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Kufera JT, Armstrong C, Wu F, Singhal A, Zhang H, Lai J, Wilkins HN, Simonetti FR, Siliciano JD, Siliciano RF. CD4+ T cells with latent HIV-1 have reduced proliferative responses to T cell receptor stimulation. J Exp Med 2024; 221:e20231511. [PMID: 38270554 PMCID: PMC10818065 DOI: 10.1084/jem.20231511] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2023] [Revised: 11/04/2023] [Accepted: 01/09/2024] [Indexed: 01/26/2024] Open
Abstract
The latent reservoir for HIV-1 in resting CD4+ T cells persists despite antiretroviral therapy as a barrier to cure. The antigen-driven proliferation of infected cells is a major mechanism of reservoir persistence. However, activation through the T cell antigen receptor (TCR) can induce latent proviruses, leading to viral cytopathic effects and immune clearance. In single-cell studies, we show that, relative to uninfected cells or cells with a defective provirus, CD4+ T cells with an intact provirus have a profound proliferative defect in response to TCR stimulation. Virion production was observed in only 16.5% of cultures with an intact provirus, but proliferation was reduced even when no virion production was detected. Proliferation was inversely correlated with in vivo clone size. These results may reflect the effects of previous in vivo proliferation and do not support attempts to reduce the reservoir with antiproliferative agents, which may have greater effects on normal T cell responses.
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Affiliation(s)
- Joshua T. Kufera
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Ciara Armstrong
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Fengting Wu
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Anushka Singhal
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Hao Zhang
- Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - Jun Lai
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Hannah N. Wilkins
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | | | - Janet D. Siliciano
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Robert F. Siliciano
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Howard Hughes Medical Institute, Baltimore, MD, USA
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2
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Board NL, Yuan Z, Wu F, Moskovljevic M, Ravi M, Sengupta S, Mun SS, Simonetti FR, Lai J, Tebas P, Lynn K, Hoh R, Deeks SG, Siliciano JD, Montaner LJ, Siliciano RF. Bispecific antibodies promote natural killer cell-mediated elimination of HIV-1 reservoir cells. Nat Immunol 2024; 25:462-470. [PMID: 38278966 PMCID: PMC10907297 DOI: 10.1038/s41590-023-01741-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2023] [Accepted: 12/28/2023] [Indexed: 01/28/2024]
Abstract
The persistence of CD4+ T cells carrying latent human immunodeficiency virus-1 (HIV-1) proviruses is the main barrier to a cure. New therapeutics to enhance HIV-1-specific immune responses and clear infected cells will probably be necessary to achieve reduction of the latent reservoir. In the present study, we report two single-chain diabodies (scDbs) that target the HIV-1 envelope protein (Env) and the human type III Fcγ receptor (CD16). We show that the scDbs promoted robust and HIV-1-specific natural killer (NK) cell activation and NK cell-mediated lysis of infected cells. Cocultures of CD4+ T cells from people with HIV-1 on antiretroviral therapy (ART) with autologous NK cells and the scDbs resulted in marked elimination of reservoir cells that was dependent on latency reversal. Treatment of human interleukin-15 transgenic NSG mice with one of the scDbs after ART initiation enhanced NK cell activity and reduced reservoir size. Thus, HIV-1-specific scDbs merit further evaluation as potential therapeutics for clearance of the latent reservoir.
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Affiliation(s)
- Nathan L Board
- Department of Medicine, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Zhe Yuan
- The Wistar Institute, Philadelphia, PA, USA
| | - Fengting Wu
- Department of Medicine, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Milica Moskovljevic
- Department of Medicine, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Meghana Ravi
- Department of Medicine, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Srona Sengupta
- Department of Medicine, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Sung Soo Mun
- Department of Medicine, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Francesco R Simonetti
- Department of Medicine, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Jun Lai
- Department of Medicine, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Pablo Tebas
- Presbyterian Hospital-University of Pennsylvania Hospital, Philadelphia, PA, USA
| | - Kenneth Lynn
- Presbyterian Hospital-University of Pennsylvania Hospital, Philadelphia, PA, USA
| | - Rebecca Hoh
- Department of Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Steven G Deeks
- Department of Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Janet D Siliciano
- Department of Medicine, The Johns Hopkins University School of Medicine, Baltimore, MD, USA.
| | | | - Robert F Siliciano
- Department of Medicine, The Johns Hopkins University School of Medicine, Baltimore, MD, USA.
- Howard Hughes Medical Institute, Baltimore, MD, USA.
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3
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Siliciano JD, Siliciano RF. HIV cure: The daunting scale of the problem. Science 2024; 383:703-705. [PMID: 38359111 DOI: 10.1126/science.adk1831] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/17/2024]
Abstract
Cure strategies are confounded by basic reservoir biology.
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Affiliation(s)
- Janet D Siliciano
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Robert F Siliciano
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Howard Hughes Medical Institute, Johns Hopkins University School of Medicine, Baltimore, MD, USA
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4
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Reeves DB, Rigau DN, Romero A, Zhang H, Simonetti FR, Varriale J, Hoh R, Zhang L, Smith KN, Montaner LJ, Rubin LH, Gange SJ, Roan NR, Tien PC, Margolick JB, Peluso MJ, Deeks SG, Schiffer JT, Siliciano JD, Siliciano RF, Antar AAR. Mild HIV-specific selective forces overlaying natural CD4+ T cell dynamics explain the clonality and decay dynamics of HIV reservoir cells. medRxiv 2024:2024.02.13.24302704. [PMID: 38405967 PMCID: PMC10888981 DOI: 10.1101/2024.02.13.24302704] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/27/2024]
Abstract
The latent reservoir of HIV persists for decades in people living with HIV (PWH) on antiretroviral therapy (ART). To determine if persistence arises from the natural dynamics of memory CD4+ T cells harboring HIV, we compared the clonal dynamics of HIV proviruses to that of memory CD4+ T cell receptors (TCRβ) from the same PWH and from HIV-seronegative people. We show that clonal dominance of HIV proviruses and antigen-specific CD4+ T cells are similar but that the field's understanding of the persistence of the less clonally dominant reservoir is significantly limited by undersampling. We demonstrate that increasing reservoir clonality over time and differential decay of intact and defective proviruses cannot be explained by mCD4+ T cell kinetics alone. Finally, we develop a stochastic model of TCRβ and proviruses that recapitulates experimental observations and suggests that HIV-specific negative selection mediates approximately 6% of intact and 2% of defective proviral clearance. Thus, HIV persistence is mostly, but not entirely, driven by natural mCD4+ T cell kinetics.
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5
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Sambaturu N, Fray EJ, Wu F, Zitzmann C, Simonetti FR, Barouch DH, Siliciano JD, Siliciano RF, Ribeiro RM, Perelson AS, Molina-París C, Leitner T. Last in first out: SIV proviruses seeded later in infection are harbored in short-lived CD4 + T cells. bioRxiv 2023:2023.11.03.565539. [PMID: 37961482 PMCID: PMC10635124 DOI: 10.1101/2023.11.03.565539] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2023]
Abstract
HIV can persist in a latent form as integrated DNA (provirus) in resting CD4+ T cells of infected individuals and as such is unaffected by antiretroviral therapy (ART). Despite being a major obstacle for eradication efforts, the genetic variation and timing of formation of this latent reservoir remains poorly understood. Previous studies on when virus is deposited in the latent reservoir have come to contradictory conclusions. To reexamine the genetic variation of HIV in CD4+ T cells during ART, we determined the divergence in envelope sequences collected from 10 SIV infected rhesus macaques. We found that the macaques displayed a biphasic decline of the viral divergence over time, where the first phase lasted for an average of 11.6 weeks (range 4-28 weeks). Motivated by recent observations that the HIV-infected CD4+ T cell population is composed of short- and long-lived subsets, we developed a model to study the divergence dynamics. We found that SIV in short-lived cells was on average more diverged, while long-lived cells harbored less diverged virus. This suggests that the long-lived cells harbor virus deposited starting earlier in infection and continuing throughout infection, while short-lived cells predominantly harbor more recent virus. As these cell populations decayed, the overall proviral divergence decline matched that observed in the empirical data. This model explains previous seemingly contradictory results on the timing of virus deposition into the latent reservoir, and should provide guidance for future eradication efforts.
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Affiliation(s)
- Narmada Sambaturu
- Theoretical Biology and Biophysics Group, Los Alamos National Laboratory, Los Alamos, NM 87545
| | - Emily J Fray
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205
| | - Fengting Wu
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205
| | - Carolin Zitzmann
- Theoretical Biology and Biophysics Group, Los Alamos National Laboratory, Los Alamos, NM 87545
| | - Francesco R Simonetti
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205
| | - Dan H Barouch
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Boston, MA 02215, USA
| | - Janet D Siliciano
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205
| | - Robert F Siliciano
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205
- Howard Hughes Medical Institute, Baltimore, MD 21205, USA
| | - Ruy M Ribeiro
- Theoretical Biology and Biophysics Group, Los Alamos National Laboratory, Los Alamos, NM 87545
| | - Alan S Perelson
- Theoretical Biology and Biophysics Group, Los Alamos National Laboratory, Los Alamos, NM 87545
| | - Carmen Molina-París
- Theoretical Biology and Biophysics Group, Los Alamos National Laboratory, Los Alamos, NM 87545
| | - Thomas Leitner
- Theoretical Biology and Biophysics Group, Los Alamos National Laboratory, Los Alamos, NM 87545
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6
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Kumar MR, Fray EJ, Bender AM, Zitzmann C, Ribeiro RM, Perelson AS, Barouch DH, Siliciano JD, Siliciano RF. Biphasic decay of intact SHIV genomes following initiation of antiretroviral therapy complicates analysis of interventions targeting the reservoir. Proc Natl Acad Sci U S A 2023; 120:e2313209120. [PMID: 37844236 PMCID: PMC10614214 DOI: 10.1073/pnas.2313209120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2023] [Accepted: 09/05/2023] [Indexed: 10/18/2023] Open
Abstract
The latent reservoir for HIV-1 in resting CD4+ T cells persists despite antiretroviral therapy (ART) and precludes cure. Reservoir-targeting interventions are evaluated in ART-treated macaques infected with simian immunodeficiency virus (SIV) or simian-human immunodeficiency virus (SHIV). Efficacy is determined by reservoir measurements before and after the intervention. However, most proviruses persisting in the setting of ART are defective. In addition, intact HIV-1 and SIV genomes undergo complex, multiphasic decay observable when new infection events are blocked by ART. Intervention-induced elimination of latently infected cells must be distinguished from natural decay. Here, we address these issues for SHIV. We describe an intact proviral DNA assay that allows digital counting of SHIV genomes lacking common fatal defects. We show that intact SHIV genomes in circulating CD4+ T cells undergo biphasic decay during the first year of ART, with a rapid first phase (t1/2 = 30.1 d) and a slower second phase (t1/2 = 8.1 mo) that is still more rapid that the slow decay observed in people with HIV-1 on long-term ART (t1/2 = 3.7 y). In SHIV models, most interventions are tested during 2nd phase decay. Natural 2nd phase decay must be considered in evaluating interventions as most infected cells present at this time do not become part of the stable reservoir. In addition, for interventions tested during 2nd phase decay, a caveat is that the intervention may not be equally effective in people with HIV on long-term ART whose reservoirs are dominated by latently infected cells with a slower decay rate.
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Affiliation(s)
- Mithra R. Kumar
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD21205
| | - Emily J. Fray
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD21205
| | - Alexandra M. Bender
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD21205
| | | | | | | | - Dan H. Barouch
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Boston, MA02215
| | - Janet D. Siliciano
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD21205
| | - Robert F. Siliciano
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD21205
- HHMI, Baltimore, MD21205
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7
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Mainou E, Berendam SJ, Obregon-Perko V, Uffman EA, Phan CT, Shaw GM, Bar KJ, Kumar MR, Fray EJ, Siliciano JM, Siliciano RF, Silvestri G, Permar SR, Fouda GG, McCarthy J, Chahroudi A, Conway JM, Chan C. Assessing the impact of autologous neutralizing antibodies on viral rebound in postnatally SHIV-infected ART-treated infant rhesus macaques. bioRxiv 2023:2023.07.22.550159. [PMID: 37502921 PMCID: PMC10370170 DOI: 10.1101/2023.07.22.550159] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/29/2023]
Abstract
While the benefits of early antiretroviral therapy (ART) initiation in perinatally infected infants are well documented, early ART initiation is not always possible in postnatal pediatric HIV infections, which account for the majority of pediatric HIV cases worldwide. The timing of onset of ART initiation is likely to affect the size of the latent viral reservoir established, as well as the development of adaptive immune responses, such as the generation of neutralizing antibody responses against the virus. How these parameters impact the ability of infants to control viremia and the time to viral rebound after ART interruption is unclear. To gain insight into the dynamics, we utilized mathematical models to investigate the effect of time of ART initiation via latent reservoir size and autologous virus neutralizing antibody responses in delaying viral rebound when treatment is interrupted. We used an infant nonhuman primate Simian/Human Immunodeficiency Virus (SHIV) infection model that mimics breast milk HIV transmission in human infants. Infant Rhesus macaques (RMs) were orally challenged with SHIV.C.CH505 375H dCT and either given ART at 4-7 days post-infection (early ART condition), at 2 weeks post-infection (intermediate ART condition), or at 8 weeks post-infection (late ART condition). These infants were then monitored for up to 60 months post-infection with serial viral load and immune measurements. We develop a stochastic mathematical model to investigate the joint effect of latent reservoir size, the autologous neutralizing antibody potency, and CD4+ T cell levels on the time to viral rebound and control of post-rebound viral loads. We find that the latent reservoir size is an important determinant in explaining time to viral rebound by affecting the growth rate of the virus. The presence of neutralizing antibodies also can delay rebound, but we find this effect for high potency antibody responses only.
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Affiliation(s)
- Ellie Mainou
- Department of Biology, Pennsylvania State University, University Park, PA, USA
| | | | | | - Emilie A Uffman
- Duke Human Vaccine Institute, Duke University Medical Center, Durham, NC, USA
| | - Caroline T Phan
- Duke Human Vaccine Institute, Duke University Medical Center, Durham, NC, USA
| | - George M Shaw
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Katherine J Bar
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Mithra R Kumar
- Department of Pharmacology and Molecular Sciences, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Emily J Fray
- Department of Biochemistry and Molecular Biology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Janet M Siliciano
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Robert F Siliciano
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Guido Silvestri
- Yerkes National Primate Research Center, Emory University, Atlanta, Georgia, USA
| | - Sallie R Permar
- Department of Pediatrics, Weill Cornell Medicine, New York, NY, USA
| | | | - Janice McCarthy
- Department of Biostatistics and Bioinformatics, Duke University Medical Center, Durham, NC, USA
| | - Ann Chahroudi
- Department of Pediatrics, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Jessica M Conway
- Department of Mathematics, Pennsylvania State University, University Park, PA, USA
| | - Cliburn Chan
- Department of Biostatistics and Bioinformatics, Duke University Medical Center, Durham, NC, USA
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8
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McMyn NF, Varriale J, Fray EJ, Zitzmann C, MacLeod H, Lai J, Singhal A, Moskovljevic M, Garcia MA, Lopez BM, Hariharan V, Rhodehouse K, Lynn K, Tebas P, Mounzer K, Montaner LJ, Benko E, Kovacs C, Hoh R, Simonetti FR, Laird GM, Deeks SG, Ribeiro RM, Perelson AS, Siliciano RF, Siliciano JM. The latent reservoir of inducible, infectious HIV-1 does not decrease despite decades of antiretroviral therapy. J Clin Invest 2023; 133:e171554. [PMID: 37463049 PMCID: PMC10471168 DOI: 10.1172/jci171554] [Citation(s) in RCA: 20] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Accepted: 07/11/2023] [Indexed: 09/02/2023] Open
Abstract
HIV-1 persists in a latent reservoir in resting CD4+ T cells despite antiretroviral therapy (ART). The reservoir decays slowly over the first 7 years of ART (t1/2 = 44 months). However, whether decay continues with long-term ART is unclear. Recent integration site studies indicate gradual selection against inducible, intact proviruses, raising speculation that decades of ART might allow treatment interruption without viral rebound. Therefore, we measured the reservoir in 42 people on long-term ART (mean 22 years) using a quantitative viral outgrowth assay. After 7 years of ART, there was no long-term decrease in the frequency of inducible, replication-competent proviruses but rather an increase with an estimated doubling time of 23 years. Another reservoir assay, the intact proviral DNA assay, confirmed that reservoir decay with t1/2 of 44 months did not continue with long-term ART. The lack of decay reflected proliferation of infected cells. Most inducible, replication-competent viruses (79.8%) had env sequences identical to those of other isolates from the same sample. Thus, although integration site analysis indicates changes in reservoir composition, the proliferation of CD4+ T cells counteracts decay, maintaining the frequency of inducible, replication-competent proviruses at roughly constant levels over the long term. These results reinforce the need for lifelong ART.
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Affiliation(s)
- Natalie F. McMyn
- Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Joseph Varriale
- Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Emily J. Fray
- Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | | | | | - Jun Lai
- Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Anushka Singhal
- Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | | | - Mauro A. Garcia
- Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Brianna M. Lopez
- Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Vivek Hariharan
- Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Kyle Rhodehouse
- Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Kenneth Lynn
- The Wistar Institute, Philadelphia, Pennsylvania, USA
- University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Pablo Tebas
- University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Karam Mounzer
- Philadelphia Field Initiating Group for HIV-1 Trials, Philadelphia, Pennsylvania, USA
| | | | - Erika Benko
- Maple Leaf Medical Clinic, Toronto, Ontario, Canada
| | - Colin Kovacs
- Maple Leaf Medical Clinic, Toronto, Ontario, Canada
| | | | | | | | | | - Ruy M. Ribeiro
- Los Alamos National Laboratory, Los Alamos, New Mexico, USA
| | | | - Robert F. Siliciano
- Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
- Howard Hughes Medical Institute, Baltimore, Maryland, USA
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9
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Wu HL, Busman-Sahay K, Weber WC, Waytashek CM, Boyle CD, Bateman KB, Reed JS, Hwang JM, Shriver-Munsch C, Swanson T, Northrup M, Armantrout K, Price H, Robertson-LeVay M, Uttke S, Kumar MR, Fray EJ, Taylor-Brill S, Bondoc S, Agnor R, Junell SL, Legasse AW, Moats C, Bochart RM, Sciurba J, Bimber BN, Sullivan MN, Dozier B, MacAllister RP, Hobbs TR, Martin LD, Panoskaltsis-Mortari A, Colgin LMA, Siliciano RF, Siliciano JD, Estes JD, Smedley JV, Axthelm MK, Meyers G, Maziarz RT, Burwitz BJ, Stanton JJ, Sacha JB. Allogeneic immunity clears latent virus following allogeneic stem cell transplantation in SIV-infected ART-suppressed macaques. Immunity 2023; 56:1649-1663.e5. [PMID: 37236188 PMCID: PMC10524637 DOI: 10.1016/j.immuni.2023.04.019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2022] [Revised: 01/30/2023] [Accepted: 04/28/2023] [Indexed: 05/28/2023]
Abstract
Allogeneic hematopoietic stem cell transplantation (alloHSCT) from donors lacking C-C chemokine receptor 5 (CCR5Δ32/Δ32) can cure HIV, yet mechanisms remain speculative. To define how alloHSCT mediates HIV cure, we performed MHC-matched alloHSCT in SIV+, anti-retroviral therapy (ART)-suppressed Mauritian cynomolgus macaques (MCMs) and demonstrated that allogeneic immunity was the major driver of reservoir clearance, occurring first in peripheral blood, then peripheral lymph nodes, and finally in mesenteric lymph nodes draining the gastrointestinal tract. While allogeneic immunity could extirpate the latent viral reservoir and did so in two alloHSCT-recipient MCMs that remained aviremic >2.5 years after stopping ART, in other cases, it was insufficient without protection of engrafting cells afforded by CCR5-deficiency, as CCR5-tropic virus spread to donor CD4+ T cells despite full ART suppression. These data demonstrate the individual contributions of allogeneic immunity and CCR5 deficiency to HIV cure and support defining targets of alloimmunity for curative strategies independent of HSCT.
