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Tzeng HE, Lee YW, Lin CT, Chuang SS, Li CC, Chuang WH, Hsu CA, Wang YH, Tien HF, Wu SJ. Multicolour and lineage-specific interphase chromosome Flow-FISH: method development and clinical validation. Pathology 2024; 56:671-680. [PMID: 38852040 DOI: 10.1016/j.pathol.2024.04.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2023] [Revised: 03/01/2024] [Accepted: 04/14/2024] [Indexed: 06/10/2024]
Abstract
Flow cytometry can be applied in the detection of fluorescence in situ hybridisation (FISH) signals to efficiently analyse chromosomal aberrations. However, such interphase chromosome (IC) Flow-FISH protocols are currently limited to detecting a single colour. Furthermore, combining IC Flow-FISH with conventional multicolour flow cytometry is difficult because the DNA-denaturation step in FISH assay also disrupts cellular integrity and protein structures, precluding subsequent antigen-antibody binding and hindering concurrent labeling of surface antigens and FISH signals. We developed a working protocol for concurrent multicolour flow cytometry detection of nuclear IC FISH signals and cell surface markers. The protocol was validated by assaying sex chromosome content of blood cells, which was indicative of chimerism status in patients who had received sex-mismatched allogeneic haematopoietic stem cell transplants (allo-HSCT). The method was also adapted to detect trisomy 12 in chronic lymphocytic leukaemia (CLL) subjects. We first demonstrated the feasibility of this protocol in detecting multiple colours and concurrent nuclear and surface signals with high agreement. In clinical validation experiments, chimerism status was identified in clinical samples (n=56) using the optimised IC Flow-FISH method; the results tightly corresponded to those of conventional slide-based FISH (R2=0.9649 for XX cells and 0.9786 for XY cells). In samples from patients who received sex-mismatched allo-HSCT, individual chimeric statuses in different lineages could be clearly distinguished with high flexibility in gating strategies. Furthermore, in CLL samples with trisomy 12, this method could demonstrate that enriched trisomy 12 FISH signal was present in B cells rather than in T cells. Finally, by performing combined labelling of chromosome 12, X chromosome, and surface markers, we could detect rare residual recipient CLL cells with trisomy 12 after allo-HSCT. This adaptable protocol for multicolour and lineage-specific IC Flow-FISH advances the technique to allow for its potential application in various clinical contexts where conventional FISH assays are currently being utilised.
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MESH Headings
- Humans
- In Situ Hybridization, Fluorescence/methods
- Flow Cytometry/methods
- Leukemia, Lymphocytic, Chronic, B-Cell/genetics
- Leukemia, Lymphocytic, Chronic, B-Cell/diagnosis
- Leukemia, Lymphocytic, Chronic, B-Cell/pathology
- Interphase
- Female
- Male
- Hematopoietic Stem Cell Transplantation
- Trisomy/diagnosis
- Trisomy/genetics
- Middle Aged
- Chromosomes, Human, Pair 12/genetics
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Affiliation(s)
- Huey-En Tzeng
- Division of Hematology/Medical Oncology, Department of Medicine, Taichung Veterans General Hospital, Taichung City, Taiwan; Ph.D. Program for Cancer Molecular Biology and Drug Discovery, and Graduate Institute of Cancer Biology and Drug Discovery, College of Medical Science and Technology, Taipei Medical University, Taipei, Taiwan; Department of Post-Baccalaureate Medicine, College of Medicine, National Chung-Hsing University, Taichung, Taiwan
| | - Yi-Wei Lee
- Department of Internal Medicine, Taipei Medical University Hospital, Taipei, Taiwan; Department of Internal Medicine, National Taiwan University Hospital, Taipei, Taiwan
| | - Chien-Ting Lin
- Department of Internal Medicine, National Taiwan University Hospital, Taipei, Taiwan; Department of Hematological Oncology, National Taiwan University Cancer Center, Taipei, Taiwan
| | - Shih-Sung Chuang
- Department of Pathology, Chi-Mei Medical Center, Tainan, Taiwan; Center of Stem Cell and Precision Medicine, Hualien Tzu Chi Hospital, Buddhist Tzu Chi Medical Foundation, Hualien, Taiwan
| | - Chi-Cheng Li
- Center of Stem Cell and Precision Medicine, Hualien Tzu Chi Hospital, Buddhist Tzu Chi Medical Foundation, Hualien, Taiwan
| | - Wen-Hui Chuang
- Department of Internal Medicine, National Taiwan University Hospital, Taipei, Taiwan
| | - Cheng-An Hsu
- Department of Laboratory Medicine, National Taiwan University Hospital, Taipei, Taiwan
| | - Yi-Hua Wang
- Department of Laboratory Medicine, National Taiwan University Hospital, Taipei, Taiwan
| | - Hwei-Fang Tien
- Department of Internal Medicine, National Taiwan University Hospital, Taipei, Taiwan; Department of Internal Medicine, Far-East Memorial Hospital, New Taipei City, Taiwan
| | - Shang-Ju Wu
- Department of Internal Medicine, National Taiwan University Hospital, Taipei, Taiwan; Department of Hematological Oncology, National Taiwan University Cancer Center, Taipei, Taiwan.
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2
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Kobayashi-Ishihara M, Tsunetsugu-Yokota Y. Post-Transcriptional HIV-1 Latency: A Promising Target for Therapy? Viruses 2024; 16:666. [PMID: 38793548 PMCID: PMC11125802 DOI: 10.3390/v16050666] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2024] [Revised: 04/19/2024] [Accepted: 04/22/2024] [Indexed: 05/26/2024] Open
Abstract
Human Immunodeficiency Virus type 1 (HIV-1) latency represents a significant hurdle in finding a cure for HIV-1 infections, despite tireless research efforts. This challenge is partly attributed to the intricate nature of HIV-1 latency, wherein various host and viral factors participate in multiple physiological processes. While substantial progress has been made in discovering therapeutic targets for HIV-1 transcription, targets for the post-transcriptional regulation of HIV-1 infections have received less attention. However, cumulative evidence now suggests the pivotal contribution of post-transcriptional regulation to the viral latency in both in vitro models and infected individuals. In this review, we explore recent insights on post-transcriptional latency in HIV-1 and discuss the potential of its therapeutic targets, illustrating some host factors that restrict HIV-1 at the post-transcriptional level.
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Affiliation(s)
- Mie Kobayashi-Ishihara
- Department of Molecular Biology, Keio University School of Medicine, Tokyo 160-8582, Japan
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3
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Roux H, Chomont N. Measuring Human Immunodeficiency Virus Reservoirs: Do We Need to Choose Between Quantity and Quality? J Infect Dis 2024; 229:635-643. [PMID: 37665978 PMCID: PMC10938203 DOI: 10.1093/infdis/jiad381] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Revised: 08/17/2023] [Accepted: 08/31/2023] [Indexed: 09/06/2023] Open
Abstract
The persistence of latent viral genomes in people receiving antiretroviral therapy (ART) is the main obstacle to a cure for human immunodeficiency virus (HIV) infection. Viral reservoirs can be defined as cells harboring HIV genomes that have the ability to produce infectious virions. Precise quantification of the cellular reservoirs of HIV is challenging because these cells are rare, heterogeneous, and outnumbered by a larger number of cells carrying defective genomes. In addition, measuring the inducibility of these proviruses requires functional assays and remains technically difficult. The recent development of single-cell and single-viral genome approaches revealed additional layers of complexity: the cell subsets that harbor proviruses are heterogeneous and their ability to be induced is variable. A substantial fraction of intact HIV genomes may be permanently silenced after years of ART, revealing the underappreciated importance of induction assays. As such, a simple approach that would assess simultaneously the genetic intactness and the inducibility of the reservoir is still lacking. In this study, we review recent advances in the development of methods to quantify and characterize persistently infected cells, and we discuss how these findings can inform the design of future assays aimed at measuring the size of the intact and inducible HIV reservoir.
