51
|
Pardons M, Baxter AE, Massanella M, Pagliuzza A, Fromentin R, Dufour C, Leyre L, Routy JP, Kaufmann DE, Chomont N. Single-cell characterization and quantification of translation-competent viral reservoirs in treated and untreated HIV infection. PLoS Pathog 2019; 15:e1007619. [PMID: 30811499 PMCID: PMC6411230 DOI: 10.1371/journal.ppat.1007619] [Citation(s) in RCA: 151] [Impact Index Per Article: 30.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2018] [Revised: 03/11/2019] [Accepted: 02/05/2019] [Indexed: 12/31/2022] Open
Abstract
The phenotypic characterization of the cells in which HIV persists during antiretroviral therapy (ART) remains technically challenging. We developed a simple flow cytometry-based assay to quantify and characterize infected cells producing HIV proteins during untreated and treated HIV infection. By combining two antibodies targeting the HIV capsid in a standard intracellular staining protocol, we demonstrate that p24-producing cells can be detected with high specificity and sensitivity in the blood from people living with HIV. In untreated individuals, the frequency of productively infected cells strongly correlated with plasma viral load. Infected cells preferentially displayed a transitional memory phenotype and were enriched in Th17, peripheral Tfh and regulatory T cells subsets. These cells also preferentially expressed activation markers (CD25, HLA-DR, Ki67), immune checkpoint molecules (PD-1, LAG-3, TIGIT, Tim-3) as well as the integrins α4β7 and α4β1. In virally suppressed individuals on ART, p24-producing cells were only detected upon stimulation (median frequency of 4.3 p24+ cells/106 cells). These measures correlated with other assays assessing the size of the persistent reservoir including total and integrated HIV DNA, Tat/rev Induced Limiting Dilution Assay (TILDA) and quantitative viral outgrowth assay (QVOA). In ART-suppressed individuals, p24-producing cells preferentially displayed a transitional and effector memory phenotype, and expressed immune checkpoint molecules (PD-1, TIGIT) as well as the integrin α4β1. Remarkably, α4β1 was expressed by more than 70% of infected cells both in untreated and ART-suppressed individuals. Altogether, these results highlight a broad diversity in the phenotypes of HIV-infected cells in treated and untreated infection and suggest that strategies targeting multiple and phenotypically distinct cellular reservoirs will be needed to exert a significant impact on the size of the reservoir. HIV persists in a small pool of infected CD4+ T cells during ART. A better characterization of these cells is a pre-requisite to the development of HIV eradication strategies. We developed a novel assay, named HIV-Flow, to simultaneously quantify and characterize reservoir cells in individuals receiving ART. With this assay, we found that a median of only 5 cells/million have the ability to produce the HIV protein Gag in individuals on suppressive ART. These frequencies correlated with other assays aimed at measuring HIV reservoirs. Importantly, we show that the HIV reservoir is phenotypically diverse, with numerous cell subsets contributing to the pool of persistently infected cells. Nonetheless, we identified several markers preferentially expressed at the surface or these rare reservoir cells, including immune checkpoint molecules and homing receptors. By combining these markers, we identified discrete cellular subsets highly enriched in HIV-infected cells. This novel assay will facilitate the identification of markers expressed by cellular HIV reservoirs.
Collapse
Affiliation(s)
- Marion Pardons
- Department of Microbiology, Infectiology and Immunology, Université de Montréal, Montreal, Quebec, Canada
| | - Amy E. Baxter
- Department of Microbiology, Infectiology and Immunology, Université de Montréal, Montreal, Quebec, Canada
| | - Marta Massanella
- Department of Microbiology, Infectiology and Immunology, Université de Montréal, Montreal, Quebec, Canada
| | - Amélie Pagliuzza
- Centre de Recherche du Centre Hospitalier de l’Université de Montréal, Montreal, Quebec, Canada
| | - Rémi Fromentin
- Centre de Recherche du Centre Hospitalier de l’Université de Montréal, Montreal, Quebec, Canada
| | - Caroline Dufour
- Department of Microbiology, Infectiology and Immunology, Université de Montréal, Montreal, Quebec, Canada
| | - Louise Leyre
- Department of Microbiology, Infectiology and Immunology, Université de Montréal, Montreal, Quebec, Canada
| | - Jean-Pierre Routy
- Division of Hematology & Chronic Viral Illness Service, McGill University Heath Centre, Montreal, Quebec, Canada
| | - Daniel E. Kaufmann
- Centre de Recherche du Centre Hospitalier de l’Université de Montréal, Montreal, Quebec, Canada
- Department of Medicine, Université de Montréal, Montreal, Quebec, Canada
| | - Nicolas Chomont
- Department of Microbiology, Infectiology and Immunology, Université de Montréal, Montreal, Quebec, Canada
- Centre de Recherche du Centre Hospitalier de l’Université de Montréal, Montreal, Quebec, Canada
- * E-mail:
| |
Collapse
|
52
|
Reconstitution of HIV-1 reservoir following high-dose chemotherapy/autologous stem cell transplantation for lymphoma. AIDS 2019; 33:247-257. [PMID: 30325771 DOI: 10.1097/qad.0000000000002051] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
OBJECTIVES Autologous stem cell transplantation following high-dose chemotherapy (HDC/ASCT) is the prime model to study the impact of HDC in HIV-1-infected participants. We analyzed the impact of HDC/ASCT on the resurgent reservoir composition and origin. DESIGN We included retrospectively a homogenous group of HIV-1-infected patients treated for high-risk lymphoma in a reference center with similar chemotherapy regimens. METHODS Thirteen participants treated with HDC/ASCT from 2012 to 2015 were included. A median seven longitudinal blood samples per participant were available. Total HIV-1 DNA levels in peripheral blood mononuclear cells (PBMCs) were quantified by quantitative PCR. In six participants with sustained viral suppression, the highly variable C2V3 viral region was subjected to next-generation sequencing. Maximum-likelihood phylogeny trees were generated from the reconstructed viral haplotypes. Lymphocyte subsets were studied by flow cytometry. RESULTS PBMC-associated HIV-1 DNA levels were stable over time. Viral diversity decreased along lymphoma treatment, but increased promptly back to prechemotherapy numbers after HDC/ASCT. Blood viral populations from all time-points were intermingled in phylogeny trees: the resurgent reservoir was similar to pre-HDC circulating proviruses. Memory subsets were the main contributor to the early restoration of the CD4+ T-cell pool, with a delayed increase in naïve cell counts. CONCLUSIONS The characterization of HIV-1 reservoir in blood revealed a fast and consistent replenishment from memory CD4+ T cells after HDC/ASCT. As HDC/ASCT is increasingly involved in HIV cure trials with gene-modified hematopoietic stem cells, the management of infected T cells in HIV-positive autologous transplants will be critical.
Collapse
|
53
|
Giacomelli A, de Rose S, Rusconi S. Clinical pharmacology in HIV cure research - what impact have we seen? Expert Rev Clin Pharmacol 2019; 12:17-29. [PMID: 30570410 DOI: 10.1080/17512433.2019.1561272] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Introduction: Combined antiretroviral therapy (cART) has transformed an inexorably fatal disease into a chronic pathology, shifting the focus of research from the control of viral replication to the possibility of HIV cure. Areas covered: The present review assesses the principal pharmacological strategies that have been tested for an HIV cure starting from the in vitro proof of concept and the potential rationale of their in vivo applicability. We evaluated the possible pharmacological procedures employed during the early-stage HIV infection and the possibility of cART-free remission. We then analyzed the shock and kill approach from the single compounds in vitro mechanism of action, to the in vivo application of single or combined actions. Finally, we briefly considered the novel immunological branch through the discovery and development of broadly neutralizing antibodies in regard to the current and future in vivo therapeutic strategies aiming to verify the clinical applicability of these compounds. Expert opinion: Despite an incredible effort in HIV research cure, the likelihood of completely eradicating HIV is unreachable within our current knowledge. A better understanding of the mechanism of viral latency and the full characterization of HIV reservoir are crucial for the discovery of new therapeutic targets and novel pharmacological entities.
Collapse
Affiliation(s)
- Andrea Giacomelli
- a Infectious Diseases Unit, DIBIC Luigi Sacco , University of Milan , Milan , Italy
| | - Sonia de Rose
- a Infectious Diseases Unit, DIBIC Luigi Sacco , University of Milan , Milan , Italy
| | - Stefano Rusconi
- a Infectious Diseases Unit, DIBIC Luigi Sacco , University of Milan , Milan , Italy
| |
Collapse
|
54
|
Rochat MA, Schlaepfer E, Kuster SP, Li D, Audige A, Ivic S, Fahrny A, Speck RF. Monitoring HIV DNA and cellular activation markers in HIV-infected humanized mice under cART. Virol J 2018; 15:191. [PMID: 30558630 PMCID: PMC6296118 DOI: 10.1186/s12985-018-1101-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2018] [Accepted: 11/27/2018] [Indexed: 12/22/2022] Open
Abstract
Background The major obstacle to cure of HIV type-1 infection is the presence of the HIV reservoir, hidden from the immune system and insensitive to combined antiretroviral therapy (cART). Eradication approaches have been hindered by the difficulty for accurately monitoring its size in vivo, especially in the lymphoid organs. Humanized mouse models are a valuable tool for systematically assess the efficacy of therapeutic interventions in reducing the HIV reservoir. Nonetheless, persistence of the HIV reservoir over time, in the presence of cART, has yet to be analyzed in this in vivo model. Findings We found that the proviral DNA as well as the total DNA were very stable in the spleen and mesenteric lymph node irrespective of the length of cART. Notably, the amount of proviral DNA was very similar in the spleen and lymph node. Furthermore, we observed a correlation between the percentage of splenic human CD4+ T-cells with total HIV DNA, between the number of human CD38 + CD8+ T-cells in the spleen with the amount of integrated HIV DNA, and eventually between the hCD4/hCD8 ratio in the spleen with integrated as well as total HIV DNA implying that the CD8+ T cells influence the size of the HIV reservoir. Conclusions Here, we demonstrated the stability of this reservoir in humanized mice irrespective of the length of cART, confirming the relevancy of this model for HIV latency eradication investigations. Notably, we also found correlates between the frequency of CD4+ T-cells, their activation status and viral parameters, which were analogous to the ones in HIV-infected patients. Thus, hu-mice represent a very valuable HIV latency model.
Collapse
Affiliation(s)
- Mary-Aude Rochat
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital of Zurich, University of Zurich, Raemistrasse 100, 8091, Zurich, Switzerland
| | - Erika Schlaepfer
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital of Zurich, University of Zurich, Raemistrasse 100, 8091, Zurich, Switzerland
| | - Stefan P Kuster
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital of Zurich, University of Zurich, Raemistrasse 100, 8091, Zurich, Switzerland
| | - Duo Li
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital of Zurich, University of Zurich, Raemistrasse 100, 8091, Zurich, Switzerland
| | - Annette Audige
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital of Zurich, University of Zurich, Raemistrasse 100, 8091, Zurich, Switzerland
| | - Sandra Ivic
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital of Zurich, University of Zurich, Raemistrasse 100, 8091, Zurich, Switzerland
| | - Audrey Fahrny
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital of Zurich, University of Zurich, Raemistrasse 100, 8091, Zurich, Switzerland
| | - Roberto F Speck
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital of Zurich, University of Zurich, Raemistrasse 100, 8091, Zurich, Switzerland.
| |
Collapse
|
55
|
Swanstrom AE, Gorelick RJ, Wu G, Howell B, Vijayagopalan A, Shoemaker R, Oswald K, Datta SA, Keele BF, Del Prete GQ, Chertova E, Bess JW, Lifson JD. Ultrasensitive Immunoassay for Simian Immunodeficiency Virus p27 CA. AIDS Res Hum Retroviruses 2018; 34:993-1001. [PMID: 29869527 DOI: 10.1089/aid.2018.0075] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
Abstract
Although effective for suppressing viral replication, combination antiretroviral treatment (cART) does not represent definitive therapy for HIV infection due to persistence of replication-competent viral reservoirs. The advent of effective cART regimens for simian immunodeficiency virus (SIV)-infected nonhuman primates (NHP) has enabled the development of relevant models for studying viral reservoirs and intervention strategies targeting them. Viral reservoir measurements are crucial for such studies but are problematic. Quantitative polymerase chain reaction (PCR) assays overestimate the size of the replication competent viral reservoir, as not all detected viral genomes are intact. Quantitative viral outgrowth assays measure replication competence, but they suffer from limited precision and dynamic range, and require large numbers of cells. Ex vivo virus induction assays to detect cells harboring inducible virus represent an experimental middle ground, but detection of inducible viral RNA in such assays does not necessarily indicate production of virions, while detection of more immunologically relevant viral proteins, including p27CA, by conventional enzyme-linked immunosorbent assays (ELISA) lacks sensitivity. An ultrasensitive digital SIV Gag p27 assay was developed, which is 100-fold more sensitive than a conventional ELISA. In ex vivo virus induction assays, the quantification of SIV Gag p27 produced by stimulated CD4+ T cells from rhesus macaques receiving cART enabled earlier and more sensitive detection than conventional ELISA-based approaches and was highly correlated with SIV RNA, as measured by quantitative reverse transcription PCR. This ultrasensitive p27 assay provides a new tool to assess ongoing replication and reactivation of infectious virus from reservoirs in SIV-infected NHP.
Collapse
Affiliation(s)
- Adrienne E. Swanstrom
- AIDS and Cancer Virus Program, Frederick National Laboratory for Cancer Research sponsored by the National Cancer Institute, Leidos Biomedical Research, Inc., Frederick, Maryland
| | - Robert J. Gorelick
- AIDS and Cancer Virus Program, Frederick National Laboratory for Cancer Research sponsored by the National Cancer Institute, Leidos Biomedical Research, Inc., Frederick, Maryland
| | - Guoxin Wu
- Department of Infectious Disease, Merck & Co., Inc., Kenilworth, New Jersey
| | - Bonnie Howell
- Department of Infectious Disease, Merck & Co., Inc., Kenilworth, New Jersey
| | - Anitha Vijayagopalan
- AIDS and Cancer Virus Program, Frederick National Laboratory for Cancer Research sponsored by the National Cancer Institute, Leidos Biomedical Research, Inc., Frederick, Maryland
| | - Rebecca Shoemaker
- AIDS and Cancer Virus Program, Frederick National Laboratory for Cancer Research sponsored by the National Cancer Institute, Leidos Biomedical Research, Inc., Frederick, Maryland
| | - Kelli Oswald
- AIDS and Cancer Virus Program, Frederick National Laboratory for Cancer Research sponsored by the National Cancer Institute, Leidos Biomedical Research, Inc., Frederick, Maryland
| | - Siddhartha A. Datta
- HIV Dynamics and Replication Program, Center for Cancer Research, National Cancer Institute, Frederick, Maryland
| | - Brandon F. Keele
- AIDS and Cancer Virus Program, Frederick National Laboratory for Cancer Research sponsored by the National Cancer Institute, Leidos Biomedical Research, Inc., Frederick, Maryland
| | - Gregory Q. Del Prete
- AIDS and Cancer Virus Program, Frederick National Laboratory for Cancer Research sponsored by the National Cancer Institute, Leidos Biomedical Research, Inc., Frederick, Maryland
| | - Elena Chertova
- AIDS and Cancer Virus Program, Frederick National Laboratory for Cancer Research sponsored by the National Cancer Institute, Leidos Biomedical Research, Inc., Frederick, Maryland
| | - Julian W. Bess
- AIDS and Cancer Virus Program, Frederick National Laboratory for Cancer Research sponsored by the National Cancer Institute, Leidos Biomedical Research, Inc., Frederick, Maryland
| | - Jeffrey D. Lifson
- AIDS and Cancer Virus Program, Frederick National Laboratory for Cancer Research sponsored by the National Cancer Institute, Leidos Biomedical Research, Inc., Frederick, Maryland
| |
Collapse
|
56
|
Dampier W, Sullivan NT, Mell JC, Pirrone V, Ehrlich GD, Chung CH, Allen AG, DeSimone M, Zhong W, Kercher K, Passic S, Williams JW, Szep Z, Khalili K, Jacobson JM, Nonnemacher MR, Wigdahl B. Broad-Spectrum and Personalized Guide RNAs for CRISPR/Cas9 HIV-1 Therapeutics. AIDS Res Hum Retroviruses 2018; 34:950-960. [PMID: 29968495 PMCID: PMC6238604 DOI: 10.1089/aid.2017.0274] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
The clustered regularly interspaced short palindromic repeats (CRISPR)-associated Cas9 system has been used to excise the HIV-1 proviral genome from latently infected cells, potentially offering a cure for HIV-infected patients. Recent studies have shown that most published HIV-1 guide RNAs (gRNAs) do not account for the diverse viral quasispecies within or among patients, which continue to diversify with time even in long-term antiretroviral therapy (ART)-suppressed patients. Given this observation, proviral genomes were deep sequenced from 23 HIV-1-infected patients in the Drexel Medicine CNS AIDS Research and Eradication Study cohort at two different visits. Based on the spectrum of integrated proviral DNA polymorphisms observed, three gRNA design strategies were explored: based on the patient's own HIV-1 sequences (personalized), based on consensus sequences from a large sample of patients [broad-spectrum (BS)], or a combination of both approaches. Using a bioinformatic algorithm, the personalized gRNA design was predicted to cut 46 of 48 patient samples at 90% efficiency, whereas the top 4 BS gRNAs (BS4) were predicted to excise provirus from 44 of 48 patient samples with 90% efficiency. Using a mixed design with the top three BS gRNAs plus one personalized gRNA (BS3 + PS1) resulted in predicted excision of provirus from 45 of 48 patient samples with 90% efficiency. In summary, these studies used an algorithmic design strategy to identify potential BS gRNAs to target a spectrum of HIV-1 long teriminal repeat (LTR) quasispecies for use with a small HIV-1-infected population. This approach should advance CRISPR/Cas9 excision technology taking into account the extensive molecular heterogeneity of HIV-1 that persists in situ after prolonged ART.
