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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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Buchholtz NVEJ, Nühn MM, de Jong TCM, Stienstra TAT, Reddy K, Ndung'u T, Ndhlovu ZM, Fisher K, Palmer S, Wensing AMJ, Symons J, Nijhuis M. Development of a highly sensitive and specific intact proviral DNA assay for HIV-1 subtype B and C. Virol J 2024; 21:36. [PMID: 38297379 PMCID: PMC10832250 DOI: 10.1186/s12985-024-02300-6] [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: 11/14/2023] [Accepted: 01/22/2024] [Indexed: 02/02/2024] Open
Abstract
INTRODUCTION HIV reservoir quantification is essential for evaluation of HIV curative strategies and may provide valuable insights about reservoir dynamics during antiretroviral therapy. The Intact Proviral DNA Assay (IPDA) provides the unique opportunity to quantify the intact and defective reservoir. The current IPDA is optimized for HIV-1 subtype B, the dominant subtype in resource-rich settings. However, subtype C is dominant in Sub-Saharan Africa, jointly accounting for around 60% of the pandemic. We developed an assay capable of quantifying intact and defective proviral HIV-1 DNA of subtype B and C. METHODS Primer and probe sequences were strategically positioned at conserved regions in psi and env and adapted to subtype B&C. In silico analysis of 752 subtype B and 697 subtype C near-full length genome sequences (nFGS) was performed to predict the specificity and sensitivity. Gblocks were used to determine the limit of blank (LoB), limit of detection (LoD), and different annealing temperatures were tested to address impact of sequence variability. RESULTS The in silico analysis showed that the HIV-1 B&C IPDA correctly identified 100% of the intact subtype B, and 86% of the subtype C sequences. In contrast, the original IPDA identified 86% and 12% of these subtype B and C sequences as intact. Furthermore, the HIV-1 B&C IPDA correctly identified hypermutated (87% and 88%) and other defective sequences (73% and 66%) for subtype B and C with comparable specificity as the original IPDA for subtype B (59% and 63%). Subtype B cis-acting sequences were more frequently identified as intact by the HIV-1 B&C IPDA compared to the original IPDA (39% and 2%). The LoB for intact proviral DNA copies was 0, and the LoD for intact proviral DNA copies was 6 (> 95% certainty) at 60 °C. Quantification of 2-6 copies can be performed with > 80% certainty. Lowering the annealing temperature to 55 °C slightly lowered the specificity but prevented exclusion of samples with single mutations in the primer/probe region. CONCLUSIONS We developed a robust and sensitive assay for the quantification of intact and defective HIV-1 subtype B and C proviral DNA, making this a suitable tool to monitor the impact of (large-scale) curative interventions.
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Affiliation(s)
- N V E J Buchholtz
- Translational Virology, Department of Medical Microbiology, University Medical Center Utrecht, Heidelberglaan 100, 3584C, Utrecht, The Netherlands
| | - M M Nühn
- Translational Virology, Department of Medical Microbiology, University Medical Center Utrecht, Heidelberglaan 100, 3584C, Utrecht, The Netherlands
| | - T C M de Jong
- Translational Virology, Department of Medical Microbiology, University Medical Center Utrecht, Heidelberglaan 100, 3584C, Utrecht, The Netherlands
| | - T A T Stienstra
- Translational Virology, Department of Medical Microbiology, University Medical Center Utrecht, Heidelberglaan 100, 3584C, Utrecht, The Netherlands
| | - K Reddy
- Africa Health Research Institute (AHRI), Durban, South Africa
| | - T Ndung'u
- Africa Health Research Institute (AHRI), Durban, South Africa
- HIV Pathogenesis Programme, The Doris Duke Medical Research Institute, University of KwaZulu-Natal, Durban, South Africa
- The Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology, Harvard University, Cambridge, MA, 01238, USA
- Division of Infection and Immunity, University College London, London, UK
| | - Z M Ndhlovu
- Africa Health Research Institute (AHRI), Durban, South Africa
| | - K Fisher
- Centre for Virus Research, The Westmead Institute for Medical Research, The University of Sydney, Sydney, NSW, Australia
| | - S Palmer
- Centre for Virus Research, The Westmead Institute for Medical Research, The University of Sydney, Sydney, NSW, Australia
| | - A M J Wensing
- Translational Virology, Department of Medical Microbiology, University Medical Center Utrecht, Heidelberglaan 100, 3584C, Utrecht, The Netherlands
- ha, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - J Symons
- Translational Virology, Department of Medical Microbiology, University Medical Center Utrecht, Heidelberglaan 100, 3584C, Utrecht, The Netherlands
| | - M Nijhuis
- Translational Virology, Department of Medical Microbiology, University Medical Center Utrecht, Heidelberglaan 100, 3584C, Utrecht, The Netherlands.