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Affiliation(s)
- Hélène Roux
- Département de Microbiologie, Infectiologie et Immunologie, Université de Montréal, Montreal, Quebec, Canada
- Centre de Recherche du CHUM, Montreal, Quebec, Canada
| | - Nicolas Chomont
- Département de Microbiologie, Infectiologie et Immunologie, Université de Montréal, Montreal, Quebec, Canada
- Centre de Recherche du CHUM, Montreal, Quebec, Canada
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4
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Tassaneetrithep B, Phuphuakrat A, Pasomsub E, Bhukhai K, Wongkummool W, Priengprom T, Khamaikawin W, Chaisavaneeyakorn S, Anurathapan U, Apiwattanakul N, Hongeng S. HIV-1 proviral DNA in purified peripheral blood CD34 + stem and progenitor cells in individuals with long-term HAART; paving the way to HIV gene therapy. Heliyon 2024; 10:e26613. [PMID: 38434025 PMCID: PMC10906414 DOI: 10.1016/j.heliyon.2024.e26613] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2023] [Revised: 02/03/2024] [Accepted: 02/16/2024] [Indexed: 03/05/2024] Open
Abstract
Human immunodeficiency virus (HIV)-1 infection is an important public health problem worldwide. After primary HIV-1 infection, transcribed HIV-1 DNA is integrated into the host genome, serving as a reservoir of the virus and hindering a definite cure. Although highly active antiretroviral therapy suppresses active viral replication, resulting in undetectable levels of HIV RNA in the blood, a viral rebound can be detected after a few weeks of treatment interruption. This supports the concept that there is a stable HIV-1 reservoir in people living with HIV-1. Recently, a few individuals with HIV infection were reported to be probably cured by hematopoietic stem transplantation (HSCT). The underlying mechanism for this success involved transfusion of uninfected hematopoietic stem and progenitor cells (HSPCs) from CCR5-mutated donors who were naturally resistant to HIV infection. Thus, gene editing technology to provide HIV-resistant HSPC has promise in the treatment of HIV infections by HSCT. In this study, we aimed to find HIV-infected individuals likely to achieve a definite cure via gene editing HSCT. We screened for total HIV proviral DNA by Alu PCR in peripheral blood mononuclear cells (PBMCs) of 20 HIV-infected individuals with prolonged viral suppression. We assessed the amount of intact proviral DNA via a modified intact proviral DNA assay (IPDA) in purified peripheral CD34+ HSPCs. PBMCs from all 20 individuals were positive for the gag gene in Alu PCR, and peripheral CD34+ HSPCs were IPDA-negative for six individuals. Our results suggested that these six HIV-infected individuals could be candidates for further studies into the ability of gene editing HSCT to lead to a definite HIV cure.
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Affiliation(s)
- Boonrat Tassaneetrithep
- Center of Research Excellence in Immunoregulation, Faculty of Medicine Siriraj Hospital, Mahidol University, Thailand
| | - Angsana Phuphuakrat
- Department of Medicine, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Thailand
| | - Ekawat Pasomsub
- Department of Pathology, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Thailand
| | - Kanit Bhukhai
- Department of Physiology, Faculty of Science, Mahidol University, Thailand
| | | | - Thongkoon Priengprom
- Center of Research Excellence in Immunoregulation, Faculty of Medicine Siriraj Hospital, Mahidol University, Thailand
| | - Wannisa Khamaikawin
- Faculty of Medicine, King Mongkut's Institute of Technology Ladkrabang, Thailand
| | | | - Usanarat Anurathapan
- Department of Pediatrics, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Thailand
| | - Nopporn Apiwattanakul
- Department of Pediatrics, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Thailand
| | - Suradej Hongeng
- Department of Pediatrics, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Thailand
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5
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Pardons M, Cole B, Lambrechts L, van Snippenberg W, Rutsaert S, Noppe Y, De Langhe N, Dhondt A, Vega J, Eyassu F, Nijs E, Van Gulck E, Boden D, Vandekerckhove L. Potent latency reversal by Tat RNA-containing nanoparticle enables multi-omic analysis of the HIV-1 reservoir. Nat Commun 2023; 14:8397. [PMID: 38110433 PMCID: PMC10728105 DOI: 10.1038/s41467-023-44020-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2023] [Accepted: 11/28/2023] [Indexed: 12/20/2023] Open
Abstract
The development of latency reversing agents that potently reactivate HIV without inducing global T cell activation would benefit the field of HIV reservoir research and could pave the way to a functional cure. Here, we explore the reactivation capacity of a lipid nanoparticle containing Tat mRNA (Tat-LNP) in CD4 T cells from people living with HIV undergoing antiretroviral therapy (ART). When combined with panobinostat, Tat-LNP induces latency reversal in a significantly higher proportion of latently infected cells compared to PMA/ionomycin (≈ 4-fold higher). We demonstrate that Tat-LNP does not alter the transcriptome of CD4 T cells, enabling the characterization of latently infected cells in their near-native state. Upon latency reversal, we identify transcriptomic differences between infected cells carrying an inducible provirus and non-infected cells (e.g. LINC02964, GZMA, CCL5). We confirm the transcriptomic differences at the protein level and provide evidence that the long non-coding RNA LINC02964 plays a role in active HIV infection. Furthermore, p24+ cells exhibit heightened PI3K/Akt signaling, along with downregulation of protein translation, suggesting that HIV-infected cells display distinct signatures facilitating their long-term persistence. Tat-LNP represents a valuable research tool for in vitro reservoir studies as it greatly facilitates the in-depth characterization of HIV reservoir cells' transcriptome and proteome profiles.