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Affiliation(s)
- Helen L Wu
- Vaccine & Gene Therapy Institute, Oregon Health & Science University, Beaverton, OR 97007, USA
| | - Kathleen Busman-Sahay
- Vaccine & Gene Therapy Institute, Oregon Health & Science University, Beaverton, OR 97007, USA
| | - Whitney C Weber
- Vaccine & Gene Therapy Institute, Oregon Health & Science University, Beaverton, OR 97007, USA
| | - Courtney M Waytashek
- Vaccine & Gene Therapy Institute, Oregon Health & Science University, Beaverton, OR 97007, USA
| | - Carla D Boyle
- Vaccine & Gene Therapy Institute, Oregon Health & Science University, Beaverton, OR 97007, USA
| | - Katherine B Bateman
- Vaccine & Gene Therapy Institute, Oregon Health & Science University, Beaverton, OR 97007, USA
| | - Jason S Reed
- Vaccine & Gene Therapy Institute, Oregon Health & Science University, Beaverton, OR 97007, USA
| | - Joseph M Hwang
- Vaccine & Gene Therapy Institute, Oregon Health & Science University, Beaverton, OR 97007, USA
| | - Christine Shriver-Munsch
- Oregon National Primate Research Center, Oregon Health & Science University, Beaverton, OR 97007, USA
| | - Tonya Swanson
- Oregon National Primate Research Center, Oregon Health & Science University, Beaverton, OR 97007, USA
| | - Mina Northrup
- Vaccine & Gene Therapy Institute, Oregon Health & Science University, Beaverton, OR 97007, USA; Oregon National Primate Research Center, Oregon Health & Science University, Beaverton, OR 97007, USA
| | - Kimberly Armantrout
- Oregon National Primate Research Center, Oregon Health & Science University, Beaverton, OR 97007, USA
| | - Heidi Price
- Oregon National Primate Research Center, Oregon Health & Science University, Beaverton, OR 97007, USA
| | - Mitch Robertson-LeVay
- Oregon National Primate Research Center, Oregon Health & Science University, Beaverton, OR 97007, USA
| | - Samantha Uttke
- Oregon National Primate Research Center, Oregon Health & Science University, Beaverton, OR 97007, USA
| | - Mithra R Kumar
- Department of Medicine and Howard Hughes Medical Institute, Johns Hopkins University School of Medicine, Baltimore, MD 21218, USA
| | - Emily J Fray
- Department of Medicine and Howard Hughes Medical Institute, Johns Hopkins University School of Medicine, Baltimore, MD 21218, USA
| | - Sol Taylor-Brill
- Vaccine & Gene Therapy Institute, Oregon Health & Science University, Beaverton, OR 97007, USA
| | - Stephen Bondoc
- Vaccine & Gene Therapy Institute, Oregon Health & Science University, Beaverton, OR 97007, USA
| | - Rebecca Agnor
- Biostatistics Shared Resource, Knight Cancer Institute, Oregon Health & Science University, Portland, OR 97239, USA
| | - Stephanie L Junell
- Division of Medical Physics, Department of Radiation Medicine, Oregon Health & Science University, Portland, OR 97239, USA
| | - Alfred W Legasse
- Oregon National Primate Research Center, Oregon Health & Science University, Beaverton, OR 97007, USA
| | - Cassandra Moats
- Oregon National Primate Research Center, Oregon Health & Science University, Beaverton, OR 97007, USA
| | - Rachele M Bochart
- Oregon National Primate Research Center, Oregon Health & Science University, Beaverton, OR 97007, USA
| | - Joseph Sciurba
- Oregon National Primate Research Center, Oregon Health & Science University, Beaverton, OR 97007, USA
| | - Benjamin N Bimber
- Oregon National Primate Research Center, Oregon Health & Science University, Beaverton, OR 97007, USA
| | - Michelle N Sullivan
- Oregon National Primate Research Center, Oregon Health & Science University, Beaverton, OR 97007, USA
| | - Brandy Dozier
- Oregon National Primate Research Center, Oregon Health & Science University, Beaverton, OR 97007, USA
| | - Rhonda P MacAllister
- Oregon National Primate Research Center, Oregon Health & Science University, Beaverton, OR 97007, USA
| | - Theodore R Hobbs
- Oregon National Primate Research Center, Oregon Health & Science University, Beaverton, OR 97007, USA
| | - Lauren D Martin
- Oregon National Primate Research Center, Oregon Health & Science University, Beaverton, OR 97007, USA
| | - Angela Panoskaltsis-Mortari
- Division of Blood and Marrow Transplantation, Department of Pediatrics, University of Minnesota, Minneapolis, MN, 55454, USA
| | - Lois M A Colgin
- Oregon National Primate Research Center, Oregon Health & Science University, Beaverton, OR 97007, USA
| | - Robert F Siliciano
- Department of Medicine and Howard Hughes Medical Institute, Johns Hopkins University School of Medicine, Baltimore, MD 21218, USA
| | - Janet D Siliciano
- Department of Medicine and Howard Hughes Medical Institute, Johns Hopkins University School of Medicine, Baltimore, MD 21218, USA
| | - Jacob D Estes
- Vaccine & Gene Therapy Institute, Oregon Health & Science University, Beaverton, OR 97007, USA; Oregon National Primate Research Center, Oregon Health & Science University, Beaverton, OR 97007, USA
| | - Jeremy V Smedley
- Oregon National Primate Research Center, Oregon Health & Science University, Beaverton, OR 97007, USA
| | - Michael K Axthelm
- Oregon National Primate Research Center, Oregon Health & Science University, Beaverton, OR 97007, USA
| | - Gabrielle Meyers
- Division of Blood and Marrow Medical Oncology, Knight Cancer Institute, Oregon Health & Science University, Portland, OR 97239, USA
| | - Richard T Maziarz
- Division of Blood and Marrow Medical Oncology, Knight Cancer Institute, Oregon Health & Science University, Portland, OR 97239, USA
| | - Benjamin J Burwitz
- Vaccine & Gene Therapy Institute, Oregon Health & Science University, Beaverton, OR 97007, USA; Oregon National Primate Research Center, Oregon Health & Science University, Beaverton, OR 97007, USA
| | - Jeffrey J Stanton
- Oregon National Primate Research Center, Oregon Health & Science University, Beaverton, OR 97007, USA
| | - Jonah B Sacha
- Vaccine & Gene Therapy Institute, Oregon Health & Science University, Beaverton, OR 97007, USA; Oregon National Primate Research Center, Oregon Health & Science University, Beaverton, OR 97007, USA.
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10
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Sengupta S, Zhang J, Reed MC, Yu J, Kim A, Boronina TN, Board NL, Wrabl JO, Shenderov K, Welsh RA, Yang W, Timmons AE, Hoh R, Cole RN, Deeks SG, Siliciano JD, Siliciano RF, Sadegh-Nasseri S. A cell-free antigen processing system informs HIV-1 epitope selection and vaccine design. J Exp Med 2023; 220:e20221654. [PMID: 37058141 PMCID: PMC10114365 DOI: 10.1084/jem.20221654] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Revised: 02/01/2023] [Accepted: 03/23/2023] [Indexed: 04/15/2023] Open
Abstract
Distinct CD4+ T cell epitopes have been associated with spontaneous control of HIV-1 replication, but analysis of antigen-dependent factors that influence epitope selection is lacking. To examine these factors, we used a cell-free antigen processing system that incorporates soluble HLA-DR (DR1), HLA-DM (DM), cathepsins, and full-length protein antigens for epitope identification by LC-MS/MS. HIV-1 Gag, Pol, Env, Vif, Tat, Rev, and Nef were examined using this system. We identified 35 novel epitopes, including glycopeptides. Epitopes from smaller HIV-1 proteins mapped to regions of low protein stability and higher solvent accessibility. HIV-1 antigens associated with limited CD4+ T cell responses were processed efficiently, while some protective epitopes were inefficiently processed. 55% of epitopes obtained from cell-free processing induced memory CD4+ T cell responses in HIV-1+ donors, including eight of 19 novel epitopes tested. Thus, an in vitro processing system utilizing the components of Class II processing reveals factors influencing epitope selection of HIV-1 and represents an approach to understanding epitope selection from non-HIV-1 antigens.
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Affiliation(s)
- Srona Sengupta
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- The Graduate Program in Immunology and Medical Scientist Training Program, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Josephine Zhang
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Madison C. Reed
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Jeanna Yu
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Aeryon Kim
- Department of Inflammation and Oncology and Genome Analysis Unit, Amgen Research, Amgen Inc., South San Francisco, CA, USA
| | - Tatiana N. Boronina
- Department of Biological Chemistry, Mass Spectrometry and Proteomics Facility, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Nathan L. Board
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - James O. Wrabl
- Department of Biology, Johns Hopkins University, Baltimore, MD, USA
| | - Kevin Shenderov
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Robin A. Welsh
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Weiming Yang
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Andrew E. Timmons
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Rebecca Hoh
- Department of Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Robert N. Cole
- Department of Biological Chemistry, Mass Spectrometry and Proteomics Facility, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Steven G. Deeks
- Department of Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Janet D. Siliciano
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Robert F. Siliciano
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Howard Hughes Medical Institute, Baltimore, MD, USA
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11
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Sanders-Beer BE, Archin NM, Brumme ZL, Busch MP, Deleage C, O'Doherty U, Hughes SH, Jerome KR, Jones RB, Karn J, Kearney MF, Keele BF, Kulpa DA, Laird GM, Li JZ, Lichterfeld MD, Nussenzweig MC, Persaud D, Yukl SA, Siliciano RF, Mellors JW. Current HIV/SIV Reservoir Assays for Preclinical and Clinical Applications: Recommendations from the Experts 2022 NIAID Workshop Summary. AIDS Res Hum Retroviruses 2023; 40:7-21. [PMID: 37126090 DOI: 10.1089/aid.2022.0188] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/02/2023] Open
Abstract
Since the first HIV-cured person was reported in 2009, a strong interest in developing highly sensitive HIV and SIV reservoir assays has emerged. In particular, the question arose about the comparative value of state-of-the-art assays to measure and characterize the HIV reservoir, and how these assays can be applied to accurately detect changes in the reservoir during efforts to develop a cure for HIV infection. Second, it is important to consider the impact on the outcome of clinical trials if these relatively new HIV reservoir assays are incorporated into clinical trial endpoints and/or used for clinical decision-making. To understand the advantages and limitations and the regulatory implications of HIV reservoir assays, the National Institute of Allergy and Infectious Diseases (NIAID) sponsored and convened a meeting on September 16, 2022, to discuss the state of knowledge concerning these questions and best practices for selecting HIV reservoir assays for a particular research question or clinical trial protocol.
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Affiliation(s)
- Brigitte E Sanders-Beer
- National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Nancie M Archin
- Division of Infectious Diseases, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Zabrina L Brumme
- Faculty of Health Sciences, Simon Fraser University, Burnaby, British Columbia, Canada
| | - Michael P Busch
- Vitalant Research Institute, University of California, San Francisco, California, USA
| | - Claire Deleage
- AIDS and Cancer Virus Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research (FNLCR), Frederick, Maryland, USA
| | - Una O'Doherty
- Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Stephen H Hughes
- HIV Dynamics and Replication Program, CCR, National Cancer Institute, Frederick, Maryland, USA
| | - Keith R Jerome
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, and Department of Laboratory Medicine and Pathology, University of Washington, Seattle, Washington, USA
| | - R Brad Jones
- Division of Infectious Diseases, Department of Medicine, Weill Cornell Medicine, New York, New York, USA
| | - Jonathan Karn
- Department of Molecular Biology and Microbiology, Case Western Reserve University, Cleveland, Ohio, USA
| | - Mary F Kearney
- HIV Dynamics and Replication Program, CCR, National Cancer Institute, Frederick, Maryland, USA
| | - Brandon F Keele
- AIDS and Cancer Virus Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research (FNLCR), Frederick, Maryland, USA
| | - Deanna A Kulpa
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, Georgia, USA
| | | | - Jonathan Z Li
- Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Mathias D Lichterfeld
- Brigham and Women's Hospital and Ragon Institute of MGH, MIT and Harvard, Boston, Massachusetts, USA
| | - Michel C Nussenzweig
- Laboratory of Molecular Immunology, The Rockefeller University, New York, New York, USA
| | - Deborah Persaud
- Department of Pediatric Infectious Disease, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Steven A Yukl
- Department of Medicine, University of California San Francisco (UCSF) and San Francisco VA Medical Center, San Francisco, California, USA
| | - Robert F Siliciano
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - John W Mellors
- Division of Infectious Diseases, Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
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12
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White JA, Wu F, Yasin S, Moskovljevic M, Varriale J, Dragoni F, Camilo-Contreras A, Duan J, Zheng MY, Tadzong NF, Patel HB, Quiambao JMC, Rhodehouse K, Zhang H, Lai J, Beg SA, Delannoy M, Kilcrease C, Hoffmann CJ, Poulin S, Chano F, Tremblay C, Cherian J, Barditch-Crovo P, Chida N, Moore RD, Summers MF, Siliciano RF, Siliciano JD, Simonetti FR. Clonally expanded HIV-1 proviruses with 5'-leader defects can give rise to nonsuppressible residual viremia. J Clin Invest 2023; 133:165245. [PMID: 36602866 PMCID: PMC10014112 DOI: 10.1172/jci165245] [Citation(s) in RCA: 33] [Impact Index Per Article: 33.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2022] [Accepted: 01/04/2023] [Indexed: 01/06/2023] Open
Abstract
BackgroundAntiretroviral therapy (ART) halts HIV-1 replication, decreasing viremia to below the detection limit of clinical assays. However, some individuals experience persistent nonsuppressible viremia (NSV) originating from CD4+ T cell clones carrying infectious proviruses. Defective proviruses represent over 90% of all proviruses persisting during ART and can express viral genes, but whether they can cause NSV and complicate ART management is unknown.MethodsWe undertook an in-depth characterization of proviruses causing NSV in 4 study participants with optimal adherence and no drug resistance. We investigated the impact of the observed defects on 5'-leader RNA properties, virus infectivity, and gene expression. Integration-site specific assays were used to track these proviruses over time and among cell subsets.ResultsClones carrying proviruses with 5'-leader defects can cause persistent NSV up to approximately 103 copies/mL. These proviruses had small, often identical deletions or point mutations involving the major splicing donor (MSD) site and showed partially reduced RNA dimerization and nucleocapsid binding. Nevertheless, they were inducible and produced noninfectious virions containing viral RNA, but lacking envelope.ConclusionThese findings show that proviruses with 5'-leader defects in CD4+ T cell clones can give rise to NSV, affecting clinical care. Sequencing of the 5'-leader can help in understanding failure to completely suppress viremia.FundingOffice of the NIH Director and National Institute of Dental and Craniofacial Research, NIH; Howard Hughes Medical Institute; Johns Hopkins University Center for AIDS Research; National Institute for Allergy and Infectious Diseases (NIAID), NIH, to the PAVE, BEAT-HIV, and DARE Martin Delaney collaboratories.
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Affiliation(s)
- Jennifer A White
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Fengting Wu
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Saif Yasin
- Department of Chemistry and Biochemistry, University of Maryland, Baltimore County, Baltimore, Maryland, USA
| | - Milica Moskovljevic
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Joseph Varriale
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Filippo Dragoni
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | | | - Jiayi Duan
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Mei Y Zheng
- Department of Chemistry and Biochemistry, University of Maryland, Baltimore County, Baltimore, Maryland, USA
| | - Ndeh F Tadzong
- Department of Chemistry and Biochemistry, University of Maryland, Baltimore County, Baltimore, Maryland, USA
| | - Heer B Patel
- Department of Chemistry and Biochemistry, University of Maryland, Baltimore County, Baltimore, Maryland, USA
| | - Jeanelle Mae C Quiambao
- Department of Chemistry and Biochemistry, University of Maryland, Baltimore County, Baltimore, Maryland, USA
| | - Kyle Rhodehouse
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Hao Zhang
- Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA
| | - Jun Lai
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Subul A Beg
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Michael Delannoy
- Institute for Basic Biomedical Sciences, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Christin Kilcrease
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Christopher J Hoffmann
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | | | | | - Cécile Tremblay
- Centre de Recherche du Centre Hospitalier de l'Université de Montréal (CHUM), Montreal, Canada.,Département de Microbiologie, Immunologie et Infectiologie, Université de Montréal, Montreal, Canada
| | - Jerald Cherian
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Patricia Barditch-Crovo
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Natasha Chida
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Richard D Moore
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Michael F Summers
- Department of Chemistry and Biochemistry, University of Maryland, Baltimore County, Baltimore, Maryland, USA.,Howard Hughes Medical Institute, Baltimore, Maryland, USA
| | - Robert F Siliciano
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA.,Howard Hughes Medical Institute, Baltimore, Maryland, USA
| | - Janet D Siliciano
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Francesco R Simonetti
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
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13
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Fray EJ, Wu F, Simonetti FR, Zitzmann C, Sambaturu N, Molina-Paris C, Bender AM, Liu PT, Ventura JD, Wiseman RW, O'Connor DH, Geleziunas R, Leitner T, Ribeiro RM, Perelson AS, Barouch DH, Siliciano JD, Siliciano RF. Antiretroviral therapy reveals triphasic decay of intact SIV genomes and persistence of ancestral variants. Cell Host Microbe 2023; 31:356-372.e5. [PMID: 36809762 PMCID: PMC10583177 DOI: 10.1016/j.chom.2023.01.016] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2022] [Revised: 12/02/2022] [Accepted: 01/24/2023] [Indexed: 02/22/2023]
Abstract
The decay kinetics of HIV-1-infected cells are critical to understand virus persistence. We evaluated the frequency of simian immunodeficiency virus (SIV)-infected cells for 4 years of antiretroviral therapy (ART). The intact proviral DNA assay (IPDA) and an assay for hypermutated proviruses revealed short- and long-term infected cell dynamics in macaques starting ART ∼1 year after infection. Intact SIV genomes in circulating CD4+T cells showed triphasic decay with an initial phase slower than the decay of the plasma virus, a second phase faster than the second phase decay of intact HIV-1, and a stable third phase reached after 1.6-2.9 years. Hypermutated proviruses showed bi- or mono-phasic decay, reflecting different selective pressures. Viruses replicating at ART initiation had mutations conferring antibody escape. With time on ART, viruses with fewer mutations became more prominent, reflecting decay of variants replicating at ART initiation. Collectively, these findings confirm ART efficacy and indicate that cells enter the reservoir throughout untreated infection.
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Affiliation(s)
- Emily J Fray
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.
| | - Fengting Wu
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Francesco R Simonetti
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | | | | | | | - Alexandra M Bender
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Po-Ting Liu
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Boston, MA 02215, USA
| | - John D Ventura
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Boston, MA 02215, USA
| | - Roger W Wiseman
- Wisconsin National Primate Research Center, Madison, WI 53715, USA
| | - David H O'Connor
- Wisconsin National Primate Research Center, Madison, WI 53715, USA
| | | | - Thomas Leitner
- Los Alamos National Laboratory, Los Alamos, NM 87545, USA
| | - Ruy M Ribeiro
- Los Alamos National Laboratory, Los Alamos, NM 87545, USA
| | | | - Dan H Barouch
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Boston, MA 02215, USA
| | - Janet D Siliciano
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Robert F Siliciano
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Howard Hughes Medical Institute, Baltimore, MD 21205, USA.
