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Abstract
Acquired immunodeficiency syndrome (AIDS), caused by the human immunodeficiency virus (HIV), has become a heavy burden of disease and an important public health problem in the world. Although current antiretroviral therapy (ART) is effective at suppressing the virus in the blood, HIV still remains in two different types of reservoirs-the latently infected cells (represented by CD4+ T cells) and the tissues containing those cells, which may block access to ART, HIV-neutralizing antibodies and latency-reversing agents. The latter is the focus of our review, as blood viral load drops below detectable levels after ART, a deeper and more systematic understanding of the HIV tissue reservoirs is imperative. In this review, we take the lymphoid system (including lymph nodes, gut-associated lymphoid tissue, spleen and bone marrow), nervous system, respiratory system, reproductive system (divided into male and female), urinary system as the order, focusing on the particularity and importance of each tissue in HIV infection, the infection target cell types of each tissue, the specific infection situation of each tissue quantified by HIV DNA or HIV RNA and the evidence of compartmentalization and pharmacokinetics. In summary, we found that the present state of HIV in different tissues has both similarities and differences. In the future, the therapeutic principle we need to follow is to respect the discrepancy on the basis of grasping the commonality. The measures taken to completely eliminate the virus in the whole body cannot be generalized. It is necessary to formulate personalized treatment strategies according to the different characteristics of the HIV in the various tissues, so as to realize the prospect of curing AIDS as soon as possible.
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Affiliation(s)
- Kangpeng Li
- Department of Orthopedics, Beijing Ditan Hospital, Capital Medical University, Beijing, China
| | - Bo Liu
- Department of Orthopedics, Beijing Ditan Hospital, Capital Medical University, Beijing, China
| | - Rui Ma
- Department of Orthopedics, Beijing Ditan Hospital, Capital Medical University, Beijing, China
| | - Qiang Zhang
- Department of Orthopedics, Beijing Ditan Hospital, Capital Medical University, Beijing, China
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2
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Ollerton MT, Folkvord JM, La Mantia A, Parry DA, Meditz AL, McCarter MD, D’Aquila R, Connick E. Follicular regulatory T cells eliminate HIV-1-infected follicular helper T cells in an IL-2 concentration dependent manner. Front Immunol 2022; 13:878273. [PMID: 36420277 PMCID: PMC9676968 DOI: 10.3389/fimmu.2022.878273] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2022] [Accepted: 10/21/2022] [Indexed: 11/09/2022] Open
Abstract
Follicular helper CD4+ T cells (TFH) are highly permissive to HIV and major foci of virus expression in both untreated and treated infection. Follicular regulatory CD4+ T cells (TFR) limit TFH numbers and function in vitro and in vivo. We evaluated the hypothesis that TFR suppress HIV replication in TFH using a well-established model of ex vivo HIV infection that employs tonsil cells from HIV uninfected individuals spinoculated with CXCR4- and CCR5-tropic HIV-GFP reporter viruses. Both CXCR4 and CCR5-tropic HIV replication were reduced in TFH cultured with TFR as compared to controls. Blocking antibodies to CD39, CTLA-4, IL-10, and TGF-beta failed to reverse suppression of HIV replication by TFR, and there were no sex differences in TFR suppressive activity. TFR reduced viability of TFH and even more so reduced HIV infected TFH as assessed by total and integrated HIV DNA. Exogenous IL-2 enhanced TFH viability and particularly numbers of GFP+ TFH in a concentration dependent manner. TFR reduced productively infected TFH at low and moderate IL-2 concentrations, and this was associated with decreases in extracellular IL-2. Both IL-2 expressing cells and larger numbers of FoxP3+CD4+ cells were detected in follicles and germinal centers of lymph nodes of people living with HIV. TFR may deplete TFH in vivo through restriction of IL-2 and thereby contribute to decay of HIV expressing cells in B cell follicles during HIV infection.