- HIV Pathogenesis Research Unit, Faculty of Health Sciences, University of Witwatersrand, Johannesburg, South Africa.
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3
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Peluso MJ, Dee L, Shao S, Taylor J, Campbell D, Collins S, Gandhi M, Johnston R, Deeks SG, Sauceda JA, Dubé K. Operationalizing Human Immunodeficiency Virus Cure-related Trials with Analytic Treatment Interruptions During the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Pandemic: A Collaborative Approach. Clin Infect Dis 2021; 72:1843-1849. [PMID: 32841311 PMCID: PMC7499539 DOI: 10.1093/cid/ciaa1260] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [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: 07/28/2020] [Accepted: 08/21/2020] [Indexed: 01/03/2023] Open
Abstract
Efforts to recognize and minimize the risk to study participants will be necessary to safely and ethically resume scientific research in the context of the ongoing severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic. These efforts are uniquely challenging in the context of human immunodeficiency virus (HIV) cure clinical trials, which often involve complex experimental therapy regimens and perhaps analytic treatment interruption, in which participants pause antiretroviral therapy. In this viewpoint, we discuss our approach to reopening an HIV cure trial in this context, with a focus on key considerations regarding study design, informed consent and participant education, and study implementation. These recommendations might be informative to other groups seeking to resume HIV cure research in settings similar to ours.
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Affiliation(s)
- Michael J Peluso
- Division of HIV, Infectious Diseases, and Global Medicine, University of California, San Francisco, San Francisco, California, USA
| | - Lynda Dee
- AIDS Action Baltimore, Baltimore, Maryland, USA
- amfAR Institute for HIV Cure Research Community Advisory Board, USA
- Delaney AIDS Research Enterprise Community Advisory Board, USA
- Martin Delaney Collaboratory Community Advisory Board, USA
| | - Shirley Shao
- Division of HIV, Infectious Diseases, and Global Medicine, University of California, San Francisco, San Francisco, California, USA
| | - Jeff Taylor
- amfAR Institute for HIV Cure Research Community Advisory Board, USA
- Martin Delaney Collaboratory Community Advisory Board, USA
- HIV + Aging Research Project, Palm Springs, California, USA
- University of California, San Diego, AntiViral Research Center Community Advisory Board, San Diego, California, USA
| | - Danielle Campbell
- Delaney AIDS Research Enterprise Community Advisory Board, USA
- Martin Delaney Collaboratory Community Advisory Board, USA
- Charles R. Drew University of Medicine and Science, Los Angeles, California, USA
| | | | - Monica Gandhi
- Division of HIV, Infectious Diseases, and Global Medicine, University of California, San Francisco, San Francisco, California, USA
| | - Rowena Johnston
- amfAR Institute for HIV Cure Research, San Francisco, California, USA
| | - Steven G Deeks
- Division of HIV, Infectious Diseases, and Global Medicine, University of California, San Francisco, San Francisco, California, USA
- amfAR Institute for HIV Cure Research, San Francisco, California, USA
| | - John A Sauceda
- Center for AIDS Prevention Studies, University of California, San Francisco, San Francisco, California, USA
| | - Karine Dubé
- Center for AIDS Prevention Studies, University of California, San Francisco, San Francisco, California, USA
- University of North Carolina Gillings School of Global Public Health, Chapel Hill, North Carolina, USA
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4
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Gonzalo-Gil E, Rapuano PB, Ikediobi U, Leibowitz R, Mehta S, Coskun AK, Porterfield JZ, Lampkin TD, Marconi VC, Rimland D, Walker BD, Deeks S, Sutton RE. Transcriptional down-regulation of ccr5 in a subset of HIV+ controllers and their family members. eLife 2019; 8:e44360. [PMID: 30964004 PMCID: PMC6456299 DOI: 10.7554/elife.44360] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [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: 12/12/2018] [Accepted: 04/01/2019] [Indexed: 11/13/2022] Open
Abstract
HIV +Elite and Viremic controllers (EC/VCs) are able to control virus infection, perhaps because of host genetic determinants. We identified 16% (21 of 131) EC/VCs with CD4 +T cells with resistance specific to R5-tropic HIV, reversed after introduction of ccr5. R5 resistance was not observed in macrophages and depended upon the method of T cell activation. CD4 +T cells of these EC/VCs had lower ccr2 and ccr5 RNA levels, reduced CCR2 and CCR5 cell-surface expression, and decreased levels of secreted chemokines. T cells had no changes in chemokine receptor mRNA half-life but instead had lower levels of active transcription of ccr2 and ccr5, despite having more accessible chromatin by ATAC-seq. Other nearby genes were also down-regulated, over a region of ~500 kb on chromosome 3p21. This same R5 resistance phenotype was observed in family members of an index VC, also associated with ccr2/ccr5 down-regulation, suggesting that the phenotype is heritable.