Collapse
Affiliation(s)
- Will Dampier
- Department of Microbiology and Immunology, Drexel University College of Medicine, Philadelphia, Pennsylvania
- Center for Molecular Virology and Translational Neuroscience, Institute for Molecular Medicine and Infectious Disease, Drexel University College of Medicine, Philadelphia, Pennsylvania
- School of Biomedical Engineering, Science, and Health Systems, Drexel University, Philadelphia, Pennsylvania
| | - Neil T. Sullivan
- Department of Microbiology and Immunology, Drexel University College of Medicine, Philadelphia, Pennsylvania
- Center for Molecular Virology and Translational Neuroscience, Institute for Molecular Medicine and Infectious Disease, Drexel University College of Medicine, Philadelphia, Pennsylvania
| | - Joshua Chang Mell
- Department of Microbiology and Immunology, Drexel University College of Medicine, Philadelphia, Pennsylvania
- Center for Genomic Sciences, Institute for Molecular Medicine and Infectious Disease, Drexel University College of Medicine, Philadelphia, Pennsylvania
- Center for Advanced Microbial Processing, Institute for Molecular Medicine and Infectious Disease, Drexel University College of Medicine, Philadelphia, Pennsylvania
- Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, Pennsylvania
| | - Vanessa Pirrone
- Department of Microbiology and Immunology, Drexel University College of Medicine, Philadelphia, Pennsylvania
- Center for Molecular Virology and Translational Neuroscience, Institute for Molecular Medicine and Infectious Disease, Drexel University College of Medicine, Philadelphia, Pennsylvania
| | - Garth D. Ehrlich
- Department of Microbiology and Immunology, Drexel University College of Medicine, Philadelphia, Pennsylvania
- Center for Genomic Sciences, Institute for Molecular Medicine and Infectious Disease, Drexel University College of Medicine, Philadelphia, Pennsylvania
- Center for Advanced Microbial Processing, Institute for Molecular Medicine and Infectious Disease, Drexel University College of Medicine, Philadelphia, Pennsylvania
- Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, Pennsylvania
- Department of Otolaryngology—Head and Neck Surgery, Drexel University College of Medicine, Philadelphia, Pennsylvania
| | - Cheng-Han Chung
- Department of Microbiology and Immunology, Drexel University College of Medicine, Philadelphia, Pennsylvania
- Center for Molecular Virology and Translational Neuroscience, Institute for Molecular Medicine and Infectious Disease, Drexel University College of Medicine, Philadelphia, Pennsylvania
| | - Alexander G. Allen
- Department of Microbiology and Immunology, Drexel University College of Medicine, Philadelphia, Pennsylvania
- Center for Molecular Virology and Translational Neuroscience, Institute for Molecular Medicine and Infectious Disease, Drexel University College of Medicine, Philadelphia, Pennsylvania
| | - Mathew DeSimone
- School of Biomedical Engineering, Science, and Health Systems, Drexel University, Philadelphia, Pennsylvania
| | - Wen Zhong
- Department of Microbiology and Immunology, Drexel University College of Medicine, Philadelphia, Pennsylvania
- Center for Molecular Virology and Translational Neuroscience, Institute for Molecular Medicine and Infectious Disease, Drexel University College of Medicine, Philadelphia, Pennsylvania
| | - Katherine Kercher
- Department of Microbiology and Immunology, Drexel University College of Medicine, Philadelphia, Pennsylvania
- Center for Molecular Virology and Translational Neuroscience, Institute for Molecular Medicine and Infectious Disease, Drexel University College of Medicine, Philadelphia, Pennsylvania
| | - Shendra Passic
- Department of Microbiology and Immunology, Drexel University College of Medicine, Philadelphia, Pennsylvania
- Center for Molecular Virology and Translational Neuroscience, Institute for Molecular Medicine and Infectious Disease, Drexel University College of Medicine, Philadelphia, Pennsylvania
| | - Jean W. Williams
- Department of Microbiology and Immunology, Drexel University College of Medicine, Philadelphia, Pennsylvania
- Center for Molecular Virology and Translational Neuroscience, Institute for Molecular Medicine and Infectious Disease, Drexel University College of Medicine, Philadelphia, Pennsylvania
| | - Zsofia Szep
- Division of Infectious Diseases and HIV Medicine, Department of Medicine, Drexel University College of Medicine, Philadelphia, Pennsylvania
- Center for Clinical and Translational Medicine, Institute for Molecular Medicine and Infectious Disease, Drexel University College of Medicine, Philadelphia, Pennsylvania
| | - Kamel Khalili
- Department of Neuroscience, Center for Neurovirology, and Comprehensive NeuroAIDS Center, Lewis Katz School of Medicine, Temple University, Philadelphia, Pennsylvania
- Center for Translational AIDS Research, Lewis Katz School of Medicine, Temple University, Philadelphia, Pennsylvania
| | - Jeffrey M. Jacobson
- Department of Neuroscience, Center for Neurovirology, and Comprehensive NeuroAIDS Center, Lewis Katz School of Medicine, Temple University, Philadelphia, Pennsylvania
- Center for Translational AIDS Research, Lewis Katz School of Medicine, Temple University, Philadelphia, Pennsylvania
- Section of Infectious Disease, Department of Medicine, Lewis Katz School of Medicine, Temple University, Philadelphia, Pennsylvania
| | - Michael R. Nonnemacher
- Department of Microbiology and Immunology, Drexel University College of Medicine, Philadelphia, Pennsylvania
- Center for Molecular Virology and Translational Neuroscience, Institute for Molecular Medicine and Infectious Disease, Drexel University College of Medicine, Philadelphia, Pennsylvania
| | - Brian Wigdahl
- Department of Microbiology and Immunology, Drexel University College of Medicine, Philadelphia, Pennsylvania
- Center for Molecular Virology and Translational Neuroscience, Institute for Molecular Medicine and Infectious Disease, Drexel University College of Medicine, Philadelphia, Pennsylvania
- Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, Pennsylvania
- Center for Clinical and Translational Medicine, Institute for Molecular Medicine and Infectious Disease, Drexel University College of Medicine, Philadelphia, Pennsylvania
| |
Collapse
|
57
|
García M, Navarrete-Muñoz MA, Ligos JM, Cabello A, Restrepo C, López-Bernaldo JC, de la Hera FJ, Barros C, Montoya M, Fernández-Guerrero M, Estrada V, Górgolas M, Benito JM, Rallón N. CD32 Expression is not Associated to HIV-DNA content in CD4 cell subsets of individuals with Different Levels of HIV Control. Sci Rep 2018; 8:15541. [PMID: 30341387 PMCID: PMC6195600 DOI: 10.1038/s41598-018-33749-5] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2018] [Accepted: 10/05/2018] [Indexed: 01/20/2023] Open
Abstract
A recent study has pointed out to CD32a as a potential biomarker of HIV-persistent CD4 cells. We have characterized the level and phenotype of CD32+ cells contained in different subsets of CD4 T-cells and its potential correlation with level of total HIV-DNA in thirty HIV patients (10 typical progressors naïve for cART, 10 cART-suppressed patients, and 10 elite controllers). Total HIV-DNA was quantified in different subsets of CD4 T-cells: Trm and pTfh cells. Level and immunephenotype of CD32+ cells were analyzed in these same subsets by flow cytometry. CD32 expression in Trm and pTfh subsets was similar in the different groups, and there was no significant correlation between the level of total HIV-DNA and the level of CD32 expression in these subsets. However, total HIV-DNA level was correlated with expression of CD127 (rho = -0.46, p = 0.043) and of CCR6 (rho = -0.418, p = 0.027) on CD32+ cells. Our results do not support CD32 as a biomarker of total HIV-DNA content. However, analyzing the expression of certain markers by CD32+ cells could improve the utility of this marker in the clinical setting, prompting the necessity of further studies to both validate our results and to explore the potential utility of certain markers expressed by CD32+ cells.
Collapse
Affiliation(s)
- Marcial García
- Instituto de Investigación Sanitaria Fundación Jiménez Díaz, Universidad Autónoma de Madrid (IIS-FJD, UAM), Madrid, Spain.,Hospital Universitario Rey Juan Carlos, Móstoles, Spain
| | - María Angeles Navarrete-Muñoz
- Instituto de Investigación Sanitaria Fundación Jiménez Díaz, Universidad Autónoma de Madrid (IIS-FJD, UAM), Madrid, Spain.,Hospital Universitario Rey Juan Carlos, Móstoles, Spain
| | - José M Ligos
- Centro Nacional de Investigaciones Cardiovasculares, Madrid, Spain
| | - Alfonso Cabello
- Hospital Universitario Fundación Jiménez Díaz, Madrid, Spain
| | - Clara Restrepo
- Instituto de Investigación Sanitaria Fundación Jiménez Díaz, Universidad Autónoma de Madrid (IIS-FJD, UAM), Madrid, Spain.,Hospital Universitario Rey Juan Carlos, Móstoles, Spain
| | | | | | | | - María Montoya
- Centro Nacional de Investigaciones Cardiovasculares, Madrid, Spain
| | | | | | - Miguel Górgolas
- Hospital Universitario Fundación Jiménez Díaz, Madrid, Spain
| | - José M Benito
- Instituto de Investigación Sanitaria Fundación Jiménez Díaz, Universidad Autónoma de Madrid (IIS-FJD, UAM), Madrid, Spain. .,Hospital Universitario Rey Juan Carlos, Móstoles, Spain.
| | - Norma Rallón
- Instituto de Investigación Sanitaria Fundación Jiménez Díaz, Universidad Autónoma de Madrid (IIS-FJD, UAM), Madrid, Spain. .,Hospital Universitario Rey Juan Carlos, Móstoles, Spain.
| |
Collapse
|
58
|
Zhang W, Svensson Akusjärvi S, Sönnerborg A, Neogi U. Characterization of Inducible Transcription and Translation-Competent HIV-1 Using the RNAscope ISH Technology at a Single-Cell Resolution. Front Microbiol 2018; 9:2358. [PMID: 30333813 PMCID: PMC6176121 DOI: 10.3389/fmicb.2018.02358] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2018] [Accepted: 09/14/2018] [Indexed: 01/17/2023] Open
Abstract
Identifying the source and dynamics of persistent HIV-1 at single-cell resolution during cART is crucial for the design of strategies to eliminate the latent HIV-1 reservoir. An assay to measure latent HIV-1 that can distinguish inducible from defective proviruses with high precision is essential to evaluate the efficacy of HIV-1 cure efforts but is presently lacking. The primary aim of this study was therefore to identify transcription and translation competent latently infected cells through detection of biomolecules that are dependent on transcriptional activation of the provirus. We investigated the applicability of two commercially available assays; PrimeFlowTM RNA Assay (RNAflow) and RNAscope® ISH (RNAscope) for evaluation of the efficacy of latency reversal agents (LRAs) to reactivate the HIV-1 latent reservoir. The J-Lat cell model (clones 6.3, 9.3, and 10.6) and four LRAs was used to evaluate the sensitivity, specificity, and lower detection limit of the RNAflow and RNAscope assays for the detection and description of the translation-competent HIV-1 reservoir. We also checked for HIV-1 subtype specificity of the RNAscope assay using patient-derived subtype A1, B, C, and CRF01_AE recombinant plasmids following transfection in 293T cells and the applicability of the method in patient-derived peripheral blood mononuclear cells (PBMCs). The lower detection limit of RNAflow was 575 HIV-1 infected cells/million and 45 cells/million for RNAscope. The RNAscope probes, designed for HIV-1B, also detected other subtypes (A1, B, C, and CRF01_AE). RNAscope was applicable for the detection of HIV-1 in patient-derived PBMCs following LRA activation. In conclusion, our study showed that RNAscope can be used to quantify the number of directly observed individual cells expressing HIV-1 mRNA following LRA activation. Therefore, it can be a useful tool for characterization of translation-competent HIV-1 in latently infected cell at single-cell resolution in the fields of HIV-1 pathogenesis and viral persistence.
Collapse
Affiliation(s)
- Wang Zhang
- Division of Clinical Microbiology, Department of Laboratory Medicine, Karolinska Institutet, Solna, Sweden.,Science for Life Laboratory, Division of Proteomics and Nanobiotechnology, KTH Royal Institute of Technology, Solna, Sweden
| | - Sara Svensson Akusjärvi
- Division of Clinical Microbiology, Department of Laboratory Medicine, Karolinska Institutet, Solna, Sweden
| | - Anders Sönnerborg
- Division of Clinical Microbiology, Department of Laboratory Medicine, Karolinska Institutet, Solna, Sweden.,Department of Medicine Huddinge, Unit of Infectious Diseases, Karolinska Institutet, Karolinska University Hospital, Solna, Sweden
| | - Ujjwal Neogi
- Division of Clinical Microbiology, Department of Laboratory Medicine, Karolinska Institutet, Solna, Sweden
| |
Collapse
|
59
|
Tagarro A, Chan M, Zangari P, Ferns B, Foster C, De Rossi A, Nastouli E, Muñoz-Fernández MA, Gibb D, Rossi P, Giaquinto C, Babiker A, Fortuny C, Freguja R, Cotugno N, Judd A, Noguera-Julian A, Navarro ML, Mellado MJ, Klein N, Palma P, Rojo P. Early and Highly Suppressive Antiretroviral Therapy Are Main Factors Associated With Low Viral Reservoir in European Perinatally HIV-Infected Children. J Acquir Immune Defic Syndr 2018; 79:269-276. [PMID: 30211778 PMCID: PMC6173292 DOI: 10.1097/qai.0000000000001789] [Citation(s) in RCA: 51] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
BACKGROUND Future strategies aiming to achieve HIV-1 remission are likely to target individuals with small reservoir size. SETTING We retrospectively investigated factors associated with HIV-1 DNA levels in European, perinatally HIV-infected children starting antiretroviral therapy (ART) <6 months of age. METHODS Total HIV-1 DNA was measured from 51 long-term suppressed children aged 6.3 years (median) after initial viral suppression. Factors associated with log10 total HIV-1 DNA were analyzed using linear regression. RESULTS At ART initiation, children were aged median [IQR] 2.3 [1.2-4.1] months, CD4% 37 [24-45] %, CD8% 28 [18-36] %, log10 plasma viral load (VL) 5.4 [4.4-5.9] copies per milliliter. Time to viral suppression was 7.98 [4.6-19.3] months. After suppression, 13 (25%) children had suboptimal response [≥2 consecutive VL 50-400 followed by VL <50] and/or experienced periods of virological failure [≥2 consecutive VL ≥400 followed by VL <50]. Median total HIV-1 DNA was 43 [6195] copies/10 PBMC. Younger age at therapy initiation was associated with lower total HIV-1 DNA (adjusted coefficient [AC] 0.12 per month older, P = 0.0091), with a month increase in age at ART start being associated with a 13% increase in HIV DNA. Similarly, a higher proportion of time spent virally suppressed (AC 0.10 per 10% higher, P = 0.0022) and the absence of viral failure/suboptimal response (AC 0.34 for those with fail/suboptimal response, P = 0.0483) were associated with lower total HIV-1 DNA. CONCLUSIONS Early ART initiation and a higher proportion of time suppressed are linked with lower total HIV-1 DNA. Early ART start and improving adherence in perinatally HIV-1-infected children minimize the size of viral reservoir.
Collapse
Affiliation(s)
- Alfredo Tagarro
- Department of Pediatrics, Hospital 12 de Octubre, Fundación para la Investigación Biomédica del Hospital Universitario 12 de Octubre. Madrid, Spain
- Biomedical School. Uiversidad Europea de Madrid. Madrid, Spain
- Translational Research Network in Pediatric Infectious Diseases (RITIP), Madrid, Spain
| | - Man Chan
- MRC Clinical Trials Unit at UCL, Institute of Clinical Trials & Methodology, London, UK
| | - Paola Zangari
- Academic Department of Pediatrics (DPUO), Research Unit in Congenital and Perinatal Infection, Children's Hospital Bambino Gesù, Rome, Italy
| | | | | | - Anita De Rossi
- University of Padova, Section of Oncology and Immunology DiSCOG, Padova, Italy
| | - Eleni Nastouli
- UCL Great Ormond Sstreet Institute of Child Health, London UK
| | - María Angeles Muñoz-Fernández
- Immunology Section, InmunoBioloy Molecular Laboratory, Hospital General Universitario Gregorio Marañón, Spanish HIV HGM BioBank, IiSGM, Madrid, Spain
| | - Diana Gibb
- MRC Clinical Trials Unit at UCL, Institute of Clinical Trials & Methodology, London, UK
| | - Paolo Rossi
- Academic Department of Pediatrics (DPUO), Research Unit in Congenital and Perinatal Infection, Children's Hospital Bambino Gesù, Rome, Italy
| | - Carlo Giaquinto
- Department of Women and Child Health, University of Padova, Padova, Italy
| | - Abdel Babiker
- MRC Clinical Trials Unit at UCL, Institute of Clinical Trials & Methodology, London, UK
| | - Claudia Fortuny
- Malalties infeccioses i resposta inflamatòria sistèmica en pediatria. Unitat d'Infeccions, Servei de Pediatria. Institut de Recerca, Pediàtrica Hospital Sant Joan de Déu, Barcelona, Spain. Departament de Pediatria, Universitat de Barcelona, Barcelona, Spain. CIBER de Epidemiología y Salud Pública Ciberesp, Spain
- Translational Research Network in Pediatric Infectious Diseases (RITIP), Madrid, Spain
| | - Riccardo Freguja
- University of Padova, Section of Oncology and Immunology DiSCOG, Padova, Italy
| | - Nicola Cotugno
- Academic Department of Pediatrics (DPUO), Research Unit in Congenital and Perinatal Infection, Children's Hospital Bambino Gesù, Rome, Italy
| | - Ali Judd
- MRC Clinical Trials Unit at UCL, Institute of Clinical Trials & Methodology, London, UK
| | - Antoni Noguera-Julian
- Malalties infeccioses i resposta inflamatòria sistèmica en pediatria. Unitat d'Infeccions, Servei de Pediatria. Institut de Recerca, Pediàtrica Hospital Sant Joan de Déu, Barcelona, Spain. Departament de Pediatria, Universitat de Barcelona, Barcelona, Spain. CIBER de Epidemiología y Salud Pública Ciberesp, Spain
- Translational Research Network in Pediatric Infectious Diseases (RITIP), Madrid, Spain
| | - María Luisa Navarro
- Pediatric Infectious Diseases Unit, Hospital Universitario Gregorio Marañón, Madrid, Spain
- Translational Research Network in Pediatric Infectious Diseases (RITIP), Madrid, Spain
| | - María José Mellado
- Pediatrics, Immunodeficiencies and Infectious Diseases Unit, Hospital Universitario La Paz, Madrid, Spain
- Translational Research Network in Pediatric Infectious Diseases (RITIP), Madrid, Spain
| | - Nigel Klein
- UCL Great Ormond Sstreet Institute of Child Health, London UK
| | - Paolo Palma
- Academic Department of Pediatrics (DPUO), Research Unit in Congenital and Perinatal Infection, Children's Hospital Bambino Gesù, Rome, Italy
| | - Pablo Rojo
- Department of Pediatrics, Hospital 12 de Octubre, Fundación para la Investigación Biomédica del Hospital Universitario 12 de Octubre. Madrid, Spain
- Medical School. Universidad Complutense de Madrid. Madrid, Spain
- Translational Research Network in Pediatric Infectious Diseases (RITIP), Madrid, Spain
| |
Collapse
|
60
|
Visualization of HIV-1 RNA Transcription from Integrated HIV-1 DNA in Reactivated Latently Infected Cells. Viruses 2018; 10:v10100534. [PMID: 30274333 PMCID: PMC6212899 DOI: 10.3390/v10100534] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2018] [Revised: 09/26/2018] [Accepted: 09/27/2018] [Indexed: 12/14/2022] Open
Abstract
We have recently developed the first microscopy-based strategy that enables simultaneous multiplex detection of viral RNA (vRNA), viral DNA (vDNA), and viral protein. Here, we used this approach to study the kinetics of latency reactivation in cells infected with the human immunodeficiency virus (HIV). We showed the transcription of nascent vRNA from individual latently integrated and reactivated vDNA sites appearing earlier than viral protein. We further demonstrated that this method can be used to quantitatively assess the efficacy of a variety of latency reactivating agents. Finally, this microscopy-based strategy was augmented with a flow-cytometry-based approach, enabling the detection of transcriptional reactivation of large numbers of latently infected cells. Hence, these approaches are shown to be suitable for qualitative and quantitative studies of HIV-1 latency and reactivation.