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Affiliation(s)
- Matthew T. Ollerton
- Department of Medicine, Division of Infectious Diseases, University of Arizona, Tucson, AZ, United States
| | - Joy M. Folkvord
- Department of Medicine, Division of Infectious Diseases, University of Arizona, Tucson, AZ, United States
| | | | - David A. Parry
- Department of Otolaryngology, University of Arizona, Tucson, AZ, United States
| | - Amie L. Meditz
- Department of Medicine, Division of Infectious Diseases, University of Colorado, Aurora, CO, United States
| | - Martin D. McCarter
- Department of Surgery, Anschutz Medical Campus, University of Colorado Denver, Aurora, CO, United States
| | - Richard T. D’Aquila
- Feinberg School of Medicine, Northwestern University, Chicago, IL, United States
| | - Elizabeth Connick
- Department of Medicine, Division of Infectious Diseases, University of Arizona, Tucson, AZ, United States
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3
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Chen J, Zhou T, Zhang Y, Luo S, Chen H, Chen D, Li C, Li W. The reservoir of latent HIV. Front Cell Infect Microbiol 2022; 12:945956. [PMID: 35967854 PMCID: PMC9368196 DOI: 10.3389/fcimb.2022.945956] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2022] [Accepted: 06/30/2022] [Indexed: 11/13/2022] Open
Abstract
The persistence of latent reservoir of the human immunodeficiency virus (HIV) is currently the major challenge in curing HIV infection. After HIV infects the human body, the latent HIV is unable to be recognized by the body’s immune system. Currently, the widely adopted antiretroviral therapy (ART) is also unble to eliminate it, thus hindering the progress of HIV treatment. This review discusses the existence of latent HIV vault for HIV treatment, its formation and factors affecting its formation, cell, and tissue localization, methods for detection and removing latent reservoir, to provide a comprehensive understanding of latent HIV vault, in order to assist in the future research and play a potential role in achieving HIV treatment.
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Affiliation(s)
- Jing Chen
- Beijing Institute of Hepatology, Beijing Youan Hospital, Capital Medical University, Beijing, China
| | - Tong Zhou
- Xiangya School of Medicine, Central South University, Changsha, China
| | - Yuan Zhang
- Beijing Youan Hospital, Capital Medical University, Beijing, China
| | - Shumin Luo
- Beijing Institute of Hepatology, Beijing Youan Hospital, Capital Medical University, Beijing, China
| | - Huan Chen
- Beijing Youan Hospital, Capital Medical University, Beijing, China
| | - Dexi Chen
- Beijing Institute of Hepatology, Beijing Youan Hospital, Capital Medical University, Beijing, China
| | - Chuanyun Li
- Beijing Youan Hospital, Capital Medical University, Beijing, China
- *Correspondence: Chuanyun Li, ; Weihua Li,
| | - Weihua Li
- Beijing Institute of Hepatology, Beijing Youan Hospital, Capital Medical University, Beijing, China
- *Correspondence: Chuanyun Li, ; Weihua Li,
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Development of Droplet Digital PCR-Based Assays to Quantify HIV Proviral and Integrated DNA in Brain Tissues from Viremic Individuals with Encephalitis and Virally Suppressed Aviremic Individuals. Microbiol Spectr 2022; 10:e0085321. [PMID: 35019681 PMCID: PMC8754137 DOI: 10.1128/spectrum.00853-21] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Although combination antiretroviral therapy (cART) can suppress the replication of HIV, the virus persists and rebounds when treatment is stopped. To find a cure that can eradicate latent reservoir, a method should be able to quantify the lingering HIV. Unlike other digital PCR technologies, droplet digital PCR (ddPCR), provides absolute quantification of target DNA molecules using fluorescent dually labeled probes by massively partitioning the sample into droplets. ddPCR enables exquisitely sensitive detection and quantification of viral DNA from very limiting clinical samples, including brain tissues. We developed and optimized duplex ddPCR assays for the detection and quantification of HIV proviral DNA and integrated DNA in the brain of HIV-1-infected patients. We have applied these approaches to successfully analyze 77 human brain tissues obtained from 27 HIV-1-infected individuals, either fully virally suppressed or with encephalitis, and were able to quantify low levels of viral DNA. Further developments and advancement of digital PCR technology is promising to aid in accurate quantification and characterization of the persistent HIV reservoir. IMPORTANCE We developed ddPCR assays to quantitatively measure HIV DNA and used this ddPCR assays to detect and quantitatively measure HIV DNA in the archived brain tissues from HIV patients. The tissue viral loads assessed by ddPCR was highly correlative with those assessed by qPCR. HIV DNA in the brain was detected more frequently by ddPCR than by qPCR. ddPCR also showed higher sensitivity than qPCR since ddPCR detected HIV DNA signals in some tissues from virally suppressed individuals while qPCR could not.