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Affiliation(s)
- Marion Pardons
- HIV Cure Research Center, Department of Internal Medicine and Pediatrics, Ghent University Hospital, Ghent University, 9000, Ghent, Belgium
| | - Basiel Cole
- HIV Cure Research Center, Department of Internal Medicine and Pediatrics, Ghent University Hospital, Ghent University, 9000, Ghent, Belgium
| | - Laurens Lambrechts
- HIV Cure Research Center, Department of Internal Medicine and Pediatrics, Ghent University Hospital, Ghent University, 9000, Ghent, Belgium
- BioBix, Department of Data Analysis and Mathematical Modelling, Faculty of Bioscience Engineering, Ghent University, 9000, Ghent, Belgium
| | - Willem van Snippenberg
- HIV Cure Research Center, Department of Internal Medicine and Pediatrics, Ghent University Hospital, Ghent University, 9000, Ghent, Belgium
| | - Sofie Rutsaert
- HIV Cure Research Center, Department of Internal Medicine and Pediatrics, Ghent University Hospital, Ghent University, 9000, Ghent, Belgium
| | - Ytse Noppe
- HIV Cure Research Center, Department of Internal Medicine and Pediatrics, Ghent University Hospital, Ghent University, 9000, Ghent, Belgium
| | - Nele De Langhe
- HIV Cure Research Center, Department of Internal Medicine and Pediatrics, Ghent University Hospital, Ghent University, 9000, Ghent, Belgium
| | - Annemieke Dhondt
- Department of Nephrology, Ghent University Hospital, 9000, Ghent, Belgium
| | - Jerel Vega
- Arcturus Therapeutics, 10628 Science Center Drive, Suite 250, San Diego, 92121, CA, USA
| | - Filmon Eyassu
- Computational biology, Johnson and Johnson, 2340, Beerse, Belgium
| | - Erik Nijs
- Janssen infectious diseases and diagnostics, Johnson and Johnson, 2340, Beerse, Belgium
| | - Ellen Van Gulck
- Janssen infectious diseases and diagnostics, Johnson and Johnson, 2340, Beerse, Belgium
| | - Daniel Boden
- Janssen Biopharma, Johnson and Johnson, South San Francisco, 94080, CA, USA
| | - Linos Vandekerckhove
- HIV Cure Research Center, Department of Internal Medicine and Pediatrics, Ghent University Hospital, Ghent University, 9000, Ghent, Belgium.
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6
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Plaza-Jennings A, Akbarian S. Genomic Exploration of the Brain in People Infected with HIV-Recent Progress and the Road Ahead. Curr HIV/AIDS Rep 2023; 20:357-367. [PMID: 37947981 PMCID: PMC10719125 DOI: 10.1007/s11904-023-00675-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/02/2023] [Indexed: 11/12/2023]
Abstract
PURPOSE OF REVIEW The adult human brain harbors billions of microglia and other myeloid and lymphoid cells highly susceptible to HIV infection and retroviral insertion into the nuclear DNA. HIV infection of the brain is important because the brain is a potentially large reservoir site that may be a barrier to HIV cure strategies and because infection can lead to the development of HIV-associated neurocognitive disorder. To better understand both the central nervous system (CNS) reservoir and how it can cause neurologic dysfunction, novel genomic, epigenomic, transcriptomic, and proteomic approaches need to be employed. Several characteristics of the reservoir are important to learn, including where the virus integrates, whether integrated proviruses are intact or defective, whether integrated proviruses can be reactivated from a latent state to seed ongoing infection, and how this all impacts brain function. RECENT FINDINGS Here, we discuss similarities and differences of viral integration sites between brain and blood and discuss evidence for and against the hypothesis that in the absence of susceptible T-lymphocytes in the periphery, the virus housing in the infected brain is not able to sustain a systemic infection. Moreover, microglia from HIV + brains across a wide range of disease severity appear to share one type of common alteration, which is defined by downregulated expression, and repressive chromosomal compartmentalization, for microglial genes regulating synaptic connectivity. Therefore, viral infection of the brain, including in immunocompetent cases with near-normal levels of CD4 blood lymphocytes, could be associated with an early disruption in microglia-dependent neuronal support functions, contributing to cognitive and neurological deficits in people living with HIV.
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Affiliation(s)
- Amara Plaza-Jennings
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Nash Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Schahram Akbarian
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA.
- Nash Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA.
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA.
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7
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Cobos Jiménez V, Geretz A, Tokarev A, Ehrenberg PK, Deletsu S, Machmach K, Mudvari P, Howard JN, Zelkoski A, Paquin-Proulx D, Del Prete GQ, Subra C, Boritz EA, Bosque A, Thomas R, Bolton DL. AP-1/c-Fos supports SIV and HIV-1 latency in CD4 T cells infected in vivo. iScience 2023; 26:108015. [PMID: 37860759 PMCID: PMC10582365 DOI: 10.1016/j.isci.2023.108015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2023] [Revised: 08/24/2023] [Accepted: 09/18/2023] [Indexed: 10/21/2023] Open
Abstract
Persistent HIV-1 reservoirs of infected CD4 T cells are a major barrier to HIV-1 cure, although the mechanisms by which they are established and maintained in vivo remain poorly characterized. To elucidate host cell gene expression patterns that govern virus gene expression, we analyzed viral RNA+ (vRNA) CD4 T cells of untreated simian immunodeficiency virus (SIV)-infected macaques by single-cell RNA sequencing. A subset of vRNA+ cells distinguished by spliced and high total vRNA (7-10% of reads) expressed diminished FOS, a component of the Activator protein 1 (AP-1) transcription factor, relative to vRNA-low and -negative cells. Conversely, FOS and JUN, another AP-1 component, were upregulated in HIV DNA+ infected cells compared to uninfected cells from people with HIV-1 on suppressive therapy. Inhibiting c-Fos in latently infected primary cells augmented reactivatable HIV-1 infection. These findings implicate AP-1 in latency establishment and maintenance and as a potential therapeutic target to limit HIV-1 reservoirs.
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Affiliation(s)
- Viviana Cobos Jiménez
- US Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD, USA
- The Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, USA
| | - Aviva Geretz
- US Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD, USA
- The Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, USA
| | - Andrey Tokarev
- US Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD, USA
- The Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, USA
| | - Philip K. Ehrenberg
- US Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD, USA
| | | | - Kawthar Machmach
- US Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD, USA
- The Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, USA
| | - Prakriti Mudvari
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | | | - Amanda Zelkoski
- US Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD, USA
- The Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, USA
| | - Dominic Paquin-Proulx
- US Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD, USA
- The Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, USA
| | - Gregory Q. Del Prete
- AIDS and Cancer Virus Program, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Caroline Subra
- US Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD, USA
- The Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, USA
| | - Eli A. Boritz
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | | | - Rasmi Thomas
- US Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD, USA
| | - Diane L. Bolton
- US Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD, USA
- The Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, USA
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8
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Otte F, Zhang Y, Spagnuolo J, Thielen A, Däumer M, Wiethe C, Stoeckle M, Kusejko K, Klein F, Metzner KJ, Klimkait T. Revealing viral and cellular dynamics of HIV-1 at the single-cell level during early treatment periods. CELL REPORTS METHODS 2023; 3:100485. [PMID: 37426753 PMCID: PMC10326345 DOI: 10.1016/j.crmeth.2023.100485] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Revised: 01/30/2023] [Accepted: 04/28/2023] [Indexed: 07/11/2023]
Abstract
While combination therapy completely suppresses HIV-1 replication in blood, functional virus persists in CD4+ T cell subsets in non-peripheral compartments that are not easily accessible. To fill this gap, we investigated tissue-homing properties of cells that transiently appear in the circulating blood. Through cell separation and in vitro stimulation, the HIV-1 "Gag and Envelope reactivation co-detection assay" (GERDA) enables sensitive detection of Gag+/Env+ protein-expressing cells down to about one cell per million using flow cytometry. By associating GERDA with proviral DNA and polyA-RNA transcripts, we corroborate the presence and functionality of HIV-1 in critical body compartments utilizing t-distributed stochastic neighbor embedding (tSNE) and density-based spatial clustering of applications with noise (DBSCAN) clustering with low viral activity in circulating cells early after diagnosis. We demonstrate transcriptional HIV-1 reactivation at any time, potentially giving rise to intact, infectious particles. With single-cell level resolution, GERDA attributes virus production to lymph-node-homing cells with central memory T cells (TCMs) as main players, critical for HIV-1 reservoir eradication.
