Towards a Functional Cure of HIV-1: Insight Into the Chromatin Landscape of the Provirus

Despite potent combination antiretroviral therapy, HIV-1 infection persists due to irreversible integration of the virus in long-living cells of the immune system. The main focus of HIV-1 cure strategies has been on HIV-1 eradication, yet without great success so far. Therefore, HIV-1 remission or a functional cure, whereby the virus is silenced rather than eradicated, is considered as an alternative strategy. Elite controllers, individuals who spontaneously control HIV-1, may point us the way toward a functional HIV-1 cure. In order to achieve such a cure, a profound understanding of the mechanisms controlling HIV-1 expression and silencing is needed. In recent years, evidence has grown that the site of integration as well as the chromatin landscape surrounding the integration site affects the transcriptional state of the provirus. Still, at present, the impact of integration site selection on the establishment and maintenance of the HIV-1 reservoirs remains poorly understood. The discovery of LEDGF/p75 as a binding partner of HIV-1 integrase has led to a better understanding of integration site selection. LEDGF/p75 is one of the important determinants of integration site selection and targets integration toward active genes. In this review, we will provide an overview of the most important determinants of integration site selection. Secondly, we will discuss the chromatin landscape at the integration site and its implications on HIV-1 gene expression and silencing. Finally, we will discuss how interventions that affect integration site selection or modifications of the chromatin could yield a functional cure of HIV-1 infection.

Download Full-text

Insight in HIV Integration Site Selection Provides a Block-and-Lock Strategy for a Functional Cure of HIV Infection

Viruses ◽

10.3390/v11010012 ◽

2018 ◽

Vol 11 (1) ◽

pp. 12 ◽

Cited By ~ 10

Author(s):

Zeger Debyser ◽

Gerlinde Vansant ◽

Anne Bruggemans ◽

Julie Janssens ◽

Frauke Christ

Keyword(s):

Hiv Infection ◽

Site Selection ◽

Integration Site ◽

Viral Reservoir ◽

Dependent Manner ◽

Functional Cure ◽

Infected Cells ◽

Hiv Integration ◽

Integration Site Selection

Despite significant improvements in therapy, the HIV/AIDS pandemic remains an important threat to public health. Current treatments fail to eradicate HIV as proviral DNA persists in long-living cellular reservoirs, leading to viral rebound whenever treatment is discontinued. Hence, a better understanding of viral reservoir establishment and maintenance is required to develop novel strategies to destroy latently infected cells, and/or to durably silence the latent provirus in infected cells. Whereas the mechanism of integration has been well studied from a catalytic point of view, it remains unknown how integration site selection and transcription are linked. In recent years, evidence has grown that lens epithelium-derived growth factor p75 (LEDGF/p75) is the main determinant of HIV integration site selection and that the integration site affects the transcriptional state of the provirus. LEDGINs have been developed as small molecule inhibitors of the interaction between LEDGF/p75 and integrase. Recently, it was shown that LEDGIN treatment in cell culture shifts the residual integrated provirus towards the inner nuclear compartment and out of transcription units in a dose dependent manner. This LEDGIN-mediated retargeting increased the proportion of provirus with a transcriptionally silent phenotype and the residual reservoir proved refractory to reactivation in vitro. LEDGINs provide us with a research tool to study the link between integration and transcription, a quintessential question in retrovirology. LEDGIN-mediated retargeting of the residual reservoirs provides a novel potential “block-and-lock” strategy as a functional cure of HIV infection.

Download Full-text

HRP-2 determines HIV-1 integration site selection in LEDGF/p75 depleted cells

Retrovirology ◽

10.1186/1742-4690-9-84 ◽

2012 ◽

Vol 9 (1) ◽

pp. 84 ◽

Cited By ~ 40

Author(s):

Rik Schrijvers ◽

Sofie Vets ◽

Jan De Rijck ◽

Nirav Malani ◽

Frederic D Bushman ◽

...