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5
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Pinzone MR, Weissman S, Pasternak AO, Zurakowski R, Migueles S, O'Doherty U. Naive infection predicts reservoir diversity and is a formidable hurdle to HIV eradication. JCI Insight 2021; 6:e150794. [PMID: 34228640 PMCID: PMC8409977 DOI: 10.1172/jci.insight.150794] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2021] [Accepted: 06/30/2021] [Indexed: 12/16/2022] Open
Abstract
Historically, naive cells have been considered inconsequential to HIV persistence. Here, we compared the contributions of naive and memory cells to the reservoirs of individuals with a spectrum of reservoir sizes and variable immunological control. We performed proviral sequencing of approximately 6000 proviruses from cellular subsets of 5 elite controllers (ECs) off antiretroviral therapy (ART) and 5 chronic progressors (CPs) on ART. The levels of naive infection were barely detectable in ECs and approximately 300-fold lower compared with those in CPs. Moreover, the ratio of infected naive to memory cells was significantly lower in ECs. Overall, the naive infection level increased as reservoir size increased, such that naive cells were a major contributor to the intact reservoir of CPs, whose reservoirs were generally very diverse. In contrast, the reservoirs of ECs were dominated by proviral clones. Critically, the fraction of proviral clones increased with cell differentiation, with naive infection predicting reservoir diversity. Longitudinal sequencing revealed that the reservoir of ECs was less dynamic compared with that of CPs. Naive cells play a critical role in HIV persistence. Their infection level predicts reservoir size and diversity. Moreover, the diminishing diversity of the reservoir as cellular subsets mature suggests that naive T cells repopulate the memory compartment and that direct infection of naive T cells occurs in vivo.
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Affiliation(s)
- Marilia R Pinzone
- Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Sam Weissman
- Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Alexander O Pasternak
- Department of Medical Microbiology, Amsterdam UMC, University of Amsterdam, Laboratory of Experimental Virology, Amsterdam, Netherlands
| | - Ryan Zurakowski
- Department of Biomedical Engineering, University of Delaware, Newark, Delaware, USA
| | - Stephen Migueles
- HIV-Specific Immunity Section of the Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, Maryland, USA
| | - Una O'Doherty
- Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
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Kojabad AA, Farzanehpour M, Galeh HEG, Dorostkar R, Jafarpour A, Bolandian M, Nodooshan MM. Droplet digital PCR of viral DNA/RNA, current progress, challenges, and future perspectives. J Med Virol 2021; 93:4182-4197. [PMID: 33538349 PMCID: PMC8013307 DOI: 10.1002/jmv.26846] [Citation(s) in RCA: 110] [Impact Index Per Article: 36.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2021] [Accepted: 02/01/2021] [Indexed: 12/18/2022]
Abstract
High-throughput droplet-based digital PCR (ddPCR) is a refinement of the conventional polymerase chain reaction (PCR) methods. In ddPCR, DNA/RNA is encapsulated stochastically inside the microdroplets as reaction chambers. A small percentage of the reaction chamber contains one or fewer copies of the DNA or RNA. After PCR amplification, concentrations are determined based on the proportion of nonfluorescent partitions through the Poisson distribution. Some of the main features of ddPCR include high sensitivity and specificity, absolute quantification without a standard curve, high reproducibility, good tolerance to PCR inhibitor, and high efficacy compared to conventional molecular methods. These advantages make ddPCR a valuable addition to the virologist's toolbox. The following review outlines the recent technological advances in ddPCR methods and their applications in viral identification.
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Affiliation(s)
- Amir Asri Kojabad
- Applied Virology Research CenterBaqiyatallah University of Medical SciencesTehranIran
| | - Mahdieh Farzanehpour
- Applied Virology Research CenterBaqiyatallah University of Medical SciencesTehranIran
| | | | - Ruhollah Dorostkar
- Applied Virology Research CenterBaqiyatallah University of Medical SciencesTehranIran
| | - Ali Jafarpour
- Research Center for Clinical VirologyTehran University of Medical SciencesTehranIran
| | - Masoumeh Bolandian
- Applied Virology Research CenterBaqiyatallah University of Medical SciencesTehranIran
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Lei S, Chen S, Zhong Q. Digital PCR for accurate quantification of pathogens: Principles, applications, challenges and future prospects. Int J Biol Macromol 2021; 184:750-759. [PMID: 34171259 DOI: 10.1016/j.ijbiomac.2021.06.132] [Citation(s) in RCA: 38] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2021] [Revised: 06/16/2021] [Accepted: 06/18/2021] [Indexed: 12/25/2022]
Abstract
Pathogens pose a severe threat to food safety and human health. The traditional methods for pathogen detection can't meet the growing diagnosis and control need. Digital PCR (dPCR) attracts a considerable attention for its ability to absolutely quantify pathogens with features of high selectivity, simplicity, accuracy and rapidity. The dPCR technique that achieves absolute quantification based on end-point measurement without standard curve offers a guideline for further genetic analysis and molecular diagnosis. It could contribute to the quantification of low level of nucleic acid, early detection and timely prevention of pathogenic diseases. In this review, 1442 publications about dPCR were selected and the detections of various pathogens by dPCR were reviewed comprehensively, including viruses, bacteria, parasites and fungi. A number of examples are cited to illustrate that dPCR is a new powerful tool with desired accuracy, sensitivity, and reproducibility for quantification of different types of pathogens. Moreover, the benefits, challenges and future prospects of the dPCR were also highlighted in this review.