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Affiliation(s)
- Fabian Otte
- Molecular Virology, Department Biomedicine, University of Basel, 4009 Basel, Switzerland
| | - Yuepeng Zhang
- Molecular Virology, Department Biomedicine, University of Basel, 4009 Basel, Switzerland
| | - Julian Spagnuolo
- Experimental Immunology, Department Biomedicine, University of Basel, 4056 Basel, Switzerland
| | | | | | | | - Marcel Stoeckle
- Infectiology, University Hospital Basel, 4031 Basel, Switzerland
| | - Katharina Kusejko
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, and Institute of Medical Virology, University of Zurich, 8091 Zurich, Switzerland
| | - Florian Klein
- Laboratory of Experimental Immunology, Institute of Virology, Faculty of Medicine and University Hospital Cologne, University of Cologne, 50931 Cologne, Germany
| | - Karin J. Metzner
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, and Institute of Medical Virology, University of Zurich, 8091 Zurich, Switzerland
| | - Thomas Klimkait
- Molecular Virology, Department Biomedicine, University of Basel, 4009 Basel, Switzerland
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9
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Kobayashi-Ishihara M, Frazão Smutná K, Alonso FE, Argilaguet J, Esteve-Codina A, Geiger K, Genescà M, Grau-Expósito J, Duran-Castells C, Rogenmoser S, Böttcher R, Jungfleisch J, Oliva B, Martinez JP, Li M, David M, Yamagishi M, Ruiz-Riol M, Brander C, Tsunetsugu-Yokota Y, Buzon MJ, Díez J, Meyerhans A. Schlafen 12 restricts HIV-1 latency reversal by a codon-usage dependent post-transcriptional block in CD4+ T cells. Commun Biol 2023; 6:487. [PMID: 37165099 PMCID: PMC10172343 DOI: 10.1038/s42003-023-04841-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2023] [Accepted: 04/13/2023] [Indexed: 05/12/2023] Open
Abstract
Latency is a major barrier towards virus elimination in HIV-1-infected individuals. Yet, the mechanisms that contribute to the maintenance of HIV-1 latency are incompletely understood. Here we describe the Schlafen 12 protein (SLFN12) as an HIV-1 restriction factor that establishes a post-transcriptional block in HIV-1-infected cells and thereby inhibits HIV-1 replication and virus reactivation from latently infected cells. The inhibitory activity is dependent on the HIV-1 codon usage and on the SLFN12 RNase active sites. Within HIV-1-infected individuals, SLFN12 expression in PBMCs correlated with HIV-1 plasma viral loads and proviral loads suggesting a link with the general activation of the immune system. Using an RNA FISH-Flow HIV-1 reactivation assay, we demonstrate that SLFN12 expression is enriched in infected cells positive for HIV-1 transcripts but negative for HIV-1 proteins. Thus, codon-usage dependent translation inhibition of HIV-1 proteins participates in HIV-1 latency and can restrict the amount of virus release after latency reversal.
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Affiliation(s)
- Mie Kobayashi-Ishihara
- Infection Biology Group, Department of Medicine and Life Sciences, Universitat Pompeu Fabra, Barcelona, Spain.
- Department of Molecular Biology, Keio University School of Medicine, Tokyo, Japan.
| | - Katarína Frazão Smutná
- Infection Biology Group, Department of Medicine and Life Sciences, Universitat Pompeu Fabra, Barcelona, Spain
| | - Florencia E Alonso
- Infection Biology Group, Department of Medicine and Life Sciences, Universitat Pompeu Fabra, Barcelona, Spain
| | - Jordi Argilaguet
- Infection Biology Group, Department of Medicine and Life Sciences, Universitat Pompeu Fabra, Barcelona, Spain
- Unitat mixta d'Investigació IRTA-UAB en Sanitat Animal. Centre de Recerca en Sanitat Animal (CReSA), Campus de la Universitat Autònoma de Barcelona (UAB), Bellaterra, Spain
- IRTA. Programa de Sanitat Animal. Centre de Recerca en Sanitat Animal (CReSA), Campus de la Universitat Autònoma de Barcelona (UAB), Bellaterra, Spain
| | - Anna Esteve-Codina
- Centro Nacional de Análisis Genómico (CNAG-CRG), Center for Genomic Regulation (CRG), Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Kerstin Geiger
- Infection Biology Group, Department of Medicine and Life Sciences, Universitat Pompeu Fabra, Barcelona, Spain
| | - Meritxell Genescà
- Infectious Disease Department, Hospital Universitari Vall d´Hebrón, Institut de Recerca (VHIR), Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Judith Grau-Expósito
- Infectious Disease Department, Hospital Universitari Vall d´Hebrón, Institut de Recerca (VHIR), Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Clara Duran-Castells
- IrsiCaixa AIDS Research Institute, Hospital Germans Trias i Pujol, Universitat Autonoma de Barcelona, Badalona, Spain
| | - Selina Rogenmoser
- Infection Biology Group, Department of Medicine and Life Sciences, Universitat Pompeu Fabra, Barcelona, Spain
| | - René Böttcher
- Molecular Virology Group, Department of Medicine and Life Sciences, Universitat Pompeu Fabra, Barcelona, Spain
| | - Jennifer Jungfleisch
- Molecular Virology Group, Department of Medicine and Life Sciences, Universitat Pompeu Fabra, Barcelona, Spain
| | - Baldomero Oliva
- Structural Bioinformatics Group, Department of Medicine and Life Sciences, Universitat Pompeu Fabra, Barcelona, Spain
| | - Javier P Martinez
- Infection Biology Group, Department of Medicine and Life Sciences, Universitat Pompeu Fabra, Barcelona, Spain
| | - Manqing Li
- Section of Molecular Biology, Division of Biological Sciences, University of California San Diego, La Jolla, CA, USA
| | - Michael David
- Section of Molecular Biology, Division of Biological Sciences, University of California San Diego, La Jolla, CA, USA
- Moores Cancer Center, University of California San Diego, La Jolla, CA, USA
| | - Makoto Yamagishi
- Graduate School of Frontier Sciences, The University of Tokyo, Tokyo, Japan
| | - Marta Ruiz-Riol
- IrsiCaixa AIDS Research Institute, Hospital Germans Trias i Pujol, Universitat Autonoma de Barcelona, Badalona, Spain
- CIBER de Enfermedades Infecciosas, Madrid, Spain
| | - Christian Brander
- IrsiCaixa AIDS Research Institute, Hospital Germans Trias i Pujol, Universitat Autonoma de Barcelona, Badalona, Spain
- Universitat de Vic-Universitat Central de Catalunya (UVic-UCC), Vic, Spain
- Institució de Recerca i Estudis Avançats (ICREA), Barcelona, Spain
| | - Yasuko Tsunetsugu-Yokota
- Department of Medical Technology, School of Human Sciences, Tokyo University of Technology, Tokyo, Japan
| | - Maria J Buzon
- Infectious Disease Department, Hospital Universitari Vall d´Hebrón, Institut de Recerca (VHIR), Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Juana Díez
- Molecular Virology Group, Department of Medicine and Life Sciences, Universitat Pompeu Fabra, Barcelona, Spain.
| | - Andreas Meyerhans
- Infection Biology Group, Department of Medicine and Life Sciences, Universitat Pompeu Fabra, Barcelona, Spain.
- Institució de Recerca i Estudis Avançats (ICREA), Barcelona, Spain.