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Affiliation(s)
- Elena Gonzalo-Gil
- Section of Infectious Diseases, Department of Internal MedicineYale University School of MedicineNew HavenUnited States
| | - Patrick B Rapuano
- Section of Infectious Diseases, Department of Internal MedicineYale University School of MedicineNew HavenUnited States
| | - Uchenna Ikediobi
- Section of Infectious Diseases, Department of Internal MedicineYale University School of MedicineNew HavenUnited States
| | - Rebecca Leibowitz
- Section of Infectious Diseases, Department of Internal MedicineYale University School of MedicineNew HavenUnited States
| | - Sameet Mehta
- Yale Center for Genome Analysis Bioinformatics groupYale University School of MedicineNew HavenUnited States
| | - Ayse K Coskun
- Section of Infectious Diseases, Department of Internal MedicineYale University School of MedicineNew HavenUnited States
| | - J Zachary Porterfield
- Section of Infectious Diseases, Department of Internal MedicineYale University School of MedicineNew HavenUnited States
| | - Teagan D Lampkin
- Infectious Diseases SectionDallas VA Medical CenterDallasUnited States
| | - Vincent C Marconi
- Atlanta VA Medical Center, Emory University School of MedicineAtlantaUnited States
| | - David Rimland
- Atlanta VA Medical Center, Emory University School of MedicineAtlantaUnited States
| | - Bruce D Walker
- Ragon Institute of MGHMIT and Harvard UniversityCambridgeUnited States
| | - Steven Deeks
- Department of MedicineUniversity of California San FranciscoSan FranciscoUnited States
- Department of Epidemiology and BiostatisticsUniversity of California San FranciscoSan FranciscoUnited States
| | - Richard E Sutton
- Section of Infectious Diseases, Department of Internal MedicineYale University School of MedicineNew HavenUnited States
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Hogan LE, Vasquez J, Hobbs KS, Hanhauser E, Aguilar-Rodriguez B, Hussien R, Thanh C, Gibson EA, Carvidi AB, Smith LCB, Khan S, Trapecar M, Sanjabi S, Somsouk M, Stoddart CA, Kuritzkes DR, Deeks SG, Henrich TJ. Increased HIV-1 transcriptional activity and infectious burden in peripheral blood and gut-associated CD4+ T cells expressing CD30. PLoS Pathog 2018; 14:e1006856. [PMID: 29470552 PMCID: PMC5823470 DOI: 10.1371/journal.ppat.1006856] [Citation(s) in RCA: 59] [Impact Index Per Article: 9.8] [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: 08/17/2017] [Accepted: 01/05/2018] [Indexed: 12/11/2022] Open
Abstract
HIV-1-infected cells persist indefinitely despite the use of combination antiretroviral therapy (ART), and novel therapeutic strategies to target and purge residual infected cells in individuals on ART are urgently needed. Here, we demonstrate that CD4+ T cell-associated HIV-1 RNA is often highly enriched in cells expressing CD30, and that cells expressing this marker considerably contribute to the total pool of transcriptionally active CD4+ lymphocytes in individuals on suppressive ART. Using in situ RNA hybridization studies, we show co-localization of CD30 with HIV-1 transcriptional activity in gut-associated lymphoid tissues. We also demonstrate that ex vivo treatment with brentuximab vedotin, an antibody-drug conjugate (ADC) that targets CD30, significantly reduces the total amount of HIV-1 DNA in peripheral blood mononuclear cells obtained from infected, ART-suppressed individuals. Finally, we observed that an HIV-1-infected individual, who received repeated brentuximab vedotin infusions for lymphoma, had no detectable virus in peripheral blood mononuclear cells. Overall, CD30 may be a marker of residual, transcriptionally active HIV-1 infected cells in the setting of suppressive ART. Given that CD30 is only expressed on a small number of total mononuclear cells, it is a potential therapeutic target of persistent HIV-1 infection. Previous studies have shown that higher levels of soluble CD30 are associated with HIV-1 disease progression. Many of these studies, however, were performed prior to the implementation of combination