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Affiliation(s)
- Shuwen Lei
- Guangdong Provincial Key Laboratory of Food Quality and Safety, College of Food Science, South China Agricultural University, Guangzhou 510642, China; Guangdong Laboratory of Lingnan Modern Agriculture, South China Agricultural University, Guangzhou 510642, China
| | - Song Chen
- Guangdong Provincial Key Laboratory of Food Quality and Safety, College of Food Science, South China Agricultural University, Guangzhou 510642, China; Guangdong Laboratory of Lingnan Modern Agriculture, South China Agricultural University, Guangzhou 510642, China
| | - Qingping Zhong
- Guangdong Provincial Key Laboratory of Food Quality and Safety, College of Food Science, South China Agricultural University, Guangzhou 510642, China; Guangdong Laboratory of Lingnan Modern Agriculture, South China Agricultural University, Guangzhou 510642, China.
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8
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Papasavvas E, Azzoni L, Ross BN, Fair M, Yuan Z, Gyampoh K, Mackiewicz A, Sciorillo AC, Pagliuzza A, Lada SM, Wu G, Goh SL, Bahnck-Teets C, Holder DJ, Zuck PD, Damra M, Lynn KM, Tebas P, Mounzer K, Kostman JR, Abdel-Mohsen M, Richman D, Chomont N, Howell BJ, Montaner LJ. Intact Human Immunodeficiency Virus (HIV) Reservoir Estimated by the Intact Proviral DNA Assay Correlates With Levels of Total and Integrated DNA in the Blood During Suppressive Antiretroviral Therapy. Clin Infect Dis 2021; 72:495-498. [PMID: 33527127 DOI: 10.1093/cid/ciaa809] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2020] [Accepted: 06/12/2020] [Indexed: 02/06/2023] Open
Abstract
Accurate characterization of the human immunodeficiency virus (HIV) reservoir is imperative to develop an effective cure. HIV was measured in antiretroviral therapy-suppressed individuals using the intact proviral DNA assay (IPDA), along with assays for total or integrated HIV DNA, and inducible HIV RNA or p24. Intact provirus correlated with total and integrated HIV.
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Affiliation(s)
| | - Livio Azzoni
- Wistar Institute, Philadelphia, Pennsylvania, USA
| | - Brian N Ross
- Wistar Institute, Philadelphia, Pennsylvania, USA
| | - Matthew Fair
- Wistar Institute, Philadelphia, Pennsylvania, USA
| | - Zhe Yuan
- Wistar Institute, Philadelphia, Pennsylvania, USA
| | | | | | | | | | - Steven M Lada
- Veterans Affairs San Diego Healthcare System and the University of California, San Diego, California, USA
| | - Guoxin Wu
- Merck & Co., Inc., Kenilworth, New Jersey, USA
| | | | | | | | - Paul D Zuck
- Merck & Co., Inc., Kenilworth, New Jersey, USA
| | | | - Kenneth M Lynn
- Presbyterian Hospital, University of Pennsylvania hospital, Philadelphia, Pennsylvania, USA
| | - Pablo Tebas
- Department of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Karam Mounzer
- Jonathan Lax Immune Disorders Treatment Center, Philadelphia Field Initiating Group for HIV-1 Trials, Philadelphia, Pennsylvania, USA
| | - Jay R Kostman
- John Bell Health Center, Philadelphia Field Initiating Group for HIV-1 Trials, Philadelphia, Pennsylvania, USA
| | | | - Douglas Richman
- Veterans Affairs San Diego Healthcare System and the University of California, San Diego, California, USA
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9
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The Intact Non-Inducible Latent HIV-1 Reservoir is Established In an In Vitro Primary T CM Cell Model of Latency. J Virol 2021; 95:JVI.01297-20. [PMID: 33441346 PMCID: PMC8092701 DOI: 10.1128/jvi.01297-20] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
The establishment of HIV-1 latency has hindered an HIV-1 cure. "Shock and Kill" strategies to target this reservoir aim to induce the latent provirus with latency reversing agents (LRAs). However, recent studies have shown that the majority of the intact HIV-1 viral reservoir found in ART-suppressed HIV infected individuals is not inducible. We sought to understand whether this non-inducible reservoir is established, and thus able to be studied, in an in vitro primary TCM model of latency. Furthermore, we wanted to expand this model system to include R5-tropic and non-B subtype viruses. To that end, we generated our TCM model of latency with an R5 subtype B virus, AD8 and an R5 subtype C virus, MJ4. Our results demonstrate that both intact and defective proviruses are generated in this model. Less than 50% of intact proviruses are inducible regardless of viral strain in the context of maximal