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10
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Gantner P, Buranapraditkun S, Pagliuzza A, Dufour C, Pardons M, Mitchell JL, Kroon E, Sacdalan C, Tulmethakaan N, Pinyakorn S, Robb ML, Phanuphak N, Ananworanich J, Hsu D, Vasan S, Trautmann L, Fromentin R, Chomont N. HIV rapidly targets a diverse pool of CD4 + T cells to establish productive and latent infections. Immunity 2023; 56:653-668.e5. [PMID: 36804957 PMCID: PMC10023508 DOI: 10.1016/j.immuni.2023.01.030] [Citation(s) in RCA: 32] [Impact Index Per Article: 32.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2022] [Revised: 10/15/2022] [Accepted: 01/25/2023] [Indexed: 02/19/2023]
Abstract
Upon infection, HIV disseminates throughout the human body within 1-2 weeks. However, its early cellular targets remain poorly characterized. We used a single-cell approach to retrieve the phenotype and TCR sequence of infected cells in blood and lymphoid tissue from individuals at the earliest stages of HIV infection. HIV initially targeted a few proliferating memory CD4+ T cells displaying high surface expression of CCR5. The phenotype of productively infected cells differed by Fiebig stage and between blood and lymph nodes. The TCR repertoire of productively infected cells was heavily biased, with preferential infection of previously expanded and disseminated clones, but composed almost exclusively of unique clonotypes, indicating that they were the product of independent infection events. Latent genetically intact proviruses were already archived early in infection. Hence, productive infection is initially established in a pool of phenotypically and clonotypically distinct T cells, and latently infected cells are generated simultaneously.
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Affiliation(s)
- Pierre Gantner
- Department of Microbiology, Infectiology and Immunology, Université de Montréal, Montreal, QC, Canada
| | - Supranee Buranapraditkun
- Department of Medicine, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand; Center of Excellence in Vaccine Research and Development, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Amélie Pagliuzza
- Centre de Recherche du Centre Hospitalier de l'Université de Montréal, Montreal, QC, Canada
| | - Caroline Dufour
- Department of Microbiology, Infectiology and Immunology, Université de Montréal, Montreal, QC, Canada
| | - Marion Pardons
- Department of Microbiology, Infectiology and Immunology, Université de Montréal, Montreal, QC, Canada
| | - Julie L Mitchell
- Vaccine and Gene Therapy Institute, Oregon Health & Science University, Beaverton, OR, USA
| | - Eugène Kroon
- SEARCH, Institute of HIV Research and Innovation, Bangkok, Thailand
| | - Carlo Sacdalan
- SEARCH, Institute of HIV Research and Innovation, Bangkok, Thailand
| | | | - Suteeraporn Pinyakorn
- Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD, USA; Henry M. Jackson Foundation for the Advancement of Military Medicine Inc., Bethesda, MD, USA
| | - Merlin L Robb
- Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD, USA; Henry M. Jackson Foundation for the Advancement of Military Medicine Inc., Bethesda, MD, USA
| | | | - Jintanat Ananworanich
- Department of Global Health, Amsterdam Medical Center, University of Amsterdam, Amsterdam, the Netherlands
| | - Denise Hsu
- Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD, USA; Henry M. Jackson Foundation for the Advancement of Military Medicine Inc., Bethesda, MD, USA
| | - Sandhya Vasan
- Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD, USA; Henry M. Jackson Foundation for the Advancement of Military Medicine Inc., Bethesda, MD, USA
| | - Lydie Trautmann
- Vaccine and Gene Therapy Institute, Oregon Health & Science University, Beaverton, OR, USA
| | - Rémi Fromentin
- Centre de Recherche du Centre Hospitalier de l'Université de Montréal, Montreal, QC, Canada
| | - Nicolas Chomont
- Department of Microbiology, Infectiology and Immunology, Université de Montréal, Montreal, QC, Canada; Centre de Recherche du Centre Hospitalier de l'Université de Montréal, Montreal, QC, Canada.
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11
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Gunst JD, Pahus MH, Rosás-Umbert M, Lu IN, Benfield T, Nielsen H, Johansen IS, Mohey R, Østergaard L, Klastrup V, Khan M, Schleimann MH, Olesen R, Støvring H, Denton PW, Kinloch NN, Copertino DC, Ward AR, Alberto WDC, Nielsen SD, Puertas MC, Ramos V, Reeves JD, Petropoulos CJ, Martinez-Picado J, Brumme ZL, Jones RB, Fox J, Tolstrup M, Nussenzweig MC, Caskey M, Fidler S, Søgaard OS. Early intervention with 3BNC117 and romidepsin at antiretroviral treatment initiation in people with HIV-1: a phase 1b/2a, randomized trial. Nat Med 2022; 28:2424-2435. [PMID: 36253609 PMCID: PMC10189540 DOI: 10.1038/s41591-022-02023-7] [Citation(s) in RCA: 39] [Impact Index Per Article: 19.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Accepted: 08/22/2022] [Indexed: 01/26/2023]
Abstract
Attempts to reduce the human immunodeficiency virus type 1 (HIV-1) reservoir and induce antiretroviral therapy (ART)-free virologic control have largely been unsuccessful. In this phase 1b/2a, open-label, randomized controlled trial using a four-group factorial design, we investigated whether early intervention in newly diagnosed people with HIV-1 with a monoclonal anti-HIV-1 antibody with a CD4-binding site, 3BNC117, followed by a histone deacetylase inhibitor, romidepsin, shortly after ART initiation altered the course of HIV-1 infection ( NCT03041012 ). The trial was undertaken in five hospitals in Denmark and two hospitals in the United Kingdom. The coprimary endpoints were analysis of initial virus decay kinetics and changes in the frequency of CD4+ T cells containing intact HIV-1 provirus from baseline to day 365. Secondary endpoints included changes in the frequency of infected CD4+ T cells and virus-specific CD8+ T cell immunity from baseline to day 365, pre-ART plasma HIV-1 3BNC117 sensitivity, safety and tolerability, and time to loss of virologic control during a 12-week analytical ART interruption that started at day 400. In 55 newly diagnosed people (5 females and 50 males) with HIV-1 who received random allocation treatment, we found that early 3BNC117 treatment with or without romidepsin enhanced plasma HIV-1 RNA decay rates compared to ART only. Furthermore, 3BNC117 treatment accelerated clearance of infected cells compared to ART only. All groups had significant reductions in the frequency of CD4+ T cells containing intact HIV-1 provirus. At day 365, early 3BNC117 + romidepsin was associated with enhanced HIV-1 Gag-specific CD8+ T cell immunity compared to ART only. The observed virological and immunological effects of 3BNC117 were most pronounced in individuals whose pre-ART plasma HIV-1 envelope sequences were antibody sensitive. The results were not disaggregated by sex. Adverse events were mild to moderate and similar between the groups. During a 12-week analytical ART interruption among 20 participants, 3BNC117-treated individuals harboring sensitive viruses were significantly more likely to maintain ART-free virologic control than other participants. We conclude that 3BNC117 at ART initiation enhanced elimination of plasma viruses and infected cells, enhanced HIV-1-specific CD8+ immunity and was associated with sustained ART-free virologic control among persons with 3BNC117-sensitive virus. These findings strongly support interventions administered at the time of ART initiation as a strategy to limit long-term HIV-1 persistence.
