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1.
J Gen Virol ; 105(5)2024 May.
Article En | MEDLINE | ID: mdl-38747699

Nasopharyngeal carcinoma (NPC) carcinogenesis and malignant transformation are intimately associated with Epstein-Barr virus (EBV) infection. A zinc-fingered transcription factor known as Krüppel-like factor 5 (KLF5) has been shown to be aberrantly expressed in a number of cancer types. However, little is known about the regulatory pathways and roles of KLF5 in EBV-positive NPC. Our study found that KLF5 expression was significantly lower in EBV-positive NPC than in EBV-negative NPC. Further investigation revealed that EBER1, which is encoded by EBV, down-regulates KLF5 via the extracellular signal-regulated kinase (ERK) signalling pathway. This down-regulation of KLF5 by EBER1 contributes to maintaining latent EBV infection in NPC. Furthermore, we uncovered the biological roles of KLF5 in NPC cells. Specifically, KLF5 may influence the cell cycle, prevent apoptosis, and encourage cell migration and proliferation - all of which have a generally pro-cancer impact. In conclusion, these findings offer novel strategies for EBV-positive NPC patients' antitumour treatment.


Down-Regulation , Epstein-Barr Virus Infections , Herpesvirus 4, Human , Kruppel-Like Transcription Factors , MAP Kinase Signaling System , Nasopharyngeal Carcinoma , Nasopharyngeal Neoplasms , Humans , Kruppel-Like Transcription Factors/metabolism , Kruppel-Like Transcription Factors/genetics , Nasopharyngeal Carcinoma/virology , Nasopharyngeal Carcinoma/metabolism , Nasopharyngeal Carcinoma/pathology , Nasopharyngeal Carcinoma/genetics , Herpesvirus 4, Human/genetics , Herpesvirus 4, Human/physiology , Epstein-Barr Virus Infections/virology , Epstein-Barr Virus Infections/metabolism , Nasopharyngeal Neoplasms/virology , Nasopharyngeal Neoplasms/metabolism , Cell Line, Tumor , Cell Movement , Cell Proliferation , Apoptosis , Virus Latency
2.
Int J Mol Sci ; 25(9)2024 May 03.
Article En | MEDLINE | ID: mdl-38732219

Epstein-Barr virus (EBV) is a ubiquitous gammaherpesvirus etiologically associated with benign and malignant diseases. Since the pathogenic mechanisms of EBV are not fully understood, understanding EBV genetic diversity is an ongoing goal. Therefore, the present work describes the genetic diversity of the lytic gene BZLF1 in a sampling of 70 EBV-positive cases from southeastern Brazil. Additionally, together with the genetic regions previously characterized, the aim of the present study was to determine the impact of viral genetic factors that may influence EBV genetic diversity. Accordingly, the phylogenetic analysis of the BZLF1 indicated two main clades with high support, BZ-A and BZ-B (PP > 0.85). Thus, the BZ-A clade was the most diverse clade associated with the main polymorphisms investigated, including the haplotype Type 1 + V3 (p < 0.001). Furthermore, the multigene phylogenetic analysis (MLA) between BZLF1 and the oncogene LMP1 showed specific clusters, revealing haplotypic segregation that previous single-gene phylogenies from both genes failed to demonstrate. Surprisingly, the LMP1 Raji-related variant clusters were shown to be more diverse, associated with BZ-A/B and the Type 2/1 + V3 haplotypes. Finally, due to the high haplotypic diversity of the Raji-related variants, the number of DNA recombination-inducing motifs (DRIMs) was evaluated within the different clusters defined by the MLA. Similarly, the haplotype BZ-A + Raji was shown to harbor a greater number of DRIMs (p < 0.001). These results call attention to the high haplotype diversity of EBV in southeast Brazil and strengthen the hypothesis of the recombinant potential of South American Raji-related variants via the LMP1 oncogene.


Epstein-Barr Virus Infections , Genetic Variation , Herpesvirus 4, Human , Phylogeny , Recombination, Genetic , Herpesvirus 4, Human/genetics , Humans , Brazil , Epstein-Barr Virus Infections/virology , Epstein-Barr Virus Infections/genetics , Trans-Activators/genetics , Male , Female , Haplotypes/genetics , Adult , Viral Matrix Proteins/genetics , Child , Middle Aged , Adolescent , Virus Latency/genetics , Child, Preschool , Young Adult
3.
Nat Commun ; 15(1): 4156, 2024 May 16.
Article En | MEDLINE | ID: mdl-38755141

Epstein-Barr virus (EBV) uses a biphasic lifecycle of latency and lytic reactivation to infect >95% of adults worldwide. Despite its central role in EBV persistence and oncogenesis, much remains unknown about how EBV latency is maintained. We used a human genome-wide CRISPR/Cas9 screen to identify that the nuclear protein SFPQ was critical for latency. SFPQ supported expression of linker histone H1, which stabilizes nucleosomes and regulates nuclear architecture, but has not been previously implicated in EBV gene regulation. H1 occupied latent EBV genomes, including the immediate early gene BZLF1 promoter. Upon reactivation, SFPQ was sequestered into sub-nuclear puncta, and EBV genomic H1 occupancy diminished. Enforced H1 expression blocked EBV reactivation upon SFPQ knockout, confirming it as necessary downstream of SFPQ. SFPQ knockout triggered reactivation of EBV in B and epithelial cells, as well as of Kaposi's sarcoma-associated herpesvirus in B cells, suggesting a conserved gamma-herpesvirus role. These findings highlight SFPQ as a major regulator of H1 expression and EBV latency.