stimulation through the TCR or with different clinically relevant LRAs including the HDAC inhibitors SAHA and MS-275, the PKC agonist Ingenol 3,20-dibenzoate or the SMAC mimetic AZD-5582. Our findings suggest that current LRA strategies are insufficient to effectively reactivate intact latent HIV-1 proviruses in primary CD4 TCM cells and that the mechanisms involved in the generation of the non-inducible HIV-1 reservoir can be studied using this primary in vitro model.Importance: HIV-1 establishes a latent reservoir that persists under antiretroviral therapy. Antiretroviral therapy is able to stop the spread of the virus and the progression of the disease but does not target this latent reservoir. If antiretroviral therapy is stopped, the virus is able to resume replication and the disease progresses. Recently, it has been demonstrated that most of the latent reservoir capable of generating replication competent virus cannot be induced in the laboratory setting. However, the mechanisms that influence the generation of this intact and non-inducible latent reservoir are still under investigation. Here we demonstrate the generation of defective, intact and intact non-inducible latent HIV-1 in a TCM model of latency using different HIV-1 strains. Thus, the mechanisms which control inducibility can be studied using this primary cell model of latency, which may accelerate our understanding of the latent reservoir and the development of curative strategies.
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10
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HIV latency reversal agents: A potential path for functional cure? Eur J Med Chem 2021; 213:113213. [PMID: 33540228 DOI: 10.1016/j.ejmech.2021.113213] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2020] [Revised: 11/16/2020] [Accepted: 01/12/2021] [Indexed: 12/28/2022]
Abstract
Despite the advances in Human Immunodeficiency Virus (HIV) treatment, the cure for all HIV patients still poses a major challenge, which needs to be surpassed in the coming years. Among the strategies pursuing this aim, the 'kick-and-kill' approach, which involves the reactivation and elimination of a latent HIV reservoir that resides in some CD4+ T cells, appears promising. The first step of this approach requires the use of latency reversal agents (LRAs) that induce the reactivation of the latent virus. Although several classes of LRAs have been reported so far, some limitations of these compounds still need to be overcome before their clinical use. The complete exhaustion of the reservoir of latent virus will contribute to promote the second step of this approach, facilitating the elimination of the reactivated HIV. Therefore, potent, safe, and non-toxic LRAs are necessary to promote efficient elimination of the HIV-1 virus from its reservoir. In this review article, we focus on the promising LRAs that have been described in the literature over the past few years, highlighting the advantages and disadvantages of their use in the 'kick and kill' approach, thus opening a new avenue in the development of a potential cure.
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Abdel-Mohsen M, Richman D, Siliciano RF, Nussenzweig MC, Howell BJ, Martinez-Picado J, Chomont N, Bar KJ, Yu XG, Lichterfeld M, Alcami J, Hazuda D, Bushman F, Siliciano JD, Betts MR, Spivak AM, Planelles V, Hahn BH, Smith DM, Ho YC, Buzon MJ, Gaebler C, Paiardini M, Li Q, Estes JD, Hope TJ, Kostman J, Mounzer K, Caskey M, Fox L, Frank I, Riley JL, Tebas P, Montaner LJ. Recommendations for measuring HIV reservoir size in cure-directed clinical trials. Nat Med 2020; 26:1339-1350. [PMID: 32895573 PMCID: PMC7703694 DOI: 10.1038/s41591-020-1022-1] [Citation(s) in RCA: 83] [Impact Index Per Article: 20.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2020] [Accepted: 07/16/2020] [Indexed: 12/28/2022]
Abstract
Therapeutic strategies are being clinically tested either to eradicate latent HIV reservoirs or to achieve virologic control in the absence of antiretroviral therapy. Attaining this goal will require a consensus on how best to measure the numbers of persistently infected cells with the potential to cause viral rebound after antiretroviral-therapy cessation in assessing the results of cure-directed strategies in vivo. Current measurements assess various aspects of the HIV provirus and its functionality and produce divergent results. Here, we provide recommendations from the BEAT-HIV Martin Delaney Collaboratory on which viral measurements should be prioritized in HIV-cure-directed clinical trials.
