1
|
Kuzmichev YV, Lackman-Smith C, Bakkour S, Wiegand A, Bale MJ, Musick A, Bernstein W, Aronson N, Ake J, Tovanabutra S, Stone M, Ptak RG, Kearney MF, Busch MP, Wonderlich ER, Kulpa DA. Application of ultrasensitive digital ELISA for p24 enables improved evaluation of HIV-1 reservoir diversity and growth kinetics in viral outgrowth assays. Sci Rep 2023; 13:10958. [PMID: 37414788 PMCID: PMC10326067 DOI: 10.1038/s41598-023-37223-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2022] [Accepted: 06/18/2023] [Indexed: 07/08/2023] Open
Abstract
The advent of combined antiretroviral therapy (cART) has been instrumental in controlling HIV-1 replication and transmission and decreasing associated morbidity and mortality. However, cART alone is not able to cure HIV-1 due to the presence of long-lived, latently infected immune cells, which re-seed plasma viremia when cART is interrupted. Assessment of HIV-cure strategies using ex vivo culture methods for further understanding of the diversity of reactivated HIV, viral outgrowth, and replication dynamics are enhanced using ultrasensitive digital ELISA based on single-molecule array (Simoa) technology to increase the sensitivity of endpoint detection. In viral outgrowth assays (VOA), exponential HIV-1 outgrowth has been shown to be dependent upon initial virus burst size surpassing a critical growth threshold of 5100 HIV-1 RNA copies. Here, we show an association between ultrasensitive HIV-1 Gag p24 concentrations and HIV-1 RNA copy number that characterize viral dynamics below the exponential replication threshold. Single-genome sequencing (SGS) revealed the presence of multiple identical HIV-1 sequences, indicative of low-level replication occurring below the threshold of exponential outgrowth early during a VOA. However, SGS further revealed diverse related HIV variants detectable by ultrasensitive methods that failed to establish exponential outgrowth. Overall, our data suggest that viral outgrowth occurring below the threshold necessary for establishing exponential growth in culture does not preclude replication competence of reactivated HIV, and ultrasensitive detection of HIV-1 p24 may provide a method to detect previously unquantifiable variants. These data strongly support the use of the Simoa platform in a multi-prong approach to measuring latent viral burden and efficacy of therapeutic interventions aimed at an HIV-1 cure.
Collapse
Affiliation(s)
- Yury V Kuzmichev
- Division of Microbiology and Immunology, Emory National Primate Research Center, Emory University, Atlanta, GA, USA.
- Department of Infectious Disease Research, Southern Research, Frederick, MD, USA.
| | - Carol Lackman-Smith
- Department of Infectious Disease Research, Southern Research, Frederick, MD, USA
| | - Sonia Bakkour
- Vitalant Research Institute, San Francisco, CA, USA
- Department of Laboratory Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Ann Wiegand
- HIV Dynamics and Replication Program, NCI at Frederick, NIH, Frederick, MD, USA
| | - Michael J Bale
- HIV Dynamics and Replication Program, NCI at Frederick, NIH, Frederick, MD, USA
- Laboratory of Epigenetics and Immunity, Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Andrew Musick
- HIV Dynamics and Replication Program, NCI at Frederick, NIH, Frederick, MD, USA
| | - Wendy Bernstein
- Uniformed Services University, Bethesda, MD, USA
- Walter Reed National Military Medical Center, Bethesda, MD, USA
| | - Naomi Aronson
- Uniformed Services University, Bethesda, MD, USA
- Walter Reed National Military Medical Center, Bethesda, MD, USA
| | - Julie Ake
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD, USA
| | - Sodsai Tovanabutra
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD, USA
| | - Mars Stone
- Vitalant Research Institute, San Francisco, CA, USA
- Department of Laboratory Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Roger G Ptak
- Department of Infectious Disease Research, Southern Research, Frederick, MD, USA
| | - Mary F Kearney
- HIV Dynamics and Replication Program, NCI at Frederick, NIH, Frederick, MD, USA
| | - Michael P Busch
- Vitalant Research Institute, San Francisco, CA, USA
- Department of Laboratory Medicine, University of California San Francisco, San Francisco, CA, USA
| | | | - Deanna A Kulpa
- Division of Microbiology and Immunology, Emory National Primate Research Center, Emory University, Atlanta, GA, USA.
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, GA, USA.
| |
Collapse
|
2
|
Dwivedi AK, Siegel DA, Thanh C, Hoh R, Hobbs KS, Pan T, Gibson EA, Martin J, Hecht F, Pilcher C, Milush J, Busch MP, Stone M, Huang ML, Levy CN, Roychoudhury P, Hladik F, Jerome KR, Henrich TJ, Deeks SG, Lee SA. Differences in expression of tumor suppressor, innate immune, inflammasome, and potassium/gap junction channel host genes significantly predict viral reservoir size during treated HIV infection. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.01.10.523535. [PMID: 36712077 PMCID: PMC9882059 DOI: 10.1101/2023.01.10.523535] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
The major barrier to an HIV cure is the persistence of infected cells that evade host immune surveillance despite effective antiretroviral therapy (ART). Most prior host genetic HIV studies have focused on identifying DNA polymorphisms (e.g., CCR5Δ32 , MHC class I alleles) associated with viral load among untreated "elite controllers" (~1% of HIV+ individuals who are able to control virus without ART). However, there have been few studies evaluating host genetic predictors of viral control for the majority of people living with HIV (PLWH) on ART. We performed host RNA sequencing and HIV reservoir quantification (total DNA, unspliced RNA, intact DNA) from peripheral CD4+ T cells from 191 HIV+ ART-suppressed non-controllers. Multivariate models included covariates for timing of ART initiation, nadir CD4+ count, age, sex, and ancestry. Lower HIV total DNA (an estimate of the total reservoir) was associated with upregulation of tumor suppressor genes NBL1 (q=0.012) and P3H3 (q=0.012). Higher HIV unspliced RNA (an estimate of residual HIV transcription) was associated with downregulation of several host genes involving inflammasome ( IL1A, CSF3, TNFAIP5, TNFAIP6, TNFAIP9 , CXCL3, CXCL10 ) and innate immune ( TLR7 ) signaling, as well as novel associations with potassium ( KCNJ2 ) and gap junction ( GJB2 ) channels, all q<0.05. Gene set enrichment analyses identified significant associations with TLR4/microbial translocation (q=0.006), IL-1β/NRLP3 inflammasome (q=0.008), and IL-10 (q=0.037) signaling. HIV intact DNA (an estimate of the "replication-competent" reservoir) demonstrated trends with thrombin degradation ( PLGLB1 ) and glucose metabolism ( AGL ) genes, but data were (HIV intact DNA detected in only 42% of participants). Our findings demonstrate that among treated PLWH, that inflammation, innate immune responses, bacterial translocation, and tumor suppression/cell proliferation host signaling play a key role in the maintenance of the HIV reservoir during ART. Further data are needed to validate these findings, including functional genomic studies, and expanded epidemiologic studies in female, non-European cohorts. Author Summary Although lifelong HIV antiretroviral therapy (ART) suppresses virus, the major barrier to an HIV cure is the persistence of infected cells that evade host immune surveillance despite effective ART, "the HIV reservoir." HIV eradication strategies have focused on eliminating residual virus to allow for HIV remission, but HIV cure trials to date have thus far failed to show a clinically meaningful reduction in the HIV reservoir. There is an urgent need for a better understanding of the host-viral dynamics during ART suppression to identify potential novel therapeutic targets for HIV cure. This is the first epidemiologic host gene expression study to demonstrate a significant link between HIV reservoir size and several well-known immunologic pathways (e.g., IL-1β, TLR7, TNF-α signaling pathways), as well as novel associations with potassium and gap junction channels (Kir2.1, connexin 26). Further data are needed to validate these findings, including functional genomic studies and expanded epidemiologic studies in female, non-European cohorts.