ART, and the relationship between surface CD30 expression, soluble CD30 and HIV-1 infection in ART suppressed individuals, or those with viremic control off ART, is not known. We demonstrate that cell-associated HIV-1 RNA is highly enriched in CD4+ T cells expressing CD30, a member of the tumor necrosis factor receptor superfamily. These findings were observed in several HIV-1 infected donor groups, regardless of whether or not the participants were receiving suppressive ART. Furthermore, we demonstrate that ex vivo treatment with brentuximab vedotin, an antibody-drug conjugate that targets CD30, reduces the total amount of HIV-1 DNA in PBMC obtained from infected individuals. Finally, we show through in situ RNA hybridization studies that CD30 and HIV transcriptional activity co-localize in cells from gut biopsies obtained from HIV-1 infected donors. These data suggest that CD30 may be a marker of residual, transcriptionally active HIV-1 infected cells in the setting of suppressive ART.
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Affiliation(s)
- Louise E. Hogan
- Division of Experimental Medicine, University of California San Francisco, San Francisco, California, United States of America
- * E-mail: (LEH); (TJH)
| | - Joshua Vasquez
- Division of Experimental Medicine, University of California San Francisco, San Francisco, California, United States of America
| | - Kristen S. Hobbs
- Division of Experimental Medicine, University of California San Francisco, San Francisco, California, United States of America
| | - Emily Hanhauser
- Division of Experimental Medicine, University of California San Francisco, San Francisco, California, United States of America
| | - Brandon Aguilar-Rodriguez
- Division of Experimental Medicine, University of California San Francisco, San Francisco, California, United States of America
| | - Rajaa Hussien
- Division of Experimental Medicine, University of California San Francisco, San Francisco, California, United States of America
| | - Cassandra Thanh
- Division of Experimental Medicine, University of California San Francisco, San Francisco, California, United States of America
| | - Erica A. Gibson
- Division of Experimental Medicine, University of California San Francisco, San Francisco, California, United States of America
| | - Alexander B. Carvidi
- Division of Experimental Medicine, University of California San Francisco, San Francisco, California, United States of America
| | - Louis C. B. Smith
- Division of Experimental Medicine, University of California San Francisco, San Francisco, California, United States of America
| | - Shahzada Khan
- Virology and Immunology, Gladstone Institutes, San Francisco, California, United States of America
| | - Martin Trapecar
- Virology and Immunology, Gladstone Institutes, San Francisco, California, United States of America
| | - Shomyseh Sanjabi
- Virology and Immunology, Gladstone Institutes, San Francisco, California, United States of America
- Department of Microbiology and Immunology, University of California San Francisco, San Francisco, California, United States of America
| | - Ma Somsouk
- Division of Gastroenterology, Department of Medicine, University of California San Francisco, San Francisco, California, United States of America
| | - Cheryl A. Stoddart
- Division of Experimental Medicine, University of California San Francisco, San Francisco, California, United States of America
| | - Daniel R. Kuritzkes
- Division of Infectious Diseases, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Steven G. Deeks
- Positive Health Program, Department of Medicine, University of California San Francisco, San Francisco, California, United States of America
| | - Timothy J. Henrich
- Division of Experimental Medicine, University of California San Francisco, San Francisco, California, United States of America
- * E-mail: (LEH); (TJH)
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6