Herpesvirus 4, Human , Histones , PTB-Associated Splicing Factor , Virus Activation , Virus Latency , Herpesvirus 4, Human/genetics , Herpesvirus 4, Human/physiology , Humans , Histones/metabolism , Virus Activation/genetics , Virus Latency/genetics , PTB-Associated Splicing Factor/metabolism , PTB-Associated Splicing Factor/genetics , Gene Expression Regulation, Viral , B-Lymphocytes/virology , B-Lymphocytes/metabolism , Epstein-Barr Virus Infections/virology , Epstein-Barr Virus Infections/genetics , Epstein-Barr Virus Infections/metabolism , CRISPR-Cas Systems , Promoter Regions, Genetic/genetics , Trans-Activators/metabolism , Trans-Activators/genetics , Genome, Viral
4.
Methods Mol Biol ; 2807: 45-59, 2024.
Article En | MEDLINE | ID: mdl-38743220

Latent HIV-1 reservoirs are a major obstacle to the eradication of HIV-1. Several cure strategies have been proposed to eliminate latent reservoirs. One of the key strategies involves the reactivation of latent HIV-1 from cells using latency-reversing agents. However, currently it is unclear whether any of the latency-reversing agents are able to completely reactivate HIV-1 provirus transcription in all latent cells. An understanding of the reactivation of HIV-1 provirus at single-cell single-molecule level is necessary to fully comprehend the reactivation of HIV-1 in the reservoirs. Furthermore, since reactivable viruses in the pool of latent reservoirs are rare, combining single-cell imaging techniques with the ability to visualize a large number of reactivated single cells that express both viral RNA and proteins in a pool of uninfected and non-reactivated cells will provide unprecedented information about cell-to-cell variability in reactivation. Here, we describe the single-cell single-molecule RNA-FISH (smRNA-FISH) method to visualize HIV-1 gag RNA combined with the immunofluorescence (IF) method to detect Gag protein to characterize the reactivated cells. This method allows the visualization of subcellular localization of RNA and proteins before and after reactivation and facilitates absolute quantitation of the number of transcripts per cell using FISH-quant. In addition, we describe a high-speed and high-resolution scanning (HSHRS) fluorescence microscopy imaging method to visualize rare and reactivated cells in a pool of non-reactivated cells with high efficiency.


Fluorescent Antibody Technique , HIV-1 , In Situ Hybridization, Fluorescence , RNA, Viral , Single Molecule Imaging , Single-Cell Analysis , Virus Activation , Virus Latency , HIV-1/physiology , HIV-1/genetics , Humans , In Situ Hybridization, Fluorescence/methods , RNA, Viral/genetics , Single-Cell Analysis/methods , Single Molecule Imaging/methods , Fluorescent Antibody Technique/methods , HIV Infections/virology , Proviruses/genetics
5.
Methods Mol Biol ; 2807: 261-270, 2024.
Article En | MEDLINE | ID: mdl-38743234

The development of 3D-organoid models has revolutionized the way diseases are studied. Recently, our brain organoid model has been shown to recapitulate in in vitro the human brain cytoarchitecture originally encountered in HIV-1 neuropathogenesis, allowing downstream applications. Infected monocytes, macrophages, and microglia are critically important immune cells for infection and dissemination of HIV-1 throughout brain during acute and chronic phase of the disease. Once in the brain parenchyma, long-lived infected monocytes/macrophages along with resident microglia contribute to the establishment of CNS latency in people with HIV (PWH). Hence, it is important to better understand how HIV-1 enters and establishes infection and latency in CNS to further develop cure strategies. Here we detailed an accessible protocol to incorporate monocytes (infected and/or labeled) as a model of transmigration of peripheral monocytes into brain organoids that can be applied to characterize HIV-1 neuroinvasion and virus dissemination.


Brain , HIV Infections , HIV-1 , Monocytes , Organoids , Organoids/virology , Organoids/pathology , Humans , HIV-1/physiology , HIV-1/pathogenicity , Monocytes/virology , Monocytes/immunology , HIV Infections/virology , HIV Infections/immunology , HIV Infections/pathology , Brain/virology , Brain/pathology , Brain/immunology , Microglia/virology , Microglia/immunology , Microglia/pathology , Macrophages/virology , Macrophages/immunology , Virus Latency
6.
Methods Mol Biol ; 2807: 343-354, 2024.
Article En | MEDLINE | ID: mdl-38743239

Assays to study HIV persistence are crucial to evaluate therapeutic strategies aimed toward an HIV cure. Several assays have been developed to date that rely on the measurement of nucleic acids. In recent years, the advancement of ultrasensitive technologies for the detection of proteins has improved our understanding of the role of translation-competent reservoirs in HIV persistence. In this chapter, we describe the development of an ultrasensitive p24 ELISA that uses planar array technology. This assay allows for the detection of HIV-1 p24 in the low fg/ml range in different biological matrixes, including cell lysates. This assay can be used to investigate the efficacy of latency reversing agents to reactivate HIV or to evaluate the persistence of translation-competent reservoirs in people living with HIV (PWH) in cells or diverse biological fluids.


