HIV DNA Subspecies Persist in both Activated and Resting Memory CD4
            <sup>+</sup>
            T Cells during Antiretroviral Therapy

Murray, John M.; Zaunders, John; McBride, Kristin; Xu, Yin; Bailey, Michelle; Suzuki, Kazuo; Cooper, David A.; Emery, Sean; Kelleher, Anthony D.; Koelsch, Kersten K.

doi:10.1128/jvi.03331-13

Cited by 75 publications

(75 citation statements)

References 44 publications

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“…Proviral sequencing data will eventually resolve these issues; however, techniques able to separate integrated from unintegrated HIV DNA robustly will be required to obtain definitive answers. Notably, different populations may have a different pattern of accumulation of integrated HIV DNA (9,53). Future studies in this direction may improve our understanding of the contribution of distinct cell subsets as well as of cellular activation status to the growth of HIV reservoirs.…”

Section: Discussionmentioning

confidence: 99%

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

Pinzone

Graf

Lynch

et al. 2016

J Virol

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The dynamics of HIV reservoir accumulation off antiretroviral therapy (ART) is underexplored. Levels of integrated HIV DNA in peripheral blood mononuclear cells (PBMCs) were longitudinally monitored before and after antiviral therapy. HIV integration increased over time in both elite controllers (ECs; n ‫؍‬ 8) and noncontrollers (NCs; n ‫؍‬ 6) before ART, whereas integration remained stable in patients on ART (n ‫؍‬ 4). The median annual fold change was higher in NCs than in ECs and negatively correlated with CD4/CD8 T-cell ratio. Cytotoxic T lymphocyte (CTL) function as assessed by infected CD4 T-cell elimination (ICE) and granzyme B activity did not significantly change over time in ECs, suggesting that the gradual increase in integrated HIV DNA observed in ECs was not a result of progressive loss of immune-mediated control. Also, acutely infected (n ‫؍‬ 7) but not chronically infected (n ‫؍‬ 6) patients exhibited a significant drop in integrated HIV DNA 12 months after ART initiation. In conclusion, in the absence of ART, integrated HIV accumulates over time both in NCs and in ECs, at variable individual rates. Starting ART early in infection leads to a greater drop in integrated HIV DNA than does initiating treatment after years of infection. The increase in integrated HIV DNA over time suggests that early treatment may be of benefit in limiting HIV reservoirs. IMPORTANCEThe establishment of a latent reservoir represents a barrier to cure among HIV-infected individuals. The dynamics of HIV reservoir accumulation over time in patients before antiviral therapy is underexplored, in large part because it is difficult to accurately and reproducibly measure the size of HIV reservoir in this setting. In our study, we compared the dynamics of integrated HIV DNA over time in ECs and NCs before and after ART was initiated. We found that integrated HIV DNA levels progressively increase over time in the absence of ART, but with a higher, albeit variable, rate in NCs compared to ECs. In addition, integrated HIV DNA declines more dramatically when ART is initiated in acute rather than chronic HIV infection, suggesting important differences between acute and chronic infection. Our study highlights the role of HIV replication and CTL control in reservoir accumulation in sanctuary sites and why ART appears to be more effective in acute infection.

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Section: Discussionmentioning

confidence: 99%

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

Pinzone

Graf

Lynch

et al. 2016

J Virol

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“…2-LTR forms decline more than integrated forms, and the decay of 2-LTR forms and integrated forms is slower in activated CD38 CD4 T cells than in nonactivated cells (115). In some patients on cART, total HIV DNA can be almost exclusively composed of integrated HIV DNA (104,114,116,117), whereas other studies suggest that some nonintegrated HIV DNA forms can also persist (115,118) and that unintegrated HIV DNA forms remain more frequent than integrated forms in quiescent CD4 T cells and monocytes after several months of cART (119,120,121). Heterogeneity among patients could explain these discrepancies.…”