Keyword(s):

Site Selection ◽

Integration Site ◽

Hiv 1 ◽

Integration Site Selection

Download Full-text

Genomic Sites of Human Immunodeficiency Virus Type 2 (HIV-2) Integration: Similarities to HIV-1 In Vitro and Possible Differences In Vivo

Journal of Virology ◽

10.1128/jvi.00604-06 ◽

2006 ◽

Vol 80 (15) ◽

pp. 7316-7321 ◽

Cited By ~ 25

Author(s):

Adam MacNeil ◽

Jean-Louis Sankalé ◽

Seema Thakore Meloni ◽

Abdoulaye Dieng Sarr ◽

Souleymane Mboup ◽

...

Keyword(s):

Human Immunodeficiency Virus ◽

Human Immunodeficiency Virus Type ◽

Site Selection ◽

Integration Site ◽

Proviral Integration ◽

Immunodeficiency Virus ◽

Hiv 1 ◽

Integration Site Selection

ABSTRACT Retroviruses have distinct preferences in integration site selection in the host cell genome during in vitro infection, with human immunodeficiency virus type 1 (HIV-1) integration strongly favoring transcriptional units. Additionally, studies with HIV-1 have shown that the genomic site of proviral integration may impact viral replication, with integration in heterochromatin associated with a block in viral transcription. HIV-2 is less pathogenic than HIV-1 and is believed to have a lower replication rate in vivo. Although differences in integration site selection between HIV-2 and HIV-1 could potentially explain the attenuated pathogenicity of HIV-2, no studies have characterized integration site selection by HIV-2. In this study, we mapped 202 HIV-2 integration sites during in vitro infection of peripheral blood mononuclear cells with a primary HIV-2 isolate. In addition, we assayed for in vivo proviral integration within heterochromatin in 21 HIV-1-infected subjects and 23 HIV-2-infected subjects, using an alphoid repeat PCR assay. During in vitro infection, HIV-2 displayed integration site preferences similar to those previously reported for HIV-1. Notably, 82% of HIV-2 integrations mapped to Refseq genes, and integration strongly favored regions of the genome with high gene density and high GC content. Though rare, the proportion of HIV-2 subjects with evidence of proviral integration within heterochromatin in vivo was higher than that of HIV-1-infected subjects. It is therefore possible that integration site selection may play a role in the differences in HIV-1 and HIV-2 in vivo pathogenesis.

Download Full-text

Nuclear architecture dictates HIV-1 integration site selection

Nature ◽

10.1038/nature14226 ◽

2015 ◽

Vol 521 (7551) ◽

pp. 227-231 ◽

Cited By ~ 179

Author(s):

Bruna Marini ◽

Attila Kertesz-Farkas ◽

Hashim Ali ◽

Bojana Lucic ◽

Kamil Lisek ◽

...

Keyword(s):

Site Selection ◽

Integration Site ◽

Nuclear Architecture ◽

Hiv 1 ◽

Integration Site Selection

Download Full-text

Nup153 Unlocks the Nuclear Pore Complex for HIV-1 Nuclear Translocation in Nondividing Cells

Journal of Virology ◽

10.1128/jvi.00648-18 ◽

2018 ◽

Vol 92 (19) ◽

Cited By ~ 21

Author(s):

Cindy Buffone ◽

Alicia Martinez-Lopez ◽

Thomas Fricke ◽

Silvana Opp ◽

Marco Severgnini ◽

...

Keyword(s):

