Longitudinal study reveals HIV-1–infected CD4+ T cell dynamics during long-term antiretroviral therapy

Antar, Annukka A.R.; Jenike, Katharine M.; Jang, Sunyoung; Rigau, Danielle; Reeves, Daniel B.; Hoh, Rebecca; Krone, Melissa; Keruly, Jeanne C.; Moore, Richard D.; Schiffer, Joshua T; Nonyane, Bareng A. S.; Hecht, Frederick; Deeks, Steven G.; Siliciano, Janet D.; Ho, Ya Chi; Siliciano, Robert F.

doi:10.1172/jci135953

Cited by 77 publications

(115 citation statements)

References 72 publications

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“…A follow-up study similarly acknowledged HIV diversity as a potential limitation, but reported no participants (of n = 81) for whom detection consistently failed for either Ψ or env amplicons 5 . By contrast, our results indicate that, as the IPDA is applied to diverse cohorts 4,5,7 , detection failures will occur, and not infrequently. The first step towards mitigation is awareness: samples that yield no Ψ or env single-positive proviruses should be flagged as ‘unreportable’ until HIV polymorphism has been addressed ( e.g .…”

contrasting

confidence: 76%

“…This duplexed droplet digital PCR (ddPCR) assay simultaneously targets the HIV Packaging Signal (Ψ) and the Rev Responsive Element (RRE) within Envelope ( env ) to distinguish genomically intact proviruses against a large background of defective ones 2 . The IPDA requires less time, resources, and biological material than the gold standard for replication-competent HIV reservoir measurement, the Quantitative Viral Outgrowth Assay (QVOA) 3 , and is being adopted in research and clinical studies 4–7 . In our cohort of HIV-1 subtype B-infected individuals from North America however, the IPDA yielded a 28% failure rate due to HIV polymorphism.…”

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confidence: 99%

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HIV Diversity Considerations in the Application of the Intact Proviral DNA Assay (IPDA)

Kinloch

Ren

Alberto

et al. 2020

Preprint

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Opening Paragraph (serves as abstract for submission) and Body 1 2The Intact Proviral DNA Assay (IPDA) was developed to address the critical need for a 3 precise and scalable method for intact HIV reservoir quantification 1 . This duplexed droplet 4 digital PCR (ddPCR) assay simultaneously targets the HIV Packaging Signal (Ψ) and the Rev 5Responsive Element (RRE) within Envelope (env) to distinguish genomically intact proviruses 6 against a large background of defective ones 2 . The IPDA requires less time, resources, and 7 biological material than the gold standard for replication-competent HIV reservoir measurement, 8the Quantitative Viral Outgrowth Assay (QVOA) 3 , and is being adopted in research and clinical 9 studies 4-7 . In our cohort of HIV-1 subtype B-infected individuals from North America however, 10 the IPDA yielded a 28% failure rate due to HIV polymorphism. We further demonstrate that 11 within-host HIV diversity can lead the IPDA to underestimate intact HIV reservoir size, which 12 could negatively impact clinical trial results interpretation. While the IPDA represents an 13 important methodological advance, HIV diversity should be addressed before its widespread 14 adoption. 15We applied the IPDA to 46 HIV subtype B-infected, virally-suppressed individuals from 16North America, yielding a median of 29 (interquartile range [IQR] 0-93) intact 17 proviruses/million CD4+ T-cells (Extended Data Figure 1). Of note, the IPDA did not detect any 18 intact (i.e. Ψ and env double-positive) proviruses in 17 participants (37%). In four of these 19 individuals, both Ψ-and env-single-positive proviruses were detected, suggesting a true negative 20 result (Extended Data Figure 3) In the remaining 13 individuals however, the IPDA did not 21 detect Ψ-and/or env-single-positive proviruses above background levels despite recovery of 22 replication competent HIV in 11/11 cases where QVOA was performed, suggesting that the 23 assay failed to detect autologous proviruses. Specifically, in eight of these participants only Ψ-24 3 positive proviruses were detected, in four only env-positive proviruses were detected, and in one 1 participant no proviruses were detected ( Figure 1B; Extended Data Figure 3). This non-detection 2 rate is consistent with Gaebler et al who reported a lack of detectable Ψ and env double-positive 3 proviruses in 2/6 individuals (33%) using a quadruplexed qPCR assay that employs the IPDA 4 probes 8 . Near-full-length single-genome proviral sequencing performed on IPDA env-negative 5 participant BC-004 revealed mismatches to the env probe, where in silico-predicted reservoir 6 distributions that took these polymorphisms into account ( Figure 1C, left) differed markedly 7 from the experimentally-obtained result (center). Substituting an autologous env probe rescued 8 detection to in silico-predicted levels ( Figure 1C, right), confirming that HIV polymorphism can 9 cause the IPDA to fail. HIV sequencing revealed mismatches in the probe and/or at the 3' end of 10 a primer in all cases of presumed ass...

