Monitoring Integration over Time Supports a Role for Cytotoxic T Lymphocytes and Ongoing Replication as Determinants of Reservoir Size

Pinzone, Marilia Rita; Graf, Erin H.; Lynch, Lindsay J.; McLaughlin, Brigit; Hecht, Frederick M.; Connors, Mark; Migueles, Stephen A.; Hwang, Wei–Ting; Nunnari, Giuseppe; O’Doherty, Una

doi:10.1128/jvi.00242-16

Cited by 21 publications

(23 citation statements)

References 54 publications

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“…Moreover, Buzon et al [ 57 ] found treating the earliest stages Fiebig III/IV resulted in a larger drop in integrated HIV DNA than treating in Fiebig V; uniquely, the decline in integrated HIV continued in those patients treated at the very earliest stages over several years. Pre-ART integration levels also correlated with viral load (r = 0.86) and negatively correlated with CD4/CD8 ratio (r = − 0.52), consistent with the idea that integrated HIV DNA can provide a surrogate marker for reservoir size [ 54 ] and consistent with [ 34 , 56 , 58 ]. These longitudinal studies highlight that integrated HIV DNA measures provide different and complementary information to total HIV DNA when an excess of unintegrated HIV DNA may exist.…”

Section: The Challenge Of Measuring Hiv Reservoir Sizesupporting

confidence: 77%

“…Meanwhile the rate of decay for total HIV was similar for both groups. Pinzone et al showed that acutely infected individuals exhibited a significant drop in integrated HIV levels 12 months after ART initiation, while integration levels barely changed in patients treated during chronic infection [ 54 ], consistent with Koelsch et al [ 55 ]. Moreover, Buzon et al [ 57 ] found treating the earliest stages Fiebig III/IV resulted in a larger drop in integrated HIV DNA than treating in Fiebig V; uniquely, the decline in integrated HIV continued in those patients treated at the very earliest stages over several years.…”

Section: The Challenge Of Measuring Hiv Reservoir Sizesupporting

confidence: 71%

“…Several studies have shown that initiating ART during acute infection is associated with a greater decline in the levels of integrated HIV DNA [ 54 – 56 ]. A limitation of these studies is their small size, but the consistent finding from all three groups that integrated HIV DNA was cleared more rapidly and effectively if patients were treated early makes these results more convincing.…”

Section: The Challenge Of Measuring Hiv Reservoir Sizementioning

confidence: 99%

“…In the absence of ART, integrated HIV DNA accumulates over time after a brief decline that may be immune-mediated [ 49 , 54 ]. Pinzone et al [ 54 ] monitored longitudinally integrated HIV DNA in 6 individuals followed from acute to chronic infection (mean observation time 6 years), showing that integrated HIV DNA increased progressively over time (from 109 to 1941 copies/million peripheral blood mononuclear cells (PBMCs)). The authors compared the increase in reservoir size observed in chronic progressors (CPs) versus long-term nonprogressors (LTNPs).…”

Section: The Challenge Of Measuring Hiv Reservoir Sizementioning

confidence: 99%

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Measuring integrated HIV DNA ex vivo and in vitro provides insights about how reservoirs are formed and maintained