Enzyme-Linked Immunosorbent Assay , HIV Core Protein p24 , HIV Infections , HIV-1 , HIV-1/drug effects , Humans , HIV Core Protein p24/metabolism , HIV Core Protein p24/analysis , Enzyme-Linked Immunosorbent Assay/methods , HIV Infections/virology , HIV Infections/drug therapy , Virus Latency
7.
Nat Commun ; 15(1): 4018, 2024 May 13.
Article En | MEDLINE | ID: mdl-38740820

Anti-HSV therapies are only suppressive because they do not eliminate latent HSV present in ganglionic neurons, the source of recurrent disease. We have developed a potentially curative approach against HSV infection, based on gene editing using HSV-specific meganucleases delivered by adeno-associated virus (AAV) vectors. Gene editing performed with two anti-HSV-1 meganucleases delivered by a combination of AAV9, AAV-Dj/8, and AAV-Rh10 can eliminate 90% or more of latent HSV DNA in mouse models of orofacial infection, and up to 97% of latent HSV DNA in mouse models of genital infection. Using a pharmacological approach to reactivate latent HSV-1, we demonstrate that ganglionic viral load reduction leads to a significant decrease of viral shedding in treated female mice. While therapy is well tolerated, in some instances, we observe hepatotoxicity at high doses and subtle histological evidence of neuronal injury without observable neurological signs or deficits. Simplification of the regimen through use of a single serotype (AAV9) delivering single meganuclease targeting a duplicated region of the HSV genome, dose reduction, and use of a neuron-specific promoter each results in improved tolerability while retaining efficacy. These results reinforce the curative potential of gene editing for HSV disease.


Dependovirus , Gene Editing , Herpes Simplex , Herpesvirus 1, Human , Viral Load , Virus Shedding , Animals , Gene Editing/methods , Female , Dependovirus/genetics , Mice , Herpesvirus 1, Human/genetics , Herpesvirus 1, Human/physiology , Herpes Simplex/genetics , Herpes Simplex/virology , Herpes Simplex/therapy , Disease Models, Animal , Virus Latency/genetics , Humans , Genetic Vectors/genetics , Vero Cells , Genetic Therapy/methods , Herpes Genitalis/therapy , Herpes Genitalis/virology , DNA, Viral/genetics
8.
Retrovirology ; 21(1): 6, 2024 Apr 05.
Article En | MEDLINE | ID: mdl-38580979

Transcriptionally latent forms of replication-competent proviruses, present primarily in a small subset of memory CD4+ T cells, pose the primary barrier to a cure for HIV-1 infection because they are the source of the viral rebound that almost inevitably follows the interruption of antiretroviral therapy. Over the last 30 years, many of the factors essential for initiating HIV-1 transcription have been identified in studies performed using transformed cell lines, such as the Jurkat T-cell model. However, as highlighted in this review, several poorly understood mechanisms still need to be elucidated, including the molecular basis for promoter-proximal pausing of the transcribing complex and the detailed mechanism of the delivery of P-TEFb from 7SK snRNP. Furthermore, the central paradox of HIV-1 transcription remains unsolved: how are the initial rounds of transcription achieved in the absence of Tat? A critical limitation of the transformed cell models is that they do not recapitulate the transitions between active effector cells and quiescent memory T cells. Therefore, investigation of the molecular mechanisms of HIV-1 latency reversal and LRA efficacy in a proper physiological context requires the utilization of primary cell models. Recent mechanistic studies of HIV-1 transcription using latently infected cells recovered from donors and ex vivo cellular models of viral latency have demonstrated that the primary blocks to HIV-1 transcription in memory CD4+ T cells are restrictive epigenetic features at the proviral promoter, the cytoplasmic sequestration of key transcription initiation factors such as NFAT and NF-κB, and the vanishingly low expression of the cellular transcription elongation factor P-TEFb. One of the foremost schemes to eliminate the residual reservoir is to deliberately reactivate latent HIV-1 proviruses to enable clearance of persisting latently infected cells-the "Shock and Kill" strategy. For "Shock and Kill" to become efficient, effective, non-toxic latency-reversing agents (LRAs) must be discovered. Since multiple restrictions limit viral reactivation in primary cells, understanding the T-cell signaling mechanisms that are essential for stimulating P-TEFb biogenesis, initiation factor activation, and reversing the proviral epigenetic restrictions have become a prerequisite for the development of more effective LRAs.