Collapse
|
3
|
Mbonye U, Kizito F, Karn J. New insights into transcription elongation control of HIV-1 latency and rebound. Trends Immunol 2023; 44:60-71. [PMID: 36503686 DOI: 10.1016/j.it.2022.11.003] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2022] [Revised: 11/07/2022] [Accepted: 11/09/2022] [Indexed: 12/13/2022]
Abstract
Antiretroviral therapy reduces circulating HIV-1 to undetectable amounts but does not eliminate the virus due to the persistence of a stable reservoir of latently infected cells. The reservoir is maintained both by proliferation of latently infected cells and by reseeding from reactivated cells. A major challenge for the field is to find safe and effective methods to eliminate this source of rebounding HIV-1. Studies on the molecular mechanisms leading to HIV-1 latency and reactivation are being transformed using latency models in primary and patient CD4+ T cells. These studies have revealed the central role played by the biogenesis of the transcription elongation factor P-TEFb (Positive Transcription Elongation Factor b) and its recruitment to proviral HIV-1, for the maintenance of viral latency and the control of viral reactivation.
Collapse
Affiliation(s)
- Uri Mbonye
- Department of Molecular Biology and Microbiology, Case Western Reserve University, Cleveland, OH, USA
| | - Fredrick Kizito
- Department of Molecular Biology and Microbiology, Case Western Reserve University, Cleveland, OH, USA
| | - Jonathan Karn
- Department of Molecular Biology and Microbiology, Case Western Reserve University, Cleveland, OH, USA.
| |
Collapse
|
4
|
Kreider EF, Bar KJ. HIV-1 Reservoir Persistence and Decay: Implications for Cure Strategies. Curr HIV/AIDS Rep 2022; 19:194-206. [PMID: 35404007 PMCID: PMC10443186 DOI: 10.1007/s11904-022-00604-2] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/25/2022] [Indexed: 02/06/2023]
Abstract
PURPOSE OF REVIEW Despite suppressive antiretroviral therapy (ART), a viral reservoir persists in individuals living with HIV that can reignite systemic replication should treatment be interrupted. Understanding how HIV-1 persists through effective ART is essential to develop cure strategies to induce ART-free virus remission. RECENT FINDINGS The HIV-1 reservoir resides in a pool of CD4-expressing cells as a range of viral species, a subset of which is genetically intact. Recent studies suggest that the reservoir on ART is highly dynamic, with expansion and contraction of virus-infected cells over time. Overall, the intact proviral reservoir declines faster than defective viruses, suggesting enhanced immune clearance or cellular turnover. Upon treatment interruption, rebound viruses demonstrate escape from adaptive and innate immune responses, implicating these selective pressures in restriction of virus reactivation. Cure strategies employing immunotherapy are poised to test whether host immune pressure can be augmented to enhance reservoir suppression or clearance. Alternatively, genomic engineering approaches are being applied to directly eliminate intact viruses and shrink the replication-competent virus pool. New evidence suggests host immunity exerts selective pressure on reservoir viruses and clears HIV-1 infected cells over years on ART. Efforts to build on the detectable, but insufficient, reservoir clearance via empiric testing in clinical trials will inform our understanding of mechanisms of viral persistence and the direction of future cure strategies.
Collapse
Affiliation(s)
- Edward F Kreider
- Perelman School of Medicine, University of Pennsylvania, Stemmler Hall Room 130-150, 3450 Hamilton Walk, Philadelphia, PA, 19104-6073, USA
| | - Katharine J Bar
- Perelman School of Medicine, University of Pennsylvania, 502D Johnson Pavilion, 3610 Hamilton Walk, Philadelphia, PA, 19104‑0673, USA.
| |
Collapse
|
5
|
Miller JS, Davis ZB, Helgeson E, Reilly C, Thorkelson A, Anderson J, Lima NS, Jorstad S, Hart GT, Lee JH, Safrit JT, Wong H, Cooley S, Gharu L, Chung H, Soon-Shiong P, Dobrowolski C, Fletcher CV, Karn J, Douek DC, Schacker TW. Safety and virologic impact of the IL-15 superagonist N-803 in people living with HIV: a phase 1 trial. Nat Med 2022; 28:392-400. [DOI: 10.1038/s41591-021-01651-9] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2020] [Accepted: 11/30/2021] [Indexed: 12/26/2022]
|
6
|
Wonderlich ER, Reece MD, Kulpa DA. Ex Vivo Differentiation of Resting CD4+ T Lymphocytes Enhances Detection of Replication Competent HIV-1 in Viral Outgrowth Assays. Methods Mol Biol 2022; 2407:315-331. [PMID: 34985673 DOI: 10.1007/978-1-0716-1871-4_21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Quantifying the number of cells harboring inducible and replication competent HIV-1 provirus is critical to evaluating HIV-1 cure interventions, but precise quantification of the latent reservoir has proven to be technically challenging. Existing protocols to quantify the frequency of replication-competent HIV-1 in resting CD4+ T cells from long-term ART treated individuals have helped to investigate the dynamics of reservoir stability, however these approaches have significant barriers to the induction of HIV-1 expression required to effectively evaluate the intact reservoir. Differentiation of CD4+ T cells to an effector memory phenotype is a successful strategy for promoting latency reversal in vitro, and significantly enhances the performance and sensitivity of viral outgrowth assays.