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14
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Benner SE, Eby Y, Zhu X, Fernandez RE, Patel EU, Ruff JE, Habtehyimer F, Schmidt HA, Kirby CS, Hussain S, Ostrander D, Desai NM, Florman S, Rana MM, Friedman-Moraco R, Pereira MR, Mehta S, Stock P, Gilbert A, Morris MI, Stosor V, Mehta SA, Small CB, Ranganna K, Santos CA, Aslam S, Husson J, Malinis M, Elias N, Blumberg EA, Doby BL, Massie AB, Smith ML, Odim J, Quinn TC, Laird GM, Siliciano RF, Segev DL, Redd AD, Durand CM, Tobian AA. The effect of induction immunosuppression for kidney transplant on the latent HIV reservoir. JCI Insight 2022; 7:162968. [PMID: 36345940 PMCID: PMC9675561 DOI: 10.1172/jci.insight.162968] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Accepted: 09/14/2022] [Indexed: 11/09/2022] Open
Abstract
The HIV latent viral reservoir (LVR) remains a major challenge in the effort to find a cure for HIV. There is interest in lymphocyte-depleting agents, used in solid organ and bone marrow transplantation to reduce the LVR. This study evaluated the LVR and T cell receptor repertoire in HIV-infected kidney transplant recipients using intact proviral DNA assay and T cell receptor sequencing in patients receiving lymphocyte-depleting or lymphocyte-nondepleting immunosuppression induction therapy. CD4+ T cells and intact and defective provirus frequencies decreased following lymphocyte-depleting induction therapy but rebounded to near baseline levels within 1 year after induction. In contrast, these biomarkers were relatively stable over time in the lymphocyte-nondepleting group. The lymphocyte-depleting group had early TCRβ repertoire turnover and newly detected and expanded clones compared with the lymphocyte-nondepleting group. No differences were observed in TCRβ clonality and repertoire richness between groups. These findings suggest that, even with significant decreases in the overall size of the circulating LVR, the reservoir can be reconstituted in a relatively short period of time. These results, while from a relatively unique population, suggest that curative strategies aimed at depleting the HIV LVR will need to achieve specific and durable levels of HIV-infected T cell depletion.
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Affiliation(s)
| | | | | | - Reinaldo E. Fernandez
- Department of Medicine, Division of Infectious Diseases, Johns Hopkins School of Medicine, Baltimore, Maryland, USA
| | - Eshan U. Patel
- Department of Pathology and
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA
| | | | - Feben Habtehyimer
- Department of Medicine, Division of Infectious Diseases, Johns Hopkins School of Medicine, Baltimore, Maryland, USA
| | | | | | - Sarah Hussain
- Department of Medicine, Division of Infectious Diseases, Johns Hopkins School of Medicine, Baltimore, Maryland, USA
| | - Darin Ostrander
- Department of Medicine, Division of Infectious Diseases, Johns Hopkins School of Medicine, Baltimore, Maryland, USA
| | - Niraj M. Desai
- Department of Surgery, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | | | - Meenakshi M. Rana
- Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | | | - Marcus R. Pereira
- Department of Medicine, Columbia University Irving Medical Center, New York, New York, USA
| | - Shikha Mehta
- Department of Medicine, University of Alabama Heersink School of Medicine, Birmingham, Alabama, USA
| | - Peter Stock
- Department of Surgery, University of California, San Francisco, San Francisco, California, USA
| | - Alexander Gilbert
- Medstar Transplant Institute, Georgetown University School of Medicine, Washington, DC, USA
| | - Michele I. Morris
- Department of Medicine, Division of Infectious Diseases, University of Miami Miller School of Medicine, Miami, Florida, USA
| | - Valentina Stosor
- Departments of Medicine and Surgery, Divisions of Infectious Diseases and Organ Transplantation, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, USA
| | - Sapna A. Mehta
- Department of Surgery, New York University Grossman School of Medicine, NYU Langone Health, New York, New York, USA
| | - Catherine B. Small
- Department of Medicine, Division of Infectious Diseases, Weill Cornell Medicine, New York, New York, USA
| | - Karthik Ranganna
- Department of Medicine, Drexel University, Philadelphia, Pennsylvania, USA
| | - Carlos A.Q. Santos
- Divison of Infectious Diseases, Rush University Medical Center, Chicago, Illinois, USA
| | - Saima Aslam
- Department of Medicine, University of California, San Diego, San Diego, California, USA
| | - Jennifer Husson
- Institute of Human Virology, University of Maryland School of Medicine, Baltimore, Maryland, USA
| | - Maricar Malinis
- Department of Internal Medicine, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Nahel Elias
- Department of Surgery and Transplant Center, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts, USA
| | - Emily A. Blumberg
- Department of Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania
| | - Brianna L. Doby
- Positive Rhetoric LLC, Bowling Green, Kentucky, USA
- Department of Public Health Sciences, College of Health, Education, and Social Transformation, New Mexico State University, Las Cruces, New Mexico, USA
| | - Allan B. Massie
- Department of Surgery, New York University Grossman School of Medicine, NYU Langone Health, New York, New York, USA
| | - Melissa L. Smith
- Department of Biochemistry and Molecular Genetics, University of Louisville, Louisville, Kentucky, USA
| | - Jonah Odim
- Division of Intramural Research, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, Maryland, USA
| | - Thomas C. Quinn
- Department of Medicine, Division of Infectious Diseases, Johns Hopkins School of Medicine, Baltimore, Maryland, USA
- Division of Intramural Research, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, Maryland, USA
| | | | - Robert F. Siliciano
- Department of Medicine, Division of Infectious Diseases, Johns Hopkins School of Medicine, Baltimore, Maryland, USA
| | - Dorry L. Segev
- Department of Surgery, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
- Department of Surgery, New York University Grossman School of Medicine, NYU Langone Health, New York, New York, USA
| | - Andrew D. Redd
- Department of Medicine, Division of Infectious Diseases, Johns Hopkins School of Medicine, Baltimore, Maryland, USA
- Division of Intramural Research, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, Maryland, USA
| | - Christine M. Durand
- Department of Medicine, Division of Infectious Diseases, Johns Hopkins School of Medicine, Baltimore, Maryland, USA
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15
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Dai W, Wu F, McMyn N, Song B, Walker-Sperling VE, Varriale J, Zhang H, Barouch DH, Siliciano JD, Li W, Siliciano RF. Genome-wide CRISPR screens identify combinations of candidate latency reversing agents for targeting the latent HIV-1 reservoir. Sci Transl Med 2022; 14:eabh3351. [PMID: 36260688 PMCID: PMC9705157 DOI: 10.1126/scitranslmed.abh3351] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Reversing HIV-1 latency promotes killing of infected cells and is essential for cure strategies; however, no single latency reversing agent (LRA) or LRA combination have been shown to reduce HIV-1 latent reservoir size in persons living with HIV-1 (PLWH). Here, we describe an approach to systematically identify LRA combinations to reactivate latent HIV-1 using genome-wide CRISPR screens. Screens on cells treated with suboptimal concentrations of an LRA can identify host genes whose knockout enhances viral gene expression. Therefore, inhibitors of these genes should synergize with the LRA. We tested this approach using AZD5582, an activator of the noncanonical nuclear factor κB (ncNF-κB) pathway, as an LRA and identified histone deacetylase 2 (HDAC2) and bromodomain-containing protein 2 (BRD2), part of the bromodomain and extra-terminal motif (BET) protein family targeted by BET inhibitors, as potential targets. Using CD4+ T cells from PLWH, we confirmed synergy between AZD5582 and several HDAC inhibitors and between AZD5582 and the BET inhibitor, JQ1. A reciprocal screen using suboptimal concentrations of an HDAC inhibitor as an LRA identified BRD2 and ncNF-κB regulators, especially BIRC2, as synergistic candidates for use in combination with HDAC inhibition. Moreover, we identified and validated additional synergistic drug candidates in latency cell line cells and primary lymphocytes isolated from PLWH. Specifically, the knockout of genes encoding CYLD or YPEL5 displayed synergy with existing LRAs in inducing HIV mRNAs. Our study provides insights into the roles of host factors in HIV-1 reactivation and validates a system for identifying drug combinations for HIV-1 latency reversal.
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Affiliation(s)
- Weiwei Dai
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205,Howard Hughes Medical Institute, Johns Hopkins University School of Medicine, Baltimore, MD 21205
| | - Fengting Wu
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205
| | - Natalie McMyn
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205
| | - Bicna Song
- Center for Genetic Medicine Research, Children’s National Hospital. 111 Michigan Ave NW, Washington, DC 20010,Department of Genomics and Precision Medicine, George Washington University. 111 Michigan Ave NW, Washington, DC 20010
| | - Victoria E. Walker-Sperling
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Boston, Massachusetts 02215, USA
| | - Joseph Varriale
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205
| | - Hao Zhang
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205
| | - Dan H. Barouch
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Boston, Massachusetts 02215, USA,Ragon Institute of Massachusetts General Hospital, MIT, and Harvard, Boston, Massachusetts 02114, USA
| | - Janet D. Siliciano
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205
| | - Wei Li
- Center for Genetic Medicine Research, Children’s National Hospital. 111 Michigan Ave NW, Washington, DC 20010,Department of Genomics and Precision Medicine, George Washington University. 111 Michigan Ave NW, Washington, DC 20010,To whom correspondence should be addressed; ;
| | - Robert F. Siliciano
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205,Howard Hughes Medical Institute, Johns Hopkins University School of Medicine, Baltimore, MD 21205,To whom correspondence should be addressed; ;
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16
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Abstract
Combination antiretroviral therapy (ART) can block multiple stages of the HIV-1 life cycle to prevent progression to AIDS in people living with HIV-1. However, owing to the persistence of a reservoir of latently infected CD4+ T cells, life-long ART is necessary to prevent viral rebound. One strategy currently under consideration for curing HIV-1 infection is known as 'shock and kill'. This strategy uses latency-reversing agents to induce expression of HIV-1 genes, allowing for infected cells to be cleared by cytolytic immune cells. The role of innate immunity in HIV-1 pathogenesis is best understood in the context of acute infection. Here, we suggest that innate immunity can also be used to improve the efficacy of HIV-1 cure strategies, with a particular focus on dendritic cells (DCs) and natural killer cells. We discuss novel latency-reversing agents targeting DCs as well as DC-based strategies to enhance the clearance of infected cells by CD8+ T cells and strategies to improve the killing activity of natural killer cells.
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Affiliation(s)
- Nathan L Board
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Milica Moskovljevic
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Fengting Wu
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Robert F Siliciano
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA. .,Howard Hughes Medical Institute, Baltimore, MD, USA.
| | - Janet D Siliciano
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
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17
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Walker-Sperling VEK, Mercado NB, Chandrashekar A, Borducchi EN, Liu J, Nkolola JP, Lewis M, Murry JP, Yang Y, Geleziunas R, Robb ML, Michael NL, Pau MG, Wegmann F, Schuitemaker H, Fray EJ, Kumar MR, Siliciano JD, Siliciano RF, Barouch DH. Therapeutic efficacy of combined active and passive immunization in ART-suppressed, SHIV-infected rhesus macaques. Nat Commun 2022; 13:3463. [PMID: 35710819 PMCID: PMC9203527 DOI: 10.1038/s41467-022-31196-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Accepted: 06/08/2022] [Indexed: 12/19/2022] Open
Abstract
The latent viral reservoir is the critical barrier for developing an HIV-1 cure. Previous studies have shown that therapeutic vaccination or broadly neutralizing antibody (bNAb) administration, together with a Toll-like receptor 7 (TLR7) agonist, enhanced virologic control or delayed viral rebound, respectively, following discontinuation of antiretroviral therapy (ART) in SIV- or SHIV-infected rhesus macaques. Here we show that the combination of active and passive immunization with vesatolimod may lead to higher rates of post-ART virologic control compared to either approach alone. Therapeutic Ad26/MVA vaccination and PGT121 administration together with TLR7 stimulation with vesatolimod resulted in 70% post-ART virologic control in SHIV-SF162P3-infected rhesus macaques. These data suggest the potential of combining active and passive immunization targeting different immunologic mechanisms as an HIV-1 cure strategy.
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Affiliation(s)
| | - Noe B Mercado
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Boston, MA, USA
| | - Abishek Chandrashekar
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Boston, MA, USA
| | - Erica N Borducchi
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Boston, MA, USA
| | - Jinyan Liu
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Boston, MA, USA
| | - Joseph P Nkolola
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Boston, MA, USA
| | | | | | | | | | - Merlin L Robb
- US Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD, 20910, USA
| | - Nelson L Michael
- US Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD, 20910, USA
| | - Maria G Pau
- Janssen Vaccines & Prevention, Leiden, The Netherlands
| | - Frank Wegmann
- Janssen Vaccines & Prevention, Leiden, The Netherlands
| | | | - Emily J Fray
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Mithra R Kumar
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Janet D Siliciano
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Robert F Siliciano
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Dan H Barouch
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Boston, MA, USA.
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA, USA.
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18
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Sengupta S, Board NL, Wu F, Moskovljevic M, Douglass J, Zhang J, Reinhold BR, Duke-Cohan J, Yu J, Reed MC, Tabdili Y, Azurmendi A, Fray EJ, Zhang H, Hsiue EHC, Jenike K, Ho YC, Gabelli SB, Kinzler KW, Vogelstein B, Zhou S, Siliciano JD, Sadegh-Nasseri S, Reinherz EL, Siliciano RF. TCR-mimic bispecific antibodies to target the HIV-1 reservoir. Proc Natl Acad Sci U S A 2022; 119:e2123406119. [PMID: 35394875 PMCID: PMC9169739 DOI: 10.1073/pnas.2123406119] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2021] [Accepted: 03/04/2022] [Indexed: 12/12/2022] Open
Abstract
HIV-1 infection is incurable due to the persistence of the virus in a latent reservoir of resting memory CD4+ T cells. “Shock-and-kill” approaches that seek to induce HIV-1 gene expression, protein production, and subsequent targeting by the host immune system have been unsuccessful due to a lack of effective latency-reversing agents (LRAs) and kill strategies. In an effort to develop reagents that could be used to promote killing of infected cells, we constructed T cell receptor (TCR)-mimic antibodies to HIV-1 peptide-major histocompatibility complexes (pMHC). Using phage display, we panned for phages expressing antibody-like variable sequences that bound HIV-1 pMHC generated using the common HLA-A*02:01 allele. We targeted three epitopes in Gag and reverse transcriptase identified and quantified via Poisson detection mass spectrometry from cells infected in vitro with a pseudotyped HIV-1 reporter virus (NL4.3 dEnv). Sequences isolated from phages that bound these pMHC were cloned into a single-chain diabody backbone (scDb) sequence, such that one fragment is specific for an HIV-1 pMHC and the other fragment binds to CD3ε, an essential signal transduction subunit of the TCR. Thus, these antibodies utilize the sensitivity of T cell signaling as readouts for antigen processing and as agents to promote killing of infected cells. Notably, these scDbs are exquisitely sensitive and specific for the peptide portion of the pMHC. Most importantly, one scDb caused killing of infected cells presenting a naturally processed target pMHC. This work lays the foundation for a novel therapeutic killing strategy toward elimination of the HIV-1 reservoir.
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Affiliation(s)
- Srona Sengupta
- Department of Medicine, The Johns Hopkins University School of Medicine, Baltimore, MD 21205
- Department of Pathology, The Johns Hopkins University School of Medicine, Baltimore, MD 21205
| | - Nathan L. Board
- Department of Medicine, The Johns Hopkins University School of Medicine, Baltimore, MD 21205
| | - Fengting Wu
- Department of Medicine, The Johns Hopkins University School of Medicine, Baltimore, MD 21205
| | - Milica Moskovljevic
- Department of Medicine, The Johns Hopkins University School of Medicine, Baltimore, MD 21205
| | - Jacqueline Douglass
- Ludwig Center, Sidney Kimmel Comprehensive Cancer Center, The Johns Hopkins University School of Medicine, Baltimore, MD 21287
- Lustgarten Pancreatic Cancer Research Laboratory, Sidney Kimmel Comprehensive Cancer Center, The Johns Hopkins University School of Medicine, Baltimore, MD 21287
| | - Josephine Zhang
- Department of Medicine, The Johns Hopkins University School of Medicine, Baltimore, MD 21205
| | - Bruce R. Reinhold
- Laboratory of Immunobiology, Dana-Farber Cancer Institute, Boston, MA 02115
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02115
- Department of Medicine, Harvard Medical School, Boston, MA 02115
| | - Jonathan Duke-Cohan
- Laboratory of Immunobiology, Dana-Farber Cancer Institute, Boston, MA 02115
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02115
- Department of Medicine, Harvard Medical School, Boston, MA 02115
| | - Jeanna Yu
- Department of Medicine, The Johns Hopkins University School of Medicine, Baltimore, MD 21205
| | - Madison C. Reed
- Department of Medicine, The Johns Hopkins University School of Medicine, Baltimore, MD 21205
| | - Yasmine Tabdili
- Department of Medicine, The Johns Hopkins University School of Medicine, Baltimore, MD 21205
| | - Aitana Azurmendi
- Department of Biophysics and Biophysical Chemistry, The Johns Hopkins University School of Medicine, Baltimore, MD 21287
| | - Emily J. Fray
- Department of Medicine, The Johns Hopkins University School of Medicine, Baltimore, MD 21205
| | - Hao Zhang
- Department of Molecular Microbiology and Immunology, The Johns Hopkins Bloomberg School of Public Health, Baltimore, MD 21205
| | - Emily Han-Chung Hsiue
- Ludwig Center, Sidney Kimmel Comprehensive Cancer Center, The Johns Hopkins University School of Medicine, Baltimore, MD 21287
- Lustgarten Pancreatic Cancer Research Laboratory, Sidney Kimmel Comprehensive Cancer Center, The Johns Hopkins University School of Medicine, Baltimore, MD 21287
| | - Katharine Jenike
- Department of Medicine, The Johns Hopkins University School of Medicine, Baltimore, MD 21205
| | - Ya-Chi Ho
- Department of Microbial Pathogenesis, Yale University School of Medicine, New Haven, CT 06519
| | - Sandra B. Gabelli
- Department of Biophysics and Biophysical Chemistry, The Johns Hopkins University School of Medicine, Baltimore, MD 21287
| | - Kenneth W. Kinzler
- Ludwig Center, Sidney Kimmel Comprehensive Cancer Center, The Johns Hopkins University School of Medicine, Baltimore, MD 21287
- Lustgarten Pancreatic Cancer Research Laboratory, Sidney Kimmel Comprehensive Cancer Center, The Johns Hopkins University School of Medicine, Baltimore, MD 21287
- Bloomberg-Kimmel Institute for Cancer Immunotherapy, Sidney Kimmel Comprehensive Cancer Center, Baltimore, MD 21287
| | - Bert Vogelstein
- Ludwig Center, Sidney Kimmel Comprehensive Cancer Center, The Johns Hopkins University School of Medicine, Baltimore, MD 21287
- Lustgarten Pancreatic Cancer Research Laboratory, Sidney Kimmel Comprehensive Cancer Center, The Johns Hopkins University School of Medicine, Baltimore, MD 21287
- Bloomberg-Kimmel Institute for Cancer Immunotherapy, Sidney Kimmel Comprehensive Cancer Center, Baltimore, MD 21287
- HHMI, The Johns Hopkins University School of Medicine, Baltimore, MD 21205
| | - Shibin Zhou
- Ludwig Center, Sidney Kimmel Comprehensive Cancer Center, The Johns Hopkins University School of Medicine, Baltimore, MD 21287
- Lustgarten Pancreatic Cancer Research Laboratory, Sidney Kimmel Comprehensive Cancer Center, The Johns Hopkins University School of Medicine, Baltimore, MD 21287
- Bloomberg-Kimmel Institute for Cancer Immunotherapy, Sidney Kimmel Comprehensive Cancer Center, Baltimore, MD 21287
| | - Janet D. Siliciano
- Department of Medicine, The Johns Hopkins University School of Medicine, Baltimore, MD 21205
| | | | - Ellis L. Reinherz
- Laboratory of Immunobiology, Dana-Farber Cancer Institute, Boston, MA 02115
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02115
- Department of Medicine, Harvard Medical School, Boston, MA 02115
| | - Robert F. Siliciano
- Department of Medicine, The Johns Hopkins University School of Medicine, Baltimore, MD 21205
- HHMI, The Johns Hopkins University School of Medicine, Baltimore, MD 21205
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19
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White JA, Simonetti FR, Beg S, McMyn NF, Dai W, Bachmann N, Lai J, Ford WC, Bunch C, Jones JL, Ribeiro RM, Perelson AS, Siliciano JD, Siliciano RF. Complex decay dynamics of HIV virions, intact and defective proviruses, and 2LTR circles following initiation of antiretroviral therapy. Proc Natl Acad Sci U S A 2022; 119:e2120326119. [PMID: 35110411 PMCID: PMC8833145 DOI: 10.1073/pnas.2120326119] [Citation(s) in RCA: 44] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2021] [Accepted: 12/21/2021] [Indexed: 02/07/2023] Open
Abstract
In persons living with HIV-1 (PLWH) who start antiretroviral therapy (ART), plasma virus decays in a biphasic fashion to below the detection limit. The first phase reflects the short half-life (<1 d) of cells that produce most of the plasma virus. The second phase represents the slower turnover (t1/2 = 14 d) of another infected cell population, whose identity is unclear. Using the intact proviral DNA assay (IPDA) to distinguish intact and defective proviruses, we analyzed viral decay in 17 PLWH initiating ART. Circulating CD4+ T cells with intact proviruses include few of the rapidly decaying first-phase cells. Instead, this population initially decays more slowly (t1/2 = 12.9 d) in a process that largely represents death or exit from the circulation rather than transition to latency. This more protracted decay potentially allows for immune selection. After ∼3 mo, the decay slope changes, and CD4+ T cells with intact proviruses decay with a half-life of 19 mo, which is still shorter than that of the latently infected cells that persist on long-term ART. Two-long-terminal repeat (2LTR) circles decay with fast and slow phases paralleling intact proviruses, a finding that precludes their use as a simple marker of ongoing viral replication. Proviruses with defects at the 5' or 3' end of the genome show equivalent monophasic decay at rates that vary among individuals. Understanding these complex early decay processes is important for correct use of reservoir assays and may provide insights into properties of surviving cells that can constitute the stable latent reservoir.