HIV Infections , HIV-1 , Humans , HIV-1/physiology , Virus Latency , Positive Transcriptional Elongation Factor B/genetics , Positive Transcriptional Elongation Factor B/metabolism , CD4-Positive T-Lymphocytes , Proviruses/metabolism , Virus Activation
9.
J Virol ; 98(5): e0003224, 2024 May 14.
Article En | MEDLINE | ID: mdl-38651900

Critical stages of lytic herpes simplex virus type 1 (HSV-1) replication are marked by the sequential expression of immediate early (IE) to early (E), then late (L) viral genes. HSV-1 can also persist in neuronal cells via a non-replicative, transcriptionally repressed infection called latency. The regulation of lytic and latent transcriptional profiles is critical to HSV-1 pathogenesis and persistence. We sought a fluorescence-based approach to observe the outcome of neuronal HSV-1 infection at the single-cell level. To achieve this goal, we constructed and characterized a novel HSV-1 recombinant that enables discrimination between lytic and latent infection. The dual reporter HSV-1 encodes a human cytomegalovirus-immediate early (hCMV-IE) promoter-driven enhanced yellow fluorescent protein (eYFP) to visualize the establishment of infection and an endogenous mCherry-VP26 fusion to report lytic replication. We confirmed that viral gene expression, replication, and spread of infection are not altered by the incorporation of the fluorescent reporters, and fluorescent protein (FP) detection virtuously reports the progression of lytic replication. We demonstrate that the outcome of HSV-1 infection of compartmentalized primary neurons is determined by viral inoculating dose: high-dose axonal inoculation proceeds to lytic replication, whereas low-dose axonal inoculation establishes a latent HSV-1 infection. Interfering with low-dose axonal inoculation via small molecule drugs reports divergent phenotypes of eYFP and mCherry reporter detection, correlating with altered states of viral gene expression. We report that the transcriptional state of neuronal HSV-1 infection is variable in response to changes in the intracellular neuronal environment.IMPORTANCEHerpes simplex virus type 1 (HSV-1) is a prevalent human pathogen that infects approximately 67% of the global human population. HSV-1 invades the peripheral nervous system, where latent HSV-1 infection persists within the host for life. Immunological evasion, viral persistence, and herpetic pathologies are determined by the regulation of HSV-1 gene expression. Studying HSV-1 gene expression during neuronal infection is challenging but essential for the development of antiviral therapeutics and interventions. We used a recombinant HSV-1 to evaluate viral gene expression during infection of primary neurons. Manipulation of cell signaling pathways impacts the establishment and transcriptional state of HSV-1 latency in neurons. The work here provides critical insight into the cellular and viral factors contributing to the establishment of latent HSV-1 infection.


Herpes Simplex , Herpesvirus 1, Human , Luminescent Proteins , Neurons , Virus Replication , Herpesvirus 1, Human/genetics , Herpesvirus 1, Human/physiology , Neurons/virology , Neurons/metabolism , Humans , Animals , Luminescent Proteins/genetics , Luminescent Proteins/metabolism , Herpes Simplex/virology , Genes, Reporter , Virus Latency/genetics , Gene Expression Regulation, Viral , Chlorocebus aethiops , Vero Cells , Cytomegalovirus/genetics , Cytomegalovirus/physiology
10.
PLoS Pathog ; 20(4): e1011939, 2024 Apr.
Article En | MEDLINE | ID: mdl-38683861

Epstein-Barr virus (EBV) persistently infects 95% of adults worldwide and is associated with multiple human lymphomas that express characteristic EBV latency programs used by the virus to navigate the B-cell compartment. Upon primary infection, the EBV latency III program, comprised of six Epstein-Barr Nuclear Antigens (EBNA) and two Latent Membrane Protein (LMP) antigens, drives infected B-cells into germinal center (GC). By incompletely understood mechanisms, GC microenvironmental cues trigger the EBV genome to switch to the latency II program, comprised of EBNA1, LMP1 and LMP2A and observed in GC-derived Hodgkin lymphoma. To gain insights into pathways and epigenetic mechanisms that control EBV latency reprogramming as EBV-infected B-cells encounter microenvironmental cues, we characterized GC cytokine effects on EBV latency protein expression and on the EBV epigenome. We confirmed and extended prior studies highlighting GC cytokine effects in support of the latency II transition. The T-follicular helper cytokine interleukin 21 (IL-21), which is a major regulator of GC responses, and to a lesser extent IL-4 and IL-10, hyper-induced LMP1 expression, while repressing EBNA expression. However, follicular dendritic cell cytokines including IL-15 and IL-27 downmodulate EBNA but not LMP1 expression. CRISPR editing highlighted that STAT3 and STAT5 were necessary for cytokine mediated EBNA silencing via epigenetic effects at the EBV genomic C promoter. By contrast, STAT3 was instead necessary for LMP1 promoter epigenetic remodeling, including gain of activating histone chromatin marks and loss of repressive polycomb repressive complex silencing marks. Thus, EBV has evolved to coopt STAT signaling to oppositely regulate the epigenetic status of key viral genomic promoters in response to GC cytokine cues.