Collapse
|
61
|
Bosman KJ, Wensing AMJ, Pijning AE, van Snippenberg WJ, van Ham PM, de Jong DMC, Hoepelman AIM, Nijhuis M. Development of sensitive ddPCR assays to reliably quantify the proviral DNA reservoir in all common circulating HIV subtypes and recombinant forms. J Int AIDS Soc 2018; 21:e25185. [PMID: 30375818 PMCID: PMC6138437 DOI: 10.1002/jia2.25185] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2018] [Accepted: 08/17/2018] [Indexed: 12/21/2022] Open
Abstract
INTRODUCTION The latent reservoir is the main barrier on the road to HIV cure, and clinical approaches towards eradication are often evaluated by their effect on proviral DNA. To ensure inclusiveness and representativeness in HIV cure studies, proviral DNA quantification assays that are able to detect all common circulating HIV clades are urgently needed. Here, three HIV DNA assays targeting three different genomic regions were evaluated for their sensitivity and subtype-tolerance using digital PCR. METHODS A subtype-B-specific assay targeting gag (GAG) and two assays targeting conserved sequences in ltr and pol (LTR and JO) were assessed for their sensitivity and subtype-tolerance in digital PCR (Bio-Rad QX200), using a panel of serially diluted subtype reference plasmids as well as a panel of clinical isolates. Both panels represent subtypes A, B, C, D, F, G and circulating recombinant forms (CRFs) AE and AG, which together are responsible for 94% of HIV infections worldwide. RESULTS HIV subtype was observed to greatly affect HIV DNA quantification results. Robust regression analysis of the serially diluted plasmid panel showed that the GAG assay was only able to linearly quantify subtype B, D and G isolates (4/13 reference plasmids, average R2 = 0.99), whereas LTR and JO were able to quantify all tested isolates (13/13 reference plasmids, respective average R2 = 0.99 and 0.98). In the clinical isolates panel, isolates were considered detectable if all replicates produced a positive result. The GAG assay could detect HIV DNA in four out of five subtype B and one out of two subtype D isolates, whereas the LTR and JO assays detected HIV DNA in all twenty-nine tested isolates. LTR and JO results were found to be equally precise but more precise than GAG. CONCLUSIONS The results demonstrate the need for a careful validation of proviral reservoir quantification assays prior to investigations into non-B subtype reservoirs. The LTR and JO assays can sensitively and reliably quantify HIV DNA in a panel that represents the worldwide most prevalent subtypes and CRFs (A, B, C, D, AE, F, G and AG), justifying their application in future trials aimed at global HIV cure.
Collapse
Affiliation(s)
- Kobus J Bosman
- Department of Medical MicrobiologyUniversity Medical Center UtrechtUtrechtthe Netherlands
| | - Annemarie MJ Wensing
- Department of Medical MicrobiologyUniversity Medical Center UtrechtUtrechtthe Netherlands
| | - Aster E Pijning
- Department of Medical MicrobiologyUniversity Medical Center UtrechtUtrechtthe Netherlands
| | | | - Petra M van Ham
- Department of Medical MicrobiologyUniversity Medical Center UtrechtUtrechtthe Netherlands
| | - Dorien MC de Jong
- Department of Medical MicrobiologyUniversity Medical Center UtrechtUtrechtthe Netherlands
| | - Andy IM Hoepelman
- Department of Internal Medicine and Infectious DiseasesUniversity Medical Center UtrechtUtrechtthe Netherlands
| | - Monique Nijhuis
- Department of Medical MicrobiologyUniversity Medical Center UtrechtUtrechtthe Netherlands
| |
Collapse
|
62
|
Rocca S, Zangari P, Cotugno N, De Rossi A, Ferns B, Petricone D, Rinaldi S, Giaquinto C, Bernardi S, Rojo P, Rossi P, Pahwa S, Nastouli E, Palma P. Human Immunodeficiency Virus (HIV)-Antibody Repertoire Estimates Reservoir Size and Time of Antiretroviral Therapy Initiation in Virally Suppressed Perinatally HIV-Infected Children. J Pediatric Infect Dis Soc 2018; 8:433-438. [PMID: 30169837 PMCID: PMC6831830 DOI: 10.1093/jpids/piy080] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/07/2018] [Accepted: 08/21/2018] [Indexed: 12/18/2022]
Abstract
BACKGROUND Assays to estimate human immunodeficiency virus (HIV) reservoir size require large amounts of blood, which represents a drawback especially in pediatric settings. We investigated whether HIV-antibody repertoire could estimate the viral reservoir size. Moreover, we assessed the magnitude of HIV-antibody response as a predictor of time of antiretroviral therapy (ART) initiation. METHODS Human immunodeficiency virus-antibody responses to 10 different viral proteins were evaluated by HIV Western blot (WB) kit and a WB score was assigned to each patient. Patients were classified in 2 subgroups based on the timing of ART initiation (early treated [ET], 0-24 weeks and late treated [LT], >24 weeks). Human immunodeficiency virus-deoxyribonucleic acid (DNA) was quantified using real-time quantitative polymerase chain reaction on total peripheral blood mononuclear cells. Logistic regression and principal component analysis were built on these data to test the ability of WB score to predict the expected value of HIV-DNA and the timing of ART initiation. RESULTS Sixty-nine perinatally HIV-infected children were evaluated. Reduced HIV-specific antibody responses and lower size of HIV-DNA were observed in ET compared with LT patients (P < .001 and P = .02, respectively). We found that WB score correlates with HIV-DNA (P = .032) and timing of ART initiation (P < .001). Based on the logistic regression analysis, we found that WB score can predict the HIV-DNA size and the timing of ART initiation with an Akaike information criterion of -118.13 and -151.51, respectively. CONCLUSIONS Western blot score can estimate HIV-DNA size and timing of ART initiation in long-term virally suppressed children. This rapid, inexpensive, and easily reproducible tool can provide useful information to identify potential candidates for HIV remission studies.
Collapse
Affiliation(s)
- Salvatore Rocca
- Department of Systems Medicine, University of Rome Tor Vergata, Rome, Italy,Research Unit in Congenital and Perinatal Infection, Immune and Infectious Diseases Division, Academic Department of Pediatrics (DPUO), Bambino Gesù Children’s Hospital, Rome, Italy
| | - Paola Zangari
- Research Unit in Congenital and Perinatal Infection, Immune and Infectious Diseases Division, Academic Department of Pediatrics (DPUO), Bambino Gesù Children’s Hospital, Rome, Italy
| | - Nicola Cotugno
- Department of Systems Medicine, University of Rome Tor Vergata, Rome, Italy,Research Unit in Congenital and Perinatal Infection, Immune and Infectious Diseases Division, Academic Department of Pediatrics (DPUO), Bambino Gesù Children’s Hospital, Rome, Italy
| | - Anita De Rossi
- Section of Oncology and Immunology, DiSCOG, University of Padova, Italy; 3bis Immunology and Molecular Oncology Unit, Istituto Oncologico Veneto (IOV)-IRCCS, Padova, Italy
| | - Bridget Ferns
- Virology Laboratory, Clinical Microbiology and Virology, University College London Hospital NHS Foundation Trust, London, United Kingdom
| | - Davide Petricone
- Department of Systems Medicine, University of Rome Tor Vergata, Rome, Italy
| | - Stefano Rinaldi
- Department of Microbiology and Immunology, Miller School of Medicine, University of Miami, Florida
| | - Carlo Giaquinto
- Department of Women’s and Children’s Health, University of Padova, Italy
| | - Stefania Bernardi
- Academic Department of Pediatrics (DPUO), Bambino Gesù Children’s Hospital-University of Rome Tor Vergata, Italy
| | - Pablo Rojo
- Department of Pediatrics, Pediatric Infectious Diseases Unit, Hospital 12 de Octubre, Universidad Complutense, Madrid, Spain
| | - Paolo Rossi
- Department of Systems Medicine, University of Rome Tor Vergata, Rome, Italy,Research Unit in Congenital and Perinatal Infection, Immune and Infectious Diseases Division, Academic Department of Pediatrics (DPUO), Bambino Gesù Children’s Hospital, Rome, Italy,Academic Department of Pediatrics (DPUO), Bambino Gesù Children’s Hospital-University of Rome Tor Vergata, Italy
| | - Savita Pahwa
- Department of Microbiology and Immunology, Miller School of Medicine, University of Miami, Florida,Miami Center for AIDS Research, Miller School of Medicine, University of Miami, Florida
| | - Eleni Nastouli
- Virology Laboratory, Clinical Microbiology and Virology, University College London Hospital NHS Foundation Trust, London, United Kingdom
| | - Paolo Palma
- Research Unit in Congenital and Perinatal Infection, Immune and Infectious Diseases Division, Academic Department of Pediatrics (DPUO), Bambino Gesù Children’s Hospital, Rome, Italy,Corresponding Author: P. Palma, MD, PhD, Research Unit in Congenital and Perinatal Infections, Academic Department of Pediatrics, Division of Immune and Infectious Diseases, IRCCS Ospedale Pediatrico Bambino Gesu’, P.zza S.Onofrio, 4 - 00165 Roma. E-mail:
| | | |
Collapse
|
63
|
Abstract
The benefits of combination antiretroviral therapy (cART) for HIV replication and transmission control have led to its universal recommendation. Many people living with HIV are, however, still undiagnosed or diagnosed late, especially in sub-Saharan Africa, where the HIV disease burden is highest. Further expansion in HIV treatment options, incorporating women-centred approaches, is essential to make individualised care a reality. With a longer life expectancy than before, people living with HIV are at an increased risk of developing non-AIDS comorbidities, such as cardiovascular diseases and cancers. Antiretroviral strategies are evolving towards a decrease in drug burden, and some two-drug combinations have proven efficacy for maintenance therapy. Investigational immune checkpoint inhibitors and broadly neutralising antibodies with effector functions have energised the HIV cure research field as the search for an effective vaccine continues. In this Seminar, we review advances and challenges relating to the goal of an AIDS-free world.
Collapse
Affiliation(s)
- Jade Ghosn
- Inserm UMR-S 1136, Institut Pierre Louis d'Epidémiologie et de Santé Publique, Paris, France; Paris Descartes University, Sorbonne Paris Cité, Paris, France
| | - Babafemi Taiwo
- Division of Infectious Diseases and Center for Global Health, Northwestern University, Chicago, Illinois, USA
| | - Soraya Seedat
- Department of Psychiatry, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
| | - Brigitte Autran
- Inserm UMR-S 1135, Centre de Recherches en Immunologie et Maladies Infectieus, CIMI-Paris, Université Pierre et Marie Curie, Paris, France
| | - Christine Katlama
- Inserm UMR-S 1136, Institut Pierre Louis d'Epidémiologie et de Santé Publique, Paris, France; Paris-Sorbonne University, Paris, France; Assistance Publique-Hôpitaux de Paris, Department of Infectious Diseases, Hôpital Pitié Salpêtrière, Paris, France.
| |
Collapse
|
64
|
Cooperative Metabolic Adaptations in the Host Can Favor Asymptomatic Infection and Select for Attenuated Virulence in an Enteric Pathogen. Cell 2018; 175:146-158.e15. [PMID: 30100182 DOI: 10.1016/j.cell.2018.07.016] [Citation(s) in RCA: 94] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2018] [Revised: 06/09/2018] [Accepted: 07/11/2018] [Indexed: 12/11/2022]
Abstract
Pathogen virulence exists on a continuum. The strategies that drive symptomatic or asymptomatic infections remain largely unknown. We took advantage of the concept of lethal dose 50 (LD50) to ask which component of individual non-genetic variation between hosts defines whether they survive or succumb to infection. Using the enteric pathogen Citrobacter, we found no difference in pathogen burdens between healthy and symptomatic populations. Iron metabolism-related genes were induced in asymptomatic hosts compared to symptomatic or naive mice. Dietary iron conferred complete protection without influencing pathogen burdens, even at 1000× the lethal dose of Citrobacter. Dietary iron induced insulin resistance, increasing glucose levels in the intestine that were necessary and sufficient to suppress pathogen virulence. A short course of dietary iron drove the selection of attenuated Citrobacter strains that can transmit and asymptomatically colonize naive hosts, demonstrating that environmental factors and cooperative metabolic strategies can drive conversion of pathogens toward commensalism.
Collapse
|
65
|
Suárez H, Rocha-Perugini V, Álvarez S, Yáñez-Mó M. Tetraspanins, Another Piece in the HIV-1 Replication Puzzle. Front Immunol 2018; 9:1811. [PMID: 30127789 PMCID: PMC6088189 DOI: 10.3389/fimmu.2018.01811] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2018] [Accepted: 07/23/2018] [Indexed: 12/12/2022] Open
Abstract
Despite the great research effort placed during the last decades in HIV-1 study, still some aspects of its replication cycle remain unknown. All this powerful research has succeeded in developing different drugs for AIDS treatment, but none of them can completely remove the virus from infected patients, who require life-long medication. The classical approach was focused on the study of virus particles as the main target, but increasing evidence highlights the importance of host cell proteins in HIV-1 cycle. In this context, tetraspanins have emerged as critical players in different steps of the viral infection cycle. Through their association with other molecules, including membrane receptors, cytoskeletal proteins, and signaling molecules, tetraspanins organize specialized membrane microdomains called tetraspanin-enriched microdomains (TEMs). Within these microdomains, several tetraspanins have been described to regulate HIV-1 entry, assembly, and transfer between cells. Interestingly, the importance of tetraspanins CD81 and CD63 in the early steps of viral replication has been recently pointed out. Indeed, CD81 can control the turnover of the HIV-1 restriction factor SAMHD1. This deoxynucleoside triphosphate triphosphohydrolase counteracts HIV-1 reverse transcription (RT) in resting cells via its dual function as dNTPase, catalyzing deoxynucleotide triphosphates into deoxynucleosides and inorganic triphosphate, and as exonuclease able to degrade single-stranded RNAs. SAMHD1 has also been related with the detection of viral nucleic acids, regulating the innate immune response and would promote viral latency. New evidences demonstrating the ability of CD81 to control SAMHD1 expression, and as a consequence, HIV-1 RT activity, highlight the importance of TEMs for viral replication. Here, we will briefly review how tetraspanins modulate HIV-1 infection, focusing on the latest findings that link TEMs to viral replication.
Collapse
Affiliation(s)
- Henar Suárez
- Departamento de Biología Molecular, Universidad Autónoma de Madrid, Madrid, Spain
| | - Vera Rocha-Perugini
- Servicio de Inmunología, Hospital de la Princesa, Instituto de Investigación Sanitaria La Princesa (IIS-IP), Madrid, Spain.,Vascular Pathophysiology Research Area, Centro Nacional de Investigaciones Cardiovasculares Carlos III, Madrid, Spain
| | - Susana Álvarez
- Servicio de Inmunobiología Molecular, Hospital General Universitario Gregorio Marañón, Madrid, Spain
| | - María Yáñez-Mó
- Departamento de Biología Molecular, Universidad Autónoma de Madrid, Madrid, Spain.,Centro de Biología Molecular Severo Ochoa, Instituto de Investigación Sanitaria La Princesa (IIS-IP), Madrid, Spain
| |
Collapse
|
66
|
Poon AFY, Prodger JL, Lynch BA, Lai J, Reynolds SJ, Kasule J, Capoferri AA, Lamers SL, Rodriguez CW, Bruno D, Porcella SF, Martens C, Quinn TC, Redd AD. Quantitation of the latent HIV-1 reservoir from the sequence diversity in viral outgrowth assays. Retrovirology 2018; 15:47. [PMID: 29976219 PMCID: PMC6034329 DOI: 10.1186/s12977-018-0426-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2018] [Accepted: 06/14/2018] [Indexed: 12/25/2022] Open
Abstract
BACKGROUND The ability of HIV-1 to integrate into the genomes of quiescent host immune cells, establishing a long-lived latent viral reservoir (LVR), is the primary obstacle to curing these infections. Quantitative viral outgrowth assays (QVOAs) are the gold standard for estimating the size of the replication-competent HIV-1 LVR, measured by the number of infectious units per million (IUPM) cells. QVOAs are time-consuming because they rely on culturing replicate wells to amplify the production of virus antigen or nucleic acid to reproducibly detectable levels. Sequence analysis can reduce the required number of culture wells because the virus genetic diversity within the LVR provides an internal replication and dilution series. Here we develop a Bayesian method to jointly estimate the IUPM and variant frequencies (a measure of clonality) from the sequence diversity of QVOAs. RESULTS Using simulation experiments, we find our Bayesian approach confers significantly greater accuracy over current methods to estimate the IUPM, particularly for reduced numbers of QVOA replicates and/or increasing actual IUPM. Furthermore, we determine that the improvement in accuracy is greater with increasing genetic diversity in the sample population. We contrast results of these different methods applied to new HIV-1 sequence data derived from QVOAs from two individuals with suppressed viral loads from the Rakai Health Sciences Program in Uganda. CONCLUSIONS Utilizing sequence variation has the additional benefit of providing information on the contribution of clonality of the LVR, where high clonality (the predominance of a single genetic variant) suggests a role for cell division in the long-term persistence of the reservoir. In addition, our Bayesian approach can be adapted to other limiting dilution assays where positive outcomes can be partitioned by their genetic heterogeneity, such as immune cell populations and other viruses.