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Affiliation(s)
- Jennifer A White
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205
| | - Francesco R Simonetti
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205
| | - Subul Beg
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205
| | - Natalie F McMyn
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205
| | - Weiwei Dai
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205
| | - Niklas Bachmann
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205
| | - Jun Lai
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205
| | - William C Ford
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205
| | - Christina Bunch
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205
| | - Joyce L Jones
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205
| | - Ruy M Ribeiro
- Department of Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, NM 87545
| | - Alan S Perelson
- Department of Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, NM 87545
| | - Janet D Siliciano
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205
| | - Robert F Siliciano
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205;
- HHMI, Baltimore, MD 21205
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20
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Abstract
Although antiretroviral therapy (ART) can reduce viremia to below the limit of detection and allow persons living with HIV-1 (PLWH) to lead relatively normal lives, viremia rebounds when treatment is interrupted. Rebound reflects viral persistence in a stable latent reservoir in resting CD4+ T cells. This reservoir is now recognized as the major barrier to cure and is the focus of intense international research efforts. Strategies to cure HIV-1 infection include interventions to eliminate this reservoir, to prevent viral rebound from the reservoir, or to enhance immune responses such that viral replication is effectively controlled. Here we consider recent developments in understanding the composition of the reservoir and how it can be measured in clinical studies. We also discuss exciting new insights into the in vivo dynamics of the reservoir and the reasons for its remarkable stability. Finally we discuss recent discoveries on the complex processes that govern viral rebound. Expected final online publication date for the Annual Review of Pathology: Mechanisms of Disease, Volume 17 is January 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
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Affiliation(s)
- Janet D Siliciano
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA;
| | - Robert F Siliciano
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA; .,Howard Hughes Medical Institute, Baltimore, Maryland 21205, USA
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21
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Simonetti FR, Zhang H, Soroosh GP, Duan J, Rhodehouse K, Hill AL, Beg SA, McCormick K, Raymond HE, Nobles CL, Everett JK, Kwon KJ, White JA, Lai J, Margolick JB, Hoh R, Deeks SG, Bushman FD, Siliciano JD, Siliciano RF. Antigen-driven clonal selection shapes the persistence of HIV-1-infected CD4+ T cells in vivo. J Clin Invest 2021; 131:145254. [PMID: 33301425 DOI: 10.1172/jci145254] [Citation(s) in RCA: 98] [Impact Index Per Article: 32.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2020] [Accepted: 12/01/2020] [Indexed: 12/23/2022] Open
Abstract
Clonal expansion of infected CD4+ T cells is a major mechanism of HIV-1 persistence and a barrier to achieving a cure. Potential causes are homeostatic proliferation, effects of HIV-1 integration, and interaction with antigens. Here, we show that it is possible to link antigen responsiveness, the full proviral sequence, the integration site, and the T cell receptor β-chain (TCRβ) sequence to examine the role of recurrent antigenic exposure in maintaining the HIV-1 reservoir. We isolated CMV- and Gag-responding CD4+ T cells from 10 treated individuals. Proviral populations in CMV-responding cells were dominated by large clones, including clones harboring replication-competent proviruses. TCRβ repertoires showed high clonality driven by converging adaptive responses. Although some proviruses were in genes linked to HIV-1 persistence (BACH2, STAT5B, MKL1), the proliferation of infected cells under antigenic stimulation occurred regardless of the site of integration. Paired TCRβ and integration site analysis showed that infection could occur early or late in the course of a clone's response to antigen and could generate infected cell populations too large to be explained solely by homeostatic proliferation. Together, these findings implicate antigen-driven clonal selection as a major factor in HIV-1 persistence, a finding that will be a difficult challenge to eradication efforts.
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Affiliation(s)
- Francesco R Simonetti
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Hao Zhang
- Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA
| | - Garshasb P Soroosh
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Jiayi Duan
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Kyle Rhodehouse
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Alison L Hill
- Institute for Computational Medicine, Johns Hopkins University, Baltimore, Maryland, USA
| | - Subul A Beg
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Kevin McCormick
- Department of Microbiology, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, USA
| | - Hayley E Raymond
- Department of Microbiology, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, USA
| | - Christopher L Nobles
- Department of Microbiology, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, USA
| | - John K Everett
- Department of Microbiology, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, USA
| | - Kyungyoon J Kwon
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Jennifer A White
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Jun Lai
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Joseph B Margolick
- Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA
| | - Rebecca Hoh
- Division of HIV, Infectious Diseases, and Global Medicine, UCSF, San Francisco, California, USA
| | - Steven G Deeks
- Division of HIV, Infectious Diseases, and Global Medicine, UCSF, San Francisco, California, USA
| | - Frederic D Bushman
- Department of Microbiology, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, USA
| | - Janet D Siliciano
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Robert F Siliciano
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA.,Howard Hughes Medical Institute, Baltimore, Maryland, USA
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22
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Abstract
The latent reservoir for human immunodeficiency virus type 1 (HIV-1) in resting CD4+ T cells is a major barrier to cure. The dimensions of the reservoir problem can be defined with 2 assays. A definitive minimal estimate of the frequency of latently infected cells is provided by the quantitative viral outgrowth assay (QVOA), which detects cells that can be induced by T-cell activation to release infectious virus. In contrast, the intact proviral DNA assay (IPDA) detects all genetically intact proviruses and provides a more accurate upper limit on reservoir size than standard single-amplicon polymerase chain reaction assays which mainly detect defective proviruses. The frequency of cells capable of initiating viral rebound on interruption of antiretroviral therapy lies between the values produced by the QVOA and the IPDA. We argue here that the 1-2-log difference between QVOA and IPDA values in part reflects that the fact that many replication-competent proviruses are not readily induced by T-cell activation. Findings of earlier studies suggest that latently infected cells can be activated to proliferate in vivo without expressing viral genes. The proliferating cells nevertheless retain the ability to produce virus on subsequent stimulation. The low inducibility of latent proviruses is a major problem for the shock-and-kill strategy for curing HIV-1 infection, which uses latency-reversing agents to induce viral gene expression and render infected cells susceptible to immune clearance. The latency-reversing agents developed to date are much less effective at reversing latency than T-cell activation. Taken together, these results indicate that HIV-1 eradication will require the discovery of much more effective ways to induce viral gene expression.
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Affiliation(s)
- Janet D Siliciano
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Robert F Siliciano
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA.,Howard Hughes Medical Institute, Baltimore, Maryland, USA
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23
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Martin AR, Bender AM, Hackman J, Kwon KJ, Lynch BA, Bruno D, Martens C, Beg S, Florman SS, Desai N, Segev D, Laird GM, Siliciano JD, Quinn TC, Tobian AAR, Durand CM, Siliciano RF, Redd AD. Similar Frequency and Inducibility of Intact Human Immunodeficiency Virus-1 Proviruses in Blood and Lymph Nodes. J Infect Dis 2021; 224:258-268. [PMID: 33269401 PMCID: PMC8280486 DOI: 10.1093/infdis/jiaa736] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2020] [Accepted: 11/25/2020] [Indexed: 01/18/2023] Open
Abstract
BACKGROUND The human immunodeficiency virus (HIV)-1 latent reservoir (LR) in resting CD4+ T cells is a barrier to cure. LR measurements are commonly performed on blood samples and therefore may miss latently infected cells residing in tissues, including lymph nodes. METHODS We determined the frequency of intact HIV-1 proviruses and proviral inducibility in matched peripheral blood (PB) and lymph node (LN) samples from 10 HIV-1-infected patients on antiretroviral therapy (ART) using the intact proviral DNA assay and a novel quantitative viral induction assay. Prominent viral sequences from induced viral RNA were characterized using a next-generation sequencing assay. RESULTS The frequencies of CD4+ T cells with intact proviruses were not significantly different in PB versus LN (61/106 vs 104/106 CD4+ cells), and they were substantially lower than frequencies of CD4+ T cells with defective proviruses. The frequencies of CD4+ T cells induced to produce high levels of viral RNA were not significantly different in PB versus LN (4.3/106 vs 7.9/106), but they were 14-fold lower than the frequencies of cells with intact proviruses. Sequencing of HIV-1 RNA from induced proviruses revealed comparable sequences in paired PB and LN samples. CONCLUSIONS These results further support the use of PB as an appropriate proxy for the HIV-1 LR in secondary lymphoid organs.
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Affiliation(s)
- Alyssa R Martin
- Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Alexandra M Bender
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
- Department of Dermatology, University of Rochester Medical Center, Rochester, New York, USA
| | - Jada Hackman
- Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Kyungyoon J Kwon
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Briana A Lynch
- Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Daniel Bruno
- Genomics Unit, Research Technologies Branch, Rocky Mountain Laboratories, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, Montana, USA
| | - Craig Martens
- Genomics Unit, Research Technologies Branch, Rocky Mountain Laboratories, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, Montana, USA
| | - Subul Beg
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | | | - Niraj Desai
- Department of Surgery, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Dorry Segev
- Department of Surgery, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | | | - Janet D Siliciano
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Thomas C Quinn
- Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Aaron A R Tobian
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Christine M Durand
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Robert F Siliciano
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
- Howard Hughes Medical Institute, Baltimore, Maryland, USA
| | - Andrew D Redd
- Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
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24
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Kirk GD, Astemborski J, Mehta SH, Ritter KD, Laird GM, Bordi R, Sekaly R, Siliciano JD, Siliciano RF. Nonstructured Treatment Interruptions Are Associated With Higher Human Immunodeficiency Virus Reservoir Size Measured by Intact Proviral DNA Assay in People Who Inject Drugs. J Infect Dis 2021; 223:1905-1913. [PMID: 33037877 PMCID: PMC8176633 DOI: 10.1093/infdis/jiaa634] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2020] [Accepted: 10/02/2020] [Indexed: 12/17/2022] Open
Abstract
The latent reservoir for human immunodeficiency virus type 1 (HIV-1) in CD4+ T cells is a major barrier to cure. HIV-1-infected persons who inject drugs (PWID) often struggle to maintain suppression of viremia and experience nonstructured treatment interruptions (NTIs). The effects of injecting drugs or NTIs on the reservoir are unclear. Using the intact proviral DNA assay, we found no apparent effect of heroin or cocaine use on reservoir size. However, we found significantly larger reservoirs in those with frequent NTIs or a shorter interval from last detectable HIV RNA measurement. These results have important implications for inclusion of PWID in HIV-1 cure studies.
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Affiliation(s)
- Gregory D Kirk
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Jacqueline Astemborski
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA
| | - Shruti H Mehta
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA
| | | | | | - Rebeka Bordi
- Department of Pathology, Case Western Reserve University, Cleveland, Ohio, USA
| | - Rafick Sekaly
- Department of Pathology, Case Western Reserve University, Cleveland, Ohio, USA
| | - Janet D Siliciano
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Robert F Siliciano
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
- Howard Hughes Medical Institute, Baltimore, Maryland, USA
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25
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Rasmussen TA, Rajdev L, Rhodes A, Dantanarayana A, Tennakoon S, Chea S, Spelman T, Lensing S, Rutishauser R, Bakkour S, Busch M, Siliciano JD, Siliciano RF, Einstein MH, Dittmer DP, Chiao E, Deeks S, Durand C, Lewin SR. Impact of anti-PD-1 and anti-CTLA-4 on the HIV reservoir in people living with HIV with cancer on antiretroviral therapy: The AIDS Malignancy Consortium-095 study. Clin Infect Dis 2021; 73:e1973-e1981. [PMID: 33677480 DOI: 10.1093/cid/ciaa1530] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2020] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND Antibodies to PD-1 and CTLA-4 may perturb HIV persistence during antiretroviral therapy (ART) by reversing HIV-latency and/or boosting HIV-specific immunity leading to clearance of infected cells. We tested this hypothesis in a clinical trial of anti-PD-1 alone or in combination with anti-CTLA-4 in people living with HIV (PLWH) and cancer. METHODS This was a substudy of the AIDS Malignancy Consortium-095 Study. ART-suppressed PLWH with advanced malignancies were assigned to nivolumab (anti-PD-1) with or without ipilimumab (anti-CTLA-4). In samples obtained pre-infusion and one and seven days after the first and fourth dose of immune checkpoint blockade (ICB), we quantified cell-associated unspliced (CA-US) HIV-RNA and HIV-DNA. Plasma HIV-RNA was quantified during the first treatment cycle. Quantitative viral outgrowth assay (QVOA) to estimate the frequency of replication-competent HIV was performed before and after ICB for participants with samples available. RESULTS Of forty participants, 33 received nivolumab and seven nivolumab plus ipilimumab. Whereas CA-US HIV RNA did not change with nivolumab monotherapy, we detected a median 1.44 fold-increase (IQR 1.16-1.89) after the first dose of nivolumab and ipilimumab combination therapy (P=0.031). There was no decrease in the frequency of cells containing replication-competent HIV, but in the two individuals on combination ICB for whom we had longitudinal QVOA, we detected decreases of 97% and 64% compared to baseline. CONCLUSION Anti-PD-1 alone showed no effect on HIV-latency or the latent HIV-reservoir, but the combination of anti-PD-1 and anti-CTL-4 induced a modest increase in CA-US HIV RNA and may potentially eliminate cells containing replication-competent HIV.
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Affiliation(s)
- Thomas A Rasmussen
- The Doherty Institute for Infection and Immunity, The University of Melbourne and Royal Melbourne Hospital, Melbourne, Australia
| | - Lakshmi Rajdev
- Department of Haematology and Oncology, Lennox Hill Hospital, New York, USA
| | - Ajantha Rhodes
- The Doherty Institute for Infection and Immunity, The University of Melbourne and Royal Melbourne Hospital, Melbourne, Australia
| | - Ashanti Dantanarayana
- The Doherty Institute for Infection and Immunity, The University of Melbourne and Royal Melbourne Hospital, Melbourne, Australia
| | - Surekha Tennakoon
- The Doherty Institute for Infection and Immunity, The University of Melbourne and Royal Melbourne Hospital, Melbourne, Australia
| | - Socheata Chea
- The Doherty Institute for Infection and Immunity, The University of Melbourne and Royal Melbourne Hospital, Melbourne, Australia
| | - Tim Spelman
- The Doherty Institute for Infection and Immunity, The University of Melbourne and Royal Melbourne Hospital, Melbourne, Australia
| | - Shelly Lensing
- Department of Biostatistics, University of Arkansas for Medical Sciences, Little Rock, Arkansas, USA
| | - Rachel Rutishauser
- Department of Medicine, University of California San Francisco, San Francisco, California, USA
| | - Sonia Bakkour
- Vitalant Research Institute and Department of Laboratory Medicine, University of California, San Francisco, California, USA
| | - Michael Busch
- Vitalant Research Institute and Department of Laboratory Medicine, University of California, San Francisco, California, USA
| | - Janet D Siliciano
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Robert F Siliciano
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Mark H Einstein
- Department of Obstetrics, Gynecology, & Reproductive Health, Rutgers New Jersey Medical School, Newark, New Jersey, USA
| | - Dirk P Dittmer
- Lineberger Comprehensive Cancer Center and Department of Microbiology and Immunology, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | | | - Steven Deeks
- Department of Medicine, University of California San Francisco, San Francisco, California, USA
| | - Christine Durand
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Sharon R Lewin
- The Doherty Institute for Infection and Immunity, The University of Melbourne and Royal Melbourne Hospital, Melbourne, Australia.,Department of Infectious Diseases, Alfred Hospital and Monash University, Melbourne, Australia
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26
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Gaebler C, Falcinelli SD, Stoffel E, Read J, Murtagh R, Oliveira TY, Ramos V, Lorenzi JCC, Kirchherr J, James KS, Allard B, Baker C, Kuruc JD, Caskey M, Archin NM, Siliciano RF, Margolis DM, Nussenzweig MC. Sequence Evaluation and Comparative Analysis of Novel Assays for Intact Proviral HIV-1 DNA. J Virol 2021; 95:e01986-20. [PMID: 33361426 PMCID: PMC8094944 DOI: 10.1128/jvi.01986-20] [Citation(s) in RCA: 38] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2020] [Accepted: 12/07/2020] [Indexed: 12/13/2022] Open
Abstract
The HIV proviral reservoir is the major barrier to cure. The predominantly replication-defective proviral landscape makes the measurement of virus that is likely to cause rebound upon antiretroviral therapy (ART)-cessation challenging. To address this issue, novel assays to measure intact HIV proviruses have been developed. The intact proviral DNA assay (IPDA) is a high-throughput assay that uses two probes to exclude the majority of defective proviruses and determine the frequency of intact proviruses, albeit without sequence confirmation. Quadruplex PCR with four probes (Q4PCR) is a lower-throughput assay that uses limiting dilution long-distance PCR amplification followed by quantitative PCR (qPCR) and near-full-length genome sequencing (nFGS) to estimate the frequency of sequence-confirmed intact proviruses and provide insight into their clonal composition. To explore the advantages and limitations of these assays, we compared IPDA and Q4PCR measurements from 39 ART-suppressed people living with HIV. We found that IPDA and Q4PCR measurements correlated with one another, but frequencies of intact proviral DNA differed by approximately 19-fold. This difference may be in part due to inefficiencies in long-distance PCR amplification of proviruses in Q4PCR, leading to underestimates of intact proviral frequencies. In addition, nFGS analysis within Q4PCR explained that some of this difference is explained by proviruses that are classified as intact by IPDA but carry defects elsewhere in the genome. Taken together, this head-to-head comparison of novel intact proviral DNA assays provides important context for their interpretation in studies to deplete the HIV reservoir and shows that together the assays bracket true reservoir size.IMPORTANCE The intact proviral DNA assay (IPDA) and quadruplex PCR (Q4PCR) represent major advances in accurately quantifying and characterizing the replication-competent HIV reservoir. This study compares the two novel approaches for measuring intact HIV proviral DNA in samples from 39 antiretroviral therapy (ART)-suppressed people living with HIV, thereby informing ongoing efforts to deplete the HIV reservoir in cure-related trials.