Epigenesis, Genetic , Epstein-Barr Virus Infections , Gene Expression Regulation, Viral , Germinal Center , Herpesvirus 4, Human , Virus Latency , Herpesvirus 4, Human/genetics , Herpesvirus 4, Human/physiology , Humans , Germinal Center/immunology , Germinal Center/virology , Epstein-Barr Virus Infections/virology , Epstein-Barr Virus Infections/genetics , Epstein-Barr Virus Infections/immunology , Cytokines/metabolism , B-Lymphocytes/virology , B-Lymphocytes/metabolism
11.
Viruses ; 16(4)2024 03 27.
Article En | MEDLINE | ID: mdl-38675857

The persistence of the latent viral reservoir is the main hurdle to curing HIV-1 infection. SIV infection of non-human primates (NHPs), namely Indian-origin rhesus macaques, is the most relevant and widely used animal model to evaluate therapies that seek to eradicate HIV-1. The utility of a model ultimately rests on how accurately it can recapitulate human disease, and while reservoirs in the NHP model behave quantitatively very similar to those of long-term suppressed persons with HIV-1 (PWH) in the most salient aspects, recent studies have uncovered key nuances at the clonotypic level that differentiate the two in qualitative terms. In this review, we will highlight differences relating to proviral intactness, clonotypic structure, and decay rate during ART between HIV-1 and SIV reservoirs and discuss the relevance of these distinctions in the interpretation of HIV-1 cure strategies. While these, to some degree, may reflect a unique biology of the virus or host, distinctions among the proviral landscape in SIV are likely to be shaped significantly by the condensed timeframe of NHP studies. ART is generally initiated earlier in the disease course, and animals are virologically suppressed for shorter periods before receiving interventions. Because these are experimental variables dictated by the investigator, we offer guidance on study design for cure-related studies performed in the NHP model. Finally, we highlight the case of GS-9620 (Vesatolimod), an antiviral TLR7 agonist tested in multiple independent pre-clinical studies in which virological outcomes may have been influenced by study-related variables.


HIV Infections , HIV-1 , Macaca mulatta , Simian Acquired Immunodeficiency Syndrome , Simian Immunodeficiency Virus , Virus Latency , Simian Immunodeficiency Virus/genetics , Simian Immunodeficiency Virus/physiology , Animals , HIV-1/genetics , HIV-1/drug effects , HIV-1/physiology , Simian Acquired Immunodeficiency Syndrome/virology , Simian Acquired Immunodeficiency Syndrome/drug therapy , Humans , HIV Infections/virology , HIV Infections/drug therapy , Virus Latency/drug effects , Disease Models, Animal , Disease Reservoirs/virology , Proviruses/genetics , Proviruses/physiology , Viral Load
12.
Viruses ; 16(4)2024 04 04.
Article En | MEDLINE | ID: mdl-38675906

The disruption of antiviral sensors and the evasion of immune defences by various tactics are hallmarks of EBV infection. One of the EBV latent gene products, LMP1, was shown to induce the activation of signalling pathways, such as NF-κB, MAPK (JNK, ERK1/2, p38), JAK/STAT and PI3K/Akt, via three subdomains of its C-terminal domain, regulating the expression of several cytokines responsible for modulation of the immune response and therefore promoting viral persistence. The aim of this review is to summarise the current knowledge on the EBV-mediated induction of immunomodulatory molecules by the activation of signal transduction pathways with a particular focus on LMP1-mediated mechanisms. A more detailed understanding of the cytokine biology molecular landscape in EBV infections could contribute to the more complete understanding of diseases associated with this virus.


Epstein-Barr Virus Infections , Herpesvirus 4, Human , Signal Transduction , Viral Matrix Proteins , Humans , Viral Matrix Proteins/metabolism , Viral Matrix Proteins/immunology , Viral Matrix Proteins/genetics , Herpesvirus 4, Human/immunology , Epstein-Barr Virus Infections/immunology , Epstein-Barr Virus Infections/virology , Epstein-Barr Virus Infections/metabolism , Cytokines/metabolism , Cytokines/immunology , Animals , Immunomodulation , Host-Pathogen Interactions/immunology , NF-kappa B/metabolism , Virus Latency/immunology
13.
Viruses ; 16(4)2024 04 08.
Article En | MEDLINE | ID: mdl-38675914

Understanding the pathophysiology of myalgic encephalomyelitis/chronic fatigue syndrome (ME/CFS) is critical for advancing treatment options. This review explores the novel hypothesis that a herpesvirus infection of endothelial cells (ECs) may underlie ME/CFS symptomatology. We review evidence linking herpesviruses to persistent EC infection and the implications for endothelial dysfunction, encompassing blood flow regulation, coagulation, and cognitive impairment-symptoms consistent with ME/CFS and Long COVID. This paper provides a synthesis of current research on herpesvirus latency and reactivation, detailing the impact on ECs and subsequent systemic complications, including latent modulation and long-term maladaptation. We suggest that the chronicity of ME/CFS symptoms and the multisystemic nature of the disease may be partly attributable to herpesvirus-induced endothelial maladaptation. Our conclusions underscore the necessity for further investigation into the prevalence and load of herpesvirus infection within the ECs of ME/CFS patients. This review offers conceptual advances by proposing an endothelial infection model as a systemic mechanism contributing to ME/CFS, steering future research toward potentially unexplored avenues in understanding and treating this complex syndrome.


