Integration in oncogenes plays only a minor role in determining the in vivo distribution of HIV integration sites before or during suppressive antiretroviral therapy

Coffin, John M.; Bale, Michael J.; Wells, Daria; Guo, Shuang; Luke, Brian T.; Zerbato, Jennifer M.; Sobolewski, Michele D.; Sia, Twan; Shao, Wei; Wu, Xiaolin; Maldarelli, Frank; Kearney, Mary F; Mellors, John W.; Hughes, Stephen H.

doi:10.1371/journal.ppat.1009141

Cited by 47 publications

(93 citation statements)

References 71 publications

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“…The ART-treated patient-derived integration site dataset was built by concatenating unique integration sites from three published datasets ( 13 , 37 , 50 ). One of these datasets was itself a concatenation of several independent datasets ( 37 ). The untreated patient-derived integration site dataset was previously published in ( 37 ) ( Supplementary Table S2 ).…”

Section: Methodsmentioning

confidence: 99%

rigrag: high-resolution mapping of genic targeting preferences during HIV-1 integration in vitro and in vivo

Bedwell

Jang

et al. 2021

Nucleic Acids Research

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HIV-1 integration favors recurrent integration gene (RIG) targets and genic proviruses can confer cell survival in vivo. However, the relationship between initial RIG integrants and how these evolve in patients over time are unknown. To address these shortcomings, we built phenomenological models of random integration in silico, which were used to identify 3718 RIGs as well as 2150 recurrent avoided genes from 1.7 million integration sites across 10 in vitro datasets. Despite RIGs comprising only 13% of human genes, they harbored 70% of genic HIV-1 integrations across in vitro and patient-derived datasets. Although previously reported to associate with super-enhancers, RIGs tracked more strongly with speckle-associated domains. While depletion of the integrase cofactor LEDGF/p75 significantly reduced recurrent HIV-1 integration in vitro, LEDGF/p75 primarily occupied non-speckle-associated regions of chromatin, suggesting a previously unappreciated dynamic aspect of LEDGF/p75 functionality in HIV-1 integration targeting. Finally, we identified only six genes from patient samples—BACH2, STAT5B, MKL1, MKL2, IL2RB and MDC1—that displayed enriched integration targeting frequencies and harbored proviruses that likely contributed to cell survival. Thus, despite the known preference of HIV-1 to target cancer-related genes for integration, we conclude that genic proviruses play a limited role to directly affect cell proliferation in vivo.

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Section: Methodsmentioning

confidence: 99%

rigrag: high-resolution mapping of genic targeting preferences during HIV-1 integration in vitro and in vivo

Bedwell

Jang

et al. 2021

Nucleic Acids Research

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“…Copies of an LTR standard were quantified using a within-run standard corresponding to position 87 through 8680 (HXB2 numbering) constructed by amplification of proviral DNA from the JLat 6. 3…”

Section: Quantification Of Individual Proviruses By Is-qpcrmentioning

confidence: 99%

“…2 NT5C3A provirus copies were determined using IS-qPCR (3 independent runs with 6 and 12 replicates) ± inter-assay standard deviation. 3 Genomic DNA extracted from an HIV-1-positive donor.…”

Section: Validation Of Is-qpcr Using the Major Ach-2 Provirus Integrated In The Nt5c3a Genementioning

confidence: 99%

“…2 Clone frequencies were calculated using the fraction of the provirus of interest and the number of LTR copies (adjusted 2-fold to account for 2 LTR copies per provirus) measured by qPCR. 3 Clone frequencies calculated from the numbers of specific proviruses present in a clone or repliclone in a sample (numerator) and the total number of integration sites obtained from the same sample (denominator) using ISA [11]. 1 Cell equivalents were determined by CCR5 quantification using qPCR (n = 3) ± intra-assay standard deviation.…”

Section: Application Of Is-qpcr Of Clones In Clinical Samplesmentioning

confidence: 99%

“…HIV-1 infection is controlled, but not cured, by antiretroviral therapy (ART) because long-lived CD4+ T cells carry replication-competent (intact) proviruses. These infected cells can clonally expand in response to antigen-driven or homeostatic stimulation, or rarely, as a consequence of the provirus integrating in one of seven oncogenes [ 1 , 2 , 3 ]. Clones of infected cells can arise early after an individual is infected and persist for many years after initiation of ART [ 4 ].…”

Section: Introductionmentioning

confidence: 99%

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Tracking HIV-1-Infected Cell Clones Using Integration Site-Specific qPCR

Brandt

Guo

Joseph

et al. 2021

Viruses

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Efforts to cure HIV-1 infection require better quantification of the HIV-1 reservoir, particularly the clones of cells harboring replication-competent (intact) proviruses, termed repliclones. The digital droplet PCR assays commonly used to quantify intact proviruses do not differentiate among specific repliclones, thus the dynamics of repliclones are not well defined. The major challenge in tracking repliclones is the relative rarity of the cells carrying specific intact proviruses. To date, detection and accurate quantification of repliclones requires in-depth integration site sequencing. Here, we describe a simplified workflow using integration site-specific qPCR (IS-qPCR) to determine the frequencies of the proviruses integrated in individual repliclones. We designed IS-qPCR to determine the frequencies of repliclones and clones of cells that carry defective proviruses in samples from three donors. Comparing the results of IS-qPCR with deep integration site sequencing data showed that the two methods yielded concordant estimates of clone frequencies (r = 0.838). IS-qPCR is a potentially valuable tool that can be applied to multiple samples and cell types over time to measure the dynamics of individual repliclones and the efficacy of treatments designed to eliminate them.

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Learning from Persistent Viremia: Mechanisms and Implications for Clinical Care and HIV-1 Cure

Wu,

Simonetti

2023

Curr HIV/AIDS Rep

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Purpose of Review In this review, we discuss what persistent viremia has taught us about the biology of the HIV-1 reservoir during antiretroviral therapy (ART). We will also discuss the implications of this phenomenon for HIV-1 cure research and its clinical management. Recent Findings While residual viremia (RV, 1–3 HIV-1 RNA copies/ml) can be detected in most of people on ART, some individuals experience non-suppressible viremia (NSV, > 20–50 copies/mL) despite optimal adherence. When issues of drug resistance and pharmacokinetics are ruled out, this persistent virus in plasma is the reflection of virus production from clonally expanded CD4+ T cells carrying proviruses. Recent work has shown that a fraction of the proviruses source of NSV are not infectious, due to defects in the 5′-Leader sequence. However, additional viruses and host determinants of NSV are not fully understood. Summary The study of NSV is of prime importance because it represents a challenge for the clinical care of people on ART, and it sheds light on virus-host interactions that could advance HIV-1 remission research.

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Integration in oncogenes plays only a minor role in determining the in vivo distribution of HIV integration sites before or during suppressive antiretroviral therapy

Cited by 47 publications

References 71 publications

rigrag: high-resolution mapping of genic targeting preferences during HIV-1 integration in vitro and in vivo

rigrag: high-resolution mapping of genic targeting preferences during HIV-1 integration in vitro and in vivo

Tracking HIV-1-Infected Cell Clones Using Integration Site-Specific qPCR

Learning from Persistent Viremia: Mechanisms and Implications for Clinical Care and HIV-1 Cure

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