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Affiliation(s)
- Christian Gaebler
- Laboratory of Molecular Immunology, The Rockefeller University, New York, New York, USA
| | - Shane D Falcinelli
- UNC HIV Cure Center, University of North Carolina, Chapel Hill, North Carolina, USA
- Department of Microbiology and Immunology, University of North Carolina, Chapel Hill, North Carolina, USA
| | - Elina Stoffel
- Laboratory of Molecular Immunology, The Rockefeller University, New York, New York, USA
| | - Jenna Read
- UNC HIV Cure Center, University of North Carolina, Chapel Hill, North Carolina, USA
| | - Ross Murtagh
- UNC HIV Cure Center, University of North Carolina, Chapel Hill, North Carolina, USA
| | - Thiago Y Oliveira
- Laboratory of Molecular Immunology, The Rockefeller University, New York, New York, USA
| | - Victor Ramos
- Laboratory of Molecular Immunology, The Rockefeller University, New York, New York, USA
| | - Julio C C Lorenzi
- Laboratory of Molecular Immunology, The Rockefeller University, New York, New York, USA
| | - Jennifer Kirchherr
- UNC HIV Cure Center, University of North Carolina, Chapel Hill, North Carolina, USA
| | - Katherine S James
- UNC HIV Cure Center, University of North Carolina, Chapel Hill, North Carolina, USA
| | - Brigitte Allard
- UNC HIV Cure Center, University of North Carolina, Chapel Hill, North Carolina, USA
| | - Caroline Baker
- UNC HIV Cure Center, University of North Carolina, Chapel Hill, North Carolina, USA
| | - JoAnn D Kuruc
- UNC HIV Cure Center, University of North Carolina, Chapel Hill, North Carolina, USA
- Department of Medicine, University of North Carolina, Chapel Hill, North Carolina, USA
| | - Marina Caskey
- Laboratory of Molecular Immunology, The Rockefeller University, New York, New York, USA
| | - Nancie M Archin
- UNC HIV Cure Center, University of North Carolina, Chapel Hill, North Carolina, USA
- Department of Medicine, University of North Carolina, Chapel Hill, North Carolina, USA
| | - Robert F Siliciano
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
- Howard Hughes Medical Institute, Baltimore, Maryland, USA
| | - David M Margolis
- UNC HIV Cure Center, University of North Carolina, Chapel Hill, North Carolina, USA
- Department of Microbiology and Immunology, University of North Carolina, Chapel Hill, North Carolina, USA
- Department of Medicine, University of North Carolina, Chapel Hill, North Carolina, USA
| | - Michel C Nussenzweig
- Laboratory of Molecular Immunology, The Rockefeller University, New York, New York, USA
- Howard Hughes Medical Institute, The Rockefeller University, New York, New York, USA
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27
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Abstract
Antiretroviral therapy (ART) generally reduces plasma HIV to undetectable levels, although virus persists in latently infected CD4+ T cells. In some individuals, viremia remains detectable despite adherence to ART and the absence of drug resistance mutations. In this issue of the JCI, Halvas et al. describe HIV RNA sequences from plasma of 8 donors with persistent viremia. Residual viremia was dominated by identical HIV-1 RNA sequences that remained relatively constant over 4 years. Plasma virus matched replication-competent virus cultured from CD4+ T cells. Integration site analysis confirmed the presence of large clones of infected cells. These results indicate that nonsuppressible viremia can be due to expanded clones of infected CD4+ T cells carrying replication-competent virus. The individuals described here represent extreme examples of a phenomenon that is seen in all infected individuals and that is a major barrier to curing HIV infection, the in vivo proliferation of latently infected cells.
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Affiliation(s)
- Janet D Siliciano
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Robert F Siliciano
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA.,Howard Hughes Medical Institute, Baltimore, Maryland, USA
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28
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Gondim MVP, Sherrill-Mix S, Bibollet-Ruche F, Russell RM, Trimboli S, Smith AG, Li Y, Liu W, Avitto AN, DeVoto JC, Connell J, Fenton-May AE, Pellegrino P, Williams I, Papasavvas E, Lorenzi JCC, Salantes DB, Mampe F, Monroy MA, Cohen YZ, Heath S, Saag MS, Montaner LJ, Collman RG, Siliciano JM, Siliciano RF, Plenderleith LJ, Sharp PM, Caskey M, Nussenzweig MC, Shaw GM, Borrow P, Bar KJ, Hahn BH. Heightened resistance to host type 1 interferons characterizes HIV-1 at transmission and after antiretroviral therapy interruption. Sci Transl Med 2021; 13:eabd8179. [PMID: 33441429 PMCID: PMC7923595 DOI: 10.1126/scitranslmed.abd8179] [Citation(s) in RCA: 46] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2020] [Revised: 10/04/2020] [Accepted: 11/30/2020] [Indexed: 12/13/2022]
Abstract
Type 1 interferons (IFN-I) are potent innate antiviral effectors that constrain HIV-1 transmission. However, harnessing these cytokines for HIV-1 cure strategies has been hampered by an incomplete understanding of their antiviral activities at later stages of infection. Here, we characterized the IFN-I sensitivity of 500 clonally derived HIV-1 isolates from the plasma and CD4+ T cells of 26 individuals sampled longitudinally after transmission or after antiretroviral therapy (ART) and analytical treatment interruption. We determined the concentration of IFNα2 and IFNβ that reduced viral replication in vitro by 50% (IC50) and found consistent changes in the sensitivity of HIV-1 to IFN-I inhibition both across individuals and over time. Resistance of HIV-1 isolates to IFN-I was uniformly high during acute infection, decreased in all individuals in the first year after infection, was reacquired concomitant with CD4+ T cell loss, and remained elevated in individuals with accelerated disease. HIV-1 isolates obtained by viral outgrowth during suppressive ART were relatively IFN-I sensitive, resembling viruses circulating just before ART initiation. However, viruses that rebounded after treatment interruption displayed the highest degree of IFNα2 and IFNβ resistance observed at any time during the infection course. These findings indicate a dynamic interplay between host innate responses and the evolving HIV-1 quasispecies, with the relative contribution of IFN-I to HIV-1 control affected by both ART and analytical treatment interruption. Although elevated at transmission, host innate pressures are the highest during viral rebound, limiting the viruses that successfully become reactivated from latency to those that are IFN-I resistant.
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Affiliation(s)
- Marcos V P Gondim
- Department of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Scott Sherrill-Mix
- Department of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
- Department of Microbiology, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Frederic Bibollet-Ruche
- Department of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
- Department of Microbiology, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Ronnie M Russell
- Department of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
- Department of Microbiology, University of Pennsylvania, Philadelphia, PA 19104, USA
| | | | | | - Yingying Li
- Department of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Weimin Liu
- Department of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Alexa N Avitto
- Gene Therapy Program, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Julia C DeVoto
- Department of Pathology and Laboratory Medicine, Tulane University School of Medicine, New Orleans, LA 70112, USA
| | - Jesse Connell
- Department of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
- Department of Microbiology, University of Pennsylvania, Philadelphia, PA 19104, USA
| | | | - Pierre Pellegrino
- Centre for Clinical Research in Infection and Sexual Health, Institute for Global Health, University College London, London WC1E 6JB, UK
| | - Ian Williams
- Centre for Clinical Research in Infection and Sexual Health, Institute for Global Health, University College London, London WC1E 6JB, UK
| | | | - Julio C C Lorenzi
- Laboratory of Molecular Immunology, Rockefeller University, New York, NY 10065, USA
| | | | - Felicity Mampe
- Department of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - M Alexandra Monroy
- Department of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | | | - Sonya Heath
- Department of Medicine, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Michael S Saag
- Department of Medicine, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Luis J Montaner
- Vaccine and Immunotherapy Center, Wistar Institute, Philadelphia, PA 19104, USA
| | - Ronald G Collman
- Department of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
- Department of Microbiology, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Janet M Siliciano
- Department of Medicine, Johns Hopkins University, Baltimore, MD 21205, USA
| | - Robert F Siliciano
- Department of Medicine, Johns Hopkins University, Baltimore, MD 21205, USA
- Howard Hughes Medical Institute, Johns Hopkins University, Baltimore, MD 21205, USA
| | - Lindsey J Plenderleith
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh EH9 3FL, UK
- Centre for Immunity, Infection and Evolution, University of Edinburgh, Edinburgh EH9 3FL, UK
| | - Paul M Sharp
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh EH9 3FL, UK
- Centre for Immunity, Infection and Evolution, University of Edinburgh, Edinburgh EH9 3FL, UK
| | - Marina Caskey
- Laboratory of Molecular Immunology, Rockefeller University, New York, NY 10065, USA
| | - Michel C Nussenzweig
- Laboratory of Molecular Immunology, Rockefeller University, New York, NY 10065, USA
- Howard Hughes Medical Institute, Rockefeller University, New York, NY 10065, USA
| | - George M Shaw
- Department of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
- Department of Microbiology, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Persephone Borrow
- Nuffield Department of Clinical Medicine, University of Oxford, Oxford OX3 7FZ, UK
| | - Katharine J Bar
- Department of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
- Department of Microbiology, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Beatrice H Hahn
- Department of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.
- Department of Microbiology, University of Pennsylvania, Philadelphia, PA 19104, USA
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29
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Yukl SA, Khan S, Chen TH, Trapecar M, Wu F, Xie G, Telwatte S, Fulop D, Pico AR, Laird GM, Ritter KD, Jones NG, Lu CM, Siliciano RF, Roan NR, Milush JM, Somsouk M, Deeks SG, Hunt PW, Sanjabi S. Shared Mechanisms Govern HIV Transcriptional Suppression in Circulating CD103 + and Gut CD4 + T Cells. J Virol 2020; 95:e01331-20. [PMID: 33115867 PMCID: PMC7944458 DOI: 10.1128/jvi.01331-20] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2020] [Accepted: 10/23/2020] [Indexed: 12/22/2022] Open
Abstract
Latent HIV infection is the main barrier to cure, and most HIV-infected cells reside in the gut, where distinct but unknown mechanisms may promote viral latency. Transforming growth factor β (TGF-β), which induces the expression of CD103 on tissue-resident memory T cells, has been implicated in HIV latency. Using CD103 as a surrogate marker to identify cells that have undergone TGF-β signaling, we compared the HIV RNA/DNA contents and cellular transcriptomes of CD103+ and CD103- CD4 T cells from the blood and rectum of HIV-negative (HIV-) and antiretroviral therapy (ART)-suppressed HIV-positive (HIV+) individuals. Like gut CD4+ T cells, circulating CD103+ cells harbored more HIV DNA than did CD103- cells but transcribed less HIV RNA per provirus. Circulating CD103+ cells also shared a gene expression profile that is closer to that of gut CD4 T cells than to that of circulating CD103- cells, with significantly lower expression levels of ribosomal proteins and transcriptional and translational pathways associated with HIV expression but higher expression levels of a subset of genes implicated in suppressing HIV transcription. These findings suggest that blood CD103+ CD4 T cells can serve as a model to study the molecular mechanisms of HIV latency in the gut and reveal new cellular factors that may contribute to HIV latency.IMPORTANCE The ability of HIV to establish a reversibly silent, "latent" infection is widely regarded as the main barrier to curing HIV. Most HIV-infected cells reside in tissues such as the gut, but it is unclear what mechanisms maintain HIV latency in the blood or gut. We found that circulating CD103+ CD4+ T cells are enriched for HIV-infected cells in a latent-like state. Using RNA sequencing (RNA-seq), we found that CD103+ T cells share a cellular transcriptome that more closely resembles that of CD4+ T cells from the gut, suggesting that they are homing to or from the gut. We also identified the cellular genes whose expression distinguishes gut CD4+ or circulating CD103+ T cells from circulating CD103- T cells, including some genes that have been implicated in HIV expression. These genes may contribute to latent HIV infection in the gut and may serve as new targets for therapies aimed at curing HIV.
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Affiliation(s)
- Steven A Yukl
- San Francisco Veterans Affairs Medical Center, San Francisco, California, USA
- Department of Medicine, University of California, San Francisco, School of Medicine, San Francisco, California, USA
| | - Shahzada Khan
- Gladstone Institutes, San Francisco, California, USA
| | - Tsui-Hua Chen
- San Francisco Veterans Affairs Medical Center, San Francisco, California, USA
- University of California, San Francisco, San Francisco, California, USA
| | | | - Frank Wu
- Gladstone Institutes, San Francisco, California, USA
| | - Guorui Xie
- Gladstone Institutes, San Francisco, California, USA
- Department of Urology, University of California, San Francisco, San Francisco, California, USA
| | - Sushama Telwatte
- San Francisco Veterans Affairs Medical Center, San Francisco, California, USA
- Department of Medicine, University of California, San Francisco, School of Medicine, San Francisco, California, USA
| | - Daniel Fulop
- Gladstone Institutes, San Francisco, California, USA
| | | | | | | | - Norman G Jones
- Department of Medicine, University of California, San Francisco, School of Medicine, San Francisco, California, USA
| | - Chuanyi M Lu
- San Francisco Veterans Affairs Medical Center, San Francisco, California, USA
- University of California, San Francisco, San Francisco, California, USA
| | - Robert F Siliciano
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
- Howard Hughes Medical Institute, Baltimore, Maryland, USA
| | - Nadia R Roan
- Gladstone Institutes, San Francisco, California, USA
- Department of Urology, University of California, San Francisco, San Francisco, California, USA
| | - Jeffrey M Milush
- Department of Medicine, University of California, San Francisco, School of Medicine, San Francisco, California, USA
| | - Ma Somsouk
- Division of Gastroenterology, University of California, San Francisco, San Francisco, California, USA
| | - Steven G Deeks
- Department of Medicine, University of California, San Francisco, School of Medicine, San Francisco, California, USA
| | - Peter W Hunt
- Department of Medicine, University of California, San Francisco, School of Medicine, San Francisco, California, USA
| | - Shomyseh Sanjabi
- Gladstone Institutes, San Francisco, California, USA
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, California, USA
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30
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Song N, Sengupta S, Khoruzhenko S, Welsh RA, Kim A, Kumar MR, Sønder SU, Sidhom JW, Zhang H, Jie C, Siliciano RF, Sadegh-Nasseri S. Multiple genetic programs contribute to CD4 T cell memory differentiation and longevity by maintaining T cell quiescence. Cell Immunol 2020; 357:104210. [PMID: 32987276 PMCID: PMC7737224 DOI: 10.1016/j.cellimm.2020.104210] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2020] [Revised: 08/14/2020] [Accepted: 08/28/2020] [Indexed: 01/12/2023]
Abstract
While memory T-cells represent a hallmark of adaptive immunity, little is known about the genetic mechanisms regulating the longevity of memory CD4 T cells. Here, we studied the dynamics of gene expression in antigen specific CD4 T cells during infection, memory differentiation, and long-term survival up to nearly a year in mice. We observed that differentiation into long lived memory cells is associated with increased expression of genes inhibiting cell proliferation and apoptosis as well as genes promoting DNA repair response, lipid metabolism, and insulin resistance. We identified several transmembrane proteins in long-lived murine memory CD4 T cells, which co-localized exclusively within the responding antigen-specific memory CD4 T cells in human. The unique gene signatures of long-lived memory CD4 T cells, along with the new markers that we have defined, will enable a deeper understanding of memory CD4 T cell biology and allow for designing novel vaccines and therapeutics.
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Affiliation(s)
- Nianbin Song
- Department of Pathology, Johns Hopkins University, United States
| | - Srona Sengupta
- The Graduate Program in Immunology, USA; Medical Scientist Training Program, USA
| | - Stanislav Khoruzhenko
- MaxCyte, Inc., Gaithersburg, MD 20878, USA; Department of Pathology, Johns Hopkins University, United States
| | | | - AeRyon Kim
- The Graduate Program in Immunology, USA; Amgen, South San Francisco, CA, USA; Department of Pathology, Johns Hopkins University, United States
| | - Mithra R Kumar
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Søren Ulrik Sønder
- Amerimmune LLC, Fairfax, VA 22030, USA; Department of Pathology, Johns Hopkins University, United States
| | - John-William Sidhom
- Medical Scientist Training Program, USA; Department of Biomedical Engineering, and Bloomberg Kimmel Institute for Cancer Immunotherapy, Sidney Kimmel Comprehensive Cancer Center, USA
| | - Hao Zhang
- Department of Molecular Microbiology and Immunology, Johns Hopkins University School of Public Health, Baltimore, MD 21205, USA
| | - Chunfa Jie
- Des Moines University, Des Moines, IA 50312, USA
| | - Robert F Siliciano
- Howard Hughes Medical Institute, Baltimore, MD, USA; Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
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31
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Durand CM, Capoferri AA, Redd AD, Zahurak M, Rosenbloom DIS, Cash A, Avery RK, Bolaños-Meade J, Bollard CM, Bullen CK, Flexner C, Fuchs EJ, Gallant J, Gladstone DE, Gocke CD, Jones RJ, Kasamon YL, Lai J, Levis M, Luznik L, Marr KA, McHugh HL, Mehta Steinke S, Pham P, Pohlmeyer C, Pratz K, Shoham S, Wagner-Johnston N, Xu D, Siliciano JD, Quinn TC, Siliciano RF, Ambinder RF. Allogeneic bone marrow transplantation with post-transplant cyclophosphamide for patients with HIV and haematological malignancies: a feasibility study. Lancet HIV 2020; 7:e602-e610. [PMID: 32649866 PMCID: PMC7484204 DOI: 10.1016/s2352-3018(20)30073-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2019] [Revised: 02/21/2020] [Accepted: 02/27/2020] [Indexed: 06/11/2023]
Abstract
BACKGROUND Allogeneic blood or marrow transplantation (alloBMT) is a potentially life-saving treatment for individuals with HIV and haematological malignancies; challenges include identifying donors and maintaining antiretroviral therapy (ART). The objectives of our study were to investigate interventions to expand donor options and to prevent ART interruptions for patients with HIV in need of alloBMT. METHODS This single-arm, interventional trial took place at the Johns Hopkins Sidney Kimmel Comprehensive Cancer Center (Baltimore, MD, USA). Individuals with HIV who were at least 18 years of age and referred for alloBMT for a standard clinical indication were eligible. The only exclusion criterion was a history of documented resistance to enfuvirtide. We used post-transplant cyclophosphamide as graft-versus-host disease (GVHD) prophylaxis to expand donor options and an optimised ART strategy of avoiding pharmacoenhancers and adding subcutaneous enfuvirtide during post-transplant cyclophosphamide and during oral medication intolerance. Our primary outcome was the proportion of participants who maintained ART through day 60 after alloBMT. We measured the HIV latent reservoir using a quantitative viral outgrowth assay. This study is registered on ClinicalTrials.gov, NCT01836068. FINDINGS Between June 1, 2013, and August 27, 2015, nine patients who were referred for transplant provided consent. Two patients had relapsed malignancy before donor searches were initiated. Seven patients had suitable donors identified (two matched sibling, two matched unrelated, two haploidentical, and one single-antigen mismatched unrelated) and proceeded to alloBMT. All patients maintained ART through day 60 and required ART changes (median 1, range 1-3) in the first 90 days. One patient stopped ART and developed HIV rebound with grade 4 meningoencephalitis at day 146. Among six patients who underwent alloBMT and had longitudinal measurements available, the HIV latent reservoir was not detected post-alloBMT in four patients with more than 95% donor chimerism, consistent with a 2·06-2·54 log10 reduction in the HIV latent reservoir. In the two patients with less than 95% donor chimerism, the HIV latent reservoir remained stable. INTERPRETATION By using post-transplant cyclophosphamide as GVHD prophylaxis, we successfully expanded alloBMT donor options for patients with HIV. Continuing ART with a regimen that includes enfuvirtide post-alloBMT was safe, but life-threatening viral rebound can occur with ART interruption. FUNDING amfAR (the Foundation for AIDS Research), Johns Hopkins University Center for AIDS Research, and National Cancer Institute.