Collapse
Affiliation(s)
| | - Monica D Reece
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, and Yerkes National Primate Research Center, Atlanta, GA, USA
| | - Deanna A Kulpa
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, and Yerkes National Primate Research Center, Atlanta, GA, USA.
| |
Collapse
|
7
|
Abstract
Recently the Tat/rev Induced Limiting Dilution Assay, or TILDA, has been proposed as a possible alternative method to quantify the HIV-1 reservoir. TILDA estimates the frequency of latently infected cells by probing, in a limiting dilution format, the presence or inducibility of tat and rev multiply spliced HIV-1 RNA. In doing so, TILDA reduces overestimation of reservoir size compared to HIV-1 DNA measurements because multiply spliced HIV-1 RNA is less likely to be transcribed from dysfunctional genomes with replication defects. TILDA is easy to perform, requires a very low input number of cells and has a fast turnaround time, making it ideal for use in clinical settings. Here we describe the execution of TILDA with particular emphasis on cell preparation and the limiting dilution scheme.
Collapse
Affiliation(s)
- Cynthia Lungu
- Department of Viroscience, Erasmus University Medical Center, Rotterdam, Netherlands
| | - Francesco A Procopio
- Department of Immunology and Allergy, Lausanne University Hospital, Lausanne, Switzerland.
| |
Collapse
|
8
|
Malatinkova E, Thomas J, De Spiegelaere W, Rutsaert S, Geretti AM, Pollakis G, Paxton WA, Vandekerckhove L, Ruggiero A. Measuring Proviral HIV-1 DNA: Hurdles and Improvements to an Assay Monitoring Integration Events Utilising Human Alu Repeat Sequences. Life (Basel) 2021; 11:life11121410. [PMID: 34947941 PMCID: PMC8706387 DOI: 10.3390/life11121410] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Revised: 12/13/2021] [Accepted: 12/13/2021] [Indexed: 12/28/2022] Open
Abstract
Integrated HIV-1 DNA persists despite antiretroviral therapy and can fuel viral rebound following treatment interruption. Hence, methods to specifically measure the integrated HIV-1 DNA portion only are important to monitor the reservoir in eradication trials. Here, we provide an up-to-date overview of the literature on the different approaches used to measure integrated HIV-1 DNA. Further, we propose an implemented standard-curve free assay to quantify integrated HIV-1 DNA, so-called Alu-5LTR PCR, which utilises novel primer combinations. We tested the Alu-5LTR PCR in 20 individuals on suppressive ART for a median of nine years; the results were compared to those produced with the standard-free Alu-gag assay. The numbers of median integrated HIV-1 DNA copies were 5 (range: 1–12) and 14 (5–26) with the Alu-gag and Alu-5LTR, respectively. The ratios between Alu-gag vs Alu-5LTR results were distributed within the cohort as follows: most patients (12/20, 60%) provided ratios between 2–5, with 3/20 (15%) and 5/20 (25%) being below or above this range, respectively. Alu-5LTR assay sensitivity was also determined using an “integrated standard”; the data confirmed the increased sensitivity of the assay, i.e., equal to 0.25 proviruses in 10,000 genomes. This work represents an improvement in the field of measuring proviral HIV-1 DNA that could be employed in future HIV-1 persistence and eradication studies.
Collapse
Affiliation(s)
- Eva Malatinkova
- HIV Cure Research Center, Department of Internal Medicine, Faculty of Medicine and Health Sciences, Ghent University, B-9000 Ghent, Belgium; (E.M.); (S.R.); (L.V.)
| | - Jordan Thomas
- Department of Clinical Infection, Microbiology and Immunology, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool L69 7BE, UK; (J.T.); (G.P.); (W.A.P.)
| | - Ward De Spiegelaere
- Laboratory of Veterinary Morphology, Faculty of Veterinary Sciences, Ghent University, B-9820 Ghent, Belgium;
| | - Sofie Rutsaert
- HIV Cure Research Center, Department of Internal Medicine, Faculty of Medicine and Health Sciences, Ghent University, B-9000 Ghent, Belgium; (E.M.); (S.R.); (L.V.)
| | - Anna Maria Geretti
- Fondazione PTV and Faculty of Medicine, University of Rome Tor Vergata, 00133 Rome, Italy;
- School of Immunology & Microbial Sciences, King’s College London, London WC2R 2LS, UK
| | - Georgios Pollakis
- Department of Clinical Infection, Microbiology and Immunology, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool L69 7BE, UK; (J.T.); (G.P.); (W.A.P.)
| | - William A. Paxton
- Department of Clinical Infection, Microbiology and Immunology, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool L69 7BE, UK; (J.T.); (G.P.); (W.A.P.)
| | - Linos Vandekerckhove
- HIV Cure Research Center, Department of Internal Medicine, Faculty of Medicine and Health Sciences, Ghent University, B-9000 Ghent, Belgium; (E.M.); (S.R.); (L.V.)
| | - Alessandra Ruggiero
- Department of Clinical Infection, Microbiology and Immunology, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool L69 7BE, UK; (J.T.); (G.P.); (W.A.P.)
- Department Neurosciences, Biomedicine and Movement Sciences, School of Medicine-University of Verona, 37129 Verona, Italy
- Correspondence: ; Tel.: +39-045-802-7190
| |
Collapse
|
9
|
Lungu C, Banga R, Gruters RA, Procopio FA. Inducible HIV-1 Reservoir Quantification: Clinical Relevance, Applications and Advancements of TILDA. Front Microbiol 2021; 12:686690. [PMID: 34211450 PMCID: PMC8239294 DOI: 10.3389/fmicb.2021.686690] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2021] [Accepted: 05/21/2021] [Indexed: 01/07/2023] Open
Abstract
The presence of a stable HIV-1 reservoir persisting over time despite effective antiretroviral suppression therapy precludes a cure for HIV-1. Characterizing and quantifying this residual reservoir is considered an essential prerequisite to develop and validate curative strategies. However, a sensitive, reproducible, cost-effective, and easily executable test is still needed. The quantitative viral outgrowth assay is considered the gold standard approach to quantify the reservoir in HIV-1-infected patients on suppressive ART, but it has several limitations. An alternative method to quantify the viral reservoir following the reactivation of latent HIV-1 provirus detects multiply-spliced tat/rev RNA (msRNA) molecules by real-time PCR [tat/rev induced limiting dilution assay (TILDA)]. This article provides a perspective overview of the clinical relevance, various applications, recent advancements of TILDA, and how the assay has contributed to our understanding of the HIV-1 reservoir.