Nuclear Import ◽

Site Selection ◽

Nuclear Translocation ◽

Integration Site ◽

The State ◽

Nuclear Pore ◽

Binding Interface ◽

Nuclear Factors ◽

Hiv 1 ◽

Integration Site Selection

ABSTRACTHuman immunodeficiency virus type 1 (HIV-1) displays the unique ability to infect nondividing cells. The capsid of HIV-1 is the viral determinant for viral nuclear import. To understand the cellular factors involved in the ability of HIV-1 to infect nondividing cells, we sought to find capsid mutations that allow the virus to infect dividing but not nondividing cells. Because the interaction of capsid with the nucleoporin protein 153 (Nup153) is important for nuclear import of HIV-1, we solved new crystal structures of hexameric HIV-1 capsid in complex with a Nup153-derived peptide containing a phenylalanine-glycine repeat (FG repeat), which we used to guide structure-based mutagenesis of the capsid-binding interface. HIV-1 viruses with mutations in these capsid residues were tested for their ability to infect dividing and nondividing cells. HIV-1 viruses with capsid N57 substitutions infected dividing but not nondividing cells. Interestingly, HIV-1 viruses with N57 mutations underwent reverse transcription but not nuclear translocation. The mutant capsids also lost the ability to interact with Nup153 and CPSF6. The use of small molecules PF74 and BI-2 prevented the interaction of FG-containing nucleoporins (Nups), such as Nup153, with the HIV-1 core. Analysis of integration sites in HIV-1 viruses with N57 mutations revealed diminished integration into transcriptionally active genes in a manner resembling that of HIV-1 in CPSF6 knockout cells or that of HIV-1-N74D. The integration pattern of the N57 mutant HIV-1 can be explained by loss of capsid interaction with CPSF6, whereas capsid interaction with Nup153 is required for HIV-1 to infect nondividing cells. Additionally, the observed viral integration profiles suggested that integration site selection is a multiparameter process that depends upon nuclear factors and the state of the cellular chromatin.IMPORTANCEOne of the key advantages that distinguish lentiviruses, such as HIV-1, from all other retroviruses is its ability to infect nondividing cells. Interaction of the HIV-1 capsid with Nup153 and CPSF6 is important for nuclear entry and integration; however, the contribution of each of these proteins to nuclear import and integration is not clear. Using genetics, we demonstrated that these proteins contribute to different processes: Nup153 is essential for the HIV-1 nuclear import in nondividing cells, and CPSF6 is important for HIV-1 integration. In addition, nuclear factors such as CPSF6 and the state of the chromatin are known to be important for integration site selection; nevertheless, the preferential determinant influencing integration site selection is not known. This work demonstrates that integration site selection is a multiparameter process that depends upon nuclear factors and the state of the cellular chromatin.

Download Full-text

GS-9822, a Preclinical LEDGIN Candidate, Displays a Block-and-Lock Phenotype in Cell Culture

Antimicrobial Agents and Chemotherapy ◽

10.1128/aac.02328-20 ◽

2021 ◽

Vol 65 (5) ◽

Author(s):

Anne Bruggemans ◽

Gerlinde Vansant ◽

Mini Balakrishnan ◽

Michael L. Mitchell ◽

Ruby Cai ◽

...

Keyword(s):

Site Selection ◽

Integration Site ◽

Binding Pocket ◽

Epigenetic Landscape ◽

Functional Cure ◽

Cellular Cofactor ◽

Integration Sites ◽

First Time ◽

Hiv Integration ◽

Integration Site Selection

ABSTRACT The ability of HIV to integrate into the host genome and establish latent reservoirs is the main hurdle preventing an HIV cure. LEDGINs are small-molecule integrase inhibitors that target the binding pocket of LEDGF/p75, a cellular cofactor that substantially contributes to HIV integration site selection. They are potent antivirals that inhibit HIV integration and maturation. In addition, they retarget residual integrants away from transcription units and toward a more repressive chromatin environment. As a result, treatment with the LEDGIN CX14442 yielded residual provirus that proved more latent and more refractory to reactivation, supporting the use of LEDGINs as research tools to study HIV latency and a functional cure strategy. In this study, we compared GS-9822, a potent, preclinical lead compound, with CX14442 with respect to antiviral potency, integration site selection, latency, and reactivation. GS-9822 was more potent than CX14442 in most assays. For the first time, the combined effects on viral replication, integrase-LEDGF/p75 interaction, integration sites, epigenetic landscape, immediate latency, and latency reversal were demonstrated at nanomolar concentrations achievable in the clinic. GS-9822 profiles as a preclinical candidate for future functional cure research.

Download Full-text

SATB1-Binding Sequences and Alu-Like Motifs Define a Unique Chromatin Context in the Vicinity of Human Immunodeficiency Virus Type 1 Integration Sites

Journal of Virology ◽

10.1128/jvi.01405-06 ◽

2007 ◽

Vol 81 (11) ◽

pp. 5617-5627 ◽

Cited By ~ 8

Author(s):

Pavan P. Kumar ◽

Sameet Mehta ◽

Prabhat Kumar Purbey ◽

Dimple Notani ◽

Ranveer S. Jayani ◽

...