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Ferdin J, Goričar K, Dolžan V, Plemenitaš A, Martin JN, Peterlin BM, Deeks SG, Lenassi M. Viral protein Nef is detected in plasma of half of HIV-infected adults with undetectable plasma HIV RNA. PLoS One 2018; 13:e0191613. [PMID: 29364927 PMCID: PMC5783402 DOI: 10.1371/journal.pone.0191613] [Citation(s) in RCA: 55] [Impact Index Per Article: 9.2] [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: 08/11/2017] [Accepted: 01/07/2018] [Indexed: 01/06/2023] Open
Abstract
OBJECTIVE To address the role of translationally active HIV reservoir in chronic inflammation and non-AIDS related disorders, we first need a simple and accurate assay to evaluate viral protein expression in virally suppressed subjects. DESIGN We optimized an HIV Nef enzyme-linked immunosorbent assay (ELISA) and used it to quantify plasma Nef levels as an indicator of the leaky HIV reservoir in an HIV-infected cohort. METHODS This study accessed 134 plasma samples from a well-characterized cohort study of HIV-infected and uninfected adults in San Francisco (the SCOPE cohort). We optimized an ELISA for detection of plasma Nef in HIV-negative subjects and HIV-infected non-controllers, and evaluated its utility to quantify plasma Nef levels in a cross-sectional study of ART-suppressed and elite controller HIV-infected subjects. RESULTS Here, we describe the performance of an optimized HIV Nef ELISA. When we applied this assay to the study cohort we found that plasma Nef levels were correlated with plasma HIV RNA levels in untreated disease. However, we were able to detect Nef in plasma of approximately half of subjects on ART or with elite control, despite the lack of detectable plasma HIV RNA levels using standard assays. Plasma Nef levels were not consistently associated with CD4+ T-cell count, CD8+ T-cell count, self-reported nadir CD4+ T-cell count or the CD4+/CD8+ T-cell ratio in HIV-infected subjects. CONCLUSION Since plasma HIV RNA levels are undetectable in virally suppressed subjects, it is reasonable to assume that viral protein expression in leaky reservoir, and not plasma virions, is the source of Nef accumulating in plasma. To examine this further, improvements of the assay sensitivity, by lowering the background through improvements in the quality of Nef antibodies, and detailed characterization of the HIV reservoirs are needed.
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Affiliation(s)
- Jana Ferdin
- Institute of Biochemistry, Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
| | - Katja Goričar
- Institute of Biochemistry, Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
| | - Vita Dolžan
- Institute of Biochemistry, Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
| | - Ana Plemenitaš
- Institute of Biochemistry, Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
| | - Jeffrey N. Martin
- Department of Epidemiology & Biostatistics, University of California, San Francisco, San Francisco, California, United States of America
| | - Boris M. Peterlin
- Department of Medicine, Microbiology and Immunology, University of California, San Francisco, San Francisco, California, United States of America
| | - Steven G. Deeks
- Department of Medicine, Microbiology and Immunology, University of California, San Francisco, San Francisco, California, United States of America
| | - Metka Lenassi
- Institute of Biochemistry, Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
- * E-mail:
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7
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Fennessey CM, Pinkevych M, Immonen TT, Reynaldi A, Venturi V, Nadella P, Reid C, Newman L, Lipkey L, Oswald K, Bosche WJ, Trivett MT, Ohlen C, Ott DE, Estes JD, Del Prete GQ, Lifson JD, Davenport MP, Keele BF. Genetically-barcoded SIV facilitates enumeration of rebound variants and estimation of reactivation rates in nonhuman primates following interruption of suppressive antiretroviral therapy. PLoS Pathog 2017; 13:e1006359. [PMID: 28472156 PMCID: PMC5433785 DOI: 10.1371/journal.ppat.1006359] [Citation(s) in RCA: 65] [Impact Index Per Article: 9.3] [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: 02/28/2017] [Revised: 05/16/2017] [Accepted: 04/17/2017] [Indexed: 01/29/2023] Open