Collapse
Affiliation(s)
- Art F Y Poon
- Department of Pathology and Laboratory Medicine, Western University, London, ON, Canada.
| | - Jessica L Prodger
- Department of Microbiology and Immunology, Western University, London, ON, Canada.,Department of Medicine, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Briana A Lynch
- Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Baltimore, MD, USA
| | - Jun Lai
- Department of Medicine, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Steven J Reynolds
- Department of Medicine, Johns Hopkins School of Medicine, Baltimore, MD, USA.,Rakai Health Sciences Program, Kalisizo, Uganda
| | | | - Adam A Capoferri
- Department of Medicine, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | | | | | - Daniel Bruno
- Genomics Unit, Research Technologies Branch, Rocky Mountain Laboratories, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, MT, USA
| | - Stephen F Porcella
- Genomics Unit, Research Technologies Branch, Rocky Mountain Laboratories, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, MT, USA
| | - Craig Martens
- Genomics Unit, Research Technologies Branch, Rocky Mountain Laboratories, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, MT, USA
| | - Thomas C Quinn
- Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Baltimore, MD, USA.,Department of Medicine, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Andrew D Redd
- Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Baltimore, MD, USA.,Department of Medicine, Johns Hopkins School of Medicine, Baltimore, MD, USA
| |
Collapse
|
67
|
De Silva Feelixge HS, Stone D, Roychoudhury P, Aubert M, Jerome KR. CRISPR/Cas9 and Genome Editing for Viral Disease-Is Resistance Futile? ACS Infect Dis 2018; 4:871-880. [PMID: 29522311 PMCID: PMC5993632 DOI: 10.1021/acsinfecdis.7b00273] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Chronic viral infections remain a major public health issue affecting millions of people worldwide. Highly active antiviral treatments have significantly improved prognosis and infection-related morbidity and mortality but have failed to eliminate persistent viral forms. Therefore, new strategies to either eradicate or control these viral reservoirs are paramount to allow patients to stop antiretroviral therapy and realize a cure. Viral genome disruption based on gene editing by programmable endonucleases is one promising curative gene therapy approach. Recent findings on RNA-guided human immunodeficiency virus 1 (HIV-1) genome cleavage by Cas9 and other gene-editing enzymes in latently infected cells have shown high levels of site-specific genome disruption and potent inhibition of virus replication. However, HIV-1 can readily develop resistance to genome editing at a single antiviral target site. Current data suggest that cellular repair associated with DNA double-strand breaks can accelerate the emergence of resistance. On the other hand, a combination antiviral target strategy can exploit the same repair mechanism to functionally cure HIV-1 infection in vitro while avoiding the development of resistance. This perspective summarizes recent findings on the biology of resistance to genome editing and discusses the significance of viral genetic diversity on the application of gene editing strategies toward cure.
Collapse
Affiliation(s)
- Harshana S De Silva Feelixge
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, 1100 Fairview Ave N, Seattle 98109, WA, USA
| | - Daniel Stone
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, 1100 Fairview Ave N, Seattle 98109, WA, USA
| | - Pavitra Roychoudhury
- Department of Laboratory Medicine, University of Washington, 1959 NE Pacific St, Seattle 98195, WA, USA
| | - Martine Aubert
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, 1100 Fairview Ave N, Seattle 98109, WA, USA
| | - Keith R Jerome
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, 1100 Fairview Ave N, Seattle 98109, WA, USA
- Department of Laboratory Medicine, University of Washington, 1959 NE Pacific St, Seattle 98195, WA, USA
- Department of Microbiology, University of Washington, 1959 NE Pacific St, Seattle 98195, WA, USA
| |
Collapse
|
68
|
Châtel L, Yang X, Cholette F, Soudeyns H, Sandstrom P, Lavigne C. Impact of pre-amplification conditions on sensitivity of the tat/rev induced limiting dilution assay. Arch Virol 2018; 163:2701-2710. [PMID: 29882046 DOI: 10.1007/s00705-018-3894-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2018] [Accepted: 04/24/2018] [Indexed: 11/29/2022]
Abstract
Antiretroviral therapy (ART) can lower a patient's HIV plasma viral load to an undetectable level, but following cessation of ART viremia rapidly rebounds. It has been shown that ART does not eliminate latent viruses sequestered into anatomical and cellular reservoirs. Therefore, in patients that have ceased ART, the following rebound in HIV viremia is caused by the activation of latent HIV reservoirs. A major issue in HIV cure research is the quantification of these latent HIV reservoirs. Various reservoir measurement methods exist, but the gold standard technique remains the culture-based quantitative viral outgrowth assay (QVOA). Recently, a new PCR-based assay, named the tat/rev induced limiting dilution assay (TILDA) was described which measures the frequency of inducible latently infected CD4+ T cells that actively produce multiply-spliced RNA coding for the Tat/Rev proteins. The objective of this study was to further optimize the assay by examining the influence of varied factors, such as the amount of products transferred from the pre-amplification step to the PCR reaction, storage of pre-amplification products prior to PCR runs, and the number of cells used, on the assay's sensitivity and reproducibility. We also investigated whether the assay could be used to quantify HIV reservoirs in monocytes/macrophages.
Collapse
Affiliation(s)
- Liam Châtel
- National HIV and Retrovirology Laboratories, National Microbiology Laboratory, JC Wilt Infectious Diseases Research Centre, Public Health Agency of Canada, 1015 Arlington Street, Winnipeg, MB, R3E 3R2, Canada
| | - Xuefen Yang
- National HIV and Retrovirology Laboratories, National Microbiology Laboratory, JC Wilt Infectious Diseases Research Centre, Public Health Agency of Canada, 1015 Arlington Street, Winnipeg, MB, R3E 3R2, Canada
| | - François Cholette
- National HIV and Retrovirology Laboratories, National Microbiology Laboratory, JC Wilt Infectious Diseases Research Centre, Public Health Agency of Canada, 1015 Arlington Street, Winnipeg, MB, R3E 3R2, Canada
| | - Hugo Soudeyns
- Centre de recherche du Centre hospitalier universitaire Sainte-Justine, Montreal, QC, Canada.,Department of Microbiology, Infectiology and Immunology, Faculty of Medicine, Université de Montréal, Montreal, QC, Canada
| | - Paul Sandstrom
- National HIV and Retrovirology Laboratories, National Microbiology Laboratory, JC Wilt Infectious Diseases Research Centre, Public Health Agency of Canada, 1015 Arlington Street, Winnipeg, MB, R3E 3R2, Canada
| | - Carole Lavigne
- National HIV and Retrovirology Laboratories, National Microbiology Laboratory, JC Wilt Infectious Diseases Research Centre, Public Health Agency of Canada, 1015 Arlington Street, Winnipeg, MB, R3E 3R2, Canada.
| |
Collapse
|
69
|
Overcoming immune tolerance in chronic hepatitis B by therapeutic vaccination. Curr Opin Virol 2018; 30:58-67. [PMID: 29751272 DOI: 10.1016/j.coviro.2018.04.003] [Citation(s) in RCA: 52] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2018] [Revised: 04/03/2018] [Accepted: 04/18/2018] [Indexed: 12/14/2022]
Abstract
The currently used nucleoside analogs (i.e. entecavir and tenofovir) with high barrier-to-resistance efficiently suppress viral replication, limit inflammation and reduce the sequelae of chronic hepatitis B, but cannot cure the disease and thus have to be applied long-term. Therapeutic vaccination as an approach to cure chronic hepatitis B has shown promising pre-clinical results, nevertheless the proof of its efficacy in clinical trials is still missing. This may be partially due to suboptimal vaccine design. A main obstacle in chronic hepatitis B, however, is the high load of viral antigens expressed and secreted, which has been proposed to cause antigen-specific immune tolerance. Reduction of the viral antigen load is therefore considered a key factor for success of immune-based therapies. Although nucleoside analogs do not reduce viral antigen expression, new antiviral strategies are becoming available. Targeting viral translation by siRNA or targeting release of HBsAg from infected hepatocytes by nucleic acid polymers both reduce the antigen load. They may be considered as pre-treatment for therapeutic vaccination to increase the potential to elicit an HBV-specific immune response able to control and cure chronic HBV infection.
Collapse
|
70
|
Shiau S, Abrams EJ, Arpadi SM, Kuhn L. Early antiretroviral therapy in HIV-infected infants: can it lead to HIV remission? Lancet HIV 2018; 5:e250-e258. [PMID: 29739699 PMCID: PMC7487171 DOI: 10.1016/s2352-3018(18)30012-2] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2017] [Accepted: 01/19/2018] [Indexed: 12/27/2022]
Abstract
Interventions to prevent mother-to-child HIV transmission have been extremely successful, but new HIV infections continue to occur in infants. Strong evidence indicates that combination antiretroviral therapy (ART) for treatment should be started in HIV-infected infants to prevent early morbidity and mortality. In 2013, the report of the Mississippi baby, who was started on ART within 30 h of life and maintained off-treatment remission for 27 months before HIV was once again detectable, generated renewed interest in very early ART initiation. The case stimulated interest in the possibility of HIV remission, which we define as maintenance of plasma viraemia below the threshold of detection in the absence of ART, after early treatment initiation. The possibility of HIV remission elicits much hope, given that children with HIV infection currently face a lifetime of treatment. The potential for early ART to lead to HIV remission in infants can be thought of in terms of six factors: rapidity of viral suppression with very early ART; initial viral suppression rate with early ART; later virological control after early treatment; the effect of early treatment on the viral reservoir size; outcomes of randomised trials of structured treatment interruption; and the likelihood of viral rebound in neonates after ART cessation. Review of existing data suggests that achieving long-term remission off treatment remains elusive, and concentrated attention and commitment of the scientific community is needed to investigate the factors that might help to reach this goal.
Collapse
Affiliation(s)
- Stephanie Shiau
- Gertrude H. Sergievsky Center, Mailman School of Public Health, Columbia University, New York, NY, USA; College of Physicians and Surgeons, and Department of Epidemiology, Mailman School of Public Health, Columbia University, New York, NY, USA; Empilweni Services and Research Unit, Rahima Moosa Mother and Child Hospital, Department of Paediatrics and Child Health, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Elaine J Abrams
- Department of Pediatrics, Mailman School of Public Health, Columbia University, New York, NY, USA; College of Physicians and Surgeons, and Department of Epidemiology, Mailman School of Public Health, Columbia University, New York, NY, USA; ICAP, Mailman School of Public Health, Columbia University, New York, NY, USA; Empilweni Services and Research Unit, Rahima Moosa Mother and Child Hospital, Department of Paediatrics and Child Health, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Stephen M Arpadi
- Gertrude H. Sergievsky Center, Mailman School of Public Health, Columbia University, New York, NY, USA; Department of Pediatrics, Mailman School of Public Health, Columbia University, New York, NY, USA; College of Physicians and Surgeons, and Department of Epidemiology, Mailman School of Public Health, Columbia University, New York, NY, USA; ICAP, Mailman School of Public Health, Columbia University, New York, NY, USA; Empilweni Services and Research Unit, Rahima Moosa Mother and Child Hospital, Department of Paediatrics and Child Health, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Louise Kuhn
- Gertrude H. Sergievsky Center, Mailman School of Public Health, Columbia University, New York, NY, USA; College of Physicians and Surgeons, and Department of Epidemiology, Mailman School of Public Health, Columbia University, New York, NY, USA; Empilweni Services and Research Unit, Rahima Moosa Mother and Child Hospital, Department of Paediatrics and Child Health, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa.
| |
Collapse
|
71
|
Wu X, Guo J, Niu M, An M, Liu L, Wang H, Jin X, Zhang Q, Lam KS, Wu T, Wang H, Wang Q, Du Y, Li J, Cheng L, Tang HY, Shang H, Zhang L, Zhou P, Chen Z. Tandem bispecific neutralizing antibody eliminates HIV-1 infection in humanized mice. J Clin Invest 2018; 128:2239-2251. [PMID: 29461979 DOI: 10.1172/jci96764] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2017] [Accepted: 02/16/2018] [Indexed: 01/01/2023] Open
Abstract
The discovery of an HIV-1 cure remains a medical challenge because the virus rebounds quickly after the cessation of combination antiretroviral therapy (cART). Here, we investigate the potential of an engineered tandem bispecific broadly neutralizing antibody (bs-bnAb) as an innovative product for HIV-1 prophylactic and therapeutic interventions. We discovered that by preserving 2 single-chain variable fragment (scFv) binding domains of each parental bnAb, a single gene-encoded tandem bs-bnAb, BiIA-SG, displayed substantially improved breadth and potency. BiIA-SG neutralized all 124 HIV-1-pseudotyped viruses tested, including global subtypes/recombinant forms, transmitted/founder viruses, variants not susceptible to parental bnAbs and to many other bnAbs with an average IC50 value of 0.073 μg/ml (range < 0.001-1.03 μg/ml). In humanized mice, an injection of BiIA-SG conferred sterile protection when administered prior to challenges with diverse live HIV-1 stains. Moreover, whereas BiIA-SG delayed viral rebound in a short-term therapeutic setting when combined with cART, a single injection of adeno-associated virus-transferred (AAV-transferred) BiIA-SG gene resulted dose-dependently in prolonged in vivo expression of BiIA-SG, which was associated with complete viremia control and subsequent elimination of infected cells in humanized mice. These results warrant the clinical development of BiIA-SG as a promising bs-bnAb-based biomedical intervention for the prevention and treatment of HIV-1 infection.