Collapse
Affiliation(s)
- Cynthia Lungu
- Department of Viroscience, Erasmus University Medical Center, Rotterdam, Netherlands
| | - Riddhima Banga
- Department of Immunology and Allergy, Lausanne University Hospital, Lausanne, Switzerland
| | - Rob A. Gruters
- Department of Viroscience, Erasmus University Medical Center, Rotterdam, Netherlands
| | - Francesco A. Procopio
- Department of Immunology and Allergy, Lausanne University Hospital, Lausanne, Switzerland,*Correspondence: Francesco A. Procopio,
| |
Collapse
|
10
|
Immonen TT, Fennessey CM, Lipkey L, Thorpe A, Del Prete GQ, Lifson JD, Davenport MP, Keele BF. Transient viral replication during analytical treatment interruptions in SIV infected macaques can alter the rebound-competent viral reservoir. PLoS Pathog 2021; 17:e1009686. [PMID: 34143853 PMCID: PMC8244872 DOI: 10.1371/journal.ppat.1009686] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Revised: 06/30/2021] [Accepted: 06/02/2021] [Indexed: 02/07/2023] Open
Abstract
Analytical treatment interruptions (ATIs) of antiretroviral therapy (ART) play a central role in evaluating the efficacy of HIV-1 treatment strategies targeting virus that persists despite ART. However, it remains unclear if ATIs alter the rebound-competent viral reservoir (RCVR), the virus population that persists during ART and from which viral recrudescence originates after ART discontinuation. To assess the impact of ATIs on the RCVR, we used a barcode sequence tagged SIV to track individual viral lineages through a series of ATIs in Rhesus macaques. We demonstrate that transient replication of individual rebounding lineages during an ATI can lead to their enrichment in the RCVR, increasing their probability of reactivating again after treatment discontinuation. These data establish that the RCVR can be altered by uncontrolled replication during ATI.
Collapse
Affiliation(s)
- Taina T. Immonen
- AIDS and Cancer Virus Program, Frederick National Laboratory, Frederick, Maryland, United States of America
| | - Christine M. Fennessey
- AIDS and Cancer Virus Program, Frederick National Laboratory, Frederick, Maryland, United States of America
| | - Leslie Lipkey
- AIDS and Cancer Virus Program, Frederick National Laboratory, Frederick, Maryland, United States of America
| | - Abigail Thorpe
- AIDS and Cancer Virus Program, Frederick National Laboratory, Frederick, Maryland, United States of America
| | - Gregory Q. Del Prete
- AIDS and Cancer Virus Program, Frederick National Laboratory, Frederick, Maryland, United States of America
| | - Jeffrey D. Lifson
- AIDS and Cancer Virus Program, Frederick National Laboratory, Frederick, Maryland, United States of America
| | - Miles P. Davenport
- Infection Analytics Program, Kirby Institute for Infection and Immunity, University of New South Wales, Sydney, New South Wales, Australia
| | - Brandon F. Keele
- AIDS and Cancer Virus Program, Frederick National Laboratory, Frederick, Maryland, United States of America
| |
Collapse
|
11
|
Lungu C, Procopio FA, Overmars RJ, Beerkens RJJ, Voermans JJC, Rao S, Prins HAB, Rokx C, Pantaleo G, van de Vijver DAMC, Mahmoudi T, Boucher CAB, Gruters RA, van Kampen JJA. Inter-Laboratory Reproducibility of Inducible HIV-1 Reservoir Quantification by TILDA. Viruses 2020; 12:v12090973. [PMID: 32887284 PMCID: PMC7552071 DOI: 10.3390/v12090973] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2020] [Revised: 08/29/2020] [Accepted: 08/31/2020] [Indexed: 12/16/2022] Open
Abstract
Substantial efforts to eliminate or reduce latent HIV-1 reservoirs are underway in clinical trials and have created a critical demand for sensitive, accurate, and reproducible tools to evaluate the efficacy of these strategies. Alternative reservoir quantification assays have been developed to circumvent limitations of the quantitative viral outgrowth assay. One such assay is tat/rev induced limiting dilution assay (TILDA), which measures the frequency of CD4+ T cells harboring inducible latent HIV-1 provirus. We modified pre-amplification reagents and conditions (TILDA v2.0) to improve assay execution and first internally validated assay performance using CD4+ T cells obtained from cART-suppressed HIV-1-infected individuals. Detection of tat/rev multiply spliced RNA was not altered by modifying pre-amplification conditions, confirming the robustness of the assay, and supporting the technique’s amenability to limited modifications to ensure better implementation for routine use in clinical studies of latent HIV-1 reservoirs. Furthermore, we cross-validated results of TILDA v2.0 and the original assay performed in two separate laboratories using samples from 15 HIV-1-infected individuals. TILDA and TILDA v2.0 showed a strong correlation (Lin’s Concordance Correlation Coefficient = 0.86). The low inter-laboratory variability between TILDAs performed at different institutes further supports use of TILDA for reservoir quantitation in multi-center interventional HIV-1 Cure trials.
Collapse
Affiliation(s)
- Cynthia Lungu
- Department of Viroscience, Erasmus University Medical Center, 3015 GD Rotterdam, The Netherlands; (R.J.O.); (R.J.J.B.); (J.J.C.V.); (D.A.M.C.v.d.V.); (C.A.B.B.); (R.A.G.); (J.J.A.v.K.)