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Affiliation(s)
| | - Douglas Richman
- VA San Diego Healthcare System and University of California, San Diego, CA, USA
| | | | | | | | - Javier Martinez-Picado
- IrsiCaixa AIDS Research Institute, Badalona, Spain
- University of Vic-Central University of Catalonia (UVic-UCC), Vic, Spain
- Catalan Institution for Research and Advanced Studies (ICREA), Barcelona, Spain
| | | | | | - Xu G Yu
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, USA
- Brigham and Women's Hospital, Boston, MA, USA
| | - Mathias Lichterfeld
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, USA
- Brigham and Women's Hospital, Boston, MA, USA
| | - Jose Alcami
- AIDS Immunopathogenesis Unit, Instituto de Salud Carlos III, Madrid and Infectious Diseases Unit, IBIDAPS, Hospital Clinic, University of Barcelona, Barcelona, Spain
| | | | | | | | | | | | | | | | - Davey M Smith
- VA San Diego Healthcare System and University of California, San Diego, CA, USA
| | - Ya-Chi Ho
- Yale School of Medicine, New Haven, CT, USA
| | - Maria J Buzon
- AIDS Immunopathogenesis Unit, Instituto de Salud Carlos III, Madrid and Infectious Diseases Unit, IBIDAPS, Hospital Clinic, University of Barcelona, Barcelona, Spain
| | | | - Mirko Paiardini
- Division of Microbiology and Immunology, Yerkes National Primate Research Center, and Emory University, Atlanta, GA, USA
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, GA, USA
| | - Qingsheng Li
- School of Biological Sciences and Nebraska Center for Virology, University of Nebraska-Lincoln, Lincoln, NE, USA
| | - Jacob D Estes
- Vaccine and Gene Therapy Institute and Oregon National Primate Research Center (ONPRC), Oregon Health and Science University (OHSU), Beaverton, OR, USA
| | | | - Jay Kostman
- Jonathan Lax Center, Philadelphia FIGHT, Philadelphia, PA, USA
| | - Karam Mounzer
- Jonathan Lax Center, Philadelphia FIGHT, Philadelphia, PA, USA
| | | | - Lawrence Fox
- Division of AIDS, NIAID, NIH, North Bethesda, MD, USA
| | - Ian Frank
- University of Pennsylvania, Philadelphia, PA, USA
| | | | - Pablo Tebas
- University of Pennsylvania, Philadelphia, PA, USA
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12
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Pinzone MR, Bertuccio MP, VanBelzen DJ, Zurakowski R, O'Doherty U. Next-Generation Sequencing in a Direct Model of HIV Infection Reveals Important Parallels to and Differences from In Vivo Reservoir Dynamics. J Virol 2020; 94:e01900-19. [PMID: 32051279 PMCID: PMC7163122 DOI: 10.1128/jvi.01900-19] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2019] [Accepted: 02/04/2020] [Indexed: 02/06/2023] Open
Abstract
Next-generation sequencing (NGS) represents a powerful tool to unravel the genetic make-up of the HIV reservoir, but limited data exist on its use in vitro Moreover, most NGS studies do not separate integrated from unintegrated DNA, even though selection pressures on these two forms should be distinct. We reasoned we could use NGS to compare the infection of resting and activated CD4 T cells in vitro to address how the metabolic state affects reservoir formation and dynamics. To address these questions, we obtained HIV sequences 2, 4, and 8 days after NL4-3 infection of metabolically activated and quiescent CD4 T cells (cultured with 2 ng/ml interleukin-7). We compared the composition of integrated and total HIV DNA by isolating integrated HIV DNA using pulsed-field electrophoresis before performing sequencing. After a single-round infection, the majority of integrated HIV DNA was intact in both resting and activated T cells. The decay of integrated intact proviruses was rapid and similar in both quiescent and activated T cells. Defective forms accumulated relative to intact ones analogously to what is observed in vivo Massively deleted viral sequences formed more frequently in resting cells, likely due to lower deoxynucleoside triphosphate (dNTP) levels and the presence of multiple restriction factors. To our surprise, the majority of these deleted sequences did not integrate into the human genome. The use of NGS to study reservoir dynamics in vitro provides a model that recapitulates important aspects of reservoir dynamics. Moreover, separating integrated from unintegrated HIV DNA is important in some clinical settings to properly study selection pressures.IMPORTANCE The major implication of our work is that the decay of intact proviruses in vitro is extremely rapid, perhaps as a result of enhanced expression. Gaining a better understanding of why intact proviruses decay faster in vitro might help the field identify strategies to purge the reservoir in vivo When used wisely, in vitro models are a powerful tool to study the selective pressures shaping the viral landscape. Our finding that massively deleted sequences rarely succeed in integrating has several ramifications. It demonstrates that the total HIV DNA can differ substantially in character from the integrated HIV DNA under certain circumstances. The presence of unintegrated HIV DNA has the potential to obscure selection pressures and confound the interpretation of clinical studies, especially in the case of trials involving treatment interruptions.