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Affiliation(s)
- Jesper D Gunst
- Department of Clinical Medicine, Aarhus University, Aarhus, Denmark
- Department of Infectious Diseases, Aarhus University Hospital, Aarhus, Denmark
| | - Marie H Pahus
- Department of Clinical Medicine, Aarhus University, Aarhus, Denmark
- Department of Infectious Diseases, Aarhus University Hospital, Aarhus, Denmark
| | - Miriam Rosás-Umbert
- Department of Clinical Medicine, Aarhus University, Aarhus, Denmark
- Department of Infectious Diseases, Aarhus University Hospital, Aarhus, Denmark
| | - I-Na Lu
- Department of Neurology with Institute of Translational Neurology, University Hospital Münster, Münster, Germany
| | - Thomas Benfield
- Department of Infectious Diseases, Copenhagen University Hospital-Amager and Hvidovre, Hvidovre, Denmark
| | - Henrik Nielsen
- Department of Infectious Diseases, Aalborg University Hospital, Aalborg, Denmark
- Department of Clinical Medicine, Aalborg University, Aalborg, Denmark
| | - Isik S Johansen
- Department of Infectious Diseases, Odense University Hospital, University of Southern Denmark, Odense, Denmark
| | - Rajesh Mohey
- Department of Internal Medicine, Regional Hospital Herning, Herning, Denmark
| | - Lars Østergaard
- Department of Clinical Medicine, Aarhus University, Aarhus, Denmark
- Department of Infectious Diseases, Aarhus University Hospital, Aarhus, Denmark
| | - Vibeke Klastrup
- Department of Infectious Diseases, Aarhus University Hospital, Aarhus, Denmark
| | - Maryam Khan
- Department of Infectious Diseases, Imperial College Hospital, London, UK
- The National Institute for Health Research, Imperial Biomedical Research Centre, London, UK
| | - Mariane H Schleimann
- Department of Clinical Medicine, Aarhus University, Aarhus, Denmark
- Department of Infectious Diseases, Aarhus University Hospital, Aarhus, Denmark
| | - Rikke Olesen
- Department of Clinical Medicine, Aarhus University, Aarhus, Denmark
- Department of Infectious Diseases, Aarhus University Hospital, Aarhus, Denmark
| | - Henrik Støvring
- Department of Public Health, Aarhus University, Aarhus, Denmark
| | - Paul W Denton
- Department of Biology, University of Nebraska at Omaha, Omaha, NE, USA
| | - Natalie N Kinloch
- Faculty of Health Sciences, Simon Fraser University, Burnaby, British Columbia, Canada
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, British Columbia, Canada
| | - Dennis C Copertino
- Infectious Diseases Division, Department of Medicine, Weill Cornell Medical College, New York, NY, USA
- Department of Microbiology and Immunology, Weill Cornell Graduate School of Medical Sciences, New York, NY, USA
| | - Adam R Ward
- Infectious Diseases Division, Department of Medicine, Weill Cornell Medical College, New York, NY, USA
| | - Winiffer D Conce Alberto
- Infectious Diseases Division, Department of Medicine, Weill Cornell Medical College, New York, NY, USA
- Department of Microbiology and Immunology, Weill Cornell Graduate School of Medical Sciences, New York, NY, USA
| | - Silke D Nielsen
- Department of Clinical Medicine, Aarhus University, Aarhus, Denmark
- Department of Infectious Diseases, Aarhus University Hospital, Aarhus, Denmark
| | - Maria C Puertas
- IrsiCaixa AIDS Research Institute, Badalona, Spain
- CIBERINFEC, Madrid, Spain
| | - Victor Ramos
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY, USA
| | | | | | - Javier Martinez-Picado
- IrsiCaixa AIDS Research Institute, Badalona, Spain
- CIBERINFEC, Madrid, Spain
- University of Vic-Central University of Catalonia, Vic, Spain
- Catalan Institution for Research and Advanced Studies, Barcelona, Spain
| | - Zabrina L Brumme
- Faculty of Health Sciences, Simon Fraser University, Burnaby, British Columbia, Canada
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, British Columbia, Canada
| | - R Brad Jones
- Infectious Diseases Division, Department of Medicine, Weill Cornell Medical College, New York, NY, USA
- Department of Microbiology and Immunology, Weill Cornell Graduate School of Medical Sciences, New York, NY, USA
| | - Julie Fox
- Department of Genitourinary Medicine and Infectious Disease, Guy's and St Thomas' National Health Service Trust, London, UK
- Department of Genitourinary Medicine and Infectious Disease, The National Institute for Health Research Biomedical Research Centre, King's College London, London, UK
| | - Martin Tolstrup
- Department of Clinical Medicine, Aarhus University, Aarhus, Denmark
- Department of Infectious Diseases, Aarhus University Hospital, Aarhus, Denmark
| | - Michel C Nussenzweig
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY, USA
- Howard Hughes Medical Institute, The Rockefeller University, New York, NY, USA
| | - Marina Caskey
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY, USA
| | - Sarah Fidler
- Department of Infectious Diseases, Imperial College Hospital, London, UK
- The National Institute for Health Research, Imperial Biomedical Research Centre, London, UK
| | - Ole S Søgaard
- Department of Clinical Medicine, Aarhus University, Aarhus, Denmark.
- Department of Infectious Diseases, Aarhus University Hospital, Aarhus, Denmark.
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12
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Real F, Zhu A, Huang B, Belmellat A, Sennepin A, Vogl T, Ransy C, Revol M, Arrigucci R, Lombès A, Roth J, Gennaro ML, Bouillaud F, Cristofari S, Bomsel M. S100A8-mediated metabolic adaptation controls HIV-1 persistence in macrophages in vivo. Nat Commun 2022; 13:5956. [PMID: 36220814 PMCID: PMC9553955 DOI: 10.1038/s41467-022-33401-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Accepted: 09/16/2022] [Indexed: 11/23/2022] Open
Abstract
HIV-1 eradication is hindered by viral persistence in cell reservoirs, established not only in circulatory CD4+T-cells but also in tissue-resident macrophages. The nature of macrophage reservoirs and mechanisms of persistence despite combined anti-retroviral therapy (cART) remain unclear. Using genital mucosa from cART-suppressed HIV-1-infected individuals, we evaluated the implication of macrophage immunometabolic pathways in HIV-1 persistence. We demonstrate that ex vivo, macrophage tissue reservoirs contain transcriptionally active HIV-1 and viral particles accumulated in virus-containing compartments, and harbor an inflammatory IL-1R+S100A8+MMP7+M4-phenotype prone to glycolysis. Reactivation of infectious virus production and release from these reservoirs in vitro are induced by the alarmin S100A8, an endogenous factor produced by M4-macrophages and implicated in “sterile” inflammation. This process metabolically depends on glycolysis. Altogether, inflammatory M4-macrophages form a major tissue reservoir of replication-competent HIV-1, which reactivate viral production upon autocrine/paracrine S100A8-mediated glycolytic stimulation. This HIV-1 persistence pathway needs to be targeted in future HIV eradication strategies. HIV-1 eradication is hindered by viral persistence in different cell reservoirs, including circulatory CD4+ T-cells and tissue-resident macrophages. Here, by analyzing male genital mucosa from cART-suppressed HIV1-infected individuals, Real et al. show that M4 macrophages represent the major macrophage HIV-1 reservoir in this tissue. These macrophages have an inflammatory IL1R+S100A8+MMP7+M4-phenotype, and contain transcriptionally active HIV-1, which reactivate infectious virus production from viral latency in response to autocrine/paracrine S100A8-mediated glycolysis.