Section: Decline In Total Hiv Dna During Cartmentioning

confidence: 99%

Total HIV-1 DNA, a Marker of Viral Reservoir Dynamics with Clinical Implications

et al. 2016

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SUMMARYHIV-1 DNA persists in infected cells despite combined antiretroviral therapy (cART), forming viral reservoirs. Recent trials of strategies targeting latent HIV reservoirs have rekindled hopes of curing HIV infection, and reliable markers are thus needed to evaluate viral reservoirs. Total HIV DNA quantification is simple, standardized, sensitive, and reproducible. Total HIV DNA load influences the course of the infection and is therefore clinically relevant. In particular, it is predictive of progression to AIDS and death, independently of HIV RNA load and the CD4 cell count. Baseline total HIV DNA load is predictive of the response to cART. It declines during cART but remains quantifiable, at a level that reflects both the history of infection (HIV RNA zenith, CD4 cell count nadir) and treatment efficacy (residual viremia, cumulative viremia, immune restoration, immune cell activation). Total HIV DNA load in blood is also predictive of the presence and severity of some HIV-1-associated end-organ disorders. It can be useful to guide individual treatment, notably, therapeutic de-escalation. Although it does not distinguish between replication-competent and -defective latent viruses, the total HIV DNA load in blood, tissues, and cells provides insights into HIV pathogenesis, probably because all viral forms participate in host cell activation and HIV pathogenesis. Total HIV DNA is thus a biomarker of HIV reservoirs, which can be defined as all infected cells and tissues containing all forms of HIV persistence that participate in pathogenesis. This participation may occur through the production of new virions, creating new cycles of infection and disseminating infected cells; maintenance or amplification of reservoirs by homeostatic cell proliferation; and viral transcription and synthesis of viral proteins without new virion production. These proteins can induce immune activation, thus participating in the vicious circle of HIV pathogenesis.

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“…Monitoring of HIV persistence by measuring the frequency of cells harboring HIV DNA (23-25, 45, 46) represents an attractive alternative but has often been criticized, as a large fraction of the viral genomes may be replication defective (26). Notwithstanding this limitation, measuring viral DNA and, in particular, integrated HIV DNA (27,28) has provided crucial information that has contributed to the understanding of the mechanisms of HIV persistence (14,15,25,(29)(30)(31)(32). Importantly, the amount of HIV DNA has been shown to predict viral rebound and the viral set point after structured treatment interruption (33,34 (20).…”

mentioning

confidence: 99%

Cross-Clade Ultrasensitive PCR-Based Assays To Measure HIV Persistence in Large-Cohort Studies

Vandergeeten

Fromentin

Merlini

et al. 2014

J Virol

204

206

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A small pool of infected cells persists in HIV-infected individuals receiving antiretroviral therapy (ART).Here, we developed ultrasensitive assays to precisely measure the frequency of cells harboring total HIV DNA, integrated HIV DNA, and two long terminal repeat (2-LTR) circles. These assays are performed on cell lysates, which circumvents the labor-intensive step of DNA extraction, and rely on the coquantification of each HIV molecular form together with CD3 gene sequences to precisely measure cell input. Using primary isolates from HIV subtypes A, B, C, D, and CRF01_A/E, we demonstrate that these assays can efficiently quantify low target copy numbers from diverse HIV subtypes. We further used these assays to measure total HIV DNA, integrated HIV DNA, and 2-LTR circles in CD4 ؉ T cells from HIV-infected subjects infected with subtype B. All samples obtained from ART-naive subjects were positive for the three HIV molecular forms (n ‫؍‬ 15). Total HIV DNA, integrated HIV DNA, and 2-LTR circles were detected in, respectively, 100%, 94%, and 77% of the samples from individuals in which HIV was suppressed by ART. Higher levels of total HIV DNA and 2-LTR circles were detected in untreated subjects than individuals on ART (P ‫؍‬ 0.0003 and P ‫؍‬ 0.0004, respectively), while the frequency of CD4 ؉ T cells harboring integrated HIV DNA did not differ between the two groups. These results demonstrate that these novel assays have the ability to quantify very low levels of HIV DNA of multiple HIV subtypes without the need for nucleic acid extraction, making them well suited for the monitoring of viral persistence in large populations of HIV-infected individuals. IMPORTANCESince the discovery of viral reservoirs in HIV-infected subjects receiving suppressive ART, measuring the degree of viral persistence has been one of the greatest challenges in the field of HIV research. Here, we report the development and validation of ultrasensitive assays to measure HIV persistence in HIV-infected individuals from multiple geographical regions. These assays are relatively inexpensive, do not require DNA extraction, and can be completed in a single day. Therefore, they are perfectly adapted to monitor HIV persistence in large cohorts of HIV-infected individuals and, given their sensitivity, can be used to monitor the efficacy of therapeutic strategies aimed at interfering with HIV persistence after prolonged ART.

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HIV DNA Subspecies Persist in both Activated and Resting Memory CD4 ⁺ T Cells during Antiretroviral Therapy

Cited by 75 publications

References 44 publications

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

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

Total HIV-1 DNA, a Marker of Viral Reservoir Dynamics with Clinical Implications

Cross-Clade Ultrasensitive PCR-Based Assays To Measure HIV Persistence in Large-Cohort Studies

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HIV DNA Subspecies Persist in both Activated and Resting Memory CD4 + T Cells during Antiretroviral Therapy

Cited by 75 publications

References 44 publications

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

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

Total HIV-1 DNA, a Marker of Viral Reservoir Dynamics with Clinical Implications

Cross-Clade Ultrasensitive PCR-Based Assays To Measure HIV Persistence in Large-Cohort Studies

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Product

Resources

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HIV DNA Subspecies Persist in both Activated and Resting Memory CD4 ⁺ T Cells during Antiretroviral Therapy