Collapse
Affiliation(s)
- Xilin Wu
- AIDS Institute and Department of Microbiology, State Key Laboratory of Emerging Infectious Diseases, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region, People's Republic of China.,The University of Hong Kong AIDS Institute Shenzhen Research Laboratory, Guangdong Key Laboratory of Emerging Infectious Diseases and Shenzhen Key Laboratory of Infection and Immunity, Shenzhen Third People's Hospital, Shenzhen, Guangdong Province, People's Republic of China
| | - Jia Guo
- AIDS Institute and Department of Microbiology, State Key Laboratory of Emerging Infectious Diseases, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region, People's Republic of China
| | - Mengyue Niu
- AIDS Institute and Department of Microbiology, State Key Laboratory of Emerging Infectious Diseases, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region, People's Republic of China.,The University of Hong Kong AIDS Institute Shenzhen Research Laboratory, Guangdong Key Laboratory of Emerging Infectious Diseases and Shenzhen Key Laboratory of Infection and Immunity, Shenzhen Third People's Hospital, Shenzhen, Guangdong Province, People's Republic of China
| | - Minghui An
- AIDS Institute and Department of Microbiology, State Key Laboratory of Emerging Infectious Diseases, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region, People's Republic of China.,Key Laboratory of AIDS Immunology of National Health and Family Planning Commission, Department of Laboratory Medicine, The First Affiliated Hospital, China Medical University, Shenyang, Liaoning Province, People's Republic of China
| | - Li Liu
- AIDS Institute and Department of Microbiology, State Key Laboratory of Emerging Infectious Diseases, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region, People's Republic of China.,The University of Hong Kong AIDS Institute Shenzhen Research Laboratory, Guangdong Key Laboratory of Emerging Infectious Diseases and Shenzhen Key Laboratory of Infection and Immunity, Shenzhen Third People's Hospital, Shenzhen, Guangdong Province, People's Republic of China
| | - Hui Wang
- The University of Hong Kong AIDS Institute Shenzhen Research Laboratory, Guangdong Key Laboratory of Emerging Infectious Diseases and Shenzhen Key Laboratory of Infection and Immunity, Shenzhen Third People's Hospital, Shenzhen, Guangdong Province, People's Republic of China
| | - Xia Jin
- Unit of Antiviral Immunity and Genetic Therapy, Institut Pasteur of Shanghai, Chinese Academy of Sciences, Shanghai, People's Republic of China
| | - Qi Zhang
- Comprehensive AIDS Research Center and Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, School of Medicine, Tsinghua University, Beijing, People's Republic of China
| | - Ka Shing Lam
- AIDS Institute and Department of Microbiology, State Key Laboratory of Emerging Infectious Diseases, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region, People's Republic of China
| | - Tongjin Wu
- AIDS Institute and Department of Microbiology, State Key Laboratory of Emerging Infectious Diseases, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region, People's Republic of China
| | - Hua Wang
- Comprehensive AIDS Research Center and Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, School of Medicine, Tsinghua University, Beijing, People's Republic of China
| | - Qian Wang
- Comprehensive AIDS Research Center and Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, School of Medicine, Tsinghua University, Beijing, People's Republic of China
| | - Yanhua Du
- AIDS Institute and Department of Microbiology, State Key Laboratory of Emerging Infectious Diseases, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region, People's Republic of China
| | - Jingjing Li
- AIDS Institute and Department of Microbiology, State Key Laboratory of Emerging Infectious Diseases, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region, People's Republic of China
| | - Lin Cheng
- The University of Hong Kong AIDS Institute Shenzhen Research Laboratory, Guangdong Key Laboratory of Emerging Infectious Diseases and Shenzhen Key Laboratory of Infection and Immunity, Shenzhen Third People's Hospital, Shenzhen, Guangdong Province, People's Republic of China
| | - Hang Ying Tang
- AIDS Institute and Department of Microbiology, State Key Laboratory of Emerging Infectious Diseases, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region, People's Republic of China
| | - Hong Shang
- Key Laboratory of AIDS Immunology of National Health and Family Planning Commission, Department of Laboratory Medicine, The First Affiliated Hospital, China Medical University, Shenyang, Liaoning Province, People's Republic of China
| | - Linqi Zhang
- Comprehensive AIDS Research Center and Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, School of Medicine, Tsinghua University, Beijing, People's Republic of China
| | - Paul Zhou
- Unit of Antiviral Immunity and Genetic Therapy, Institut Pasteur of Shanghai, Chinese Academy of Sciences, Shanghai, People's Republic of China
| | - Zhiwei Chen
- AIDS Institute and Department of Microbiology, State Key Laboratory of Emerging Infectious Diseases, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region, People's Republic of China.,The University of Hong Kong AIDS Institute Shenzhen Research Laboratory, Guangdong Key Laboratory of Emerging Infectious Diseases and Shenzhen Key Laboratory of Infection and Immunity, Shenzhen Third People's Hospital, Shenzhen, Guangdong Province, People's Republic of China
| |
Collapse
|
72
|
Vadrevu SK, Trbojevic-Akmacic I, Kossenkov AV, Colomb F, Giron LB, Anzurez A, Lynn K, Mounzer K, Landay AL, Kaplan RC, Papasavvas E, Montaner LJ, Lauc G, Abdel-Mohsen M. Frontline Science: Plasma and immunoglobulin G galactosylation associate with HIV persistence during antiretroviral therapy. J Leukoc Biol 2018; 104:461-471. [PMID: 29633346 DOI: 10.1002/jlb.3hi1217-500r] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2017] [Revised: 02/12/2018] [Accepted: 02/14/2018] [Indexed: 12/26/2022] Open
Abstract
Global antibody glycosylation is dynamic and plays critical roles in shaping different immunological outcomes and direct antibody functionality during HIV infection. However, the relevance of global antibody or plasma glycosylation patterns to HIV persistence after antiretroviral therapy (ART) has not been characterized. First, we compared glycomes of total plasma and isolated immunoglobulin G (IgG) from HIV+ ART-suppressed, HIV+ viremic, and HIV-negative individuals. Second, in ART-suppressed individuals, we examined the associations between glycomes and (1) levels of cell-associated HIV DNA and RNA in PBMCs and isolated CD4+ T cells, (2) CD4 count and CD4%, and (3) expression of CD4+ T-cell activation markers. HIV infection is associated with persistent alterations in the IgG glycome including decreased levels of disialylated glycans, which is associated with a lower anti-inflammatory activity, and increased levels of fucosylated glycans, which is associated with lower antibody-dependent cell-mediated cytotoxicity (ADCC). We also show that levels of certain mono- and digalactosylated nonfucosylated glycomic traits (A2G1, A2G2, and A2BG2), which have been reported to be associated with higher ADCC and higher anti-inflammatory activities, exhibit significant negative correlations with levels of cell-associated total HIV DNA and HIV RNA in ART-suppressed individuals. Finally, levels of certain circulating anti-inflammatory glycans are associated with higher levels of CD4 T cells and lower levels of T-cell activation. Our findings represent the first proof-of-concept evidence that glycomic alterations, known to be associated with differential states of inflammation and ADCC activities, are also associated with levels of HIV persistence in the setting of ART suppression.
Collapse
Affiliation(s)
| | | | | | | | - Leila B Giron
- The Wistar Institute, Philadelphia, Pennsylvania, USA
| | | | - Kenneth Lynn
- The Wistar Institute, Philadelphia, Pennsylvania, USA.,Department of Medicine, University of Pennsylvania, Pennsylvania, USA
| | - Karam Mounzer
- Jonathan Lax Center, Philadelphia FIGHT, Pennsylvania, USA
| | - Alan L Landay
- Department of Microbial Pathogens and Immunity, Rush University Medical Center, Chicago, Illinois, USA
| | | | | | | | - Gordan Lauc
- Genos Glycoscience Research Laboratory, Zagreb, Croatia.,Faculty of Pharmacy and Biochemistry, University of Zagreb, Zagreb, Croatia
| | | |
Collapse
|
73
|
Cummins NW, Badley AD. Allogeneic stem cell transplantation alone is unlikely to provide the HIV-1 cure. Future Virol 2018. [DOI: 10.2217/fvl-2018-0005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Affiliation(s)
- Nathan W Cummins
- Division of Infectious Diseases, Mayo Clinic, Rochester, MN 55905, USA
| | - Andrew D Badley
- Division of Infectious Diseases, Mayo Clinic, Rochester, MN 55905, USA
- Office of Translation to Practice, Mayo Clinic, Rochester, MN 55905, USA
| |
Collapse
|
74
|
Darcis G, Das AT, Berkhout B. Tackling HIV Persistence: Pharmacological versus CRISPR-Based Shock Strategies. Viruses 2018; 10:v10040157. [PMID: 29596334 PMCID: PMC5923451 DOI: 10.3390/v10040157] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2018] [Revised: 03/26/2018] [Accepted: 03/28/2018] [Indexed: 02/07/2023] Open
Abstract
Jan Svoboda studied aspects of viral latency, in particular with respect to disease induction by avian RNA tumor viruses, which were later renamed as part of the extended retrovirus family. The course of retroviral pathogenesis is intrinsically linked to their unique property of integrating the DNA copy of the retroviral genome into that of the host cell, thus forming the provirus. Retroviral latency has recently become of major clinical interest to allow a better understanding of why we can effectively block the human immunodeficiency virus type 1 (HIV-1) in infected individuals with antiviral drugs, yet never reach a cure. We will discuss HIV-1 latency and its direct consequence—the formation of long-lasting HIV-1 reservoirs. We next focus on one of the most explored strategies in tackling HIV-1 reservoirs—the “shock and kill” strategy—which describes the broadly explored pharmacological way of kicking the latent provirus, with subsequent killing of the virus-producing cell by the immune system. We furthermore present how the clustered regularly interspaced palindromic repeats (CRISPR) and associated protein (Cas) system can be harnessed to reach the same objective by reactivating HIV-1 gene expression from latency. We will review the benefits and drawbacks of these different cure strategies.
Collapse
Affiliation(s)
- Gilles Darcis
- Laboratory of Experimental Virology, Department of Medical Microbiology, Academic Medical Center, University of Amsterdam, 1105 AZ Amsterdam, The Netherlands.
- Infectious Diseases Department, Liège University Hospital, 4000 Liege, Belgium.
| | - Atze T Das
- Laboratory of Experimental Virology, Department of Medical Microbiology, Academic Medical Center, University of Amsterdam, 1105 AZ Amsterdam, The Netherlands.
| | - Ben Berkhout
- Laboratory of Experimental Virology, Department of Medical Microbiology, Academic Medical Center, University of Amsterdam, 1105 AZ Amsterdam, The Netherlands.
| |
Collapse
|
75
|
Schmitt K, Akkina R. Ultra-Sensitive HIV-1 Latency Viral Outgrowth Assays Using Humanized Mice. Front Immunol 2018; 9:344. [PMID: 29556230 PMCID: PMC5844934 DOI: 10.3389/fimmu.2018.00344] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2017] [Accepted: 02/07/2018] [Indexed: 11/16/2022] Open
Abstract
In the current quest for a complete cure for HIV/AIDS, highly sensitive HIV-1 latency detection methods are critical to verify full viral eradication. Until now, the in vitro quantitative viral outgrowth assays (qVOA) have been the gold standard for assessing latent HIV-1 viral burden. However, these assays have been inadequate in detecting the presence of ultralow levels of latent virus in a number of patients who were initially thought to have been cured, but eventually showed viral rebound. In this context, new approaches utilizing in vivo mouse-based VOAs are promising. In the murine VOA (mVOA), large numbers of CD4+ T cells or PBMC from aviremic subjects are xenografted into immunodeficient NSG mice, whereas in the humanized mouse-based VOA (hmVOA) patient CD4+ T cell samples are injected into BLT or hu-hematopoetic stem cells (hu-HSC) humanized mice. While latent virus could be recovered in both of these systems, the hmVOA provides higher sensitivity than the mVOA using a fewer number of input cells. In contrast to the mVOA, the hmVOA provides a broader spectrum of highly susceptible HIV-1 target cells and enables newly engrafted cells to home into preformed human lymphoid organs where they can infect cells in situ after viral activation. Hu-mice also allow for both xenograft- and allograft-driven cell expansions with less severe GvH providing a longer time frame for potential viral outgrowth from cells with a delayed latent viral activation. Based on these advantages, the hmVOA has great potential in playing an important role in HIV-1 latency and cure research.
Collapse
Affiliation(s)
- Kimberly Schmitt
- Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, CO, United States
| | - Ramesh Akkina
- Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, CO, United States
| |
Collapse
|
76
|
Vibholm L, Schleimann MH, Højen JF, Benfield T, Offersen R, Rasmussen K, Olesen R, Dige A, Agnholt J, Grau J, Buzon M, Wittig B, Lichterfeld M, Petersen AM, Deng X, Abdel-Mohsen M, Pillai SK, Rutsaert S, Trypsteen W, De Spiegelaere W, Vandekerchove L, Østergaard L, Rasmussen TA, Denton PW, Tolstrup M, Søgaard OS. Short-Course Toll-Like Receptor 9 Agonist Treatment Impacts Innate Immunity and Plasma Viremia in Individuals With Human Immunodeficiency Virus Infection. Clin Infect Dis 2018; 64:1686-1695. [PMID: 28329286 DOI: 10.1093/cid/cix201] [Citation(s) in RCA: 115] [Impact Index Per Article: 19.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2017] [Accepted: 03/03/2017] [Indexed: 12/22/2022] Open
Abstract
Background. Treatment with latency reversing agents (LRAs) enhances human immunodeficiency virus type 1 (HIV-1) transcription in vivo but leads to only modest reductions in the size of the reservoir, possibly due to insufficient immune-mediated elimination of infected cells. We hypothesized that a single drug molecule-a novel Toll-like receptor 9 (TLR9) agonist, MGN1703-could function as an enhancer of innate immunity and an LRA in vivo. Methods. We conducted a single-arm, open-label study in which 15 virologically suppressed HIV-1-infected individuals on antiretroviral therapy received 60 mg MGN1703 subcutaneously twice weekly for 4 weeks. We characterized plasmacytoid dendritic cell, natural killer (NK), and T-cell activation using flow cytometry on baseline and after 4 weeks of treatment. HIV-1 transcription was quantified by measuring plasma HIV-1 RNA during MGN1703 administration. Results. In accordance with the cell type-specific expression of TLR9, MGN1703 treatment led to pronounced activation of plasmacytoid dendritic cells and substantial increases in plasma interferon-α2 levels (P < .0001). Consistently, transcription of interferon-stimulated genes (eg, OAS1, ISG15, Mx1; each P < .0001) were upregulated in CD4+ T cells as demonstrated by RNA sequencing. Further, proportions of activated cytotoxic NK cells and CD8+ T cells increased significantly during MGN1703 dosing, suggesting an enhancement of cellular immune responses. In 6 of 15 participants, plasma HIV-1 RNA increased from <20 copies/mL to >1500 copies/mL (range, 21-1571 copies/mL) during treatment. Conclusions. TLR9 agonist treatment in HIV infection has a dual potential by increasing HIV-1 transcription and enhancing cytotoxic NK cell activation, both of which are key outcomes in HIV-1 eradication therapy. Clinical Trials Registration. NCT02443935.
Collapse
Affiliation(s)
- Line Vibholm
- Department of Infectious Diseases, Aarhus University Hospital.,Institute of Clinical Medicine, Aarhus University
| | - Mariane H Schleimann
- Department of Infectious Diseases, Aarhus University Hospital.,Institute of Clinical Medicine, Aarhus University
| | - Jesper F Højen
- Department of Infectious Diseases, Aarhus University Hospital.,Institute of Clinical Medicine, Aarhus University
| | - Thomas Benfield
- Department of Infectious Diseases, Hvidovre Hospital, University of Copenhagen, and
| | - Rasmus Offersen
- Department of Infectious Diseases, Aarhus University Hospital.,Institute of Clinical Medicine, Aarhus University
| | | | - Rikke Olesen
- Department of Infectious Diseases, Aarhus University Hospital
| | - Anders Dige
- Institute of Clinical Medicine, Aarhus University.,Department of Hepatology and Gastroenterology, Aarhus University Hospital, Denmark
| | - Jørgen Agnholt
- Institute of Clinical Medicine, Aarhus University.,Department of Hepatology and Gastroenterology, Aarhus University Hospital, Denmark
| | - Judith Grau
- Hebron Institute of Research, Department of Infectious Diseases, Barcelona, Spain
| | - Maria Buzon
- Hebron Institute of Research, Department of Infectious Diseases, Barcelona, Spain
| | - Burghardt Wittig
- Foundation Institute Molecular Biology and Bioinformatics, Freie Universitaet, Berlin, Germany
| | - Mathias Lichterfeld
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology, and Harvard University, Boston; Departments of
| | - Andreas Munk Petersen
- Gastroenterology and.,Microbiology, Hvidovre Hospital, University of Copenhagen, Hvidovre, Denmark
| | - Xutao Deng
- Blood Systems Research Institute, San Francisco, California, and.,University of California, San Francisco
| | - Mohamed Abdel-Mohsen
- Blood Systems Research Institute, San Francisco, California, and.,University of California, San Francisco.,The Wistar Institute, Philadelphia, Pennsylvania; and Departments of
| | - Satish K Pillai
- Blood Systems Research Institute, San Francisco, California, and.,University of California, San Francisco
| | | | | | - Ward De Spiegelaere
- Internal Medicine; and.,Morphology, Faculty of Veterinary Medicine, Ghent University, Belgium
| | | | - Lars Østergaard
- Department of Infectious Diseases, Aarhus University Hospital.,Institute of Clinical Medicine, Aarhus University
| | | | - Paul W Denton
- Department of Infectious Diseases, Aarhus University Hospital.,Institute of Clinical Medicine, Aarhus University
| | - Martin Tolstrup
- Department of Infectious Diseases, Aarhus University Hospital.,Institute of Clinical Medicine, Aarhus University
| | - Ole S Søgaard
- Department of Infectious Diseases, Aarhus University Hospital.,Institute of Clinical Medicine, Aarhus University
| |
Collapse
|
77
|
Jiang G, Nguyen D, Archin NM, Yukl SA, Méndez-Lagares G, Tang Y, Elsheikh MM, Thompson GR, Hartigan-O'Connor DJ, Margolis DM, Wong JK, Dandekar S. HIV latency is reversed by ACSS2-driven histone crotonylation. J Clin Invest 2018; 128:1190-1198. [PMID: 29457784 DOI: 10.1172/jci98071] [Citation(s) in RCA: 99] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2017] [Accepted: 01/09/2018] [Indexed: 12/21/2022] Open
Abstract
Eradication of HIV-1 (HIV) is hindered by stable viral reservoirs. Viral latency is epigenetically regulated. While the effects of histone acetylation and methylation at the HIV long-terminal repeat (LTR) have been described, our knowledge of the proviral epigenetic landscape is incomplete. We report that a previously unrecognized epigenetic modification of the HIV LTR, histone crotonylation, is a regulator of HIV latency. Reactivation of latent HIV was achieved following the induction of histone crotonylation through increased expression of the crotonyl-CoA-producing enzyme acyl-CoA synthetase short-chain family member 2 (ACSS2). This reprogrammed the local chromatin at the HIV LTR through increased histone acetylation and reduced histone methylation. Pharmacologic inhibition or siRNA knockdown of ACSS2 diminished histone crotonylation-induced HIV replication and reactivation. ACSS2 induction was highly synergistic in combination with either a protein kinase C agonist (PEP005) or a histone deacetylase inhibitor (vorinostat) in reactivating latent HIV. In the SIV-infected nonhuman primate model of AIDS, the expression of ACSS2 was significantly induced in intestinal mucosa in vivo, which correlated with altered fatty acid metabolism. Our study links the HIV/SIV infection-induced fatty acid enzyme ACSS2 to HIV latency and identifies histone lysine crotonylation as a novel epigenetic regulator for HIV transcription that can be targeted for HIV eradication.
