIV latency. Recent reports have shed further light on how HIV latency might be epigenetically regulated. In this review, we discuss how these recent reports broaden our understanding of how HIV latency is regulated. Here, we review how histone modifications and chromatin remodeling affect the transcriptional activity of the HIV promoter in the context of HIV latency. SUMMARY: These new epigenetic regulators of HIV latency pose as potential interesting candidates for therapeutics against HIV latency.

Opposing functions of TFII-I spliced isoforms in growth factor-induced gene expression.

Multifunctional transcription factor TFII-I has two spliced isoforms (Delta and beta) in murine fibroblasts. Here we show that these isoforms have distinct subcellular localization and mutually exclusive transcription functions in the context of growth factor signaling. In the absence of signaling, TFII-Ibeta is nuclear and recruited to the c-fos promoter in vivo. But upon growth factor stimulation, the promoter recruitment is abolished and it is exported out of the nucleus. Moreover, isoform-specific silencing of TFII-Ibeta results in transcriptional activation of the c-fos gene. In contrast, TFII-IDelta is largely cytoplasmic in the resting state but translocates to the nucleus upon growth factor signaling, undergoes signal-induced recruitment to the same site on the c-fos promoter, and activates the gene. Importantly, activated TFII-IDelta interacts with Erk1/2 (MAPK) kinase in the cell cytoplasm and imports the Erk1/2 to the nucleus, thereby transducing growth factor signaling. Our results identify a unique growth factor signaling pathway controlled by opposing activities of two TFII-I spliced isoforms.

An FF domain-dependent protein interaction mediates a signaling pathway for growth factor-induced gene expression.

FF domains are poorly understood protein motifs found in all eukaryotes but in a very small number of proteins. They typically occur in tandem arrays and appear predominantly in splicing and transcription factors. Curiously, they are also present in the p190 family of cytoplasmic Rho GTPase activating proteins (GAPs). We identified the serum-responsive transcriptional regulator TFII-I as a specific interactor with the p190 RhoGAP FF domains. p190 sequesters TFII-I in the cytoplasm via the FF domains, but upon PDGF receptor-mediated phosphorylation of an FF domain, TFII-I is released from p190 and translocates to the nucleus where it can activate transcription of serum-inducible genes including c-fos. These findings reveal a pathway by which mitogens promote gene transcription and indicate a role for FF domains in phosphorylation-mediated signal transduction.

Transcriptional regulation of the Grp78 promoter by endoplasmic reticulum stress: role of TFII-I and its tyrosine phosphorylation.

TFII-I is a signal-induced multi-functional transcription factor that has recently been implicated as a regulatory component of the endoplasmic reticulum (ER) stress response. TFII-I acts through ER stress-induced binding to the ER stress element, which is highly conserved in promoters of ER stress-inducible genes such as Grp78/BiP. Interestingly, its tyrosine phosphorylation sites are required for its activation of the Grp78 promoter. Toward understanding the link between TFII-I, the tyrosine kinase signaling pathway, and Grp78 activation, we discovered that Tg stress induces a dramatic increase of TFII-I phosphorylation at Tyr248 and localization of this form of TFII-I to the nucleus. Chromatin immunoprecipitation analysis further reveals enhanced TFII-I binding to the Grp78 promoter in vivo upon ER stress. Previously, we reported that genistein, a general inhibitor of tyrosine kinase, could suppress ER stress induction of Grp78 by inhibiting complex formation on the ER stress element; however, the mechanism is not known. Consistent with TFII-I being a target of genistein suppression, we observed that genistein could suppress Tg stress-induced phosphorylation of TFII-I. We further demonstrate that c-Src, which is one of kinases identified to mediate phosphorylation of TFII-I at Tyr248, is activated by Tg stress and is able to stimulate the Grp78 promoter activity. Lastly, using stable cell lines with suppressed TFII-I levels, we show that TFII-I is required for optimal induction of Grp78 by ER stress. Our studies provide a molecular link that connects the c-Src tyrosine kinase transduction pathway to ER stress-induced transcriptional activation of Grp78 mediated by TFII-I.

The SUMO ubiquitin-protein isopeptide ligase family member Miz1/PIASxbeta /Siz2 is a transcriptional cofactor for TFII-I.

We have shown previously that a TFII-I-related protein, hMusTRD1/BEN, represses transcriptional activity of TFII-I. The repression by hMusTRD1/BEN was hypothesized to occur via a two-step competition mechanism involving a cytoplasmic shuttling factor and a nuclear cofactor required for transcriptional activation of TFII-I. Employing a two-hybrid approach with both yeast genomic and mouse cDNA libraries in parallel, we have identified the RING-like zinc finger containing Miz1/PIASxbeta/Siz2, which is a ubiquitin-protein isopeptide ligase in the SUMO pathway, as the potential nuclear cofactor that interacts with both TFII-I and hMusTRD1/BEN. Our conclusion is based on the following observations. First, the interactions are biochemically confirmed in mammalian cells where Miz1/mPIASxbeta interacts with both TFII-I and hMusTRD1/BEN when these proteins are ectopically co-expressed. Second, co-expression of a nuclear localization signal-deficient mutant of Miz1/mPIASxbeta with wild type TFII-I fails to alter the subcellular localization of the former. Finally, ectopically expressed Miz1/mPIASxbeta augments the transcriptional activity of TFII-I and relieves the repression exerted by a mutant hMusTRD1/BEN that co-localized with TFII-I in the nucleus.