Abstract
HIV and SIV infection dynamics are commonly investigated by measuring plasma viral loads. However, this total viral load value represents the sum of many individual infection events, which are difficult to independently track using conventional sequencing approaches. To overcome this challenge, we generated a genetically tagged virus stock (SIVmac239M) with a 34-base genetic barcode inserted between the vpx and vpr accessory genes of the infectious molecular clone SIVmac239. Next-generation sequencing of the virus stock identified at least 9,336 individual barcodes, or clonotypes, with an average genetic distance of 7 bases between any two barcodes. In vitro infection of rhesus CD4+ T cells and in vivo infection of rhesus macaques revealed levels of viral replication of SIVmac239M comparable to parental SIVmac239. After intravenous inoculation of 2.2x105 infectious units of SIVmac239M, an average of 1,247 barcodes were identified during acute infection in 26 infected rhesus macaques. Of the barcodes identified in the stock, at least 85.6% actively replicated in at least one animal, and on average each barcode was found in 5 monkeys. Four infected animals were treated with combination antiretroviral therapy (cART) for 82 days starting on day 6 post-infection (study 1). Plasma viremia was reduced from >106 to <15 vRNA copies/mL by the time treatment was interrupted. Virus rapidly rebounded following treatment interruption and between 87 and 136 distinct clonotypes were detected in plasma at peak rebound viremia. This study confirmed that SIVmac239M viremia could be successfully curtailed with cART, and that upon cART discontinuation, rebounding viral variants could be identified and quantified. An additional 6 animals infected with SIVmac239M were treated with cART beginning on day 4 post-infection for 305, 374, or 482 days (study 2). Upon treatment interruption, between 4 and 8 distinct viral clonotypes were detected in each animal at peak rebound viremia. The relative proportions of the rebounding viral clonotypes, spanning a range of 5 logs, were largely preserved over time for each animal. The viral growth rate during recrudescence and the relative abundance of each rebounding clonotype were used to estimate the average frequency of reactivation per animal. Using these parameters, reactivation frequencies were calculated and ranged from 0.33–0.70 events per day, likely representing reactivation from long-lived latently infected cells. The use of SIVmac239M therefore provides a powerful tool to investigate SIV latency and the frequency of viral reactivation after treatment interruption. Elucidation of HIV dynamics is essential for a thorough understanding of viral transmission, therapeutic interventions, pathogenesis, and immune evasion. The complex dynamics of reservoir establishment and viral recrudescence upon therapy removal present the primary obstacles to developing a functional cure. We sought to develop a virus model system for use in nonhuman primates that allows for the genetic discrimination of nearly 10,000 otherwise isogenic clones. This “synthetic swarm” adds a genetic component to viral dynamics where individual viral lineages can be tracked and monitored during infection. Here we utilized this model to identify the dynamics of viral reservoir establishment and rebound. We found that after 300 or more days of therapy, between 4 and 8 distinct viral lineages could be detected upon therapeutic intervention. Using the relative proportion of each distinct genetic barcoded virus and the overall viral load curve, we could estimate the time and rate of reactivation from latency. On average, we found 1 reactivation event every 2 days with reactivation of the first rebounding variant within days of therapeutic interruption. This virus model will be useful for testing various approaches to reduce the latent viral reservoir and to molecularly track viral dynamics in all stages of infection.