Endothelial Cells , Fatigue Syndrome, Chronic , Herpesviridae Infections , Humans , Endothelial Cells/virology , Fatigue Syndrome, Chronic/virology , Fatigue Syndrome, Chronic/physiopathology , Herpesviridae/physiology , Herpesviridae Infections/virology , Virus Latency , Post-Acute COVID-19 Syndrome/pathology , Post-Acute COVID-19 Syndrome/physiopathology
14.
PLoS Pathog ; 20(4): e1012132, 2024 Apr.
Article En | MEDLINE | ID: mdl-38620028

Epstein-Barr virus (EBV) is an important cause of human lymphomas, including Burkitt lymphoma (BL). EBV+ BLs are driven by Myc translocation and have stringent forms of viral latency that do not express either of the two major EBV oncoproteins, EBNA2 (which mimics Notch signaling) and LMP1 (which activates NF-κB signaling). Suppression of Myc-induced apoptosis, often through mutation of the TP53 (p53) gene or inhibition of pro-apoptotic BCL2L11 (BIM) gene expression, is required for development of Myc-driven BLs. EBV+ BLs contain fewer cellular mutations in apoptotic pathways compared to EBV-negative BLs, suggesting that latent EBV infection inhibits Myc-induced apoptosis. Here we use an EBNA2-deleted EBV virus (ΔEBNA2 EBV) to create the first in vivo model for EBV+ BL-like lymphomas derived from primary human B cells. We show that cord blood B cells infected with both ΔEBNA2 EBV and a Myc-expressing vector proliferate indefinitely on a CD40L/IL21 expressing feeder layer in vitro and cause rapid onset EBV+ BL-like tumors in NSG mice. These LMP1/EBNA2-negative Myc-driven lymphomas have wild type p53 and very low BIM, and express numerous germinal center B cell proteins (including TCF3, BACH2, Myb, CD10, CCDN3, and GCSAM) in the absence of BCL6 expression. Myc-induced activation of Myb mediates expression of many of these BL-associated proteins. We demonstrate that Myc blocks LMP1 expression both by inhibiting expression of cellular factors (STAT3 and Src) that activate LMP1 transcription and by increasing expression of proteins (DNMT3B and UHRF1) known to enhance DNA methylation of the LMP1 promoters in human BLs. These results show that latent EBV infection collaborates with Myc over-expression to induce BL-like human B-cell lymphomas in mice. As NF-κB signaling retards the growth of EBV-negative BLs, Myc-mediated repression of LMP1 may be essential for latent EBV infection and Myc translocation to collaboratively induce human BLs.


B-Lymphocytes , Burkitt Lymphoma , Epstein-Barr Virus Infections , Herpesvirus 4, Human , Proto-Oncogene Proteins c-myc , Virus Latency , Animals , Burkitt Lymphoma/virology , Burkitt Lymphoma/metabolism , Burkitt Lymphoma/pathology , Burkitt Lymphoma/genetics , Humans , Mice , Epstein-Barr Virus Infections/virology , Epstein-Barr Virus Infections/metabolism , Epstein-Barr Virus Infections/complications , Epstein-Barr Virus Infections/genetics , Herpesvirus 4, Human/genetics , Proto-Oncogene Proteins c-myc/metabolism , Proto-Oncogene Proteins c-myc/genetics , B-Lymphocytes/virology , B-Lymphocytes/metabolism , Epstein-Barr Virus Nuclear Antigens/metabolism , Epstein-Barr Virus Nuclear Antigens/genetics , Apoptosis , Viral Proteins/metabolism , Viral Proteins/genetics
15.
Proc Natl Acad Sci U S A ; 121(18): e2202003121, 2024 Apr 30.
Article En | MEDLINE | ID: mdl-38669184

Using an immunofluorescence assay based on CRISPR-dCas9-gRNA complexes that selectively bind to the HIV LTR (HIV Cas-FISH), we traced changes in HIV DNA localization in primary effector T cells from early infection until the cells become quiescent as they transition to memory cells. Unintegrated HIV DNA colocalized with CPSF6 and HIV capsid (CA, p24) was found in the cytoplasm and nuclear periphery at days 1 and 3 post infection. From days 3 to 7, most HIV DNA was distributed primarily in the nuclear intermediate euchromatic compartment and was transcribed. By day 21, the cells had entered quiescence, and HIV DNA accumulated in the perinucleolar compartment (PNC). The localization of proviruses to the PNC was blocked by integrase inhibitor Raltegravir, suggesting it was due to chromosomal rearrangements. During the reactivation of latently infected cells through the T cell receptor (TCR), nascent viral mRNA transcripts associated with HIV DNA in the PNC were detected. The viral trans-activator Tat and its regulatory partners, P-TEFb and 7SK snRNA, assembled in large interchromatin granule clusters near the provirus within 2 h of TCR activation. As T cell activation progressed, the HIV DNA shifted away from the PNC. HIV DNA in latently infected memory T cells from patients also accumulated in the PNC and showed identical patterns of nuclear rearrangements after cellular reactivation. Thus, in contrast to transformed cells where proviruses are found primarily at the nuclear periphery, in primary memory T cells, the nuclear architecture undergoes rearrangements that shape the transcriptional silencing and reactivation of proviral HIV.