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Affiliation(s)
- Christine M Durand
- Johns Hopkins University School of Medicine, Baltimore, MD, USA; Sidney Kimmel Cancer Center, Baltimore, MD, USA.
| | | | - Andrew D Redd
- Johns Hopkins University School of Medicine, Baltimore, MD, USA; Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | | | - Daniel I S Rosenbloom
- Department of Pharmacokinetics, Pharmacodynamics and Drug Metabolism, Merck & Co, Kenilworth, NJ, USA
| | - Ayla Cash
- Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Robin K Avery
- Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Javier Bolaños-Meade
- Johns Hopkins University School of Medicine, Baltimore, MD, USA; Sidney Kimmel Cancer Center, Baltimore, MD, USA
| | - Catherine M Bollard
- Sidney Kimmel Cancer Center, Baltimore, MD, USA; Program for Cell Enhancement and Technologies for Immunotherapy Children's National Health System, George Washington University Washington, DC, USA
| | - C Korin Bullen
- Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Charles Flexner
- Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | | | - Joel Gallant
- Johns Hopkins University School of Medicine, Baltimore, MD, USA; Gilead Sciences, Foster City, CA, USA
| | | | | | | | | | - Jun Lai
- Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Mark Levis
- Sidney Kimmel Cancer Center, Baltimore, MD, USA
| | - Leo Luznik
- Sidney Kimmel Cancer Center, Baltimore, MD, USA
| | - Kieren A Marr
- Johns Hopkins University School of Medicine, Baltimore, MD, USA; Sidney Kimmel Cancer Center, Baltimore, MD, USA
| | - Holly L McHugh
- Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | | | - Paul Pham
- Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | | | - Keith Pratz
- Sidney Kimmel Cancer Center, Baltimore, MD, USA
| | - Shmuel Shoham
- Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | | | - Daniel Xu
- Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | | | - Thomas C Quinn
- Johns Hopkins University School of Medicine, Baltimore, MD, USA; Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Robert F Siliciano
- Johns Hopkins University School of Medicine, Baltimore, MD, USA; Howard Hughes Medical Institute, Baltimore, MD, USA
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Abdel-Mohsen M, Richman D, Siliciano RF, Nussenzweig MC, Howell BJ, Martinez-Picado J, Chomont N, Bar KJ, Yu XG, Lichterfeld M, Alcami J, Hazuda D, Bushman F, Siliciano JD, Betts MR, Spivak AM, Planelles V, Hahn BH, Smith DM, Ho YC, Buzon MJ, Gaebler C, Paiardini M, Li Q, Estes JD, Hope TJ, Kostman J, Mounzer K, Caskey M, Fox L, Frank I, Riley JL, Tebas P, Montaner LJ. Recommendations for measuring HIV reservoir size in cure-directed clinical trials. Nat Med 2020; 26:1339-1350. [PMID: 32895573 PMCID: PMC7703694 DOI: 10.1038/s41591-020-1022-1] [Citation(s) in RCA: 75] [Impact Index Per Article: 18.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2020] [Accepted: 07/16/2020] [Indexed: 12/28/2022]
Abstract
Therapeutic strategies are being clinically tested either to eradicate latent HIV reservoirs or to achieve virologic control in the absence of antiretroviral therapy. Attaining this goal will require a consensus on how best to measure the numbers of persistently infected cells with the potential to cause viral rebound after antiretroviral-therapy cessation in assessing the results of cure-directed strategies in vivo. Current measurements assess various aspects of the HIV provirus and its functionality and produce divergent results. Here, we provide recommendations from the BEAT-HIV Martin Delaney Collaboratory on which viral measurements should be prioritized in HIV-cure-directed clinical trials.
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Affiliation(s)
| | - Douglas Richman
- VA San Diego Healthcare System and University of California, San Diego, CA, USA
| | | | | | | | - Javier Martinez-Picado
- IrsiCaixa AIDS Research Institute, Badalona, Spain
- University of Vic-Central University of Catalonia (UVic-UCC), Vic, Spain
- Catalan Institution for Research and Advanced Studies (ICREA), Barcelona, Spain
| | | | | | - Xu G Yu
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, USA
- Brigham and Women's Hospital, Boston, MA, USA
| | - Mathias Lichterfeld
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, USA
- Brigham and Women's Hospital, Boston, MA, USA
| | - Jose Alcami
- AIDS Immunopathogenesis Unit, Instituto de Salud Carlos III, Madrid and Infectious Diseases Unit, IBIDAPS, Hospital Clinic, University of Barcelona, Barcelona, Spain
| | | | | | | | | | | | | | | | - Davey M Smith
- VA San Diego Healthcare System and University of California, San Diego, CA, USA
| | - Ya-Chi Ho
- Yale School of Medicine, New Haven, CT, USA
| | - Maria J Buzon
- AIDS Immunopathogenesis Unit, Instituto de Salud Carlos III, Madrid and Infectious Diseases Unit, IBIDAPS, Hospital Clinic, University of Barcelona, Barcelona, Spain
| | | | - Mirko Paiardini
- Division of Microbiology and Immunology, Yerkes National Primate Research Center, and Emory University, Atlanta, GA, USA
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, GA, USA
| | - Qingsheng Li
- School of Biological Sciences and Nebraska Center for Virology, University of Nebraska-Lincoln, Lincoln, NE, USA
| | - Jacob D Estes
- Vaccine and Gene Therapy Institute and Oregon National Primate Research Center (ONPRC), Oregon Health and Science University (OHSU), Beaverton, OR, USA
| | | | - Jay Kostman
- Jonathan Lax Center, Philadelphia FIGHT, Philadelphia, PA, USA
| | - Karam Mounzer
- Jonathan Lax Center, Philadelphia FIGHT, Philadelphia, PA, USA
| | | | - Lawrence Fox
- Division of AIDS, NIAID, NIH, North Bethesda, MD, USA
| | - Ian Frank
- University of Pennsylvania, Philadelphia, PA, USA
| | | | - Pablo Tebas
- University of Pennsylvania, Philadelphia, PA, USA
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33
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Jiang C, Lian X, Gao C, Sun X, Einkauf KB, Chevalier JM, Chen SMY, Hua S, Rhee B, Chang K, Blackmer JE, Osborn M, Peluso MJ, Hoh R, Somsouk M, Milush J, Bertagnolli LN, Sweet SE, Varriale JA, Burbelo PD, Chun TW, Laird GM, Serrao E, Engelman AN, Carrington M, Siliciano RF, Siliciano JM, Deeks SG, Walker BD, Lichterfeld M, Yu XG. Distinct viral reservoirs in individuals with spontaneous control of HIV-1. Nature 2020; 585:261-267. [PMID: 32848246 PMCID: PMC7837306 DOI: 10.1038/s41586-020-2651-8] [Citation(s) in RCA: 211] [Impact Index Per Article: 52.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2019] [Accepted: 07/15/2020] [Indexed: 02/01/2023]
Abstract
Sustained, drug-free control of HIV-1 replication is naturally achieved in less than 0.5% of infected individuals (here termed 'elite controllers'), despite the presence of a replication-competent viral reservoir1. Inducing such an ability to spontaneously maintain undetectable plasma viraemia is a major objective of HIV-1 cure research, but the characteristics of proviral reservoirs in elite controllers remain to be determined. Here, using next-generation sequencing of near-full-length single HIV-1 genomes and corresponding chromosomal integration sites, we show that the proviral reservoirs of elite controllers frequently consist of oligoclonal to near-monoclonal clusters of intact proviral sequences. In contrast to individuals treated with long-term antiretroviral therapy, intact proviral sequences from elite controllers were integrated at highly distinct sites in the human genome and were preferentially located in centromeric satellite DNA or in Krüppel-associated box domain-containing zinc finger genes on chromosome 19, both of which are associated with heterochromatin features. Moreover, the integration sites of intact proviral sequences from elite controllers showed an increased distance to transcriptional start sites and accessible chromatin of the host genome and were enriched in repressive chromatin marks. These data suggest that a distinct configuration of the proviral reservoir represents a structural correlate of natural viral control, and that the quality, rather than the quantity, of viral reservoirs can be an important distinguishing feature for a functional cure of HIV-1 infection. Moreover, in one elite controller, we were unable to detect intact proviral sequences despite analysing more than 1.5 billion peripheral blood mononuclear cells, which raises the possibility that a sterilizing cure of HIV-1 infection, which has previously been observed only following allogeneic haematopoietic stem cell transplantation2,3, may be feasible in rare instances.
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Affiliation(s)
- Chenyang Jiang
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, USA
- Infectious Disease Division, Brigham and Women's Hospital, Boston, MA, USA
| | - Xiaodong Lian
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, USA
- Infectious Disease Division, Brigham and Women's Hospital, Boston, MA, USA
| | - Ce Gao
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, USA
| | - Xiaoming Sun
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, USA
| | - Kevin B Einkauf
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, USA
- Infectious Disease Division, Brigham and Women's Hospital, Boston, MA, USA
| | - Joshua M Chevalier
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, USA
- Infectious Disease Division, Brigham and Women's Hospital, Boston, MA, USA
| | | | - Stephane Hua
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, USA
| | - Ben Rhee
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, USA
- Infectious Disease Division, Brigham and Women's Hospital, Boston, MA, USA
| | - Kaylee Chang
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, USA
| | | | - Matthew Osborn
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, USA
| | - Michael J Peluso
- Department of Medicine, University of California at San Francisco, San Francisco, CA, USA
| | - Rebecca Hoh
- Department of Medicine, University of California at San Francisco, San Francisco, CA, USA
| | - Ma Somsouk
- Department of Medicine, University of California at San Francisco, San Francisco, CA, USA
| | - Jeffrey Milush
- Department of Medicine, University of California at San Francisco, San Francisco, CA, USA
| | - Lynn N Bertagnolli
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Sarah E Sweet
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Joseph A Varriale
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Peter D Burbelo
- Dental Clinical Research Core, National Institute of Dental and Craniofacial Research, National Institutes of Health, Bethesda, MD, USA
| | - Tae-Wook Chun
- National Institute of Allergies and Infectious Diseases, Bethesda, MD, USA
| | | | - Erik Serrao
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Alan N Engelman
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Mary Carrington
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, USA
- Basic Science Program, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Robert F Siliciano
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | - Janet M Siliciano
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | - Steven G Deeks
- Department of Medicine, University of California at San Francisco, San Francisco, CA, USA
| | - Bruce D Walker
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
- Institute for Medical Engineering and Sciences, Massachusetts Institute of Technology, Cambridge, MA, USA
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Mathias Lichterfeld
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, USA
- Infectious Disease Division, Brigham and Women's Hospital, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Xu G Yu
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, USA.
- Infectious Disease Division, Brigham and Women's Hospital, Boston, MA, USA.
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Simonetti FR, White JA, Tumiotto C, Ritter KD, Cai M, Gandhi RT, Deeks SG, Howell BJ, Montaner LJ, Blankson JN, Martin A, Laird GM, Siliciano RF, Mellors JW, Siliciano JD. Intact proviral DNA assay analysis of large cohorts of people with HIV provides a benchmark for the frequency and composition of persistent proviral DNA. Proc Natl Acad Sci U S A 2020; 117:18692-18700. [PMID: 32690683 PMCID: PMC7414172 DOI: 10.1073/pnas.2006816117] [Citation(s) in RCA: 59] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
A scalable approach for quantifying intact HIV-1 proviruses is critical for basic research and clinical trials directed at HIV-1 cure. The intact proviral DNA assay (IPDA) is a novel approach to characterizing the HIV-1 reservoir, focusing on the genetic integrity of individual proviruses independent of transcriptional status. It uses multiplex digital droplet PCR to distinguish and separately quantify intact proviruses, defined by a lack of overt fatal defects such as large deletions and APOBEC3G-mediated hypermutation, from the majority of proviruses that have such defects. This distinction is important because only intact proviruses cause viral rebound on ART interruption. To evaluate IPDA performance and provide benchmark data to support its implementation, we analyzed peripheral blood samples from 400 HIV-1+ adults on ART from several diverse cohorts, representing a robust sample of treated HIV-1 infection in the United States. We provide direct quantitative evidence that defective proviruses greatly outnumber intact proviruses (by >12.5 fold). However, intact proviruses are present at substantially higher frequencies (median, 54/106 CD4+ T cells) than proviruses detected by the quantitative viral outgrowth assay, which requires induction and in vitro growth (∼1/106 CD4+ T cells). IPDA amplicon signal issues resulting from sequence polymorphisms were observed in only 6.3% of individuals and were readily apparent and easily distinguished from low proviral frequency, an advantage of the IPDA over standard PCR assays which generate false-negative results in such situations. The large IPDA dataset provided here gives the clearest quantitative picture to date of HIV-1 proviral persistence on ART.
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Affiliation(s)
- Francesco R Simonetti
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205
| | - Jennifer A White
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205
| | - Camille Tumiotto
- Division of Infectious Diseases, University of Pittsburgh, Pittsburgh, PA 15260
| | | | - Mian Cai
- AccelevirDx, Baltimore, MD 21205
| | - Rajesh T Gandhi
- Division of Infectious Diseases, Massachusetts General Hospital, Boston, MA 02114
| | - Steven G Deeks
- Division of HIV, Infectious Diseases, and Global Medicine, University of California, San Francisco, CA 94118
| | | | | | - Joel N Blankson
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205
| | | | | | - Robert F Siliciano
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205;
- HHMI, Baltimore, MD 21205
| | - John W Mellors
- Division of Infectious Diseases, University of Pittsburgh, Pittsburgh, PA 15260
| | - Janet D Siliciano
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205
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35
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Antar AA, Jenike KM, Jang S, Rigau DN, Reeves DB, Hoh R, Krone MR, Keruly JC, Moore RD, Schiffer JT, Nonyane BA, Hecht FM, Deeks SG, Siliciano JD, Ho YC, Siliciano RF. Longitudinal study reveals HIV-1-infected CD4+ T cell dynamics during long-term antiretroviral therapy. J Clin Invest 2020; 130:3543-3559. [PMID: 32191639 PMCID: PMC7324206 DOI: 10.1172/jci135953] [Citation(s) in RCA: 61] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2019] [Accepted: 03/17/2020] [Indexed: 12/11/2022] Open
Abstract
Proliferation of CD4+ T cells harboring HIV-1 proviruses is a major contributor to viral persistence in people on antiretroviral therapy (ART). To determine whether differential rates of clonal proliferation or HIV-1-specific cytotoxic T lymphocyte (CTL) pressure shape the provirus landscape, we performed an intact proviral DNA assay (IPDA) and obtained 661 near-full-length provirus sequences from 8 individuals with suppressed viral loads on ART at time points 7 years apart. We observed slow decay of intact proviruses but no changes in the proportions of various types of defective proviruses. The proportion of intact proviruses in expanded clones was similar to that of defective proviruses in clones. Intact proviruses observed in clones did not have more escaped CTL epitopes than intact proviruses observed as singlets. Concordantly, total proviruses at later time points or observed in clones were not enriched in escaped or unrecognized epitopes. Three individuals with natural control of HIV-1 infection (controllers) on ART, included because controllers have strong HIV-1-specific CTL responses, had a smaller proportion of intact proviruses but a distribution of defective provirus types and escaped or unrecognized epitopes similar to that of the other individuals. This work suggests that CTL selection does not significantly check clonal proliferation of infected cells or greatly alter the provirus landscape in people on ART.
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Affiliation(s)
- Annukka A.R. Antar
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Katharine M. Jenike
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Sunyoung Jang
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Danielle N. Rigau
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Daniel B. Reeves
- Vaccine and Infectious Diseases Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | | | - Melissa R. Krone
- Department of Epidemiology and Biostatistics, UCSF, San Francisco, California, USA
| | - Jeanne C. Keruly
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Richard D. Moore
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Joshua T. Schiffer
- Vaccine and Infectious Diseases Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
- Department of Medicine, University of Washington, Seattle, Washington, USA
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - Bareng A.S. Nonyane
- Department of International Health, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA
| | | | | | - Janet D. Siliciano
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Ya-Chi Ho
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Robert F. Siliciano
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
- Howard Hughes Medical Institute, Baltimore, Maryland, USA
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Peluso MJ, Bacchetti P, Ritter KD, Beg S, Lai J, Martin JN, Hunt PW, Henrich TJ, Siliciano JD, Siliciano RF, Laird GM, Deeks SG. Differential decay of intact and defective proviral DNA in HIV-1-infected individuals on suppressive antiretroviral therapy. JCI Insight 2020; 5:132997. [PMID: 32045386 PMCID: PMC7101154 DOI: 10.1172/jci.insight.132997] [Citation(s) in RCA: 122] [Impact Index Per Article: 30.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2019] [Accepted: 01/29/2020] [Indexed: 12/24/2022] Open
Abstract
BACKGROUNDThe relative stabilities of the intact and defective HIV genomes over time during effective antiretroviral therapy (ART) have not been fully characterized.METHODSWe used the intact proviral DNA assay (IPDA) to estimate the rate of change of intact and defective proviruses in HIV-infected adults on ART. We used linear spline models with a knot at seven years and a random intercept and slope up to the knot. We estimated the influence of covariates on rates of change.RESULTSWe studied 81 individuals for a median of 7.3 (IQR 5.9-9.6) years. Intact genomes declined more rapidly from initial suppression through seven years (15.7% per year decline; 95% CI -22.8%, -8.0%) and more slowly after seven years (3.6% per year; 95% CI -8.1%, +1.1%). The estimated half-life of the reservoir was 4.0 years (95% CI 2.7-8.3) until year seven and 18.7 years (95% CI 8.2-infinite) thereafter. There was substantial variability between individuals in the rate of decline until year seven. Intact provirus declined more rapidly than defective provirus (P < 0.001) and showed a faster decline in individuals with higher CD4+ T cell nadirs.CONCLUSIONThe biology of the replication-competent (intact) reservoir differs from that of the replication-incompetent (non-intact) pool of proviruses. The IPDA will likely be informative when investigating the impact of interventions targeting the reservoir.FUNDINGDelaney AIDS Research Enterprise, UCSF/Gladstone Institute of Virology & Immunology CFAR, CFAR Network of Integrated Systems, amfAR Institute for HIV Cure Research, I4C and Beat-HIV Collaboratories, Howard Hughes Medical Institute, Gilead Sciences, Bill and Melinda Gates Foundation.