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Affiliation(s)
- Fernando Real
- Laboratory of Mucosal Entry of HIV and Mucosal Immunity, Institut Cochin, Université Paris Cité, 75014, Paris, France.,CNRS, UMR8104, 75014, Paris, France.,Inserm, U1016, Institut Cochin, 75014, Paris, France
| | - Aiwei Zhu
- Laboratory of Mucosal Entry of HIV and Mucosal Immunity, Institut Cochin, Université Paris Cité, 75014, Paris, France.,CNRS, UMR8104, 75014, Paris, France.,Inserm, U1016, Institut Cochin, 75014, Paris, France
| | - Boxin Huang
- Laboratory of Mucosal Entry of HIV and Mucosal Immunity, Institut Cochin, Université Paris Cité, 75014, Paris, France.,CNRS, UMR8104, 75014, Paris, France.,Inserm, U1016, Institut Cochin, 75014, Paris, France
| | - Ania Belmellat
- Laboratory of Mucosal Entry of HIV and Mucosal Immunity, Institut Cochin, Université Paris Cité, 75014, Paris, France.,CNRS, UMR8104, 75014, Paris, France.,Inserm, U1016, Institut Cochin, 75014, Paris, France
| | - Alexis Sennepin
- Laboratory of Mucosal Entry of HIV and Mucosal Immunity, Institut Cochin, Université Paris Cité, 75014, Paris, France.,CNRS, UMR8104, 75014, Paris, France.,Inserm, U1016, Institut Cochin, 75014, Paris, France
| | - Thomas Vogl
- Institute of Immunology and Interdisciplinary Center for Clinical Research, University of Münster, Münster, Germany
| | - Céline Ransy
- CNRS, UMR8104, 75014, Paris, France.,Inserm, U1016, Institut Cochin, 75014, Paris, France
| | - Marc Revol
- Plastic, Reconstructive and Aesthetic Surgery Department, Saint Louis Hospital, Paris, France
| | - Riccardo Arrigucci
- Public Health Research Institute, New Jersey Medical School, Rutgers, The State University of New Jersey, Newark, NJ, USA
| | - Anne Lombès
- CNRS, UMR8104, 75014, Paris, France.,Inserm, U1016, Institut Cochin, 75014, Paris, France
| | - Johannes Roth
- Institute of Immunology and Interdisciplinary Center for Clinical Research, University of Münster, Münster, Germany
| | - Maria Laura Gennaro
- Public Health Research Institute, New Jersey Medical School, Rutgers, The State University of New Jersey, Newark, NJ, USA
| | - Frédéric Bouillaud
- CNRS, UMR8104, 75014, Paris, France.,Inserm, U1016, Institut Cochin, 75014, Paris, France
| | - Sarra Cristofari
- Plastic, Reconstructive and Aesthetic Surgery Department, Saint Louis Hospital, Paris, France
| | - Morgane Bomsel
- Laboratory of Mucosal Entry of HIV and Mucosal Immunity, Institut Cochin, Université Paris Cité, 75014, Paris, France. .,CNRS, UMR8104, 75014, Paris, France. .,Inserm, U1016, Institut Cochin, 75014, Paris, France.
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13
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Closing the Door with CRISPR: Genome Editing of CCR5 and CXCR4 as a Potential Curative Solution for HIV. BIOTECH 2022; 11:biotech11030025. [PMID: 35892930 PMCID: PMC9326690 DOI: 10.3390/biotech11030025] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2022] [Revised: 07/10/2022] [Accepted: 07/12/2022] [Indexed: 11/17/2022] Open
Abstract
Human immunodeficiency virus (HIV) infection can be controlled by anti-retroviral therapy. Suppressing viral replication relies on life-long medication, but anti-retroviral therapy is not without risks to the patient. Therefore, it is important that permanent cures for HIV infection are developed. Three patients have been described to be completely cured from HIV infection in recent years. In all cases, patients received a hematopoietic stem cell (HSC) transplantation due to a hematological malignancy. The HSCs were sourced from autologous donors that expressed a homozygous mutation in the CCR5 gene. This mutation results in a non-functional receptor, and confers resistance to CCR5-tropic HIV strains that rely on CCR5 to enter host cells. The Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR)/CRISPR-associated (Cas) system is one of the methods of choice for gene editing, and the CRISPR/Cas system has been employed to target loci of interest in the context of HIV. Here, the current literature regarding CRISPR-mediated genome editing to render cells resistant to HIV (re)-infection by knocking out the co-receptors CCR5 and CXCR4 is summarized, and an outlook is provided regarding future (research) directions.
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14
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Tokarev A, Machmach K, Creegan M, Kim D, Eller MA, Bolton DL. Single-Cell Profiling of Latently SIV-Infected CD4 + T Cells Directly Ex Vivo to Reveal Host Factors Supporting Reservoir Persistence. Microbiol Spectr 2022; 10:e0060422. [PMID: 35510859 PMCID: PMC9241701 DOI: 10.1128/spectrum.00604-22] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2022] [Accepted: 04/02/2022] [Indexed: 11/20/2022] Open
Abstract
HIV-1 cure strategies aiming to eliminate persistent infected cell reservoirs are hampered by a poor understanding of cells harboring viral DNA in vivo. We describe a novel method to identify, enumerate, and characterize in detail individual cells infected in vivo using a combination of single-cell multiplexed assays for integrated proviral DNA, quantitative viral and host gene expression, and quantitative surface protein expression without any in vitro manipulation. Latently infected CD4+ T cells, defined as harboring integrated provirus in the absence of spliced viral mRNA, were identified from macaque lymph nodes during acute, chronic, and combination antiretroviral therapy (cART)-suppressed simian immunodeficiency virus (SIV) infection. Latently infected CD4+ T cells were most abundant during acute SIV (~8% of memory CD4+ T cells) and persisted in chronic and cART-suppressed infection. Productively infected cells actively transcribing viral mRNA, by contrast, were much more labile and declined substantially between acute and chronic or cART-suppressed infection. Expression of most surface proteins and host genes was similar between latently infected cells and uninfected cells. Elevated FLIP mRNA and surface CD3 expression among latently infected cells suggest increased survival potential and capacity to respond to T cell receptor stimulation. These findings point to a large pool of latently infected CD4+ T cells established very early in acute infection and upregulated host factors that may facilitate their persistence in vivo, both of which pose potential challenges to eliminating HIV-1 reservoirs. IMPORTANCE Effective combination antiretroviral therapy controls HIV-1 infection but fails to eliminate latent viral reservoirs that give rise to viremia upon treatment interruption. Strategies to eradicate latently infected cells require a better understanding of their biology and distinguishing features to promote their elimination. Tools for studying these cells from patients are currently limited. Here, we developed a single-cell method to identify cells latently infected in vivo and to characterize these cells for expression of surface proteins and host genes without in vitro manipulation, capturing their in vivo state from SIV-infected macaques. Host factors involved in cell survival and proliferation were upregulated in latently infected cells, which were abundant in the earliest stages of acute infection. These studies provide insight into the basic biology of latently infected cells as well as potential mechanisms underlying the persistence of HIV-1/SIV reservoirs to inform development of novel HIV-1 cure strategies.