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confidence: 76%

mentioning

confidence: 99%

HIV Diversity Considerations in the Application of the Intact Proviral DNA Assay (IPDA)

Kinloch

Ren

Alberto

et al. 2020

Preprint

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“…These studies showed that the HIV-1 reservoir is mostly formed at the time of ART initiation ( Brodin et al, 2016 ; Abrahams et al, 2019 ; Pankau et al, 2020 ) and its subsequent rate of decay is very slow ( Crooks et al, 2015 ; Siliciano and Siliciano, 2015 ; Siliciano and Siliciano, 2004 ), with only limited variation in the number of proviruses, or the types of proviral defects observed in PLWH on ART over time ( Lu et al, 2018 ). More recently, longitudinal analyses of near full-length proviral sequences in PLWH on ART showed no enrichment in escaped epitopes over time suggesting that HIV-1-specific T cells do not significantly alter the provirus landscape in people durably suppressed ( Antar et al, 2020 ). Furthermore, a recent study reported that brief analytical treatment interruption (ATI) (median of 5 weeks) does not significantly impact the composition of virus populations (phylogenetic analyses sequencing of HIV-1 env) or size (total DNA, cell-associated RNA, IUPM) of the latent HIV-1 reservoir ( Salantes et al, 2018 ).…”

Section: Discussionmentioning

confidence: 99%

The HIV-1 latent reservoir is largely sensitive to circulating T cells

Warren

Zhou²,

et al. 2020

eLife

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HIV-1 specific CD8+ T cells are an important component of HIV-1 curative strategies. Viral variants in the HIV-1 reservoir may limit the capacity of T cells to detect and clear virus-infected cells. We investigated the patterns of T cell escape variants in the replication-competent reservoir of 25 persons living with HIV-1 (PLWH) durably suppressed on ART. We identified all reactive T cell epitopes in the HIV-1 proteome for each participant and sequenced HIV-1 outgrowth viruses from resting CD4+ T cells. All non-synonymous mutations in reactive T cell epitopes were tested for their effect on the size of the T cell response, with a ≥50% loss defined as an escape mutation. The majority (68%) of T cell epitopes harbored no detectable escape mutations. These findings suggest that circulating T cells in PLWH on ART could contribute to control of rebound and could be targeted for boosting in curative strategies.

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“…Thus, HIV-specific T-cells may frequently eliminate infected cells, only to have these replaced by clonal expansion of other reservoir-harboring cells. There have been somewhat conflicting recent reports regarding this possibility -from groups that approached the question from different angles -highlighting the need for further study (42,49,50).…”

Section: Discussionmentioning

confidence: 99%

HIV-specific T-cell responses reflect substantive in vivo interactions with infected cells despite long-term therapy

Stevenson

Ward

Truong

et al. 2020

Preprint

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Antiretroviral therapies (ART) durably suppress HIV replication to undetectable levels – however, infection persists in the form of long-lived reservoirs of infected cells with integrated proviruses, that re-seed systemic replication if ART is interrupted. A central tenet of our current understanding of this persistence is that infected cells are shielded from immune recognition and elimination through a lack of antigen expression from proviruses. Efforts to cure HIV infection have therefore focused on reactivating latent proviruses to enable immune-mediated clearance, but these have yet to succeed in driving reductions in viral reservoirs. Here, we revisited the question of whether HIV reservoirs are predominately immunologically silent from a new angle, by querying the dynamics of HIV-specific T-cell responses over long-term ART for evidence of ongoing recognition of HIV-infected cells. We show that T-cell responses to autologous reservoir viruses persist over years, and that the maintenance of HIV-Nef-specific responses was uniquely associated with residual frequencies of infected cells. These responses disproportionately exhibited a cytotoxic, effector functional profile, indicative of recent in vivo recognition of HIV-infected cells. These results indicate substantial visibility of the HIV reservoir to T-cells on stable ART, presenting both opportunities and challenges for the development of therapeutic approaches to curing HIV infection.

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Longitudinal study reveals HIV-1–infected CD4+ T cell dynamics during long-term antiretroviral therapy

Cited by 77 publications

References 72 publications

HIV Diversity Considerations in the Application of the Intact Proviral DNA Assay (IPDA)

HIV Diversity Considerations in the Application of the Intact Proviral DNA Assay (IPDA)

The HIV-1 latent reservoir is largely sensitive to circulating T cells

HIV-specific T-cell responses reflect substantive in vivo interactions with infected cells despite long-term therapy

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