Cell Nucleus , HIV Infections , HIV-1 , Proviruses , Virus Activation , Virus Latency , Humans , Proviruses/genetics , Cell Nucleus/metabolism , Cell Nucleus/virology , HIV-1/genetics , HIV-1/physiology , HIV-1/metabolism , HIV Infections/virology , HIV Infections/metabolism , DNA, Viral/genetics , DNA, Viral/metabolism , HIV Long Terminal Repeat/genetics
16.
PLoS Pathog ; 20(4): e1012172, 2024 Apr.
Article En | MEDLINE | ID: mdl-38662769

The implementation of antiretroviral therapy (ART) has effectively restricted the transmission of Human Immunodeficiency Virus (HIV) and improved overall clinical outcomes. However, a complete cure for HIV remains out of reach, as the virus persists in a stable pool of infected cell reservoir that is resistant to therapy and thus a main barrier towards complete elimination of viral infection. While the mechanisms by which host proteins govern viral gene expression and latency are well-studied, the emerging regulatory functions of non-coding RNAs (ncRNA) in the context of T cell activation, HIV gene expression and viral latency have not yet been thoroughly explored. Here, we report the identification of the Cytoskeleton Regulator (CYTOR) long non-coding RNA (lncRNA) as an activator of HIV gene expression that is upregulated following T cell stimulation. Functional studies show that CYTOR suppresses viral latency by directly binding to the HIV promoter and associating with the cellular positive transcription elongation factor (P-TEFb) to activate viral gene expression. CYTOR also plays a global role in regulating cellular gene expression, including those involved in controlling actin dynamics. Depletion of CYTOR expression reduces cytoplasmic actin polymerization in response to T cell activation. In addition, treating HIV-infected cells with pharmacological inhibitors of actin polymerization reduces HIV gene expression. We conclude that both direct and indirect effects of CYTOR regulate HIV gene expression.


Gene Expression Regulation, Viral , HIV Infections , HIV-1 , RNA, Long Noncoding , Virus Latency , Humans , RNA, Long Noncoding/genetics , HIV Infections/virology , HIV Infections/genetics , HIV-1/genetics , HIV-1/physiology , Promoter Regions, Genetic , Lymphocyte Activation , Jurkat Cells
17.
Virol J ; 21(1): 80, 2024 04 05.
Article En | MEDLINE | ID: mdl-38581045

BACKGROUND: Although macrophages are now recognized as an essential part of the HIV latent reservoir, whether and how viral latency is established and reactivated in these cell types is poorly understood. To understand the fundamental mechanisms of viral latency in macrophages, there is an urgent need to develop latency models amenable to genetic manipulations and screening for appropriate latency-reversing agents (LRAs). Given that differentiated THP-1 cells resemble monocyte-derived macrophages in HIV replication mechanisms, we set out to establish a macrophage cell model for HIV latency using THP-1 cells. METHODS: We created single-cell clones of THP-1 cells infected with a single copy of the dual-labeled HIVGKO in which a codon switched eGFP (csGFP) is under the control of the HIV-1 5' LTR promoter, and a monomeric Kusabira orange 2 (mKO2) under the control of cellular elongation factor one alpha promoter (EF1α). Latently infected cells are csGFP-, mKO2+, while cells with actively replicating HIV (or reactivated virus) are csGFP+,mKO2+. After sorting for latently infected cells, each of the THP-1 clones with unique integration sites for HIV was differentiated into macrophage-like cells with phorbol 12-myristate 13-acetate (PMA) and treated with established LRAs to stimulate HIV reactivation. Monocyte-derived macrophages (MDMs) harboring single copies of HIVGKO were used to confirm our findings. RESULTS: We obtained clones of THP-1 cells with latently infected HIV with unique integration sites. When the differentiated THP-1 or primary MDMs cells were treated with various LRAs, the bromodomain inhibitors JQ1 and I-BET151 were the most potent compounds. Knockdown of BRD4, the target of JQ1, resulted in increased reactivation, thus confirming the pharmacological effect. The DYRK1A inhibitor Harmine and lipopolysaccharide (LPS) also showed significant reactivation across all three MDM donors. Remarkably, LRAs like PMA/ionomycin, bryostatin-1, and histone deacetylase inhibitors known to potently reactivate latent HIV in CD4 + T cells showed little activity in macrophages. CONCLUSIONS: Our results indicate that this model could be used to screen for appropriate LRAs for macrophages and show that HIV latency and reactivation mechanisms in macrophages may be distinct from those of CD4 + T cells.