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Affiliation(s)
- Michael J. Peluso
- Division of HIV, Infectious Diseases, and Global Medicine, Department of Medicine, and
| | - Peter Bacchetti
- Department of Epidemiology and Biostatistics, UCSF, San Francisco, California, USA
| | | | - Subul Beg
- Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Jun Lai
- Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Jeffrey N. Martin
- Department of Epidemiology and Biostatistics, UCSF, San Francisco, California, USA
| | - Peter W. Hunt
- Division of Experimental Medicine, Department of Medicine, UCSF, San Francisco, California, USA
| | - Timothy J. Henrich
- Division of Experimental Medicine, Department of Medicine, UCSF, San Francisco, California, USA
| | | | - Robert F. Siliciano
- Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
- Howard Hughes Medical Institute, Chevy Chase, Maryland, USA
| | | | - Steven G. Deeks
- Division of HIV, Infectious Diseases, and Global Medicine, Department of Medicine, and
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37
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Kwon KJ, Timmons AE, Sengupta S, Simonetti FR, Zhang H, Hoh R, Deeks SG, Siliciano JD, Siliciano RF. Different human resting memory CD4 + T cell subsets show similar low inducibility of latent HIV-1 proviruses. Sci Transl Med 2020; 12:eaax6795. [PMID: 31996465 PMCID: PMC7875249 DOI: 10.1126/scitranslmed.aax6795] [Citation(s) in RCA: 67] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2019] [Revised: 07/10/2019] [Accepted: 10/03/2019] [Indexed: 12/15/2022]
Abstract
The latent reservoir of HIV-1 in resting CD4+ T cells is a major barrier to cure. It is unclear whether the latent reservoir resides principally in particular subsets of CD4+ T cells, a finding that would have implications for understanding its stability and developing curative therapies. Recent work has shown that proliferation of HIV-1-infected CD4+ T cells is a major factor in the generation and persistence of the latent reservoir and that latently infected T cells that have clonally expanded in vivo can proliferate in vitro without producing virions. In certain CD4+ memory T cell subsets, the provirus may be in a deeper state of latency, allowing the cell to proliferate without producing viral proteins, thus permitting escape from immune clearance. To evaluate this possibility, we used a multiple stimulation viral outgrowth assay to culture resting naïve, central memory (TCM), transitional memory (TTM), and effector memory (TEM) CD4+ T cells from 10 HIV-1-infected individuals on antiretroviral therapy. On average, only 1.7% of intact proviruses across all T cell subsets were induced to transcribe viral genes and release replication-competent virus after stimulation of the cells. We found no consistent enrichment of intact or inducible proviruses in any T cell subset. Furthermore, we observed notable plasticity among the canonical memory T cell subsets after activation in vitro and saw substantial person-to-person variability in the inducibility of infectious virus release. This finding complicates the vision for a targeted approach for HIV-1 cure based on T cell memory subsets.
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Affiliation(s)
- Kyungyoon J Kwon
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Andrew E Timmons
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Srona Sengupta
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Francesco R Simonetti
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Hao Zhang
- Flow Cytometry and Immunology Core, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - Rebecca Hoh
- Department of Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Steven G Deeks
- Department of Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Janet D Siliciano
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Robert F Siliciano
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
- Howard Hughes Medical Institute, Baltimore, MD, USA
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38
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Bender AM, Simonetti FR, Kumar MR, Fray EJ, Bruner KM, Timmons AE, Tai KY, Jenike KM, Antar AAR, Liu PT, Ho YC, Raugi DN, Seydi M, Gottlieb GS, Okoye AA, Del Prete GQ, Picker LJ, Mankowski JL, Lifson JD, Siliciano JD, Laird GM, Barouch DH, Clements JE, Siliciano RF. The Landscape of Persistent Viral Genomes in ART-Treated SIV, SHIV, and HIV-2 Infections. Cell Host Microbe 2019; 26:73-85.e4. [PMID: 31295427 DOI: 10.1016/j.chom.2019.06.005] [Citation(s) in RCA: 57] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2019] [Revised: 04/21/2019] [Accepted: 05/31/2019] [Indexed: 12/27/2022]
Abstract
Evaluation of HIV cure strategies is complicated by defective proviruses that persist in ART-treated patients but are irrelevant to cure. Non-human primates (NHP) are essential for testing cure strategies. However, the persisting proviral landscape in ART-treated NHPs is uncharacterized. Here, we describe viral genomes persisting in ART-treated, simian immunodeficiency virus (SIV)-infected NHPs, simian-human immunodeficiency virus (SHIV)-infected NHPs, and humans infected with HIV-2, an SIV-related virus. The landscapes of persisting SIV, SHIV, and HIV-2 genomes are also dominated by defective sequences. However, there was a significantly higher fraction of intact SIV proviral genomes compared to ART-treated HIV-1 or HIV-2 infected humans. Compared to humans with HIV-1, SIV-infected NHPs had more hypermutated genomes, a relative paucity of clonal SIV sequences, and a lower frequency of deleted genomes. Finally, we report an assay for measuring intact SIV genomes which may have value in cure research.
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Affiliation(s)
- Alexandra M Bender
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Francesco R Simonetti
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Mithra R Kumar
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Emily J Fray
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Katherine M Bruner
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Andrew E Timmons
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Katherine Y Tai
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Katharine M Jenike
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Annukka A R Antar
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Po-Ting Liu
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA
| | - Ya-Chi Ho
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Dana N Raugi
- Department of Medicine & Center of Emerging & Re-Emerging Infectious Diseases, University of Washington, Seattle, WA, USA
| | - Moussa Seydi
- Service de Maladies Infectieuses et Tropicales, CHNU-Fann, Dakar, Senegal
| | - Geoffrey S Gottlieb
- Department of Medicine & Center of Emerging & Re-Emerging Infectious Diseases, University of Washington, Seattle, WA, USA
| | - Afam A Okoye
- Vaccine and Gene Therapy Institute, Oregon Health and Sciences University, Beaverton, OR, USA
| | - Gregory Q Del Prete
- AIDS and Cancer Virus Program, Frederick National Laboratory, Frederick, MD, USA
| | - Louis J Picker
- Vaccine and Gene Therapy Institute, Oregon Health and Sciences University, Beaverton, OR, USA
| | - Joseph L Mankowski
- Department of Molecular and Comparative Pathobiology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Jeffrey D Lifson
- AIDS and Cancer Virus Program, Frederick National Laboratory, Frederick, MD, USA
| | - Janet D Siliciano
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Greg M Laird
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Accelevir Diagnostics, Baltimore, MD, USA
| | - Dan H Barouch
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA
| | - Janice E Clements
- Department of Molecular and Comparative Pathobiology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Robert F Siliciano
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Howard Hughes Medical Institute, Baltimore, MD 21205, USA.
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39
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Silverman K, Holtyn AF, Rodewald AM, Siliciano RF, Jarvis BP, Subramaniam S, Leoutsakos JM, Getty CA, Ruhs S, Marzinke MA, Fingerhood M. Incentives for Viral Suppression in People Living with HIV: A Randomized Clinical Trial. AIDS Behav 2019; 23:2337-2346. [PMID: 31297681 DOI: 10.1007/s10461-019-02592-8] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
The HIV/AIDS epidemic can be eliminated if 73% of people living with HIV take antiretroviral medications and achieve undetectable viral loads. This study assessed the effects of financial incentives in suppressing viral load. People living with HIV with detectable viral loads (N = 102) were randomly assigned to Usual Care or Incentive groups. Incentive participants earned up to $10 per day for 2 years for providing blood samples that showed either reduced or undetectable viral loads. This report presents data on the 1st year after random assignment. Incentive participants provided more (adjusted OR = 15.6, CI 4.2-58.8, p < 0.001) blood samples at 3-month assessments with undetectable viral load (72.1%) than usual care control participants (39.0%). We collected most blood samples. The study showed that incentives can substantially increase undetectable viral loads in people living with HIV. Financial incentives for suppressed viral loads could contribute to the eradication of the HIV/AIDS epidemic.
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Affiliation(s)
- Kenneth Silverman
- Department of Psychiatry and Behavioral Sciences, Center for Learning and Health, Johns Hopkins University School of Medicine, 5200 Eastern Avenue, Suite 350 East, Baltimore, MD, 21224, USA.
| | - August F Holtyn
- Department of Psychiatry and Behavioral Sciences, Center for Learning and Health, Johns Hopkins University School of Medicine, 5200 Eastern Avenue, Suite 350 East, Baltimore, MD, 21224, USA
| | - Andrew M Rodewald
- Department of Psychiatry and Behavioral Sciences, Center for Learning and Health, Johns Hopkins University School of Medicine, 5200 Eastern Avenue, Suite 350 East, Baltimore, MD, 21224, USA
| | - Robert F Siliciano
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Brantley P Jarvis
- Department of Psychiatry and Behavioral Sciences, Center for Learning and Health, Johns Hopkins University School of Medicine, 5200 Eastern Avenue, Suite 350 East, Baltimore, MD, 21224, USA
- Knowesis, LLC, Fairfax, VA, USA
| | - Shrinidhi Subramaniam
- Department of Psychiatry and Behavioral Sciences, Center for Learning and Health, Johns Hopkins University School of Medicine, 5200 Eastern Avenue, Suite 350 East, Baltimore, MD, 21224, USA
- Department of Psychology and Child Development, California State University Stanislaus, Turlock, CA, USA
| | - Jeannie-Marie Leoutsakos
- Department of Psychiatry and Behavioral Sciences, Center for Learning and Health, Johns Hopkins University School of Medicine, 5200 Eastern Avenue, Suite 350 East, Baltimore, MD, 21224, USA
| | - Carol-Ann Getty
- Department of Psychiatry and Behavioral Sciences, Center for Learning and Health, Johns Hopkins University School of Medicine, 5200 Eastern Avenue, Suite 350 East, Baltimore, MD, 21224, USA
- Addictions Department, Kings College, London, England, UK
| | | | - Mark A Marzinke
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Michael Fingerhood
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
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40
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Abstract
The odds of living a long and healthy life with HIV infection have dramatically improved with the advent of combination antiretroviral therapy. Along with the early development and clinical trials of these drugs, and new field of research emerged called viral dynamics, which uses mathematical models to interpret and predict the time-course of viral levels during infection and how they are altered by treatment. In this review, we summarize the contributions that virus dynamics models have made to understanding the pathophysiology of infection and to designing effective therapies. This includes studies of the multiphasic decay of viral load when antiretroviral therapy is given, the evolution of drug resistance, the long-term persistence latently infected cells, and the rebound of viremia when drugs are stopped. We additionally discuss new work applying viral dynamics models to new classes of investigational treatment for HIV, including latency-reversing agents and immunotherapy.
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Affiliation(s)
- Alison L. Hill
- Program for Evolutionary DynamicsHarvard UniversityCambridgeMassachusetts
| | - Daniel I. S. Rosenbloom
- Department of PharmacokineticsPharmacodynamics, & Drug MetabolismMerck Research LaboratoriesKenilworthNew Jersey
| | - Martin A. Nowak
- Program for Evolutionary DynamicsHarvard UniversityCambridgeMassachusetts
| | - Robert F. Siliciano
- Department of MedicineJohns Hopkins University School of MedicineBaltimoreMaryland
- Howard Hughes Medical InstituteBaltimoreMaryland
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41
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El-Diwany R, Soliman M, Sugawara S, Breitwieser F, Skaist A, Coggiano C, Sangal N, Chattergoon M, Bailey JR, Siliciano RF, Blankson JN, Ray SC, Wheelan SJ, Thomas DL, Balagopal A. CMPK2 and BCL-G are associated with type 1 interferon-induced HIV restriction in humans. Sci Adv 2018; 4:eaat0843. [PMID: 30083606 PMCID: PMC6070316 DOI: 10.1126/sciadv.aat0843] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/22/2018] [Accepted: 06/19/2018] [Indexed: 05/14/2023]
Abstract
Type 1 interferons (IFN) are critical for host control of HIV and simian immunodeficiency virus. However, it is unknown which of the hundreds of interferon-stimulated genes (ISGs) restrict HIV in vivo. We sequenced RNA from cells that support HIV replication (activated CD4+ T cells) in 19 HIV-infected people before and after interferon-α2b (IFN-α2b) injection. IFN-α2b administration reduced plasma HIV RNA and induced mRNA expression in activated CD4+ T cells: The IFN-α2b-induced change of each mRNA was compared to the change in plasma HIV RNA. Of 99 ISGs, 13 were associated in magnitude with plasma HIV RNA decline. In addition to well-known restriction factors among the 13 ISGs, two novel genes, CMPK2 and BCL-G, were identified and confirmed for their ability to restrict HIV in vitro: The effect of IFN on HIV restriction in culture was attenuated with RNA interference to CMPK2, and overexpression of BCL-G diminished HIV replication. These studies reveal novel antiviral molecules that are linked with IFN-mediated restriction of HIV in humans.
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Affiliation(s)
- Ramy El-Diwany
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Mary Soliman
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Sho Sugawara
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Florian Breitwieser
- Center for Computational Biology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Alyza Skaist
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Candelaria Coggiano
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Neel Sangal
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Michael Chattergoon
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Justin R. Bailey
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Robert F. Siliciano
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- Howard Hughes Medical Institute, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Joel N. Blankson
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Stuart C. Ray
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Sarah J. Wheelan
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - David L. Thomas
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Ashwin Balagopal
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- Corresponding author.
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42
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Salantes DB, Zheng Y, Mampe F, Srivastava T, Beg S, Lai J, Li JZ, Tressler RL, Koup RA, Hoxie J, Abdel-Mohsen M, Sherrill-Mix S, McCormick K, Overton ET, Bushman FD, Learn GH, Siliciano RF, Siliciano JM, Tebas P, Bar KJ. HIV-1 latent reservoir size and diversity are stable following brief treatment interruption. J Clin Invest 2018; 128:3102-3115. [PMID: 29911997 PMCID: PMC6026010 DOI: 10.1172/jci120194] [Citation(s) in RCA: 76] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2018] [Accepted: 04/24/2018] [Indexed: 01/25/2023] Open
Abstract
BACKGROUND The effect of a brief analytical treatment interruption (ATI) on the HIV-1 latent reservoir of individuals who initiate antiretroviral therapy (ART) during chronic infection is unknown. METHODS We evaluated the impact of transient viremia on the latent reservoir in participants who underwent an ATI and at least 6 months of subsequent viral suppression in a clinical trial testing the effect of passive infusion of the broadly neutralizing Ab VRC01 during ATI. RESULTS Measures of total HIV-1 DNA, cell-associated RNA, and infectious units per million cells (IUPM) (measured by quantitative viral outgrowth assay [QVOA]) were not statistically different before or after ATI. Phylogenetic analyses of HIV-1 env sequences from QVOA and proviral DNA demonstrated little change in the composition of the virus populations comprising the pre- and post-ATI reservoir. Expanded clones were common in both QVOA and proviral DNA sequences. The frequency of clonal populations differed significantly between QVOA viruses, proviral DNA sequences, and the viruses that reactivated in vivo. CONCLUSIONS The results indicate that transient viremia from ATI does not substantially alter measures of the latent reservoir, that clonal expansion is prevalent within the latent reservoir, and that characterization of latent viruses that can reactivate in vivo remains challenging. TRIAL REGISTRATION ClinicalTrials.gov NCT02463227FUNDING. Funding was provided by the NIH.
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Affiliation(s)
| | - Yu Zheng
- Harvard University, Cambridge, Massachusetts, USA
| | - Felicity Mampe
- University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | | | - Subul Beg
- Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Jun Lai
- Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | | | - Randall L. Tressler
- Division of AIDS (DAIDS), National Institute of Allergy and Infectious Diseases (NIAID), NIH, Bethesda, Maryland, USA
| | | | - James Hoxie
- University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | | | | | | | | | | | | | - Robert F. Siliciano
- Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
- Howard Hughes Medical Institute, The Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | | | - Pablo Tebas
- University of Pennsylvania, Philadelphia, Pennsylvania, USA
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43
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Abstract
Antiretroviral therapy can effectively block HIV-1 replication and prevent or reverse immunodeficiency in HIV-1-infected individuals. However, viral replication resumes within weeks of treatment interruption. The major barrier to a cure is a small pool of resting memory CD4+ T cells that harbor latent HIV-1 proviruses. This latent reservoir is now the focus of an intense international research effort. We describe how the reservoir is established, challenges involved in eliminating it, and pharmacologic and immunologic strategies for targeting this reservoir. The development of a successful cure strategy will most likely require understanding the mechanisms that maintain HIV-1 proviruses in a latent state and pathways that drive the proliferation of infected cells, which slows reservoir decay. In addition, a cure will require the development of effective immunologic approaches to eliminating infected cells. There is renewed optimism about the prospect of a cure, and the interventions discussed here could pave the way.
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Affiliation(s)
- Srona Sengupta
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Graduate Program in Immunology and Medical Scientist Training Program, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Robert F Siliciano
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Howard Hughes Medical Institute, Baltimore, MD 21205, USA.
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44
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Sengupta S, Boronina T, Cole RN, Siliciano RF, Sadegh-Nasseri S. Assessing non-classical antigen presentation in HIV-infected CD4+ T cells. The Journal of Immunology 2018. [DOI: 10.4049/jimmunol.200.supp.99.8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Abstract
CD4+T cells recognize peptides presented by MHC Class II (MHC-II) molecules on B cells, dendritic cells, and macrophages. Interestingly, in humans, activated CD4+ T cells themselves express MHC-II molecules (HLA-DR, -DP, -DQ), but their potential role as antigen processing cells has not been well characterized. Recent promising data in a simian immunodeficiency (SIV) model suggest that antigen presentation by CD4+ T cells may be important in immunity. In these studies, a vaccine incorporating SIV antigens into a cytomegalovirus vector induced MHC-II restricted CD8+ T cells in macaques. Notably, these non-canonical cells were also observed in HIV patients. Clones generated from these MHC-II restricted CD8+ T cells killed autologous HIV-infected CD4+ T cells, suggesting that HIV is processed and presented on MHC-II on CD4+ T cells. To investigate this potentially novel form of antigen presentation, we eluted peptides from HLA-DR on activated CD4+T cells and sequenced them by LC-MS/MS. We show for the first time that human primary CD4+ T cells indeed process and present peptides on HLA-DR. We are currently applying this approach to HIV-infected cells to detect HIV peptides. Given the low sensitivity of untargeted MS for rare viral peptides, we are also generating a library of MHC-II HIV epitopes presented on HLA-DR to help guide more targeted MS analysis. To create this library, we are using a MHC-II cell-free processing system. We have already identified several epitopes from HIV Gag, Pol, Env, Vif, Rev, and Tat, some of which we show elicit memory responses in HIV patients. Our studies reveal a novel role for CD4+ T cells in antigen presentation and show that a cell-free processing system can predict HIV epitopes that may be presented on these cells.
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45
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Pohlmeyer CW, Laskey SB, Beck SE, Xu DC, Capoferri AA, Garliss CC, May ME, Livingston A, Lichmira W, Moore RD, Leffell MS, Butler NJ, Thorne JE, Flynn JA, Siliciano RF, Blankson JN. Cross-reactive microbial peptides can modulate HIV-specific CD8+ T cell responses. PLoS One 2018; 13:e0192098. [PMID: 29466365 PMCID: PMC5821448 DOI: 10.1371/journal.pone.0192098] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2017] [Accepted: 01/02/2018] [Indexed: 11/19/2022] Open
Abstract
Heterologous immunity is an important aspect of the adaptive immune response. We hypothesized that this process could modulate the HIV-1-specific CD8+ T cell response, which has been shown to play an important role in HIV-1 immunity and control. We found that stimulation of peripheral blood mononuclear cells (PBMCs) from HIV-1-positive subjects with microbial peptides that were cross-reactive with immunodominant HIV-1 epitopes resulted in dramatic expansion of HIV-1-specific CD8+ T cells. Interestingly, the TCR repertoire of HIV-1-specific CD8+ T cells generated by ex vivo stimulation of PBMCs using HIV-1 peptide was different from that of cells stimulated with cross-reactive microbial peptides in some HIV-1-positive subjects. Despite these differences, CD8+ T cells stimulated with either HIV-1 or cross-reactive peptides effectively suppressed HIV-1 replication in autologous CD4+ T cells. These data suggest that exposure to cross-reactive microbial antigens can modulate HIV-1-specific immunity.