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Affiliation(s)
- Marilia Rita Pinzone
- Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Maria Paola Bertuccio
- Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
- Department of Biomedical and Dental Sciences and Morphofunctional Imaging, University of Messina, Messina, Italy
| | - D Jake VanBelzen
- Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
- Department of Molecular Biosciences, Northwestern University, Evanston, Illinois, USA
| | - Ryan Zurakowski
- Delaware Biotechnology Institute, University of Delaware, Newark, Delaware, USA
| | - Una O'Doherty
- Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
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13
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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.
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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
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Anderson EM, Simonetti FR, Gorelick RJ, Hill S, Gouzoulis MA, Bell J, Rehm C, Pérez L, Boritz E, Wu X, Wells D, Hughes SH, Rao V, Coffin JM, Kearney MF, Maldarelli F. Dynamic Shifts in the HIV Proviral Landscape During Long Term Combination Antiretroviral Therapy: Implications for Persistence and Control of HIV Infections. Viruses 2020; 12:v12020136. [PMID: 31991737 PMCID: PMC7077288 DOI: 10.3390/v12020136] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2019] [Revised: 01/13/2020] [Accepted: 01/16/2020] [Indexed: 12/19/2022] Open
Abstract
Combination antiretroviral therapy (cART) controls but does not eradicate HIV infection; HIV persistence is the principal obstacle to curing infections. The proportion of defective proviruses increases during cART, but the dynamics of this process are not well understood, and a quantitative analysis of how the proviral landscape is reshaped after cART is initiated is critical to understanding how HIV persists. Here, we studied longitudinal samples from HIV infected individuals undergoing long term cART using multiplexed Droplet Digital PCR (ddPCR) approaches to quantify the proportion of deleted proviruses in lymphocytes. In most individuals undergoing cART, HIV proviruses that contain gag are lost more quickly than those that lack gag. Increases in the fraction of gag-deleted proviruses occurred only after 1–2 years of therapy, suggesting that the immune system, and/or toxicity of viral re-activation helps to gradually shape the proviral landscape. After 10–15 years on therapy, there were as many as 3.5–5 times more proviruses in which gag was deleted or highly defective than those containing intact gag. We developed a provirus-specific ddPCR approach to quantify individual clones. Investigation of a clone of cells containing a deleted HIV provirus integrated in the HORMAD2 gene revealed that the cells underwent a massive expansion shortly after cART was initiated until the clone, which was primarily in effector memory cells, dominated the population of proviruses for over 6 years. The expansion of this HIV-infected clone had substantial effects on the overall proviral population.
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Affiliation(s)
- Elizabeth M. Anderson
- HIV Dynamics and Replication Program, NCI, NIH, Frederick, MD 21702, USA; (E.M.A.); (F.R.S.); (S.H.); (M.A.G.); (S.H.H.); (M.F.K.)
- Department of Biology, The Catholic University of America, Washington, DC 20064, USA;
| | - Francesco R. Simonetti
- HIV Dynamics and Replication Program, NCI, NIH, Frederick, MD 21702, USA; (E.M.A.); (F.R.S.); (S.H.); (M.A.G.); (S.H.H.); (M.F.K.)
| | - Robert J. Gorelick
- Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA; (R.J.G.); (J.B.)
| | - Shawn Hill
- HIV Dynamics and Replication Program, NCI, NIH, Frederick, MD 21702, USA; (E.M.A.); (F.R.S.); (S.H.); (M.A.G.); (S.H.H.); (M.F.K.)
| | - Monica A. Gouzoulis
- HIV Dynamics and Replication Program, NCI, NIH, Frederick, MD 21702, USA; (E.M.A.); (F.R.S.); (S.H.); (M.A.G.); (S.H.H.); (M.F.K.)
| | - Jennifer Bell
- Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA; (R.J.G.); (J.B.)
| | - Catherine Rehm
- Laboratory of Immunoregulation, NIAID, NIH, Bethesda, MD 20814, USA;
| | - Liliana Pérez
- Virus Persistence and Dynamics Section, VRC, NIAID, NIH, Bethesda, MD 20814, USA; (L.P.); (E.B.)