Pinzone

O’Doherty

2018

Retrovirology

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The identification of the most appropriate marker to measure reservoir size has been a great challenge for the HIV field. Quantitative viral outgrowth assay (QVOA), the reference standard to quantify the amount of replication-competent virus, has several limitations, as it is laborious, expensive, and unable to robustly reactivate every single integrated provirus. PCR-based assays have been developed as an easier, cheaper and less error-prone alternative to QVOA, but also have limitations. Historically, measuring integrated HIV DNA has provided insights about how reservoirs are formed and maintained. In the 1990s, measuring integrated HIV DNA was instrumental in understanding that a subset of resting CD4 T cells containing integrated HIV DNA were the major source of replication-competent virus. Follow-up studies have further characterized the phenotype of these cells containing integrated HIV DNA, as well as shown the correlation between the integration levels and clinical parameters, such as duration of infection, CD4 count and viral load. Integrated HIV DNA correlates with total HIV measures and with QVOA. The integration assay has several limitations. First, it largely overestimates the reservoir size, as both defective and replication-competent proviruses are detected. Since defective proviruses are the majority in patients on ART, it follows that the number of proviruses capable of reactivating and releasing new virions is significantly smaller than the number of integrated proviruses. Second, in patients on ART clonal expansion could theoretically lead to the preferential amplification of proviruses close to an Alu sequence though longitudinal studies have not captured this effect. Proviral sequencing combined with integration measures is probably the best estimate of reservoir size, but it is expensive, time-consuming and requires considerable bioinformatics expertise. All these reasons limit its use on a large scale. Herein, we review the utility of measuring HIV integration and suggest combining it with sequencing and total HIV measurements can provide insights that underlie reservoir maintenance.

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Section: The Challenge Of Measuring Hiv Reservoir Sizesupporting

confidence: 77%

Section: The Challenge Of Measuring Hiv Reservoir Sizesupporting

confidence: 71%

Section: The Challenge Of Measuring Hiv Reservoir Sizementioning

confidence: 99%

Section: The Challenge Of Measuring Hiv Reservoir Sizementioning

confidence: 99%

See 2 more Smart Citations

Measuring integrated HIV DNA ex vivo and in vitro provides insights about how reservoirs are formed and maintained

Pinzone

O’Doherty

2018

Retrovirology

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“…Prior to treatment initiation, total and integrated HIV DNA levels are higher in individuals treated during chronic HIV infection and decrease to a lower extent than those treated in primary HIV infection [ 71 – 73 ]. Furthermore, integrated HIV DNA continues to decay after prolonged therapy in individuals treated during primary infection suggesting that enhanced immune responses in these individuals are able to clear HIV infected cells more effectively [ 72 , 74 , 75 ]. During this same period, CD4 cell numbers typically increase with a measure of immune restoration.…”

Section: Dynamics Of Hiv Infected Populationsmentioning

confidence: 99%

The role of integration and clonal expansion in HIV infection: live long and prosper

Anderson¹,

Maldarelli²

2018

Retrovirology

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Integration of viral DNA into the host genome is a central event in the replication cycle and the pathogenesis of retroviruses, including HIV. Although most cells infected with HIV are rapidly eliminated in vivo, HIV also infects long-lived cells that persist during combination antiretroviral therapy (cART). Cells with replication competent HIV proviruses form a reservoir that persists despite cART and such reservoirs are at the center of efforts to eradicate or control infection without cART. The mechanisms of persistence of these chronically infected long-lived cells is uncertain, but recent research has demonstrated that the presence of the HIV provirus has enduring effects on infected cells. Cells with integrated proviruses may persist for many years, undergo clonal expansion, and produce replication competent HIV. Even proviruses with defective genomes can produce HIV RNA and may contribute to ongoing HIV pathogenesis. New analyses of HIV infected cells suggest that over time on cART, there is a shift in the composition of the population of HIV infected cells, with the infected cells that persist over prolonged periods having proviruses integrated in genes associated with regulation of cell growth. In several cases, strong evidence indicates the presence of the provirus in specific genes may determine persistence, proliferation, or both. These data have raised the intriguing possibility that after cART is introduced, a selection process enriches for cells with proviruses integrated in genes associated with cell growth regulation. The dynamic nature of populations of cells infected with HIV during cART is not well understood, but is likely to have a profound influence on the composition of the HIV reservoir with critical consequences for HIV eradication and control strategies. As such, integration studies will shed light on understanding viral persistence and inform eradication and control strategies. Here we review the process of HIV integration, the role that integration plays in persistence, clonal expansion of the HIV reservoir, and highlight current challenges and outstanding questions for future research.