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Affiliation(s)
- Christopher W. Pohlmeyer
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
| | - Sarah B. Laskey
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
| | - Sarah E. Beck
- Department of Molecular and Comparative Pathobiology. Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
| | - Daniel C. Xu
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
| | - Adam A. Capoferri
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
| | - Caroline C. Garliss
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
| | - Megan E. May
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
| | - Alison Livingston
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
| | - Walt Lichmira
- Spondylitis Association of America, Philadelphia, Pennsylvania United States of America
| | - Richard D. Moore
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
| | - M. Sue Leffell
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
| | - Nicholas J. Butler
- Department of Ophthalmology. Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
| | - Jennifer E. Thorne
- Department of Ophthalmology. Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
| | - John A. Flynn
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
| | - Robert F. Siliciano
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
- Howard Hughes Medical Institute, Baltimore, Maryland, United States of America
| | - Joel N. Blankson
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
- Department of Molecular and Comparative Pathobiology. Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
- * E-mail:
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46
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Wang Z, Simonetti FR, Siliciano RF, Laird GM. Measuring replication competent HIV-1: advances and challenges in defining the latent reservoir. Retrovirology 2018; 15:21. [PMID: 29433524 PMCID: PMC5810003 DOI: 10.1186/s12977-018-0404-7] [Citation(s) in RCA: 48] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2017] [Accepted: 02/06/2018] [Indexed: 12/24/2022] Open
Abstract
Antiretroviral therapy cannot cure HIV-1 infection due to the persistence of a small number of latently infected cells harboring replication-competent proviruses. Measuring persistent HIV-1 is challenging, as it consists of a mosaic population of defective and intact proviruses that can shift from a state of latency to active HIV-1 transcription. Due to this complexity, most of the current assays detect multiple categories of persistent HIV-1, leading to an overestimate of the true size of the latent reservoir. Here, we review the development of the viral outgrowth assay, the gold-standard quantification of replication-competent proviruses, and discuss the insights provided by full-length HIV-1 genome sequencing methods, which allowed us to unravel the composition of the proviral landscape. In this review, we provide a dissection of what defines HIV-1 persistence and we examine the unmet needs to measure the efficacy of interventions aimed at eliminating the HIV-1 reservoir.
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Affiliation(s)
- Zheng Wang
- Department of Pharmacology and Molecular Sciences, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
| | - Francesco R Simonetti
- Department of Medicine, Johns Hopkins University School of Medicine, Room 879, Edward D. Miller Research Building, 733 N. Broadway, Baltimore, MD, 21205, USA
| | - Robert F Siliciano
- Department of Medicine, Johns Hopkins University School of Medicine, Room 879, Edward D. Miller Research Building, 733 N. Broadway, Baltimore, MD, 21205, USA. .,Howard Hughes Medical Institute, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA.
| | - Gregory M Laird
- Department of Medicine, Johns Hopkins University School of Medicine, Room 879, Edward D. Miller Research Building, 733 N. Broadway, Baltimore, MD, 21205, USA
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47
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Huang SH, Ren Y, Thomas AS, Chan D, Mueller S, Ward AR, Patel S, Bollard CM, Cruz CR, Karandish S, Truong R, Macedo AB, Bosque A, Kovacs C, Benko E, Piechocka-Trocha A, Wong H, Jeng E, Nixon DF, Ho YC, Siliciano RF, Walker BD, Jones RB. Latent HIV reservoirs exhibit inherent resistance to elimination by CD8+ T cells. J Clin Invest 2018; 128:876-889. [PMID: 29355843 DOI: 10.1172/jci97555] [Citation(s) in RCA: 132] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2017] [Accepted: 12/05/2017] [Indexed: 02/06/2023] Open
Abstract
The presence of persistent, latent HIV reservoirs in CD4+ T cells obstructs current efforts to cure infection. The so-called kick-and-kill paradigm proposes to purge these reservoirs by combining latency-reversing agents with immune effectors such as cytotoxic T lymphocytes. Support for this approach is largely based on success in latency models, which do not fully reflect the makeup of latent reservoirs in individuals on long-term antiretroviral therapy (ART). Recent studies have shown that CD8+ T cells have the potential to recognize defective proviruses, which comprise the vast majority of all infected cells, and that the proviral landscape can be shaped over time due to in vivo clonal expansion of infected CD4+ T cells. Here, we have shown that treating CD4+ T cells from ART-treated individuals with combinations of potent latency-reversing agents and autologous CD8+ T cells consistently reduced cell-associated HIV DNA, but failed to deplete replication-competent virus. These CD8+ T cells recognized and potently eliminated CD4+ T cells that were newly infected with autologous reservoir virus, ruling out a role for both immune escape and CD8+ T cell dysfunction. Thus, our results suggest that cells harboring replication-competent HIV possess an inherent resistance to CD8+ T cells that may need to be addressed to cure infection.
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Affiliation(s)
- Szu-Han Huang
- Department of Microbiology, Immunology and Tropical Medicine, The George Washington University, Washington DC, USA
| | - Yanqin Ren
- Department of Microbiology, Immunology and Tropical Medicine, The George Washington University, Washington DC, USA
| | - Allison S Thomas
- Department of Microbiology, Immunology and Tropical Medicine, The George Washington University, Washington DC, USA
| | - Dora Chan
- Department of Microbiology, Immunology and Tropical Medicine, The George Washington University, Washington DC, USA
| | - Stefanie Mueller
- Ragon Institute of Massachusetts Institute of Technology (MIT), Massachusetts General Hospital (MGH), and Harvard University, Cambridge, Massachusetts, USA
| | - Adam R Ward
- Department of Microbiology, Immunology and Tropical Medicine, The George Washington University, Washington DC, USA
| | - Shabnum Patel
- Department of Microbiology, Immunology and Tropical Medicine, The George Washington University, Washington DC, USA.,Children's National Health System, Washington DC, USA
| | - Catherine M Bollard
- Department of Microbiology, Immunology and Tropical Medicine, The George Washington University, Washington DC, USA.,Children's National Health System, Washington DC, USA
| | - Conrad Russell Cruz
- Department of Microbiology, Immunology and Tropical Medicine, The George Washington University, Washington DC, USA.,Children's National Health System, Washington DC, USA
| | - Sara Karandish
- Department of Microbiology, Immunology and Tropical Medicine, The George Washington University, Washington DC, USA
| | - Ronald Truong
- Department of Microbiology, Immunology and Tropical Medicine, The George Washington University, Washington DC, USA
| | - Amanda B Macedo
- Department of Microbiology, Immunology and Tropical Medicine, The George Washington University, Washington DC, USA
| | - Alberto Bosque
- Department of Microbiology, Immunology and Tropical Medicine, The George Washington University, Washington DC, USA
| | - Colin Kovacs
- Maple Leaf Medical Clinic, Toronto, Ontario, Canada
| | - Erika Benko
- Maple Leaf Medical Clinic, Toronto, Ontario, Canada
| | - Alicja Piechocka-Trocha
- Ragon Institute of Massachusetts Institute of Technology (MIT), Massachusetts General Hospital (MGH), and Harvard University, Cambridge, Massachusetts, USA
| | - Hing Wong
- Altor Bioscience Corporation, Miramar, Florida, USA
| | - Emily Jeng
- Altor Bioscience Corporation, Miramar, Florida, USA
| | - Douglas F Nixon
- Department of Microbiology, Immunology and Tropical Medicine, The George Washington University, Washington DC, USA
| | - Ya-Chi Ho
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Robert F Siliciano
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA.,Howard Hughes Medical Institute, Chevy Chase, Maryland, USA
| | - Bruce D Walker
- Ragon Institute of Massachusetts Institute of Technology (MIT), Massachusetts General Hospital (MGH), and Harvard University, Cambridge, Massachusetts, USA.,Howard Hughes Medical Institute, Chevy Chase, Maryland, USA.,Institute for Medical Engineering and Sciences, MIT, Cambridge, Massachusetts, USA
| | - R Brad Jones
- Department of Microbiology, Immunology and Tropical Medicine, The George Washington University, Washington DC, USA.,Ragon Institute of Massachusetts Institute of Technology (MIT), Massachusetts General Hospital (MGH), and Harvard University, Cambridge, Massachusetts, USA
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48
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Shan L, Deng K, Gao H, Xing S, Capoferri AA, Durand CM, Rabi SA, Laird GM, Kim M, Hosmane NN, Yang HC, Zhang H, Margolick JB, Li L, Cai W, Ke R, Flavell RA, Siliciano JD, Siliciano RF. Transcriptional Reprogramming during Effector-to-Memory Transition Renders CD4 + T Cells Permissive for Latent HIV-1 Infection. Immunity 2017; 47:766-775.e3. [PMID: 29045905 DOI: 10.1016/j.immuni.2017.09.014] [Citation(s) in RCA: 124] [Impact Index Per Article: 17.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2017] [Revised: 05/26/2017] [Accepted: 09/25/2017] [Indexed: 11/19/2022]
Abstract
The latent reservoir for HIV-1 in resting memory CD4+ T cells is the major barrier to curing HIV-1 infection. Studies of HIV-1 latency have focused on regulation of viral gene expression in cells in which latent infection is established. However, it remains unclear how infection initially becomes latent. Here we described a unique set of properties of CD4+ T cells undergoing effector-to-memory transition including temporary upregulation of CCR5 expression and rapid downregulation of cellular gene transcription. These cells allowed completion of steps in the HIV-1 life cycle through integration but suppressed HIV-1 gene transcription, thus allowing the establishment of latency. CD4+ T cells in this stage were substantially more permissive for HIV-1 latent infection than other CD4+ T cells. Establishment of latent HIV-1 infection in CD4+ T could be inhibited by viral-specific CD8+ T cells, a result with implications for elimination of latent HIV-1 infection by T cell-based vaccines.
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Affiliation(s)
- Liang Shan
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Department of Immunobiology, Yale University School of Medicine, New Haven, CT 06510, USA
| | - Kai Deng
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Institute of Human Virology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, 510080, China
| | - Hongbo Gao
- Institute of Human Virology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, 510080, China
| | - Sifei Xing
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Adam A Capoferri
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Christine M Durand
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - S Alireza Rabi
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Gregory M Laird
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Michelle Kim
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Nina N Hosmane
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | | | - Hao Zhang
- Department of Molecular Microbiology and Immunology, Johns Hopkins University Bloomberg School of Public Health, Baltimore, MD 21205, USA
| | - Joseph B Margolick
- Department of Molecular Microbiology and Immunology, Johns Hopkins University Bloomberg School of Public Health, Baltimore, MD 21205, USA
| | - Linghua Li
- Department of Infectious Diseases, Guangzhou Eighth People's Hospital, Guangzhou Medical University, Guangzhou, Guangdong 510060, China
| | - Weiping Cai
- Department of Infectious Diseases, Guangzhou Eighth People's Hospital, Guangzhou Medical University, Guangzhou, Guangdong 510060, China
| | - Ruian Ke
- Department of Mathematics, North Carolina State University, Raleigh, NC 27695, USA
| | - Richard A Flavell
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT 06510, USA; Howard Hughes Medical Institute, Yale University, New Haven, CT 06520, USA
| | - Janet D Siliciano
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Robert F Siliciano
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Howard Hughes Medical Institute, Johns Hopkins University, Baltimore, MD 21205, USA.
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Henrich TJ, Hatano H, Bacon O, Hogan LE, Rutishauser R, Hill A, Kearney MF, Anderson EM, Buchbinder SP, Cohen SE, Abdel-Mohsen M, Pohlmeyer CW, Fromentin R, Hoh R, Liu AY, McCune JM, Spindler J, Metcalf-Pate K, Hobbs KS, Thanh C, Gibson EA, Kuritzkes DR, Siliciano RF, Price RW, Richman DD, Chomont N, Siliciano JD, Mellors JW, Yukl SA, Blankson JN, Liegler T, Deeks SG. HIV-1 persistence following extremely early initiation of antiretroviral therapy (ART) during acute HIV-1 infection: An observational study. PLoS Med 2017; 14:e1002417. [PMID: 29112956 PMCID: PMC5675377 DOI: 10.1371/journal.pmed.1002417] [Citation(s) in RCA: 157] [Impact Index Per Article: 22.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/19/2017] [Accepted: 09/29/2017] [Indexed: 12/29/2022] Open
Abstract
BACKGROUND It is unknown if extremely early initiation of antiretroviral therapy (ART) may lead to long-term ART-free HIV remission or cure. As a result, we studied 2 individuals recruited from a pre-exposure prophylaxis (PrEP) program who started prophylactic ART an estimated 10 days (Participant A; 54-year-old male) and 12 days (Participant B; 31-year-old male) after infection with peak plasma HIV RNA of 220 copies/mL and 3,343 copies/mL, respectively. Extensive testing of blood and tissue for HIV persistence was performed, and PrEP Participant A underwent analytical treatment interruption (ATI) following 32 weeks of continuous ART. METHODS AND FINDINGS Colorectal and lymph node tissues, bone marrow, cerebral spinal fluid (CSF), plasma, and very large numbers of peripheral blood mononuclear cells (PBMCs) were obtained longitudinally from both participants and were studied for HIV persistence in several laboratories using molecular and culture-based detection methods, including a murine viral outgrowth assay (mVOA). Both participants initiated PrEP with tenofovir/emtricitabine during very early Fiebig stage I (detectable plasma HIV-1 RNA, antibody negative) followed by 4-drug ART intensification. Following peak viral loads, both participants experienced full suppression of HIV-1 plasma viremia. Over the following 2 years, no further HIV could be detected in blood or tissue from PrEP Participant A despite extensive sampling from ileum, rectum, lymph nodes, bone marrow, CSF, circulating CD4+ T cell subsets, and plasma. No HIV was detected from tissues obtained from PrEP Participant B, but low-level HIV RNA or DNA was intermittently detected from various CD4+ T cell subsets. Over 500 million CD4+ T cells were assayed from both participants in a humanized mouse outgrowth assay. Three of 8 mice infused with CD4+ T cells from PrEP Participant B developed viremia (50 million input cells/surviving mouse), but only 1 of 10 mice infused with CD4+ T cells from PrEP Participant A (53 million input cells/mouse) experienced very low level viremia (201 copies/mL); sequence confirmation was unsuccessful. PrEP Participant A stopped ART and remained aviremic for 7.4 months, rebounding with HIV RNA of 36 copies/mL that rose to 59,805 copies/mL 6 days later. ART was restarted promptly. Rebound plasma HIV sequences were identical to those obtained during acute infection by single-genome sequencing. Mathematical modeling predicted that the latent reservoir size was approximately 200 cells prior to ATI and that only around 1% of individuals with a similar HIV burden may achieve lifelong ART-free remission. Furthermore, we observed that lymphocytes expressing the tumor marker CD30 increased in frequency weeks to months prior to detectable HIV-1 RNA in plasma. This study was limited by the small sample size, which was a result of the rarity of individuals presenting during hyperacute infection. CONCLUSIONS We report HIV relapse despite initiation of ART at one of the earliest stages of acute HIV infection possible. Near complete or complete loss of detectable HIV in blood and tissues did not lead to indefinite ART-free HIV remission. However, the small numbers of latently infected cells in individuals treated during hyperacute infection may be associated with prolonged ART-free remission.
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Affiliation(s)
- Timothy J. Henrich
- Division of Experimental Medicine, University of California, San Francisco, California, United States of America
- * E-mail:
| | - Hiroyu Hatano
- Division of HIV, Infectious Diseases and Global Medicine, University of California, San Francisco, California, United States of America
| | - Oliver Bacon
- Division of HIV, Infectious Diseases and Global Medicine, University of California, San Francisco, California, United States of America
- San Francisco Department of Public Health, San Francisco, California, United States of America
| | - Louise E. Hogan
- Division of Experimental Medicine, University of California, San Francisco, California, United States of America
| | - Rachel Rutishauser
- Division of Experimental Medicine, University of California, San Francisco, California, United States of America
- Division of HIV, Infectious Diseases and Global Medicine, University of California, San Francisco, California, United States of America
| | - Alison Hill
- Program for Evolutionary Dynamics, Harvard University, Cambridge, Massachusetts, United States of America
| | - Mary F. Kearney
- HIV Dynamics and Replication Program, Center for Cancer Research, National Cancer Institute, Frederick, Maryland, United States of America
| | - Elizabeth M. Anderson
- HIV Dynamics and Replication Program, Center for Cancer Research, National Cancer Institute, Frederick, Maryland, United States of America
| | - Susan P. Buchbinder
- Division of HIV, Infectious Diseases and Global Medicine, University of California, San Francisco, California, United States of America
- San Francisco Department of Public Health, San Francisco, California, United States of America
| | - Stephanie E. Cohen
- Division of HIV, Infectious Diseases and Global Medicine, University of California, San Francisco, California, United States of America
- San Francisco Department of Public Health, San Francisco, California, United States of America
| | - Mohamed Abdel-Mohsen
- Division of HIV, Infectious Diseases and Global Medicine, University of California, San Francisco, California, United States of America
- The Wistar Institute, Philadelphia, Pennsylvania, United States of America
| | - Christopher W. Pohlmeyer
- Center for AIDS Research, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
| | - Remi Fromentin
- Centre de Recherche du CHUM and Department of Microbiology, Infectiology and Immunology, Université de Montréal, Montreal, Quebec, Canada
| | - Rebecca Hoh
- Division of HIV, Infectious Diseases and Global Medicine, University of California, San Francisco, California, United States of America
| | - Albert Y. Liu
- Division of HIV, Infectious Diseases and Global Medicine, University of California, San Francisco, California, United States of America
- San Francisco Department of Public Health, San Francisco, California, United States of America
| | - Joseph M. McCune
- Division of Experimental Medicine, University of California, San Francisco, California, United States of America
| | - Jonathan Spindler
- HIV Dynamics and Replication Program, Center for Cancer Research, National Cancer Institute, Frederick, Maryland, United States of America
| | - Kelly Metcalf-Pate
- Center for AIDS Research, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
| | - Kristen S. Hobbs
- Division of Experimental Medicine, University of California, San Francisco, California, United States of America
| | - Cassandra Thanh
- Division of Experimental Medicine, University of California, San Francisco, California, United States of America
| | - Erica A. Gibson
- Division of Experimental Medicine, University of California, San Francisco, California, United States of America
| | - Daniel R. Kuritzkes
- Division of Infectious Diseases, Brigham and Women's Hospital, Boston, Massachusetts, United States of America
- Harvard Medical School, Boston, Massachusetts, United States of America
| | - Robert F. Siliciano
- Division of Infectious Diseases, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
- Howard Hughes Medical Institute, Baltimore, Maryland, United States of America
| | - Richard W. Price
- Department of Neurology, University of California, San Francisco, California, United States of America
| | - Douglas D. Richman
- University of California San Diego, La Jolla, California, United States of America
- Veterans Affairs San Diego Healthcare System, San Diego, California, United States of America
| | - Nicolas Chomont
- Centre de Recherche du CHUM and Department of Microbiology, Infectiology and Immunology, Université de Montréal, Montreal, Quebec, Canada
| | | | - John W. Mellors
- Department of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Steven A. Yukl
- San Francisco Veterans Affairs Medical Center, San Francisco, California, United States of America
- University of California, San Francisco, California, Unites States of America
| | - Joel N. Blankson
- Center for AIDS Research, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
| | - Teri Liegler
- Division of HIV, Infectious Diseases and Global Medicine, University of California, San Francisco, California, United States of America
| | - Steven G. Deeks
- Division of HIV, Infectious Diseases and Global Medicine, University of California, San Francisco, California, United States of America
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50
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Rosenbloom DIS, Hill AL, Laskey SB, Siliciano RF. Re-evaluating evolution in the HIV reservoir. Nature 2017; 551:E6-E9. [PMID: 29168805 DOI: 10.1038/nature24634] [Citation(s) in RCA: 58] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2016] [Accepted: 05/23/2017] [Indexed: 12/18/2022]
Affiliation(s)
- Daniel I S Rosenbloom
- Department of Biomedical Informatics, Columbia University Medical Center, New York, New York, USA
| | - Alison L Hill
- Program for Evolutionary Dynamics, Harvard University, Cambridge, Massachusetts, USA
| | - Sarah B Laskey
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Robert F Siliciano
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA.,Howard Hughes Medical Institute, Baltimore, Maryland, USA
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