Keyword(s):

Site Selection ◽

Binding Sites ◽

Integration Site ◽

Viral Integration ◽

Immunodeficiency Virus ◽

Integration Sites ◽

Hiv 1 ◽

Integration Site Selection

ABSTRACT Retroviral integration has recently been shown to be nonrandom, favoring transcriptionally active regions of chromatin. However, the mechanism for integration site selection by retroviruses is not clear. We show here the occurrence of Alu-like motifs in the sequences flanking the reported viral integration sites that are significantly different from those obtained from the randomly picked sequences from the human genome, suggesting that unique primary sequence features exist in the genomic regions targeted by human immunodeficiency virus type 1 (HIV-1). Additionally, these sequences were preferentially bound by SATB1, the T lineage-restricted chromatin organizer, in vitro and in vivo. Alu repeats make up nearly 10% of the human genome and have been implicated in the regulation of transcription. To specifically isolate sequences flanking the viral integration sites and also harboring both Alu-like repeats and SATB1-binding sites, we combined chromatin immunoprecipitation with sequential PCRs. The cloned sequences flanking HIV-1 integration sites were specifically immunoprecipitated and amplified from the pool of anti-SATB1-immunoprecipitated genomic DNA fragments isolated from HIV-1 NL4.3-infected Jurkat T-cell chromatin. Moreover, many of these sequences were preferentially partitioned in the DNA associated tightly with the nuclear matrix and not in the chromatin loops. Strikingly, many of these regions were disfavored for integration when SATB1 was silenced, providing unequivocal evidence for its role in HIV-1 integration site selection. We propose that definitive sequence features such as the Alu-like motifs and SATB1-binding sites provide a unique chromatin context in vivo which is preferentially targeted by the HIV-1 integration machinery.

Download Full-text

Light and shadow on the mechanisms of integration site selection in yeast Ty retrotransposon families

Current Genetics ◽

10.1007/s00294-021-01154-7 ◽

2021 ◽

Cited By ~ 1

Author(s):

Amandine Bonnet ◽

Pascale Lesage

Keyword(s):

Site Selection ◽

Integration Site ◽

Light And Shadow ◽

Integration Site Selection

Download Full-text

Integrase-Specific Enhancement and Suppression of Retroviral DNA Integration by Compacted Chromatin Structure In Vitro

Journal of Virology ◽

10.1128/jvi.78.11.5848-5855.2004 ◽

2004 ◽

Vol 78 (11) ◽

pp. 5848-5855 ◽

Cited By ~ 39

Author(s):

Konstantin D. Taganov ◽

Isabel Cuesta ◽

René Daniel ◽

Lisa Ann Cirillo ◽

Richard A. Katz ◽

...

Keyword(s):

Transcription Factors ◽

Chromatin Structure ◽

Site Selection ◽

Integration Site ◽

Histone H1 ◽

Detectable Effect ◽

Host Chromosome ◽

Dna Integration ◽

Hiv 1

ABSTRACT Integration of viral DNA into the host chromosome is an obligatory step in retroviral replication and is dependent on the activity of the viral enzyme integrase. To examine the influence of chromatin structure on retroviral DNA integration in vitro, we used a model target comprising a 13-nucleosome extended array that includes binding sites for specific transcription factors and can be compacted into a higher-ordered structure. We found that the efficiency of in vitro integration catalyzed by human immunodeficiency virus type 1 (HIV-1) integrase was decreased after compaction of this target with histone H1. In contrast, integration by avian sarcoma virus (ASV) integrase was more efficient after compaction by either histone H1 or a high salt concentration, suggesting that the compacted structure enhances this reaction. Furthermore, although site-specific binding of transcription factors HNF3 and GATA4 blocked ASV DNA integration in extended nucleosome arrays, local opening of H1-compacted chromatin by HNF3 had no detectable effect on integration, underscoring the preference of ASV for compacted chromatin. Our results indicate that chromatin structure affects integration site selection of the HIV-1 and ASV integrases in opposite ways. These distinct properties of integrases may also affect target site selection in vivo, resulting in an important bias against or in favor of integration into actively transcribed host DNA.

Download Full-text