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Affiliation(s)
- Christine M. Fennessey
- AIDS and Cancer Virus Program, Leidos Biomedical Research Inc., Frederick National Laboratory for Cancer Research, Frederick, Maryland, United States of America
| | - Mykola Pinkevych
- Infection Analytics Program, Kirby Institute for Infection and Immunity, UNSW Australia, Sydney, NSW, Australia
| | - Taina T. Immonen
- AIDS and Cancer Virus Program, Leidos Biomedical Research Inc., Frederick National Laboratory for Cancer Research, Frederick, Maryland, United States of America
| | - Arnold Reynaldi
- Infection Analytics Program, Kirby Institute for Infection and Immunity, UNSW Australia, Sydney, NSW, Australia
| | - Vanessa Venturi
- Infection Analytics Program, Kirby Institute for Infection and Immunity, UNSW Australia, Sydney, NSW, Australia
| | - Priyanka Nadella
- AIDS and Cancer Virus Program, Leidos Biomedical Research Inc., Frederick National Laboratory for Cancer Research, Frederick, Maryland, United States of America
| | - Carolyn Reid
- AIDS and Cancer Virus Program, Leidos Biomedical Research Inc., Frederick National Laboratory for Cancer Research, Frederick, Maryland, United States of America
| | - Laura Newman
- AIDS and Cancer Virus Program, Leidos Biomedical Research Inc., Frederick National Laboratory for Cancer Research, Frederick, Maryland, United States of America
| | - Leslie Lipkey
- AIDS and Cancer Virus Program, Leidos Biomedical Research Inc., Frederick National Laboratory for Cancer Research, Frederick, Maryland, United States of America
| | - Kelli Oswald
- AIDS and Cancer Virus Program, Leidos Biomedical Research Inc., Frederick National Laboratory for Cancer Research, Frederick, Maryland, United States of America
| | - William J. Bosche
- AIDS and Cancer Virus Program, Leidos Biomedical Research Inc., Frederick National Laboratory for Cancer Research, Frederick, Maryland, United States of America
| | - Matthew T. Trivett
- AIDS and Cancer Virus Program, Leidos Biomedical Research Inc., Frederick National Laboratory for Cancer Research, Frederick, Maryland, United States of America
| | - Claes Ohlen
- AIDS and Cancer Virus Program, Leidos Biomedical Research Inc., Frederick National Laboratory for Cancer Research, Frederick, Maryland, United States of America
| | - David E. Ott
- AIDS and Cancer Virus Program, Leidos Biomedical Research Inc., Frederick National Laboratory for Cancer Research, Frederick, Maryland, United States of America
| | - Jacob D. Estes
- AIDS and Cancer Virus Program, Leidos Biomedical Research Inc., Frederick National Laboratory for Cancer Research, Frederick, Maryland, United States of America
| | - Gregory Q. Del Prete
- AIDS and Cancer Virus Program, Leidos Biomedical Research Inc., Frederick National Laboratory for Cancer Research, Frederick, Maryland, United States of America
| | - Jeffrey D. Lifson
- AIDS and Cancer Virus Program, Leidos Biomedical Research Inc., Frederick National Laboratory for Cancer Research, Frederick, Maryland, United States of America
| | - Miles P. Davenport
- Infection Analytics Program, Kirby Institute for Infection and Immunity, UNSW Australia, Sydney, NSW, Australia
- * E-mail: (BFK); (MPD)
| | - Brandon F. Keele
- AIDS and Cancer Virus Program, Leidos Biomedical Research Inc., Frederick National Laboratory for Cancer Research, Frederick, Maryland, United States of America
- * E-mail: (BFK); (MPD)
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Abstract
HIV is a devastating worldwide epidemic that has had substantial social and economic impacts throughout the globe. Due to the presence of a small pool of latently infected cells that persists during antiretroviral therapy (ART), HIV is not curable. Because of the high cost of ART and the lack of reliable accessibility across the globe, life-long ART is unfortunately not a feasible solution for the epidemic. Therefore, new strategies need to be developed and implemented to address HIV-1 infection. Several approaches toward this end are currently under investigation (Ebina et al. in Sci Rep 3:2510, 2013; Archin et al. in Nature 487:482–5, 2012; Elliott et al. in PLoS Pathog 10:e1004473, 2014; Rasmussen et al. in Lancet HIV 1:e13–e21, 2014; Tebas et al. in N Engl J Med 370:901–10, 2014; Archin et al. in Nat Rev Microbiol 12:750–64, 2014; Barton et al. in PLoS One 9:e102684, 2014; Sogaard et al. in PLoS Pathog 11:e1005142, 2015). Initial studies have proven promising, but have highlighted the need for sensitive and accurate assays to detect changes in very low concentrations of virus to allow confident interpretation of the success of curative approaches. This review will focus on assays that are currently available and the advantages and limitations of each.