Collapse
Affiliation(s)
- Guochun Jiang
- Department of Medical Microbiology and Immunology, UCD, Davis, California, USA
| | - Don Nguyen
- Department of Medical Microbiology and Immunology, UCD, Davis, California, USA
| | - Nancie M Archin
- Department of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Steven A Yukl
- Department of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Gema Méndez-Lagares
- Department of Medical Microbiology and Immunology, UCD, Davis, California, USA
| | - Yuyang Tang
- Department of Medical Microbiology and Immunology, UCD, Davis, California, USA
| | - Maher M Elsheikh
- Department of Medical Microbiology and Immunology, UCD, Davis, California, USA
| | - George R Thompson
- Department of Medical Microbiology and Immunology, UCD, Davis, California, USA
| | | | - David M Margolis
- Department of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Joseph K Wong
- Department of Medicine, UCSF, and San Francisco Veterans Affairs Medical Center, San Francisco, California, USA
| | - Satya Dandekar
- Department of Medical Microbiology and Immunology, UCD, Davis, California, USA
| |
Collapse
|
78
|
Pinzone MR, O’Doherty U. Measuring integrated HIV DNA ex vivo and in vitro provides insights about how reservoirs are formed and maintained. Retrovirology 2018; 15:22. [PMID: 29452580 PMCID: PMC5816390 DOI: 10.1186/s12977-018-0396-3] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2017] [Accepted: 01/19/2018] [Indexed: 11/29/2022] Open
Abstract
The identification of the most appropriate marker to measure reservoir size has been a great challenge for the HIV field. Quantitative viral outgrowth assay (QVOA), the reference standard to quantify the amount of replication-competent virus, has several limitations, as it is laborious, expensive, and unable to robustly reactivate every single integrated provirus. PCR-based assays have been developed as an easier, cheaper and less error-prone alternative to QVOA, but also have limitations. Historically, measuring integrated HIV DNA has provided insights about how reservoirs are formed and maintained. In the 1990s, measuring integrated HIV DNA was instrumental in understanding that a subset of resting CD4 T cells containing integrated HIV DNA were the major source of replication-competent virus. Follow-up studies have further characterized the phenotype of these cells containing integrated HIV DNA, as well as shown the correlation between the integration levels and clinical parameters, such as duration of infection, CD4 count and viral load. Integrated HIV DNA correlates with total HIV measures and with QVOA. The integration assay has several limitations. First, it largely overestimates the reservoir size, as both defective and replication-competent proviruses are detected. Since defective proviruses are the majority in patients on ART, it follows that the number of proviruses capable of reactivating and releasing new virions is significantly smaller than the number of integrated proviruses. Second, in patients on ART clonal expansion could theoretically lead to the preferential amplification of proviruses close to an Alu sequence though longitudinal studies have not captured this effect. Proviral sequencing combined with integration measures is probably the best estimate of reservoir size, but it is expensive, time-consuming and requires considerable bioinformatics expertise. All these reasons limit its use on a large scale. Herein, we review the utility of measuring HIV integration and suggest combining it with sequencing and total HIV measurements can provide insights that underlie reservoir maintenance.
Collapse
Affiliation(s)
- Marilia Rita Pinzone
- Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, PA USA
| | - Una O’Doherty
- Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, PA USA
| |
Collapse
|
79
|
Baxter AE, O'Doherty U, Kaufmann DE. Beyond the replication-competent HIV reservoir: transcription and translation-competent reservoirs. Retrovirology 2018; 15:18. [PMID: 29394935 PMCID: PMC5797386 DOI: 10.1186/s12977-018-0392-7] [Citation(s) in RCA: 64] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2017] [Accepted: 01/08/2018] [Indexed: 12/20/2022] Open
Abstract
Recent years have seen a substantial increase in the number of tools available to monitor and study HIV reservoirs. Here, we discuss recent technological advances that enable an understanding of reservoir dynamics beyond classical assays to measure the frequency of cells containing provirus able to propagate a spreading infection (replication-competent reservoir). Specifically, we focus on the characterization of cellular reservoirs containing proviruses able to transcribe viral mRNAs (so called transcription-competent) and translate viral proteins (translation-competent). We suggest that the study of these alternative reservoirs provides complementary information to classical approaches, crucially at a single-cell level. This enables an in-depth characterization of the cellular reservoir, both following reactivation from latency and, importantly, directly ex vivo at baseline. Furthermore, we propose that the study of cellular reservoirs that may not contain fully replication-competent virus, but are able to produce HIV mRNAs and proteins, is of biological importance. Lastly, we detail some of the key contributions that the study of these transcription and translation-competent reservoirs has made thus far to investigations into HIV persistence, and outline where these approaches may take the field next.
Collapse
Affiliation(s)
- Amy E Baxter
- CR-CHUM, Université de Montréal, Montréal, QC, Canada.,Scripps CHAVI-ID, La Jolla, CA, USA
| | - Una O'Doherty
- Department of Pathology and Laboratory Medicine, Division of Transfusion Medicine and Therapeutic Pathology, University of Pennsylvania, Philadelphia, PA, USA.
| | - Daniel E Kaufmann
- CR-CHUM, Université de Montréal, Montréal, QC, Canada. .,Scripps CHAVI-ID, La Jolla, CA, USA.
| |
Collapse
|
80
|
Bekele Y, Graham RL, Soeria-Atmadja S, Nasi A, Zazzi M, Vicenti I, Naver L, Nilsson A, Chiodi F. Hepatitis B Virus Vaccination in HIV-1-Infected Young Adults: A Tool to Reduce the Size of HIV-1 Reservoirs? Front Immunol 2018; 8:1966. [PMID: 29375579 PMCID: PMC5767726 DOI: 10.3389/fimmu.2017.01966] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2017] [Accepted: 12/19/2017] [Indexed: 01/12/2023] Open
Abstract
During anti-retroviral therapy (ART) HIV-1 persists in cellular reservoirs, mostly represented by CD4+ memory T cells. Several approaches are currently being undertaken to develop a cure for HIV-1 infection through elimination (or reduction) of these reservoirs. Few studies have so far been conducted to assess the possibility of reducing the size of HIV-1 reservoirs through vaccination in virologically controlled HIV-1-infected children. We recently conducted a vaccination study with a combined hepatitis A virus (HAV) and hepatitis B virus (HBV) vaccine in 22 HIV-1-infected children. We assessed the size of the virus reservoir, measured as total HIV-1 DNA copies in blood cells, pre- and postvaccination. In addition, we investigated by immunostaining whether the frequencies of CD4+ and CD8+ T cells and parameters of immune activation and proliferation on these cells were modulated by vaccination. At 1 month from the last vaccination dose, we found that 20 out of 22 children mounted a serological response to HBV; a majority of children had antibodies against HAV at baseline. The number of HIV-1 DNA copies in blood at 1 month postvaccination was reduced in comparison to baseline although this reduction was not statistically significant. A significant reduction of HIV-1 DNA copies in blood following vaccination was found in 12 children. The frequencies of CD4+ (naïve, effector memory) and CD8+ (central memory) T-cell subpopulations changed following vaccinations and a reduction in the activation and proliferation pattern of these cells was also noticed. Multivariate linear regression analysis revealed that the frequency of CD8+ effector memory T cells prior to vaccination was strongly predictive of the reduction of HIV-1 DNA copies in blood following vaccination of the 22 HIV-1-infected children. The results of this study suggest a beneficial effect of vaccination to reduce the size of virus reservoir in HIV-1-infected children receiving ART. A reduced frequency of activated CD4+ cells and an increase in central memory CD8+ T cells were associated with this finding. Further studies should assess whether vaccination is a possible tool to reduce HIV-1 reservoirs.
Collapse
Affiliation(s)
- Yonas Bekele
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Rebecka Lantto Graham
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Sandra Soeria-Atmadja
- Department of Clinical Science, Intervention and Technology (CLINTEC), Karolinska Institutet, Stockholm, Sweden.,Department of Pediatrics, Karolinska University Hospital, Stockholm, Sweden
| | - Aikaterini Nasi
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Maurizio Zazzi
- Department of Medical Biotechnology, University of Siena, Siena, Italy
| | - Ilaria Vicenti
- Department of Medical Biotechnology, University of Siena, Siena, Italy
| | - Lars Naver
- Department of Clinical Science, Intervention and Technology (CLINTEC), Karolinska Institutet, Stockholm, Sweden.,Department of Pediatrics, Karolinska University Hospital, Stockholm, Sweden
| | - Anna Nilsson
- Department of Women's and Children Health, Karolinska Institutet, Stockholm, Sweden
| | - Francesca Chiodi
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| |
Collapse
|
81
|
Genetically Intact but Functionally Impaired HIV-1 Env Glycoproteins in the T-Cell Reservoir. J Virol 2018; 92:JVI.01684-17. [PMID: 29187544 DOI: 10.1128/jvi.01684-17] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2017] [Accepted: 11/20/2017] [Indexed: 01/16/2023] Open
Abstract
HIV-infected subjects under antiretroviral treatment (ART) harbor a persistent viral reservoir in resting CD4+ T cells, which accounts for the resurgence of HIV replication after ART interruption. A large majority of HIV reservoir genomes are genetically defective, but even among intact proviruses few seem able to generate infectious virus. To understand this phenomenon, we examined the function and expression of HIV envelope glycoproteins reactivated from the reservoir of four HIV-infected subjects under suppressive ART. We studied full-length genetically intact env sequences from both replicative viruses and cell-associated mRNAs. We found that these Env proteins varied extensively in fusogenicity and infectivity, with strongest functional defects found in Envs from cell-associated mRNAs. Env functional impairments were essentially explained by defects in Env protein expression. Our results support the idea that defects in HIV Env expression, preventing cytopathic or immune HIV clearance, contribute to the persistence of the HIV T-cell reservoir in vivoIMPORTANCE In most individuals, evolution of HIV infection is efficiently controlled on the long-term by combination antiviral therapies. These treatments, however, fail to eradicate HIV from the infected subjects, a failure that results both in resurgence of virus replication and in resumption of HIV pathogenicity when the treatment is stopped. HIV resurgence, in these instances, is widely assumed to emerge from a reservoir of silent virus integrated in the genomes of a small number of T lymphocytes. The silent HIV reservoir is mostly composed of heavily deleted or mutated HIV DNA. Moreover, among the seemingly intact remaining HIV, only very few are actually able to efficiently propagate in tissue culture. In this study, we find that intact HIV in the reservoir often carry strong defects in their capacity to promote fusion to neighboring cells and infection of target cells, a defect related to the function and expression of the HIV envelope glycoprotein. Impaired envelope glycoprotein expression and function could explain why cells harboring these viruses tend to remain undetected and unharmed in the reservoir.
Collapse
|
82
|
Clarridge KE, Blazkova J, Einkauf K, Petrone M, Refsland EW, Justement JS, Shi V, Huiting ED, Seamon CA, Lee GQ, Yu XG, Moir S, Sneller MC, Lichterfeld M, Chun TW. Effect of analytical treatment interruption and reinitiation of antiretroviral therapy on HIV reservoirs and immunologic parameters in infected individuals. PLoS Pathog 2018; 14:e1006792. [PMID: 29324842 PMCID: PMC5764487 DOI: 10.1371/journal.ppat.1006792] [Citation(s) in RCA: 68] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2017] [Accepted: 12/06/2017] [Indexed: 01/08/2023] Open
Abstract
Therapeutic strategies aimed at achieving antiretroviral therapy (ART)-free HIV remission in infected individuals are under active investigation. Considering the vast majority of HIV-infected individuals experience plasma viral rebound upon cessation of therapy, clinical trials evaluating the efficacy of curative strategies would likely require inclusion of ART interruption. However, it is unclear what impact short-term analytical treatment interruption (ATI) and subsequent reinitiation of ART have on immunologic and virologic parameters of HIV-infected individuals. Here, we show a significant increase of HIV burden in the CD4+ T cells of infected individuals during ATI that was correlated with the level of plasma viral rebound. However, the size of the HIV reservoirs as well as immune parameters, including markers of exhaustion and activation, returned to pre-ATI levels 6–12 months after the study participants resumed ART. Of note, the proportions of near full-length, genome-intact and structurally defective HIV proviral DNA sequences were similar prior to ATI and following reinitiation of ART. In addition, there was no evidence of emergence of antiretroviral drug resistance mutations within intact HIV proviral DNA sequences following reinitiation of ART. These data demonstrate that short-term ATI does not necessarily lead to expansion of the persistent HIV reservoir nor irreparable damages to the immune system in the peripheral blood, warranting the inclusion of ATI in future clinical trials evaluating curative strategies. While we have made considerable advancements in the treatment of HIV, most infected individuals require life-long treatment to suppress plasma viremia, underscoring the need for the development of additional therapeutic strategies that would allow durable virologic remission in the absence of antiretroviral therapy (ART). While a definitive cure has not yet been identified, the field is moving in a promising direction, and with continued efforts we may arrive at a clinically acceptable alternative to ART. Clinical validation of new treatment options likely requires patients to stop therapy while monitoring for viral rebound, but the effect of treatment interruption and its precise impact on immunologic and virologic parameters in HIV-infected individuals has not been fully delineated. In this work, we measured a significant increase of HIV burden in the CD4+ T cells of infected individuals who underwent ATI with subsequent plasma viral rebound. However, the size of the HIV reservoirs as well as immune parameters returned to pre-ATI levels 6–12 months after the participants resumed ART. These data suggest ATI does not lead to expansion of the persistent HIV reservoir nor irreversible damages to the immune system in the peripheral blood.
Collapse
Affiliation(s)
- Katherine E. Clarridge
- Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases, National Institutes of Health (NIH), Bethesda, Maryland, United States of America
| | - Jana Blazkova
- Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases, National Institutes of Health (NIH), Bethesda, Maryland, United States of America
| | - Kevin Einkauf
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, Massachusetts, United States of America
| | - Mary Petrone
- Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases, National Institutes of Health (NIH), Bethesda, Maryland, United States of America
| | - Eric W. Refsland
- Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases, National Institutes of Health (NIH), Bethesda, Maryland, United States of America
| | - J. Shawn Justement
- Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases, National Institutes of Health (NIH), Bethesda, Maryland, United States of America
| | - Victoria Shi
- Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases, National Institutes of Health (NIH), Bethesda, Maryland, United States of America
| | - Erin D. Huiting
- Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases, National Institutes of Health (NIH), Bethesda, Maryland, United States of America
| | - Catherine A. Seamon
- Critical Care Medicine Department, Clinical Center, NIH, Bethesda, Maryland, United States of America
| | - Guinevere Q. Lee
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, Massachusetts, United States of America
| | - Xu G. Yu
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, Massachusetts, United States of America
| | - Susan Moir
- Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases, National Institutes of Health (NIH), Bethesda, Maryland, United States of America
| | - Michael C. Sneller
- Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases, National Institutes of Health (NIH), Bethesda, Maryland, United States of America
| | - Mathias Lichterfeld
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, Massachusetts, United States of America
- Infectious Disease Division, Brigham and Women’s Hospital, Boston, Massachusetts, United States of America
| | - Tae-Wook Chun
- Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases, National Institutes of Health (NIH), Bethesda, Maryland, United States of America
- * E-mail:
| |
Collapse
|
83
|
Exploring viral reservoir: The combining approach of cell sorting and droplet digital PCR. Methods 2017; 134-135:98-105. [PMID: 29197654 DOI: 10.1016/j.ymeth.2017.11.014] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2017] [Revised: 10/24/2017] [Accepted: 11/27/2017] [Indexed: 12/12/2022] Open
Abstract
Combined antiretroviral therapy (cART) blocks different steps of HIV replication and maintains plasma viral RNA at undetectable levels. The virus can remain in long-living cells and create a reservoir where HIV can restart replicating after cART discontinuation. A persistent viral production triggers and maintains a persistent immune activation, which is a well-known feature of chronic HIV infection, and contributes either to precocious aging, or to the increased incidence of morbidity and mortality of HIV positive patients. The new frontier of the treatment of HIV infection is nowadays eradication of the virus from all host cells and tissues. For this reason, it is crucial to have a clear and precise idea of where the virus hides, and which are the cells that keep it silent. Important efforts have been made to improve the detection of viral reservoirs, and new techniques are now giving the opportunity to characterize viral reservoirs. Among these techniques, a strategic approach based upon cell sorting and droplet digital PCR (ddPCR) is opening new horizons and opportunities of research. This review provides an overview of the methods that combine cell sorting and ddPCR for the quantification of HIV DNA in different cell types, and for the detection of its maintenance.
Collapse
|
84
|
Tunneling nanotubes (TNT) mediate long-range gap junctional communication: Implications for HIV cell to cell spread. Sci Rep 2017; 7:16660. [PMID: 29192225 PMCID: PMC5709493 DOI: 10.1038/s41598-017-16600-1] [Citation(s) in RCA: 60] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2017] [Accepted: 11/15/2017] [Indexed: 12/24/2022] Open
Abstract
Cell-to-cell communication is essen for the development of multicellular systems and is coordinated by soluble factors, exosomes, gap junction (GJ) channels, and the recently described tunneling nanotubes (TNTs). We and others have demonstrated that TNT-like structures are mostly present during pathogenic conditions, including HIV infection. However, the nature, function, and communication properties of TNTs are still poorly understood. In this manuscript, we demonstrate that TNTs induced by HIV infection have functional GJs at the ends of their membrane extensions and that TNTs mediate long-range GJ communication during HIV infection. Blocking or reducing GJ communication during HIV infection resulted in aberrant TNT cell-to-cell contact, compromising HIV spread and replication. Thus, TNTs and associated GJs are required for the efficient cell-to-cell communication and viral spread. Our data indicate that targeting TNTs/GJs may provide new therapeutic opportunities for the treatment of HIV.
Collapse
|
85
|
Cummins NW, Rizza S, Litzow MR, Hua S, Lee GQ, Einkauf K, Chun TW, Rhame F, Baker JV, Busch MP, Chomont N, Dean PG, Fromentin R, Haase AT, Hampton D, Keating SM, Lada SM, Lee TH, Natesampillai S, Richman DD, Schacker TW, Wietgrefe S, Yu XG, Yao JD, Zeuli J, Lichterfeld M, Badley AD. Extensive virologic and immunologic characterization in an HIV-infected individual following allogeneic stem cell transplant and analytic cessation of antiretroviral therapy: A case study. PLoS Med 2017; 14:e1002461. [PMID: 29182633 PMCID: PMC5705162 DOI: 10.1371/journal.pmed.1002461] [Citation(s) in RCA: 49] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/09/2017] [Accepted: 10/25/2017] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND Notwithstanding 1 documented case of HIV-1 cure following allogeneic stem cell transplantation (allo-SCT), several subsequent cases of allo-SCT in HIV-1 positive individuals have failed to cure HIV-1 infection. The aim of our study was to describe changes in the HIV reservoir in a single chronically HIV-infected patient on suppressive antiretroviral therapy who underwent allo-SCT for treatment of acute lymphoblastic leukemia. METHODS AND FINDINGS We prospectively collected peripheral blood mononuclear cells (PBMCs) by leukapheresis from a 55-year-old man with chronic HIV infection before and after allo-SCT to measure the size of the HIV-1 reservoir and characterize viral phylogeny and phenotypic changes in immune cells. At day 784 post-transplant, when HIV-1 was undetectable by multiple measures-including PCR measurements of both total and integrated HIV-1 DNA, replication-competent virus measurement by large cell input quantitative viral outgrowth assay, and in situ hybridization of colon tissue-the patient consented to an analytic treatment interruption (ATI) with frequent clinical monitoring. He remained aviremic off antiretroviral therapy until ATI day 288, when a low-level virus rebound of 60 HIV-1 copies/ml occurred, which increased to 1,640 HIV-1 copies/ml 5 days later, prompting reinitiation of ART. Rebounding plasma HIV-1 sequences were phylogenetically distinct from proviral HIV-1 DNA detected in circulating PBMCs before transplantation. The main limitations of this study are the insensitivity of reservoir measurements, and the fact that it describes a single case. CONCLUSIONS allo-SCT led to a significant reduction in the size of the HIV-1 reservoir and a >9-month-long ART-free remission from HIV-1 replication. Phylogenetic analyses suggest that the origin of rebound virus was distinct from the viruses identified pre-transplant in the PBMCs.