- Correspondence:
| | - Francesco A. Procopio
- Service of Immunology and Allergy, Lausanne University Hospital, University of Lausanne, 1011 Lausanne, Switzerland; (F.A.P.); (G.P.)
| | - Ronald J. Overmars
- Department of Viroscience, Erasmus University Medical Center, 3015 GD Rotterdam, The Netherlands; (R.J.O.); (R.J.J.B.); (J.J.C.V.); (D.A.M.C.v.d.V.); (C.A.B.B.); (R.A.G.); (J.J.A.v.K.)
| | - Rob J. J. Beerkens
- Department of Viroscience, Erasmus University Medical Center, 3015 GD Rotterdam, The Netherlands; (R.J.O.); (R.J.J.B.); (J.J.C.V.); (D.A.M.C.v.d.V.); (C.A.B.B.); (R.A.G.); (J.J.A.v.K.)
| | - Jolanda J. C. Voermans
- Department of Viroscience, Erasmus University Medical Center, 3015 GD Rotterdam, The Netherlands; (R.J.O.); (R.J.J.B.); (J.J.C.V.); (D.A.M.C.v.d.V.); (C.A.B.B.); (R.A.G.); (J.J.A.v.K.)
| | - Shringar Rao
- Department of Biochemistry, Erasmus University Medical Center, 3015 GD Rotterdam, The Netherlands; (S.R.); (T.M.)
| | - Henrieke A. B. Prins
- Department of Internal Medicine, Section of Infectious Diseases, Erasmus University Medical Center, 3015 GD Rotterdam, The Netherlands; (H.A.B.P.); (C.R.)
| | - Casper Rokx
- Department of Internal Medicine, Section of Infectious Diseases, Erasmus University Medical Center, 3015 GD Rotterdam, The Netherlands; (H.A.B.P.); (C.R.)
| | - Giuseppe Pantaleo
- Service of Immunology and Allergy, Lausanne University Hospital, University of Lausanne, 1011 Lausanne, Switzerland; (F.A.P.); (G.P.)
| | - David A. M. C. van de Vijver
- Department of Viroscience, Erasmus University Medical Center, 3015 GD Rotterdam, The Netherlands; (R.J.O.); (R.J.J.B.); (J.J.C.V.); (D.A.M.C.v.d.V.); (C.A.B.B.); (R.A.G.); (J.J.A.v.K.)
| | - Tokameh Mahmoudi
- Department of Biochemistry, Erasmus University Medical Center, 3015 GD Rotterdam, The Netherlands; (S.R.); (T.M.)
| | - Charles A. B. Boucher
- Department of Viroscience, Erasmus University Medical Center, 3015 GD Rotterdam, The Netherlands; (R.J.O.); (R.J.J.B.); (J.J.C.V.); (D.A.M.C.v.d.V.); (C.A.B.B.); (R.A.G.); (J.J.A.v.K.)
| | - Rob A. Gruters
- Department of Viroscience, Erasmus University Medical Center, 3015 GD Rotterdam, The Netherlands; (R.J.O.); (R.J.J.B.); (J.J.C.V.); (D.A.M.C.v.d.V.); (C.A.B.B.); (R.A.G.); (J.J.A.v.K.)
| | - Jeroen J. A. van Kampen
- Department of Viroscience, Erasmus University Medical Center, 3015 GD Rotterdam, The Netherlands; (R.J.O.); (R.J.J.B.); (J.J.C.V.); (D.A.M.C.v.d.V.); (C.A.B.B.); (R.A.G.); (J.J.A.v.K.)
| |
Collapse
|
12
|
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] [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.
Collapse
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
| | | |
Collapse
|
13
|
Stuelke EL, James KS, Kirchherr JL, Allard B, Baker C, Kuruc JD, Gay CL, Margolis DM, Archin NM. Measuring the Inducible, Replication-Competent HIV Reservoir Using an Ultra-Sensitive p24 Readout, the Digital ELISA Viral Outgrowth Assay. Front Immunol 2020; 11:1971. [PMID: 32849659 PMCID: PMC7423995 DOI: 10.3389/fimmu.2020.01971] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2020] [Accepted: 07/21/2020] [Indexed: 12/16/2022] Open
Abstract
Quantifying the inducible HIV reservoir provides an estimate of the frequency of quiescent HIV-infected cells in humans as well as in animal models, and can help ascertain the efficacy of latency reversing agents (LRAs). The quantitative viral outgrowth assay (QVOA) is used to measure inducible, replication competent HIV and generate estimations of reservoir size. However, traditional QVOA is time and labor intensive and requires large amounts of lymphocytes. Given the importance of reproducible and accurate assessment of both reservoir size and LRA activity in cure strategies, efforts to streamline the QVOA are of high priority. We developed a modified QVOA, the Digital ELISA Viral Outgrowth or DEVO assay, with ultra-sensitive p24 readout, capable of femtogram detection of HIV p24 protein in contrast to the picogram limitations of traditional ELISA. For each DEVO assay, 8–12 × 106 resting CD4 + T cells from aviremic, ART-treated HIV + participants are plated in limiting dilution and maximally stimulated with PHA, IL-2 and uninfected allogeneic irradiated PBMC. CD8-depleted PHA blasts from an uninfected donor or HIV-permissive cells (e.g., Molt4/CCR5) are added to the cultures and virus allowed to amplify for 8–12 days. HIV p24 from culture supernatant is measured at day 8 by Simoa (single molecule array, ultra-sensitive p24 assay) confirmed at day 12, and infectious units per million CD4 + T cells (IUPM) are calculated using the maximum likelihood method. In all DEVO assays performed, HIV p24 was detected in the supernatant of cultures as early as 8 days post stimulation. Importantly, DEVO IUPM values at day 8 were comparable or higher than traditional QVOA IUPM values obtained at day 15. Interestingly, DEVO IUPM values were similar with or without the addition of allogeneic CD8-depleted target PHA blasts or HIV permissive cells traditionally used to expand virus. The DEVO assay uses fewer resting CD4 + T cells and provides an assessment of reservoir size in less time than standard QVOA. This assay offers a new platform to quantify replication competent HIV during limited cell availability. Other potential applications include evaluating LRA activity, and measuring clearance of infected cells during latency clearance assays.
