Emerging PCR-Based Techniques to Study HIV-1 Reservoir Persistence

Lambrechts, Laurens; Cole, Basiel; Rutsaert, Sofie; Trypsteen, Wim; Vandekerckhove, Linos

doi:10.3390/v12020149

Cited by 21 publications

(21 citation statements)

References 42 publications

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“…Several sequencing-based assays have been developed to study the HIV reservoir, each focusing on different aspects of the infected cells and the proviruses within 27 . Near full-length (NFL) provirus sequencing enables the identification of genomeintact and potentially replication-competent proviruses [28][29][30][31] .…”

Section: Introductionmentioning

confidence: 99%

In-depth single-cell analysis of translation-competent HIV-1 reservoirs identifies cellular sources of plasma viremia

Cole

Lambrechts

Gantner

et al. 2021

Preprint

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Clonal expansion of HIV-infected cells contributes to the long-term persistence of the HIV reservoir in ART-suppressed individuals. However, the contribution to plasma viremia from cell clones that harbor inducible proviruses is poorly understood. Here, we describe a single-cell approach to simultaneously sequence the TCR, integration sites and proviral genomes from translation-competent reservoir cells, called STIP-Seq. By applying this approach to blood samples from eight participants, we showed that the translation-competent reservoir mainly consists of proviruses with short deletions at the 5-prime-end of the genome, often involving the major splice donor site. TCR and integration site sequencing revealed that antigen-responsive cells can harbor inducible proviruses integrated into cancer-related genes. Furthermore, we found several matches between proviruses retrieved with STIP-Seq and plasma viruses obtained during ART and upon treatment interruption, showing that STIP-Seq can capture clones that are responsible for low-level viremia or viral rebound.

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Section: Introductionmentioning

confidence: 99%

In-depth single-cell analysis of translation-competent HIV-1 reservoirs identifies cellular sources of plasma viremia

Cole

Lambrechts

Gantner

et al. 2021

Preprint

Self Cite

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“…Previously, full-length sequencing of proviral DNA has provided invaluable insight into the composition of the LR (Ho et al, 2013) but the methods used are time consuming and technically challenging. The advent of various NGS technologies, however, has also paved the way for novel methods to measure the HIV-1 LR with relative ease and high throughput (Lambrechts et al, 2020). The use of Illumina based sequencing techniques has so far been used in LR studies to measure fulllength, individual proviral sequences, helping to elucidate the driving force of LR persistence and latency maintenance (Hiener et al, 2017;Lee et al, 2017;Einkauf et al, 2019).…”

Section: Bridging the Gap Between Culture And Pcr Based Assaysmentioning

confidence: 99%

Measuring the Success of HIV-1 Cure Strategies

Thomas

Ruggiero

Paxton

et al. 2020

Front. Cell. Infect. Microbiol.

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HIV-1 eradication strategies aim to achieve viral remission in the absence of antiretroviral therapy (ART). The development of an HIV-1 cure remains challenging due to the latent reservoir (LR): long-lived CD4 T cells that harbor transcriptionally silent HIV-1 provirus. The LR is stable despite years of suppressive ART and is the source of rebound viremia following therapy interruption. Cure strategies such as "shock and kill" aim to eliminate or reduce the LR by reversing latency, exposing the infected cells to clearance via the immune response or the viral cytopathic effect. Alternative strategies include therapeutic vaccination, which aims to prime the immune response to facilitate control of the virus in the absence of ART. Despite promising advances, these strategies have been unable to significantly reduce the LR or increase the time to viral rebound but have provided invaluable insight in the field of HIV-1 eradication. The development and assessment of an HIV-1 cure requires robust assays that can measure the LR with sufficient sensitivity to detect changes that may occur following treatment. The viral outgrowth assay (VOA) is considered the gold standard method for LR quantification due to its ability to distinguish intact and defective provirus. However, the VOA is time consuming and resource intensive, therefore several alternative assays have been developed to bridge the gap between practicality and accuracy. Whilst a cure for HIV-1 infection remains elusive, recent advances in our understanding of the LR and methods for its eradication have offered renewed hope regarding achieving ART free viral remission.

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“…The functionality of latent reservoirs is in large part determined by the intactness of the proviral sequences. Therefore, efforts were made to develop more sensitive and accurate assays to obtain full sequencing of the HIV-1 genome in patient samples ( Lambrechts et al, 2020 ). Remarkably, only 10% of the proviral sequences exhibit an intact genome and are thus theoretically able to produce replication-competent virus.…”

Section: Introductionmentioning

confidence: 99%

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

et al. 2021

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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.

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Emerging PCR-Based Techniques to Study HIV-1 Reservoir Persistence

Cited by 21 publications

References 42 publications

In-depth single-cell analysis of translation-competent HIV-1 reservoirs identifies cellular sources of plasma viremia

In-depth single-cell analysis of translation-competent HIV-1 reservoirs identifies cellular sources of plasma viremia

Measuring the Success of HIV-1 Cure Strategies

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

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