| | - Eli Boritz
- Virus Persistence and Dynamics Section, VRC, NIAID, NIH, Bethesda, MD 20814, USA; (L.P.); (E.B.)
| | - Xiaolin Wu
- Cancer Research Technology Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA; (X.W.); (D.W.)
| | - Daria Wells
- Cancer Research Technology Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA; (X.W.); (D.W.)
| | - Stephen H. Hughes
- HIV Dynamics and Replication Program, NCI, NIH, Frederick, MD 21702, USA; (E.M.A.); (F.R.S.); (S.H.); (M.A.G.); (S.H.H.); (M.F.K.)
| | - Venigalla Rao
- Department of Biology, The Catholic University of America, Washington, DC 20064, USA;
| | - John M. Coffin
- Department of Biology, Tufts University, Boston, MA 02155, USA;
| | - Mary F. Kearney
- HIV Dynamics and Replication Program, NCI, NIH, Frederick, MD 21702, USA; (E.M.A.); (F.R.S.); (S.H.); (M.A.G.); (S.H.H.); (M.F.K.)
| | - Frank Maldarelli
- HIV Dynamics and Replication Program, NCI, NIH, Frederick, MD 21702, USA; (E.M.A.); (F.R.S.); (S.H.); (M.A.G.); (S.H.H.); (M.F.K.)
- Correspondence: ; Tel.: +01-301-846-5611
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Beliakova-Bethell N, Mukim A, White CH, Deshmukh S, Abewe H, Richman DD, Spina CA. Histone deacetylase inhibitors induce complex host responses that contribute to differential potencies of these compounds in HIV reactivation. J Biol Chem 2019; 294:5576-5589. [PMID: 30745362 PMCID: PMC6462528 DOI: 10.1074/jbc.ra118.005185] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2018] [Revised: 02/07/2019] [Indexed: 12/23/2022] Open
Abstract
Histone deacetylase (HDAC) inhibitors (HDACis) have been widely tested in clinical trials for their ability to reverse HIV latency but have yielded only limited success. One HDACi, suberoylanilide hydroxamic acid (SAHA), exhibits off-target effects on host gene expression predicted to interfere with induction of HIV transcription. Romidepsin (RMD) has higher potency and specificity for class I HDACs implicated in maintaining HIV provirus in the latent state. More robust HIV reactivation has indeed been achieved with RMD use ex vivo than with SAHA; however, reduction of viral reservoir size has not been observed in clinical trials. Therefore, using RNA-Seq, we sought to compare the effects of SAHA and RMD on gene expression in primary CD4+ T cells. Among the genes whose expression was modulated by both HDACi agents, we identified genes previously implicated in HIV latency. Two genes, SMARCB1 and PARP1, whose modulation by SAHA and RMD is predicted to inhibit HIV reactivation, were evaluated in the major maturation subsets of CD4+ T cells and were consistently either up- or down-regulated by both HDACi compounds. Our results indicate that despite having different potencies and HDAC specificities, SAHA and RMD modulate an overlapping set of genes, implicated in HIV latency regulation. Some of these genes merit exploration as additional targets to improve the therapeutic outcomes of "shock and kill" strategies. The overall complexity of HDACi-induced responses among host genes with predicted stimulatory or inhibitory effects on HIV expression likely contributes to differential HDACi potencies and dictates the outcome of HIV reactivation.
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Affiliation(s)
- Nadejda Beliakova-Bethell
- From the Veterans Affairs San Diego Healthcare System and Veterans Medical Research Foundation, San Diego, California 92161 and
- the University of California San Diego, La Jolla, California 92093
| | - Amey Mukim
- From the Veterans Affairs San Diego Healthcare System and Veterans Medical Research Foundation, San Diego, California 92161 and
| | - Cory H White
- the University of California San Diego, La Jolla, California 92093
| | - Savitha Deshmukh
- From the Veterans Affairs San Diego Healthcare System and Veterans Medical Research Foundation, San Diego, California 92161 and
| | - Hosiana Abewe
- From the Veterans Affairs San Diego Healthcare System and Veterans Medical Research Foundation, San Diego, California 92161 and
- the University of California San Diego, La Jolla, California 92093
| | - Douglas D Richman
- From the Veterans Affairs San Diego Healthcare System and Veterans Medical Research Foundation, San Diego, California 92161 and
- the University of California San Diego, La Jolla, California 92093
| | - Celsa A Spina
- From the Veterans Affairs San Diego Healthcare System and Veterans Medical Research Foundation, San Diego, California 92161 and
- the University of California San Diego, La Jolla, California 92093
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