Collapse
Affiliation(s)
- Erin L Stuelke
- University of North Carolina HIV Cure Center, UNC Institute for Global Health and Infectious Diseases, Chapel Hill, NC, United States
| | - Katherine S James
- University of North Carolina HIV Cure Center, UNC Institute for Global Health and Infectious Diseases, Chapel Hill, NC, United States
| | - Jennifer L Kirchherr
- University of North Carolina HIV Cure Center, UNC Institute for Global Health and Infectious Diseases, Chapel Hill, NC, United States
| | - Brigitte Allard
- University of North Carolina HIV Cure Center, UNC Institute for Global Health and Infectious Diseases, Chapel Hill, NC, United States
| | - Caroline Baker
- University of North Carolina HIV Cure Center, UNC Institute for Global Health and Infectious Diseases, Chapel Hill, NC, United States
| | - Joann D Kuruc
- University of North Carolina HIV Cure Center, UNC Institute for Global Health and Infectious Diseases, Chapel Hill, NC, United States.,Department of Medicine, UNC Chapel Hill School of Medicine, Chapel Hill, NC, United States
| | - Cindy L Gay
- University of North Carolina HIV Cure Center, UNC Institute for Global Health and Infectious Diseases, Chapel Hill, NC, United States.,Department of Medicine, UNC Chapel Hill School of Medicine, Chapel Hill, NC, United States
| | - David M Margolis
- University of North Carolina HIV Cure Center, UNC Institute for Global Health and Infectious Diseases, Chapel Hill, NC, United States.,Department of Medicine, UNC Chapel Hill School of Medicine, Chapel Hill, NC, United States.,Department of Microbiology and Immunology, UNC Chapel Hill School of Medicine, Chapel Hill, NC, United States.,Department of Epidemiology, UNC Chapel Hill School of Public Health, The University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Nancie M Archin
- University of North Carolina HIV Cure Center, UNC Institute for Global Health and Infectious Diseases, Chapel Hill, NC, United States.,Department of Medicine, UNC Chapel Hill School of Medicine, Chapel Hill, NC, United States
| |
Collapse
|
14
|
Thomas J, Ruggiero A, Paxton WA, Pollakis G. Measuring the Success of HIV-1 Cure Strategies. Front Cell Infect Microbiol 2020; 10:134. [PMID: 32318356 PMCID: PMC7154081 DOI: 10.3389/fcimb.2020.00134] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2020] [Accepted: 03/13/2020] [Indexed: 01/10/2023] Open
Abstract
HIV-1 eradication strategies aim to achieve viral remission in the absence of antiretroviral therapy (ART). The development of an HIV-1 cure remains challenging due to the latent reservoir (LR): long-lived CD4 T cells that harbor transcriptionally silent HIV-1 provirus. The LR is stable despite years of suppressive ART and is the source of rebound viremia following therapy interruption. Cure strategies such as "shock and kill" aim to eliminate or reduce the LR by reversing latency, exposing the infected cells to clearance via the immune response or the viral cytopathic effect. Alternative strategies include therapeutic vaccination, which aims to prime the immune response to facilitate control of the virus in the absence of ART. Despite promising advances, these strategies have been unable to significantly reduce the LR or increase the time to viral rebound but have provided invaluable insight in the field of HIV-1 eradication. The development and assessment of an HIV-1 cure requires robust assays that can measure the LR with sufficient sensitivity to detect changes that may occur following treatment. The viral outgrowth assay (VOA) is considered the gold standard method for LR quantification due to its ability to distinguish intact and defective provirus. However, the VOA is time consuming and resource intensive, therefore several alternative assays have been developed to bridge the gap between practicality and accuracy. Whilst a cure for HIV-1 infection remains elusive, recent advances in our understanding of the LR and methods for its eradication have offered renewed hope regarding achieving ART free viral remission.
Collapse
Affiliation(s)
- Jordan Thomas
- Department of Clinical Infection, Microbiology and Immunology, Institute of Infection and Global Health, University of Liverpool, Liverpool, United Kingdom
| | - Alessandra Ruggiero
- Department of Clinical Infection, Microbiology and Immunology, Institute of Infection and Global Health, University of Liverpool, Liverpool, United Kingdom.,Immune and Infectious Disease Division, Academic Department of Pediatrics (DPUO), Bambino Gesù Children's Hospital, Rome, Italy
| | - William A Paxton
- Department of Clinical Infection, Microbiology and Immunology, Institute of Infection and Global Health, University of Liverpool, Liverpool, United Kingdom
| | - Georgios Pollakis
- Department of Clinical Infection, Microbiology and Immunology, Institute of Infection and Global Health, University of Liverpool, Liverpool, United Kingdom
| |
Collapse
|
15
|
Stone M, Rosenbloom D, Bacchetti P, Deng X, Dimapasoc M, Keating S, Bakkour S, Richman D, Mellors J, Deeks S, Lai J, Beg S, Siliciano J, Pagliuzza A, Chomont N, Lackman-Smith C, Ptak RG, Busch MP. Assessing suitability of next-generation viral outgrowth assays as proxies for classic QVOA to measure HIV-1 latent reservoir size. J Infect Dis 2020; 224:1209-1218. [PMID: 32147687 PMCID: PMC8514180 DOI: 10.1093/infdis/jiaa089] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2019] [Accepted: 03/06/2020] [Indexed: 01/20/2023] Open
Abstract
Background Evaluations of human immunodeficiency virus (HIV) curative interventions require reliable and efficient quantification of replication-competent latent reservoirs. The “classic” quantitative viral outgrowth assay (QVOA) has been regarded as the reference standard, although prohibitively resource and labor intensive. We compared 6 “next-generation” viral outgrowth assays, using polymerase chain reaction or ultrasensitive p24 to assess their suitability as scalable proxies for QVOA. Methods Next-generation QVOAs were compared with classic QVOA using single leukapheresis-derived samples from 5 antiretroviral therapy–suppressed HIV-infected participants and 1 HIV-uninfected control; each laboratory tested blinded batches of 3 frozen and 1 fresh sample. Markov chain Monte Carlo methods estimated extra-Poisson variation at aliquot, batch, and laboratory levels. Models also estimated the effect of testing frozen versus fresh samples. Results Next-generation QVOAs had similar estimates of variation to QVOA. Assays with ultrasensitive readout reported higher infectious units per million values than classic QVOA. Within-batch testing had 2.5-fold extra-Poisson variation (95% credible interval [CI], 2.1–3.5-fold) for next-generation assays. Between-laboratory variation increased extra-Poisson variation to 3.4-fold (95% CI, 2.6–5.4-fold). Frozen storage did not substantially alter infectious units per million values (−18%; 95% CI, −52% to 39%). Conclusions The data offer cautious support for use of next-generation QVOAs as proxies for more laborious QVOA, while providing greater sensitivities and dynamic ranges. Measurement of latent reservoirs in eradication strategies would benefit from high throughput and scalable assays.