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HIV‐DNA decrease during treatment in primary HIV‐1 infection with three different drug regimens: Italian Network of Acute HIV Infection (INACTION) clinical trial

Bruzzesi,

Gabrieli,

Bernasconi

et al. 2023

Journal of Medical Virology

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As the introduction of antiretroviral therapy (ART) during primary HIV‐1 infection (PHI) could restrict the establishment of HIV reservoirs, we aimed to assess the effect of three different ART regimens on HIV‐DNA load in people living with HIV (PLWH), who started ART in PHI. Randomized, open‐label, multicentric study, including subjects in PHI (defined as an incomplete HIV‐1 Western blot and detectable plasma HIV‐RNA) in the Italian Network of Acute HIV Infection cohort. Participants were randomly assigned (10:10:8) to a fixed‐dose combination of tenofovir alafenamide fumarate (TAF) 10 mg plus emtricitabine (FTC) 200 mg, darunavir 800 mg, and cobicistat 150 mg once daily (group A), or TAF 25 mg plus FTC 200 mg, dolutegravir 50 mg once daily (group B), or an intensified four‐drug regimen (TAF 10 mg plus FTC 200 mg, dolutegravir 50 mg, darunavir 800 mg, and cobicistat 150 mg once daily) (group C). The primary endpoint was the decrease of HIV‐DNA copies/106 peripheral blood mononuclear cells (PBMCs) at weeks (W) 12 and 48. Secondary endpoints were increased in CD4+ cells and in CD4+/CD8+ ratio and percentage of PLWH reaching undetectable HIV‐RNA. HIV‐DNA was quantified by Droplet Digital PCR (Biorad QX100) and normalized to RPP30 reference gene. This study was registered in ClinicalTrials.gov (number NCT04225325). Among 78 participants enrolled, 30 were randomized to group 1, 28 to group 2, and 20 to group 3. At baseline, median CD4+ count was 658/µL (476–790), HIV‐RNA 5.37 (4.38, 6.12) log10 copies/mL, without statistical difference in their change among groups at weeks 12 and 48 (p = 0.432 and 0.234, respectively). The trial was prematurely discontinued for slow accrual and for COVID‐19 pandemic‐associated restrictions. In the per‐protocol analysis, PLWH (n = 72) with undetectable viral load was 54.3% at W12 and 86.4% at W48. Interestingly, the CD4/CD8 ratio progressively increased over time, up to normalization in almost half of the cohort by week 48, despite a deflection in group 3; no difference was observed by the Fiebig stage (I–III vs. IV–VI). HIV‐DNA decreased from 4.46 (4.08, 4.81) log10 copies/106 PBMCs to 4.22 (3.79, 4.49) at week 12, and 3.87 (3.46, 4.34) at week 48, without difference among groups. At multivariable analysis, HIV‐DNA delta at W48 was associated only with the increase of CD4+ count by 100 cells/mm3 but not with the Fiebig stage, the CD4+/CD8+ ratio, and treatment arm, despite a higher decrease in group 3. Six adverse events were recorded during our study, which did not cause any withdrawal from the study. We observed a decrease in HIV‐DNA from baseline to W48 in PLWH treated during PHI, associated with an increase in CD4+ count, unrelated to the treatment arm.

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Monitoring Integration over Time Supports a Role for Cytotoxic T Lymphocytes and Ongoing Replication as Determinants of Reservoir Size

Cited by 21 publications

References 54 publications

Measuring integrated HIV DNA ex vivo and in vitro provides insights about how reservoirs are formed and maintained

Measuring integrated HIV DNA ex vivo and in vitro provides insights about how reservoirs are formed and maintained

The role of integration and clonal expansion in HIV infection: live long and prosper

HIV‐DNA decrease during treatment in primary HIV‐1 infection with three different drug regimens: Italian Network of Acute HIV Infection (INACTION) clinical trial

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