Collapse
Affiliation(s)
- Nathan W. Cummins
- Division of Infectious Diseases, Mayo Clinic, Rochester, Minnesota, United States of America
| | - Stacey Rizza
- Division of Infectious Diseases, Mayo Clinic, Rochester, Minnesota, United States of America
| | - Mark R. Litzow
- Division of Hematology, Mayo Clinic, Rochester, Minnesota, United States of America
| | - Stephane Hua
- Ragon Institute of MGH, MIT and Harvard, Cambridge, Massachusetts, United States of America
| | - Guinevere Q. Lee
- Ragon Institute of MGH, MIT and Harvard, Cambridge, Massachusetts, United States of America
| | - Kevin Einkauf
- Ragon Institute of MGH, MIT and Harvard, Cambridge, Massachusetts, United States of America
| | - Tae-Wook Chun
- HIV Immunovirology Unit, Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Frank Rhame
- Abbott Northwestern Hospital, Allina Health, Minneapolis, Minnesota, United States of America
- Department of Microbiology and Immunology, University of Minnesota, Minneapolis, Minnesota, United States of America
| | - Jason V. Baker
- Division of Infectious Diseases, Hennepin County Medical Center, Minneapolis, Minnesota, United States of America
| | - Michael P. Busch
- Blood Systems 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
| | - Nicolas Chomont
- Centre de Recherche du CHUM, University of Montreal Hospital Centre, Montreal, Canada
- Department of Microbiology, Infectious Diseases and Immunology, University of Montreal, Montreal, Canada
| | - Patrick G. Dean
- Division of Transplantation Surgery, Mayo Clinic, Rochester, Minnesota, United States of America
| | - Rémi Fromentin
- Centre de Recherche du CHUM, University of Montreal Hospital Centre, Montreal, Canada
- Department of Microbiology, Infectious Diseases and Immunology, University of Montreal, Montreal, Canada
| | - Ashley T. Haase
- Department of Microbiology and Immunology, University of Minnesota, Minneapolis, Minnesota, United States of America
| | - Dylan Hampton
- Blood Systems Research Institute, San Francisco, California, United States of America
| | - Sheila M. Keating
- Blood Systems 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
| | - Steven M. Lada
- University of California, San Diego, San Diego, California, United States of America
- VA San Diego Healthcare System, San Diego, California, United States of America
| | - Tzong-Hae Lee
- Blood Systems Research Institute, San Francisco, California, United States of America
| | - Sekar Natesampillai
- Division of Infectious Diseases, Mayo Clinic, Rochester, Minnesota, United States of America
| | - Douglas D. Richman
- University of California, San Diego, San Diego, California, United States of America
- VA San Diego Healthcare System, San Diego, California, United States of America
| | - Timothy W. Schacker
- Department of Medicine, University of Minnesota, Minneapolis, Minnesota, United States of America
| | - Stephen Wietgrefe
- Department of Microbiology and Immunology, University of Minnesota, Minneapolis, Minnesota, United States of America
| | - Xu G. Yu
- Ragon Institute of MGH, MIT and Harvard, Cambridge, Massachusetts, United States of America
- Infectious Disease Division, Brigham and Women’s Hospital, Boston, Massachusetts, United States of America
| | - Joseph D. Yao
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota, United States of America
| | - John Zeuli
- Division of Infectious Diseases, Mayo Clinic, Rochester, Minnesota, United States of America
| | - Mathias Lichterfeld
- Ragon Institute of MGH, MIT and Harvard, Cambridge, Massachusetts, United States of America
- Infectious Disease Division, Brigham and Women’s Hospital, Boston, Massachusetts, United States of America
| | - Andrew D. Badley
- Division of Infectious Diseases, Mayo Clinic, Rochester, Minnesota, United States of America
| |
Collapse
|
86
|
Abstract
INTRODUCTION HIV eradication and remission research has largely taken place in high-income countries. In low- and middle-income countries (LMIC), there may be factors that have a substantial impact on the size of the latent HIV reservoir and the immunological response to infection. If a curative strategy is to be available to all HIV-infected individuals, these factors must be understood. METHODS We use a scoping review to examine the literature on biological factors that may have an impact on HIV persistence in LMIC. Three databases were searched without date restrictions. RESULTS Uncontrolled viral replication and higher coinfection prevalence may alter the immunological milieu of individuals in LMIC and increase the size of the HIV reservoir. Differences in HIV subtype could also influence the measurement and size of the HIV reservoir. Immune activation may differ due to late presentation to care, presence of chronic infections, increased gut translocation of bacterial products and poor nutrition. CONCLUSIONS Research on HIV remission is urgently needed in LMIC. Research into chronic immune activation in resource poor environments, the immune response to infection, the mechanisms of HIV persistence and latency in different viral clades and the effect of the microbiological milieu must be performed. Geographic differences, which may be substantial and may delay access to curative strategies, should be identified.
Collapse
|
87
|
Gupta P, Sanyal A, Mailliard RB. TZA: a novel assay for measuring the latent HIV-1 reservoir. Expert Rev Mol Diagn 2017; 17:1033-1035. [PMID: 28937839 DOI: 10.1080/14737159.2017.1384315] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Affiliation(s)
- Phalguni Gupta
- a Department of Infectious Diseases and Microbiology , University of Pittsburgh Graduate School of Public Health , Pittsburgh , PA , USA.,b Department of Pathology , University of Pittsburgh School of Medicine , Pittsburgh , PA , USA
| | - Anwesha Sanyal
- a Department of Infectious Diseases and Microbiology , University of Pittsburgh Graduate School of Public Health , Pittsburgh , PA , USA
| | - Robbie B Mailliard
- a Department of Infectious Diseases and Microbiology , University of Pittsburgh Graduate School of Public Health , Pittsburgh , PA , USA
| |
Collapse
|
88
|
Hu TY. Can sugarcoated fingerprints be used to identify lurking viruses? Proteomics 2017; 16:1947-8. [PMID: 27297056 DOI: 10.1002/pmic.201600197] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2016] [Accepted: 06/10/2016] [Indexed: 11/11/2022]
Abstract
Comparative proteomics is increasingly used to detect biomarkers and therapeutic targets that differ between healthy and diseased populations; however, differences in posttranslational modifications have received less attention. In this issue, Yang et al. (Proteomics 2016, 16, 1872-1880) present data indicating that a glycoproteomics approach can detect N-glycosylated membrane protein differences between non-HIV-infected and latently infected human CD4(+) T-cell lines, identifying 172 proteins differentially expressed by these cells. Latently infected CD4(+) T cells are thought to represent the major barrier to eventual HIV cure, but do not express detectable levels of viral protein and have not been shown to express biomarkers that can distinguish them from the vastly more abundant uninfected CD4(+) T-cell population. The findings of Yang et al. suggest that glycoproteomic analyses may have untapped potential to identify novel biomarkers and therapeutic targets in cell populations not readily distinguishable be standard proteomic analyses.
Collapse
Affiliation(s)
- Tony Y Hu
- Department of Nanomedicine, Houston Methodist Research Institute, Houston, TX, USA.,Department of Cell and Developmental Biology, Weill Cornell Medical College of Cornell University, New York, NY, USA
| |
Collapse
|
89
|
Baxter AE, Niessl J, Morou A, Kaufmann DE. RNA flow cytometric FISH for investigations into HIV immunology, vaccination and cure strategies. AIDS Res Ther 2017; 14:40. [PMID: 28893281 PMCID: PMC5594475 DOI: 10.1186/s12981-017-0171-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2017] [Accepted: 08/11/2017] [Indexed: 12/22/2022] Open
Abstract
Despite the tremendous success of anti-retroviral therapy (ART) no current treatment can eradicate latent HIV reservoirs from HIV-infected individuals or generate, effective HIV-specific immunity. Technological limitations have hampered the identification and characterization of both HIV-infected cells and HIV-specific responses in clinical samples directly ex vivo. RNA-flow cytometric fluorescence in situ hybridisation (RNA Flow-FISH) is a powerful technique, which enables detection of mRNAs in conjunction with proteins at a single-cell level. Here, we describe how we are using this technology to address some of the major questions remaining in the HIV field in the era of ART. We discuss how CD4 T cell responses to HIV antigens, both following vaccination and HIV infection, can be characterized by measurement of cytokine mRNAs. We describe how our development of a dual HIV mRNA/protein assay (HIVRNA/Gag assay) enables high sensitivity detection of very rare HIV-infected cells and aids investigations into the translation-competent latent reservoir in the context of HIV cure.
Collapse
|
90
|
Baxter AE, Niessl J, Fromentin R, Richard J, Porichis F, Massanella M, Brassard N, Alsahafi N, Routy JP, Finzi A, Chomont N, Kaufmann DE. Multiparametric characterization of rare HIV-infected cells using an RNA-flow FISH technique. Nat Protoc 2017; 12:2029-2049. [PMID: 28880280 DOI: 10.1038/nprot.2017.079] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Efforts to cure HIV are hampered by limited characterization of the cells supporting HIV replication in vivo and inadequate methods for quantifying the latent viral reservoir in individuals receiving antiretroviral therapy (ART). We describe a protocol for flow cytometric identification of viral reservoirs, based on concurrent detection of cellular HIV Gagpol mRNA by in situ RNA hybridization combined with antibody staining for the HIV Gag protein. By simultaneously detecting both HIV RNA and protein, the CD4 T cells harboring translation-competent virus can be identified. The HIVRNA/Gag method is 1,000-fold more sensitive than Gag protein staining alone, with a detection limit of 0.5-1 Gagpol mRNA+/Gag protein+ cells per million CD4 T cells. Uniquely, the HIVRNA/Gag assay also allows parallel phenotyping of viral reservoirs, including reactivated latent reservoirs in clinical samples. The assay takes 2 d, and requires antibody labeling for surface and intracellular markers, followed by mRNA labeling and multiple signal amplification steps.
Collapse
Affiliation(s)
- Amy E Baxter
- Research Centre of the Centre Hospitalier de l'Université de Montréal (CRCHUM) and Université de Montréal, Montreal, Quebec, Canada.,Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery (CHAVI-ID), La Jolla, California, USA
| | - Julia Niessl
- Research Centre of the Centre Hospitalier de l'Université de Montréal (CRCHUM) and Université de Montréal, Montreal, Quebec, Canada.,Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery (CHAVI-ID), La Jolla, California, USA
| | - Rémi Fromentin
- Research Centre of the Centre Hospitalier de l'Université de Montréal (CRCHUM) and Université de Montréal, Montreal, Quebec, Canada
| | - Jonathan Richard
- Research Centre of the Centre Hospitalier de l'Université de Montréal (CRCHUM) and Université de Montréal, Montreal, Quebec, Canada
| | - Filippos Porichis
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology and Harvard University, Cambridge, Massachusetts, USA
| | - Marta Massanella
- Research Centre of the Centre Hospitalier de l'Université de Montréal (CRCHUM) and Université de Montréal, Montreal, Quebec, Canada
| | - Nathalie Brassard
- Research Centre of the Centre Hospitalier de l'Université de Montréal (CRCHUM) and Université de Montréal, Montreal, Quebec, Canada
| | - Nirmin Alsahafi
- Research Centre of the Centre Hospitalier de l'Université de Montréal (CRCHUM) and Université de Montréal, Montreal, Quebec, Canada.,Department of Microbiology and Immunology, McGill University, Montreal, Quebec, Canada
| | - Jean-Pierre Routy
- Chronic Viral Illnesses Service and Division of Hematology, McGill University Health Centre, Montreal, Quebec, Canada
| | - Andrés Finzi
- Research Centre of the Centre Hospitalier de l'Université de Montréal (CRCHUM) and Université de Montréal, Montreal, Quebec, Canada.,Department of Microbiology and Immunology, McGill University, Montreal, Quebec, Canada
| | - Nicolas Chomont
- Research Centre of the Centre Hospitalier de l'Université de Montréal (CRCHUM) and Université de Montréal, Montreal, Quebec, Canada
| | - Daniel E Kaufmann
- Research Centre of the Centre Hospitalier de l'Université de Montréal (CRCHUM) and Université de Montréal, Montreal, Quebec, Canada.,Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery (CHAVI-ID), La Jolla, California, USA
| |
Collapse
|
91
|
Abstract
PURPOSE OF REVIEW This article provides an overview of anticancer therapies in various stages of clinical development as potential interventions to target HIV persistence. RECENT FINDINGS Epigenetic drugs developed for cancer have been investigated in vitro, ex vivo and in clinical trials as interventions aimed at reversing HIV latency and depleting the amount of virus that persists on antiretroviral therapy. Treatment with histone deacetylase inhibitors induced HIV expression in patients on antiretroviral therapy but did not reduce the frequency of infected cells. Other interventions that may accelerate the decay of latently infected cells, in the presence or absence of latency-reversing therapy, are now being explored. These include apoptosis-promoting agents, nonhistone deacetylase inhibitor compounds to reverse HIV latency and immunotherapy interventions to enhance antiviral immunity such as immune checkpoint inhibitors and Toll-like receptor agonists. SUMMARY A curative strategy in HIV will likely need to both reduce the amount of virus that persists on antiretroviral therapy and improve anti-HIV immune surveillance. Although we continue to explore advances in the field of oncology including cancer immunotherapy, there are major differences in the risk-benefit assessment between HIV-infected individuals and patients with malignancies. Drug development specifically targeting HIV persistence will be the key to developing effective interventions with an appropriate safety profile.
Collapse
|
92
|
Beliakova-Bethell N, Hezareh M, Wong JK, Strain MC, Lewinski MK, Richman DD, Spina CA. Relative efficacy of T cell stimuli as inducers of productive HIV-1 replication in latently infected CD4 lymphocytes from patients on suppressive cART. Virology 2017; 508:127-133. [PMID: 28527342 DOI: 10.1016/j.virol.2017.05.008] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2016] [Revised: 05/09/2017] [Accepted: 05/10/2017] [Indexed: 10/19/2022]
Abstract
Quantification of cell-associated replication-competent HIV, in blood samples from patients with undetectable plasma viremia, requires specialized culture conditions that include exogenous pan T cell stimulation. Different research groups have used several stimuli for this purpose; however, the relative efficacies of these T cell stimuli to induce productive HIV replication from latently infected cells ex vivo have not been systematically evaluated. To this end, we compared four commonly used T cell stimuli: 1) irradiated allogeneic cells plus phytohaemagglutinin (PHA); 2) PHA alone; 3) phorbol myristate acetate plus Ionomycin; and 4) immobilized αCD3 plus αCD28 antibodies. End-point dilutions of patient CD4 T cells were performed, using virion RNA production to quantify HIV induction. Our results demonstrated that these activation approaches were not equivalent and that antibody cross-linking of CD3 and CD28 membrane receptors was the most effective means to activate HIV replication from a resting cell state, closely followed by stimulation with irradiated allogeneic cells plus PHA.
Collapse
Affiliation(s)
- Nadejda Beliakova-Bethell
- VA San Diego Healthcare System, 3350 La Jolla Village Dr., San Diego, CA 92161, USA; University of California San Diego, 9500 Gilman Dr., La Jolla, CA 92093, USA
| | - Marjan Hezareh
- University of California San Diego, 9500 Gilman Dr., La Jolla, CA 92093, USA
| | - Joseph K Wong
- VA San Diego Healthcare System, 3350 La Jolla Village Dr., San Diego, CA 92161, USA; University of California San Diego, 9500 Gilman Dr., La Jolla, CA 92093, USA
| | - Matthew C Strain
- University of California San Diego, 9500 Gilman Dr., La Jolla, CA 92093, USA
| | - Mary K Lewinski
- VA San Diego Healthcare System, 3350 La Jolla Village Dr., San Diego, CA 92161, USA; University of California San Diego, 9500 Gilman Dr., La Jolla, CA 92093, USA
| | - Douglas D Richman
- VA San Diego Healthcare System, 3350 La Jolla Village Dr., San Diego, CA 92161, USA; University of California San Diego, 9500 Gilman Dr., La Jolla, CA 92093, USA
| | - Celsa A Spina
- VA San Diego Healthcare System, 3350 La Jolla Village Dr., San Diego, CA 92161, USA; University of California San Diego, 9500 Gilman Dr., La Jolla, CA 92093, USA.
| |
Collapse
|
93
|
Datta PK, Kaminski R, Hu W, Pirrone V, Sullivan NT, Nonnemacher MR, Dampier W, Wigdahl B, Khalili K. HIV-1 Latency and Eradication: Past, Present and Future. Curr HIV Res 2017; 14:431-441. [PMID: 27009094 DOI: 10.2174/1570162x14666160324125536] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2015] [Revised: 12/04/2015] [Accepted: 01/16/2016] [Indexed: 02/06/2023]
Abstract
BACKGROUND It is well established that antiretroviral therapy (ART), while highly effective in controlling HIV replication, cannot eliminate virus from the body. Therefore, the majority of HIV-1-infected individuals remain at risk for developing AIDS due to persistence of infected reservoir cells serving as a source of virus re-emergence. Several reservoirs containing replication competent HIV-1 have been identified, most notably CD4+ T cells. Cells of the myeloid lineage, which are the first line of defense against pathogens and participate in HIV dissemination into sanctuary organs, also serve as cellular reservoirs of HIV-1. In latently infected resting CD4+ T cells, the integrated copies of proviral DNA remain in a dormant state, yet possess the ability to produce replication competent virus after cellular activation. Studies have demonstrated that modification of chromatin structure plays a role in establishing persistence, in part suggesting that latency is, controlled epigenetically. CONCLUSION Current efforts to eradicate HIV-1 from this cell population focus primarily on a &quot;shock and kill&quot; approach through cellular reactivation to trigger elimination of virus producing cells by cytolysis or host immune responses. However, studies revealed several limitations to this approach that require more investigation to assess its clinical application. Recent advances in gene editing technology prompted use of this approach for inactivating integrated proviral DNA in the genome of latently infected cells. This technology, which requires a detailed understanding of the viral genetics and robust delivery, may serve as a powerful strategy to eliminate the latent reservoir in the host leading to a sterile cure of AIDS.