Collapse
Affiliation(s)
- Mars Stone
- Vitalant Research Institute, San Francisco, CA, USA.,University of California San Francisco, Department of Laboratory Medicine
| | - Daniel Rosenbloom
- Department of Biomedical Informatics, Columbia University College of Physicians and Surgeons, New York, NY, USA
| | - Peter Bacchetti
- Department of Epidemiology and Biostatistics, University of California San Francisco, San Francisco, CA, USA
| | - Xutao Deng
- Vitalant Research Institute, San Francisco, CA, USA.,University of California San Francisco, Department of Laboratory Medicine
| | | | - Sheila Keating
- Vitalant Research Institute, San Francisco, CA, USA.,University of California San Francisco, Department of Laboratory Medicine
| | - Sonia Bakkour
- Vitalant Research Institute, San Francisco, CA, USA.,University of California San Francisco, Department of Laboratory Medicine
| | - Douglas Richman
- VA San Diego Healthcare System, San Diego CA and Center for AIDS Research, University of California San Diego, La Jolla, CA, USA
| | - John Mellors
- Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Steven Deeks
- Department of Medicine, University of California San Francisco School of Medicine, San Francisco, CA, USA
| | - Jun Lai
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Subul Beg
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Janet Siliciano
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Amélie Pagliuzza
- Centre de Recherche du CHUM and Department of Microbiology, Infectiology and Immunology, Université de Montréal, Faculty of Medicine, Montreal, Quebec, Canada
| | - Nicolas Chomont
- Centre de Recherche du CHUM and Department of Microbiology, Infectiology and Immunology, Université de Montréal, Faculty of Medicine, Montreal, Quebec, Canada
| | | | | | - Michael P Busch
- Vitalant Research Institute, San Francisco, CA, USA.,University of California San Francisco, Department of Laboratory Medicine
| | | |
Collapse
|
16
|
Dhummakupt A, Rubens JH, Anderson T, Powell L, Nonyane BA, Siems LV, Collinson-Streng A, Nilles T, Jones RB, Tepper V, Agwu A, Persaud D. Differences in inducibility of the latent HIV reservoir in perinatal and adult infection. JCI Insight 2020; 5:134105. [PMID: 31999647 DOI: 10.1172/jci.insight.134105] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2019] [Accepted: 01/24/2020] [Indexed: 12/13/2022] Open
Abstract
The HIV latent reservoir in resting memory CD4+ T cells precludes cure. Therapeutics to reactivate and eliminate this reservoir are in clinical trials in adults, but not yet in pediatric populations. We determined, ex vivo, the inducibility of the latent reservoir in perinatal infection as compared with adult infections using the Tat/rev induced limiting dilution assay (TILDA), in which a single round (12 hours) of CD4+ T cell stimulation with PMA/ionomycin maximally activates T cells and leads to proviral expression with multiply spliced HIV RNA production. Markers of immune activation and exhaustion were measured to assess interactions with inducibility. Although rates of T cell activation with PMA/ionomycin were similar, the latent reservoir in perinatal infection was slower to reactivate and of lower magnitude compared with adult infection, independent of proviral load. An enhanced TILDA with the addition of phytohemagglutin and a duration of 18 hours augmented proviral expression in perinatal but not adult infection. The baseline HLA-DR+CD4+ T cell level was significantly lower in perinatal compared with adult infections, but not correlated with induced reservoir size. These data support the hypothesis that there are differences in kinetics of latency reversal and baseline immune activation in perinatal compared with adult infections, with implications for latency reversal strategies toward reservoir clearance and remission.
Collapse
Affiliation(s)
- Adit Dhummakupt
- Division of Infectious Diseases, Department of Pediatrics, School of Medicine
| | - Jessica H Rubens
- Division of Infectious Diseases, Department of Pediatrics, School of Medicine
| | - Thuy Anderson
- Division of Infectious Diseases, Department of Pediatrics, School of Medicine
| | - Laura Powell
- Division of Infectious Diseases, Department of Pediatrics, School of Medicine
| | - Bareng As Nonyane
- Bloomberg School of Public Health, Johns Hopkins University, Baltimore, Maryland, USA
| | - Lilly V Siems
- Division of Infectious Diseases, Department of Pediatrics, School of Medicine
| | | | - Tricia Nilles
- Bloomberg School of Public Health, Johns Hopkins University, Baltimore, Maryland, USA
| | - R Brad Jones
- Division of Infectious Diseases, Department of Medicine, Weill Cornell Medicine, New York, New York, USA
| | - Vicki Tepper
- Department of Pediatrics, School of Medicine, University of Maryland, Baltimore, Maryland, USA
| | - Allison Agwu
- Division of Infectious Diseases, Department of Pediatrics, School of Medicine
| | - Deborah Persaud
- Division of Infectious Diseases, Department of Pediatrics, School of Medicine
| |
Collapse
|
17
|
Falcinelli SD, Ceriani C, Margolis DM, Archin NM. New Frontiers in Measuring and Characterizing the HIV Reservoir. Front Microbiol 2019; 10:2878. [PMID: 31921056 PMCID: PMC6930150 DOI: 10.3389/fmicb.2019.02878] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2019] [Accepted: 11/28/2019] [Indexed: 12/13/2022] Open
Abstract
A cure for HIV infection remains elusive due to the persistence of replication-competent HIV proviral DNA during suppressive antiretroviral therapy (ART). With the exception of rare elite or post-treatment controllers of viremia, withdrawal of ART invariably results in the rebound of viremia and progression of HIV disease. A thorough understanding of the reservoir is necessary to develop new strategies in order to reduce or eliminate the reservoir. However, there is significant heterogeneity in the sequence composition, genomic location, stability, and expression of the HIV reservoir both within and across individuals, and a majority of proviral sequences are replication-defective. These factors, and the low frequency of persistently infected cells in individuals on suppressive ART, make understanding the reservoir and its response to experimental reservoir reduction interventions challenging. Here, we review the characteristics of the HIV reservoir, state-of-the-art assays to measure and characterize the reservoir, and how these assays can be applied to accurately detect reductions in reservoir during efforts to develop a cure for HIV infection. In particular, we highlight recent advances in the development of direct measures of provirus, including intact proviral DNA assays and full-length HIV DNA sequencing with integration site analysis. We also focus on novel techniques to quantitate persistent and inducible HIV, including RNA sequencing and RNA/gag protein staining techniques, as well as modified viral outgrowth methods that seek to improve upon throughput, sensitivity and dynamic range.