HIV Infections , HIV-1 , Humans , Virus Latency/genetics , Virus Activation , Transcription Factors , Nuclear Proteins , HIV-1/genetics , Macrophages , CD4-Positive T-Lymphocytes , Bromodomain Containing Proteins , Cell Cycle Proteins
18.
Proc Natl Acad Sci U S A ; 121(19): e2313823121, 2024 May 07.
Article En | MEDLINE | ID: mdl-38683980

HIV latency regulation in monocytes and macrophages can vary according to signals directing differentiation, polarization, and function. To investigate these processes, we generated an HIV latency model in THP-1 monocytes and showed differential levels of HIV reactivation among clonal populations. Monocyte-to-macrophage differentiation of HIV-infected primary human CD14+ and THP-1 cells induced HIV reactivation and showed that virus production increased concomitant with macrophage differentiation. We applied the HIV-infected THP-1 monocyte-to-macrophage (MLat) model to assess the biological mechanisms regulating HIV latency dynamics during monocyte-to-macrophage differentiation. We pinpointed protein kinase C signaling pathway activation and Cyclin T1 upregulation as inherent differentiation mechanisms that regulate HIV latency reactivation. Macrophage polarization regulated latency, revealing proinflammatory M1 macrophages suppressed HIV reactivation while anti-inflammatory M2 macrophages promoted HIV reactivation. Because macrophages rely on reactive-oxygen species (ROS) to exert numerous cellular functions, we disrupted redox pathways and found that inhibitors of the thioredoxin (Trx) system acted as latency-promoting agents in T-cells and monocytes, but opposingly acted as latency-reversing agents in macrophages. We explored this mechanism with Auranofin, a clinical candidate for reducing HIV reservoirs, and demonstrated Trx reductase inhibition led to ROS induced NF-κB activity, which promoted HIV reactivation in macrophages, but not in T-cells and monocytes. Collectively, cell type-specific differences in HIV latency regulation could pose a barrier to HIV eradication strategies.


Cell Differentiation , HIV Infections , HIV-1 , Homeostasis , Macrophages , Monocytes , Oxidation-Reduction , Reactive Oxygen Species , Virus Activation , Virus Latency , Humans , Virus Latency/physiology , Macrophages/virology , Macrophages/metabolism , Monocytes/virology , Monocytes/metabolism , HIV-1/physiology , HIV Infections/virology , HIV Infections/metabolism , Virus Activation/physiology , Reactive Oxygen Species/metabolism , THP-1 Cells , Signal Transduction , Protein Kinase C/metabolism
19.
Emerg Microbes Infect ; 13(1): 2327371, 2024 Dec.
Article En | MEDLINE | ID: mdl-38444369

To date, an affordable, effective treatment for an HIV-1 cure remains only a concept with most "latency reversal" agents (LRAs) lacking specificity for the latent HIV-1 reservoir and failing in early clinical trials. We assessed HIV-1 latency reversal using a multivalent HIV-1-derived virus-like particle (HLP) to treat samples from 32 people living with HIV-1 (PLWH) in Uganda, US and Canada who initiated combined antiretroviral therapy (cART) during chronic infection. Even after 5-20 years on stable cART, HLP could target CD4+ T cells harbouring latent HIV-1 reservoir resulting in 100-fold more HIV-1 release into culture supernatant than by common recall antigens, and 1000-fold more than by chemotherapeutic LRAs. HLP induced release of a divergent and replication-competent HIV-1 population from PLWH on cART. These findings suggest HLP provides a targeted approach to reactivate the majority of latent HIV-1 proviruses among individuals infected with HIV-1.


HIV Infections , HIV-1 , Humans , Virus Latency , CD4-Positive T-Lymphocytes , Canada
20.
Curr Opin HIV AIDS ; 19(3): 95-101, 2024 May 01.
Article En | MEDLINE | ID: mdl-38457209

PURPOSE OF REVIEW: Currently, HIV-infected patients are treated with antiretroviral therapy. However, when the treatment is interrupted, viral rebound occurs from latently infected cells. Therefore, scientists aim to develop an HIV-1 cure which eradicates or permanently silences the latent reservoir. RECENT FINDINGS: Previously, scientists focused on the shock-and-kill cure strategy, which aims to eradicate the latent reservoir using latency-reactivating agents. Limited success shifts the interest towards the block-and-lock cure approach, which aims to achieve a functional cure by "blocking" HIV-1 transcription and "locking" the provirus in a deep latent state, resistant to treatment-interruption. In this strategy, latency promoting agents are used to induce transcriptional silencing and alter the epigenetics environment at the HIV promotor. SUMMARY: For the block-and-lock cure strategy to succeed more investigation into the transcriptional and epigenetic regulation of HIV-1 gene expression is necessary to design optimal latency-promoting agents. In this review, we will discuss the latency promoting agents that have been described in literature during the past 2 years (2022-2023).


HIV Infections , Virus Activation , Humans , Virus Activation/genetics , Virus Latency/genetics , Epigenesis, Genetic , Proviruses/genetics , CD4-Positive T-Lymphocytes
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