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Affiliation(s)
- Kirston M. Barton
- Westmead Millennium Institute/University of Sydney, 176 Hawkesbury Road, Westmead, NSW 2145 Australia
| | - Sarah E. Palmer
- Westmead Millennium Institute/University of Sydney, 176 Hawkesbury Road, Westmead, NSW 2145 Australia
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9
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Pereira Ribeiro S, M. Milush J, Cunha-Neto E, G. Kallas E, Kalil J, D. Passero LF, W. Hunt P, G. Deeks S, F. Nixon D, SenGupta D. p16INK4a Expression and Immunologic Aging in Chronic HIV Infection. PLoS One 2016; 11:e0166759. [PMID: 27861555 PMCID: PMC5115792 DOI: 10.1371/journal.pone.0166759] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2016] [Accepted: 11/03/2016] [Indexed: 01/01/2023] Open
Abstract
Chronic HIV infection is characterized by increased immune activation and immunosenescence. p16 INK4a (p16) is a member of the cyclin-dependent kinase antagonist family that inhibits cellular proliferation, and its protein expression increases during normal chronological aging. However, some infectious diseases can increase the expression of this anti-proliferative protein, potentially accelerating immunological aging and dysfunction. In order to investigate the immunological aging in HIV patients, p16 protein expression was evaluated by flow cytometry, in T cell subsets in a cohort of chronically HIV-infected patients on and off ART as well as age-matched healthy controls. Results showed that untreated HIV-infected subjects exhibited increased per-cell p16 protein expression that was discordant with chronological aging. ART restored p16 protein expression to levels comparable with HIV-negative subjects in the CD4 compartment, but not in CD8 T cells, which can be an indicative of an irreversible activation/exhaustion status on these cells. Additionally, the frequency of activated CD4+ and CD8+ T cells was positively correlated with p16 expression in CD4+ and CD8+ T cells in untreated subjects. In contrast to healthy controls, untreated HIV-infected individuals had increased p16 levels within the effector memory (TEM) subset, indicating a possible role for this marker in impaired clonal expansion during antiviral effector function. Taken together, these data demonstrate that chronic HIV infection is associated with elevated expression of the cellular aging marker p16 in T cells. ART restored normal p16 levels in the CD4+ T cell compartment, indicating that use of therapy can be of fundamental importance to normal cell cycling and maintaining immune homeostasis.
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Affiliation(s)
- Susan Pereira Ribeiro
- Laboratory of Clinical Immunology and Allergy-LIM60/ University of Sao Paulo School of Medicine, São Paulo, Brazil
- Institute of Investigation in Immunology–iii-INCT, São Paulo, Brazil
- Department of Pathology, Case Western Reserve University, Cleveland, Ohio, United States of America
- * E-mail:
| | - Jeffrey M. Milush
- Division of Experimental Medicine, Department of Medicine, University of California San Francisco, San Francisco, California, United States of America
| | - Edecio Cunha-Neto
- Laboratory of Clinical Immunology and Allergy-LIM60/ University of Sao Paulo School of Medicine, São Paulo, Brazil
- Institute of Investigation in Immunology–iii-INCT, São Paulo, Brazil
- Laboratory of Immunology, Heart Institute, University of Sao Paulo School of Medicine, São Paulo, Brazil
| | - Esper G. Kallas
- Laboratory of Clinical Immunology and Allergy-LIM60/ University of Sao Paulo School of Medicine, São Paulo, Brazil
- Institute of Investigation in Immunology–iii-INCT, São Paulo, Brazil
| | - Jorge Kalil
- Laboratory of Clinical Immunology and Allergy-LIM60/ University of Sao Paulo School of Medicine, São Paulo, Brazil
- Institute of Investigation in Immunology–iii-INCT, São Paulo, Brazil
- Laboratory of Immunology, Heart Institute, University of Sao Paulo School of Medicine, São Paulo, Brazil
- Butantan Institute, Butantan, São Paulo, SP, Brazil
| | - Luiz Felipe D. Passero
- São Vicent Unit, Paulista Coastal Campus, São Paulo State University "Julio de Mesquita Filho", Sao Paulo, Brazil
| | - Peter W. Hunt
- HIV/AIDS Division, Department of Medicine, San Francisco General Hospital, University of California, San Francisco, California, United States of America
| | - Steven G. Deeks
- HIV/AIDS Division, Department of Medicine, San Francisco General Hospital, University of California, San Francisco, California, United States of America
| | - Douglas F. Nixon
- Department of Microbiology, Immunology & Tropical Medicine, The George Washington University, Washington DC, United States of America
| | - Devi SenGupta
- Division of Experimental Medicine, Department of Medicine, University of California San Francisco, San Francisco, California, United States of America
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