Collapse
Affiliation(s)
- Shane D Falcinelli
- UNC HIV Cure Center, The University of North Carolina at Chapel Hill, Chapel Hill, NC, United States.,Department of Microbiology and Immunology, The University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Cristina Ceriani
- UNC HIV Cure Center, The University of North Carolina at Chapel Hill, Chapel Hill, NC, United States.,Department of Medicine, The University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - David M Margolis
- UNC HIV Cure Center, The University of North Carolina at Chapel Hill, Chapel Hill, NC, United States.,Department of Microbiology and Immunology, The University of North Carolina at Chapel Hill, Chapel Hill, NC, United States.,Department of Medicine, The University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Nancie M Archin
- UNC HIV Cure Center, The University of North Carolina at Chapel Hill, Chapel Hill, NC, United States.,Department of Medicine, The University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| |
Collapse
|
18
|
Wonderlich ER, Subramanian K, Cox B, Wiegand A, Lackman-Smith C, Bale MJ, Stone M, Hoh R, Kearney MF, Maldarelli F, Deeks SG, Busch MP, Ptak RG, Kulpa DA. Effector memory differentiation increases detection of replication-competent HIV-l in resting CD4+ T cells from virally suppressed individuals. PLoS Pathog 2019; 15:e1008074. [PMID: 31609991 PMCID: PMC6812841 DOI: 10.1371/journal.ppat.1008074] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2019] [Revised: 10/24/2019] [Accepted: 09/10/2019] [Indexed: 12/15/2022] Open
Abstract
Studies have demonstrated that intensive ART alone is not capable of eradicating HIV-1, as the virus rebounds within a few weeks upon treatment interruption. Viral rebound may be induced from several cellular subsets; however, the majority of proviral DNA has been found in antigen experienced resting CD4+ T cells. To achieve a cure for HIV-1, eradication strategies depend upon both understanding mechanisms that drive HIV-1 persistence as well as sensitive assays to measure the frequency of infected cells after therapeutic interventions. Assays such as the quantitative viral outgrowth assay (QVOA) measure HIV-1 persistence during ART by ex vivo activation of resting CD4+ T cells to induce latency reversal; however, recent studies have shown that only a fraction of replication-competent viruses are inducible by primary mitogen stimulation. Previous studies have shown a correlation between the acquisition of effector memory phenotype and HIV-1 latency reversal in quiescent CD4+ T cell subsets that harbor the reservoir. Here, we apply our mechanistic understanding that differentiation into effector memory CD4+ T cells more effectively promotes HIV-1 latency reversal to significantly improve proviral measurements in the QVOA, termed differentiation QVOA (dQVOA), which reveals a significantly higher frequency of the inducible HIV-1 replication-competent reservoir in resting CD4+ T cells.
Collapse
Affiliation(s)
| | | | - Bryan Cox
- Department of Pediatrics, Emory University, Atlanta, Georgia, United States of America
| | - Ann Wiegand
- HIV DRP, NCI at Frederick, NIH, Frederick, Maryland, United States of America
| | | | - Michael J Bale
- HIV DRP, NCI at Frederick, NIH, Frederick, Maryland, United States of America
| | - Mars Stone
- Vitalant Research Institute, San Francisco, California, United States of America.,Department of Laboratory Medicine, University of California, San Francisco, San Francisco, California, United States of America
| | - Rebecca Hoh
- University of California, San Francisco (UCSF), San Francisco, California, United States of America
| | - Mary F Kearney
- HIV DRP, NCI at Frederick, NIH, Frederick, Maryland, United States of America
| | - Frank Maldarelli
- HIV DRP, NCI at Frederick, NIH, Frederick, Maryland, United States of America
| | - Steven G Deeks
- University of California, San Francisco (UCSF), San Francisco, California, United States of America
| | - Michael P Busch
- Vitalant Research Institute, San Francisco, California, United States of America.,Department of Laboratory Medicine, University of California, San Francisco, San Francisco, California, United States of America
| | - Roger G Ptak
- Southern Research, Frederick, Maryland, United States of America
| | - Deanna A Kulpa
- Department of Pediatrics, Emory University, Atlanta, Georgia, United States of America
| |
Collapse
|
19
|
Gaebler C, Lorenzi JCC, Oliveira TY, Nogueira L, Ramos V, Lu CL, Pai JA, Mendoza P, Jankovic M, Caskey M, Nussenzweig MC. Combination of quadruplex qPCR and next-generation sequencing for qualitative and quantitative analysis of the HIV-1 latent reservoir. J Exp Med 2019; 216:2253-2264. [PMID: 31350309 PMCID: PMC6781006 DOI: 10.1084/jem.20190896] [Citation(s) in RCA: 85] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2019] [Revised: 06/12/2019] [Accepted: 06/19/2019] [Indexed: 11/22/2022] Open
Abstract
HIV-1 cure research seeks to decrease or eliminate the latent reservoir. The evaluation of such curative strategies requires accurate measures of the reservoir. Gaebler et al. describe a combined multicolor qPCR and next-generation sequencing method that enables the sensitive and specific characterization of the HIV-1 latent reservoir. HIV-1 infection requires lifelong therapy with antiretroviral drugs due to the existence of a latent reservoir of transcriptionally inactive integrated proviruses. The goal of HIV-1 cure research is to eliminate or functionally silence this reservoir. To this end, there are numerous ongoing studies to evaluate immunological approaches, including monoclonal antibody therapies. Evaluating the results of these studies requires sensitive and specific measures of the reservoir. Here, we describe a relatively high-throughput combined quantitative PCR (qPCR) and next-generation sequencing method. Four different qPCR probes covering the packaging signal (PS), group-specific antigen (gag), polymerase (pol), and envelope (env) are combined in a single multiplex reaction to detect the HIV-1 genome in limiting dilution samples followed by sequence verification of individual reactions that are positive for combinations of any two of the four probes (Q4PCR). This sensitive and specific approach allows for an unbiased characterization of the HIV-1 latent reservoir.
Collapse
Affiliation(s)
- Christian Gaebler
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY
| | - Julio C C Lorenzi
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY
| | - Thiago Y Oliveira
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY
| | - Lilian Nogueira
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY
| | - Victor Ramos
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY
| | - Ching-Lan Lu
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY
| | - Joy A Pai
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY
| | - Pilar Mendoza
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY
| | - Mila Jankovic
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY
| | - Marina Caskey
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY
| | - Michel C Nussenzweig
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY .,Howard Hughes Medical Institute, The Rockefeller University, New York, NY
| |
Collapse
|