Collapse
Affiliation(s)
| | | | | | | | | | | | | | | | - Kamel Khalili
- Department of Neuroscience, Center for Neurovirology and Comprehensive NeuroAIDS Center, Lewis Katz School of Medicine at Temple University, 3500 N. Broad Street, 7th Floor, Philadelphia, PA 19140, USA.
| |
Collapse
|
94
|
Eckstrand CD, Sparger EE, Murphy BG. Central and peripheral reservoirs of feline immunodeficiency virus in cats: a review. J Gen Virol 2017; 98:1985-1996. [DOI: 10.1099/jgv.0.000866] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Affiliation(s)
- Chrissy D. Eckstrand
- Veterinary Microbiology and Pathology, College of Veterinary Medicine, 4003 Animal Disease Biotechnology Facility, Washington State University, Pullman, WA 99163, USA
| | - Ellen E. Sparger
- Department of Medicine and Epidemiology, School of Veterinary Medicine, University of California, 3115 Tupper Hall, Davis, CA 95616, USA
| | - Brian G. Murphy
- Department of Pathology, Microbiology, and Immunology, School of Veterinary Medicine, 4206 Vet Med 3A, University of California, Davis, CA 95616, USA
| |
Collapse
|
95
|
Wang J, Holmes MC. Engineering hematopoietic stem cells toward a functional cure of human immunodeficiency virus infection. Cytotherapy 2017; 18:1370-1381. [PMID: 27745602 DOI: 10.1016/j.jcyt.2016.07.007] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2016] [Revised: 07/05/2016] [Accepted: 07/21/2016] [Indexed: 12/23/2022]
Abstract
The battle with human immunodeficiency virus (HIV) has been ongoing for more than 30 years, and although progress has been made, there are still significant challenges remaining. A few unique features render HIV to be one of the toughest viruses to conquer in the modern medicine era, such as the ability to target the host immune system, persist by integrating into the host genome and adapt to a hostile environment such as a single anti-HIV medication by continuously evolving. The finding of combination anti-retroviral therapy (cART) about 2 decades ago has transformed the treatment options for HIV-infected patients and significantly improved patient outcomes. However, finding an HIV cure has proven to be extremely challenging with the only known exception being the so-called "Berlin patient," whose immune system was replaced by stem cell transplants from a donor missing one of HIV's key co-receptors (CCR5). The broad application of this approach is limited by the requirement of an HLA-matched donor who is also homozygous for the rare CCR5 delta32 deletion. On the other hand, the Berlin patient provided the proof of concept of a potential cure for HIV using HIV-resistant hematopoietic stem cells (HSCs), revitalizing the hope to find an HIV cure that is broadly applicable. Here we will review strategies and recent attempts to engineer HIV-resistant HSCs as a path to an HIV cure.
Collapse
Affiliation(s)
- Jianbin Wang
- Sangamo BioSciences Inc., Richmond, California, USA.
| | | |
Collapse
|
96
|
Archin NM, Kirchherr JL, Sung JA, Clutton G, Sholtis K, Xu Y, Allard B, Stuelke E, Kashuba AD, Kuruc JD, Eron J, Gay CL, Goonetilleke N, Margolis DM. Interval dosing with the HDAC inhibitor vorinostat effectively reverses HIV latency. J Clin Invest 2017; 127:3126-3135. [PMID: 28714868 DOI: 10.1172/jci92684] [Citation(s) in RCA: 148] [Impact Index Per Article: 21.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2017] [Accepted: 06/01/2017] [Indexed: 11/17/2022] Open
Abstract
BACKGROUND The histone deacetylase (HDAC) inhibitor vorinostat (VOR) can increase HIV RNA expression in vivo within resting CD4+ T cells of aviremic HIV+ individuals. However, while studies of VOR or other HDAC inhibitors have reported reversal of latency, none has demonstrated clearance of latent infection. We sought to identify the optimal dosing of VOR for effective serial reversal of HIV latency. METHODS In a study of 16 HIV-infected, aviremic individuals, we measured resting CD4+ T cell-associated HIV RNA ex vivo and in vivo following a single exposure to VOR, and then in vivo after a pair of doses separated by 48 or 72 hours, and finally following a series of 10 doses given at 72-hour intervals. RESULTS Serial VOR exposures separated by 72 hours most often resulted in an increase in cell-associated HIV RNA within circulating resting CD4+ T cells. VOR was well tolerated by all participants. However, despite serial reversal of latency over 1 month of VOR dosing, we did not observe a measurable decrease (>0.3 log10) in the frequency of latent infection within resting CD4+ T cells. CONCLUSIONS These findings outline parameters for the experimental use of VOR to clear latent infection. Latency reversal can be achieved by VOR safely and repeatedly, but effective depletion of persistent HIV infection will require additional advances. In addition to improvements in latency reversal, these advances may include the sustained induction of potent antiviral immune responses capable of recognizing and clearing the rare cells in which HIV latency has been reversed. TRIAL REGISTRATION Clinicaltrials.gov NCT01319383. FUNDING NIH grants U01 AI095052, AI50410, and P30 CA016086 and National Center for Advancing Translational Sciences grant KL2 TR001109.
Collapse
Affiliation(s)
- Nancie M Archin
- University of North Carolina (UNC) HIV Cure Center, UNC Institute of Global Health and Infectious Diseases.,Departments of Medicine and
| | - Jennifer L Kirchherr
- University of North Carolina (UNC) HIV Cure Center, UNC Institute of Global Health and Infectious Diseases
| | - Julia Am Sung
- University of North Carolina (UNC) HIV Cure Center, UNC Institute of Global Health and Infectious Diseases.,Departments of Medicine and
| | - Genevieve Clutton
- University of North Carolina (UNC) HIV Cure Center, UNC Institute of Global Health and Infectious Diseases.,Microbiology and Immunology, UNC Chapel Hill School of Medicine
| | - Katherine Sholtis
- University of North Carolina (UNC) HIV Cure Center, UNC Institute of Global Health and Infectious Diseases
| | - Yinyan Xu
- University of North Carolina (UNC) HIV Cure Center, UNC Institute of Global Health and Infectious Diseases
| | - Brigitte Allard
- University of North Carolina (UNC) HIV Cure Center, UNC Institute of Global Health and Infectious Diseases
| | - Erin Stuelke
- University of North Carolina (UNC) HIV Cure Center, UNC Institute of Global Health and Infectious Diseases
| | - Angela D Kashuba
- Division of Pharmacotherapy and Experimental Therapeutics, UNC Eshelman School of Pharmacy
| | - Joann D Kuruc
- University of North Carolina (UNC) HIV Cure Center, UNC Institute of Global Health and Infectious Diseases.,Departments of Medicine and
| | - Joseph Eron
- University of North Carolina (UNC) HIV Cure Center, UNC Institute of Global Health and Infectious Diseases.,Departments of Medicine and.,Department of Epidemiology, UNC Chapel Hill School of Public Health, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Cynthia L Gay
- University of North Carolina (UNC) HIV Cure Center, UNC Institute of Global Health and Infectious Diseases.,Departments of Medicine and
| | - Nilu Goonetilleke
- University of North Carolina (UNC) HIV Cure Center, UNC Institute of Global Health and Infectious Diseases.,Microbiology and Immunology, UNC Chapel Hill School of Medicine
| | - David M Margolis
- University of North Carolina (UNC) HIV Cure Center, UNC Institute of Global Health and Infectious Diseases.,Departments of Medicine and.,Microbiology and Immunology, UNC Chapel Hill School of Medicine.,Department of Epidemiology, UNC Chapel Hill School of Public Health, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| |
Collapse
|
97
|
Sanyal A, Mailliard RB, Rinaldo CR, Ratner D, Ding M, Chen Y, Zerbato JM, Giacobbi NS, Venkatachari NJ, Patterson BK, Chargin A, Sluis-Cremer N, Gupta P. Novel assay reveals a large, inducible, replication-competent HIV-1 reservoir in resting CD4 + T cells. Nat Med 2017; 23:885-889. [PMID: 28553933 PMCID: PMC5505781 DOI: 10.1038/nm.4347] [Citation(s) in RCA: 62] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2017] [Accepted: 03/07/2017] [Indexed: 12/14/2022]
Abstract
Although antiretroviral therapy can suppress HIV-1 infection to undetectable levels of plasma viremia, integrated latent HIV-1 genomes that encode replication competent virus persist in resting CD4+ T cells. This latent HIV-1 reservoir represents a major barrier to a cure. Currently, there are substantial ongoing efforts to identify therapeutic approaches that will eliminate or reduce the size of this latent HIV-1 reservoir. In this regard, a sensitive assay which can accurately and rapidly quantify inducible replication competent latent HIV-1 from resting CD4+ T cells is essential for HIV-1 eradication studies. Here we describe a reporter cell-based assay to quantify inducible replication competent latent HIV-1. This assay has several advantages over existing technology in that it: (i) is sensitive; (ii) requires only a small blood volume; (iii) is faster, less labor intensive, and less expensive, and (iv) can be readily adapted to a high-throughput format. Using this assay we show that the size of the inducible latent HIV-1 reservoir in aviremic participants on therapy is approximately 70-fold larger than previous estimates.
Collapse
Affiliation(s)
- Anwesha Sanyal
- Department of Infectious Diseases and Microbiology, University of Pittsburgh Graduate School of Public Health, Pittsburgh, Pennsylvania, USA
| | - Robbie B Mailliard
- Department of Infectious Diseases and Microbiology, University of Pittsburgh Graduate School of Public Health, Pittsburgh, Pennsylvania, USA
| | - Charles R Rinaldo
- Department of Infectious Diseases and Microbiology, University of Pittsburgh Graduate School of Public Health, Pittsburgh, Pennsylvania, USA.,Department of Pathology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Deena Ratner
- Department of Infectious Diseases and Microbiology, University of Pittsburgh Graduate School of Public Health, Pittsburgh, Pennsylvania, USA
| | - Ming Ding
- Department of Infectious Diseases and Microbiology, University of Pittsburgh Graduate School of Public Health, Pittsburgh, Pennsylvania, USA
| | - Yue Chen
- Department of Infectious Diseases and Microbiology, University of Pittsburgh Graduate School of Public Health, Pittsburgh, Pennsylvania, USA
| | - Jennifer M Zerbato
- Division of Infectious Diseases, Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Nicholas S Giacobbi
- Division of Infectious Diseases, Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Narasimhan J Venkatachari
- Department of Infectious Diseases and Microbiology, University of Pittsburgh Graduate School of Public Health, Pittsburgh, Pennsylvania, USA
| | | | | | - Nicolas Sluis-Cremer
- Division of Infectious Diseases, Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Phalguni Gupta
- Department of Infectious Diseases and Microbiology, University of Pittsburgh Graduate School of Public Health, Pittsburgh, Pennsylvania, USA.,Department of Pathology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| |
Collapse
|
98
|
Busby E, Whale AS, Ferns RB, Grant PR, Morley G, Campbell J, Foy CA, Nastouli E, Huggett JF, Garson JA. Instability of 8E5 calibration standard revealed by digital PCR risks inaccurate quantification of HIV DNA in clinical samples by qPCR. Sci Rep 2017; 7:1209. [PMID: 28446770 PMCID: PMC5430807 DOI: 10.1038/s41598-017-01221-5] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2016] [Accepted: 03/22/2017] [Indexed: 11/09/2022] Open
Abstract
ABTRACT Establishing a cure for HIV is hindered by the persistence of latently infected cells which constitute the viral reservoir. Real-time qPCR, used for quantification of this reservoir by measuring HIV DNA, requires external calibration; a common choice of calibrator is the 8E5 cell line, which is assumed to be stable and to contain one HIV provirus per cell. In contrast, digital PCR requires no external calibration and potentially provides 'absolute' quantification. We compared the performance of qPCR and dPCR in quantifying HIV DNA in 18 patient samples. HIV DNA was detected in 18 by qPCR and in 15 by dPCR, the difference being due to the smaller sample volume analysed by dPCR. There was good quantitative correlation (R2 = 0.86) between the techniques but on average dPCR values were only 60% of qPCR values. Surprisingly, investigation revealed that this discrepancy was due to loss of HIV DNA from the 8E5 cell calibrant. 8E5 extracts from two other sources were also shown to have significantly less than one HIV DNA copy per cell and progressive loss of HIV from 8E5 cells during culture was demonstrated. We therefore suggest that the copy number of HIV in 8E5 extracts be established by dPCR prior to use as calibrator.
Collapse
Affiliation(s)
- Eloise Busby
- Molecular and Cell Biology Team, LGC, Teddington, UK
| | | | - R Bridget Ferns
- Department of Infection, Division of Infection and Immunity, University College London, London, UK
| | - Paul R Grant
- Department of Clinical Virology, University College London Hospital NHS Foundation Trust, and the UCL/UCLH NIHR Biomedical Research Centre, London, UK
| | - Gary Morley
- Molecular and Cell Biology Team, LGC, Teddington, UK
| | | | - Carole A Foy
- Molecular and Cell Biology Team, LGC, Teddington, UK
| | - Eleni Nastouli
- Department of Clinical Virology, University College London Hospital NHS Foundation Trust, and the UCL/UCLH NIHR Biomedical Research Centre, London, UK.,Department of Population Policy and Practice, UCL GOS Institute of Child Health, London, UK
| | - Jim F Huggett
- Molecular and Cell Biology Team, LGC, Teddington, UK. .,School of Biosciences & Medicine, Faculty of Health & Medical Science, University of Surrey, Guildford, GU2 7XH, UK.
| | - Jeremy A Garson
- Department of Infection, Division of Infection and Immunity, University College London, London, UK. .,National Transfusion Microbiology Laboratories, NHS Blood and Transplant, Colindale, London, UK.
| |
Collapse
|
99
|
Levels of HIV-1 persistence on antiretroviral therapy are not associated with markers of inflammation or activation. PLoS Pathog 2017; 13:e1006285. [PMID: 28426825 PMCID: PMC5398724 DOI: 10.1371/journal.ppat.1006285] [Citation(s) in RCA: 137] [Impact Index Per Article: 19.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2016] [Accepted: 03/09/2017] [Indexed: 11/19/2022] Open
Abstract
Antiretroviral therapy (ART) reduces levels of HIV-1 and immune activation but both can persist despite clinically effective ART. The relationships among pre-ART and on-ART levels of HIV-1 and activation are incompletely understood, in part because prior studies have been small or cross-sectional. To address these limitations, we evaluated measures of HIV-1 persistence, inflammation, T cell activation and T cell cycling in a longitudinal cohort of 101 participants who initiated ART and had well-documented sustained suppression of plasma viremia for a median of 7 years. During the first 4 years following ART initiation, HIV-1 DNA declined by 15-fold (93%) whereas cell-associated HIV-1 RNA (CA-RNA) fell 525-fold (>99%). Thereafter, HIV-1 DNA levels continued to decline slowly (5% per year) with a half-life of 13 years. Participants who had higher HIV-1 DNA and CA-RNA before starting treatment had higher levels while on ART, despite suppression of plasma viremia for many years. Markers of inflammation and T cell activation were associated with plasma HIV-1 RNA levels before ART was initiated but there were no consistent associations between these markers and HIV-1 DNA or CA-RNA during long-term ART, suggesting that HIV-1 persistence is not driving or driven by inflammation or activation. Higher levels of inflammation, T cell activation and cycling before ART were associated with higher levels during ART, indicating that immunologic events that occurred well before ART initiation had long-lasting effects despite sustained virologic suppression. These findings should stimulate studies of viral and host factors that affect virologic, inflammatory and immunologic set points prior to ART initiation and should inform the design of strategies to reduce HIV-1 reservoirs and dampen immune activation that persists despite ART.
Collapse
|
100
|
Ruggiero A, Malatinkova E, Rutsaert S, Paxton WA, Vandekerckhove L, De Spiegelaere W. Utility of integrated HIV-1 DNA quantification in cure studies. Future Virol 2017. [DOI: 10.2217/fvl-2016-0130] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Numerous HIV-1 curative strategies have been proposed to eradicate the virus reservoir pool that remains integrated within target cells, despite successful antiretroviral therapy. To test the impact of such interventions on this reservoir, a universal marker of persistence is needed. Quantifying integrated HIV-1 DNA load has been proposed as a strong virological marker. In this paper, we provide a detailed description of the most commonly used assays to quantify integrated HIV-1 DNA and applications in relevant clinical studies produced over the last 20 years with a major focus on the recent literature. We discuss the potential for using this marker of virological persistence and the technical limitations that need to be addressed.
Collapse
Affiliation(s)
- Alessandra Ruggiero
- Department of Clinical Infection, Microbiology & Immunology (CIMI), Institute of Infection & Global Health, University of Liverpool, Liverpool, UK
| | - Eva Malatinkova
- HIV Cure Research Center, Department of Internal Medicine, Faculty of Medicine & Health Sciences, Ghent University, Belgium
| | - Sofie Rutsaert
- HIV Cure Research Center, Department of Internal Medicine, Faculty of Medicine & Health Sciences, Ghent University, Belgium
| | - William A Paxton
- Department of Clinical Infection, Microbiology & Immunology (CIMI), Institute of Infection & Global Health, University of Liverpool, Liverpool, UK
| | - Linos Vandekerckhove
- HIV Cure Research Center, Department of Internal Medicine, Faculty of Medicine & Health Sciences, Ghent University, Belgium
| | - Ward De Spiegelaere
- Department of Morphology, Faculty of Veterinary Sciences, Ghent University, Belgium
| |
Collapse
|