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Affiliation(s)
- Andrey Tokarev
- US Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, Maryland, USA
- The Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, Maryland, USA
| | - Kawthar Machmach
- US Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, Maryland, USA
- The Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, Maryland, USA
| | - Matthew Creegan
- US Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, Maryland, USA
- The Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, Maryland, USA
| | - Dohoon Kim
- US Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, Maryland, USA
- The Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, Maryland, USA
| | - Michael A. Eller
- US Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, Maryland, USA
- The Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, Maryland, USA
| | - Diane L. Bolton
- US Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, Maryland, USA
- The Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, Maryland, USA
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15
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Kreider EF, Bar KJ. HIV-1 Reservoir Persistence and Decay: Implications for Cure Strategies. Curr HIV/AIDS Rep 2022; 19:194-206. [PMID: 35404007 PMCID: PMC10443186 DOI: 10.1007/s11904-022-00604-2] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/25/2022] [Indexed: 02/06/2023]
Abstract
PURPOSE OF REVIEW Despite suppressive antiretroviral therapy (ART), a viral reservoir persists in individuals living with HIV that can reignite systemic replication should treatment be interrupted. Understanding how HIV-1 persists through effective ART is essential to develop cure strategies to induce ART-free virus remission. RECENT FINDINGS The HIV-1 reservoir resides in a pool of CD4-expressing cells as a range of viral species, a subset of which is genetically intact. Recent studies suggest that the reservoir on ART is highly dynamic, with expansion and contraction of virus-infected cells over time. Overall, the intact proviral reservoir declines faster than defective viruses, suggesting enhanced immune clearance or cellular turnover. Upon treatment interruption, rebound viruses demonstrate escape from adaptive and innate immune responses, implicating these selective pressures in restriction of virus reactivation. Cure strategies employing immunotherapy are poised to test whether host immune pressure can be augmented to enhance reservoir suppression or clearance. Alternatively, genomic engineering approaches are being applied to directly eliminate intact viruses and shrink the replication-competent virus pool. New evidence suggests host immunity exerts selective pressure on reservoir viruses and clears HIV-1 infected cells over years on ART. Efforts to build on the detectable, but insufficient, reservoir clearance via empiric testing in clinical trials will inform our understanding of mechanisms of viral persistence and the direction of future cure strategies.
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Affiliation(s)
- Edward F Kreider
- Perelman School of Medicine, University of Pennsylvania, Stemmler Hall Room 130-150, 3450 Hamilton Walk, Philadelphia, PA, 19104-6073, USA
| | - Katharine J Bar
- Perelman School of Medicine, University of Pennsylvania, 502D Johnson Pavilion, 3610 Hamilton Walk, Philadelphia, PA, 19104‑0673, USA.
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16
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Ne E, Crespo R, Izquierdo-Lara R, Rao S, Koçer S, Górska A, van Staveren T, Kan TW, van de Vijver D, Dekkers D, Rokx C, Moulos P, Hatzis P, Palstra RJ, Demmers J, Mahmoudi T. Catchet-MS identifies IKZF1-targeting thalidomide analogues as novel HIV-1 latency reversal agents. Nucleic Acids Res 2022; 50:5577-5598. [PMID: 35640596 PMCID: PMC9177988 DOI: 10.1093/nar/gkac407] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2021] [Revised: 04/11/2022] [Accepted: 05/24/2022] [Indexed: 12/27/2022] Open
Abstract
A major pharmacological strategy toward HIV cure aims to reverse latency in infected cells as a first step leading to their elimination. While the unbiased identification of molecular targets physically associated with the latent HIV-1 provirus would be highly valuable to unravel the molecular determinants of HIV-1 transcriptional repression and latency reversal, due to technical limitations, this has been challenging. Here we use a dCas9 targeted chromatin and histone enrichment strategy coupled to mass spectrometry (Catchet-MS) to probe the differential protein composition of the latent and activated HIV-1 5′LTR. Catchet-MS identified known and novel latent 5′LTR-associated host factors. Among these, IKZF1 is a novel HIV-1 transcriptional repressor, required for Polycomb Repressive Complex 2 recruitment to the LTR. We find the clinically advanced thalidomide analogue iberdomide, and the FDA approved analogues lenalidomide and pomalidomide, to be novel LRAs. We demonstrate that, by targeting IKZF1 for degradation, these compounds reverse HIV-1 latency in CD4+ T-cells isolated from virally suppressed people living with HIV-1 and that they are able to synergize with other known LRAs.
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Affiliation(s)
- Enrico Ne
- Department of Biochemistry, Erasmus University Medical Center, Ee622 PO Box 2040, 3000CA Rotterdam, The Netherlands
| | - Raquel Crespo
- Department of Biochemistry, Erasmus University Medical Center, Ee622 PO Box 2040, 3000CA Rotterdam, The Netherlands
| | - Ray Izquierdo-Lara
- Department of Biochemistry, Erasmus University Medical Center, Ee622 PO Box 2040, 3000CA Rotterdam, The Netherlands
| | - Shringar Rao
- Department of Biochemistry, Erasmus University Medical Center, Ee622 PO Box 2040, 3000CA Rotterdam, The Netherlands
| | - Selin Koçer
- Department of Biochemistry, Erasmus University Medical Center, Ee622 PO Box 2040, 3000CA Rotterdam, The Netherlands
| | - Alicja Górska
- Department of Biochemistry, Erasmus University Medical Center, Ee622 PO Box 2040, 3000CA Rotterdam, The Netherlands
| | - Thomas van Staveren
- Department of Biochemistry, Erasmus University Medical Center, Ee622 PO Box 2040, 3000CA Rotterdam, The Netherlands
| | - Tsung Wai Kan
- Department of Biochemistry, Erasmus University Medical Center, Ee622 PO Box 2040, 3000CA Rotterdam, The Netherlands.,Department of Pathology, Erasmus University Medical Center, The Netherlands.,Department of Urology, Erasmus University Medical Center, The Netherlands
| | - David van de Vijver
- Department of Viroscience, Erasmus University Medical Center, The Netherlands
| | - Dick Dekkers
- Proteomics Center, Erasmus University Medical Center, Ee679a PO Box 2040, 3000CA Rotterdam, The Netherlands
| | - Casper Rokx
- Department of Internal Medicine, Section of Infectious Diseases, Erasmus University Medical Center, Rg-530, PO Box 2040, 3000CA Rotterdam, The Netherlands
| | - Panagiotis Moulos
- Institute for Fundamental Biomedical Research, Biomedical Sciences Research Center "Alexander Fleming", 16672, Vari, Greece
| | - Pantelis Hatzis
- Institute for Fundamental Biomedical Research, Biomedical Sciences Research Center "Alexander Fleming", 16672, Vari, Greece
| | - Robert-Jan Palstra
- Department of Biochemistry, Erasmus University Medical Center, Ee622 PO Box 2040, 3000CA Rotterdam, The Netherlands.,Department of Pathology, Erasmus University Medical Center, The Netherlands.,Department of Urology, Erasmus University Medical Center, The Netherlands
| | - Jeroen Demmers
- Proteomics Center, Erasmus University Medical Center, Ee679a PO Box 2040, 3000CA Rotterdam, The Netherlands
| | - Tokameh Mahmoudi
- Department of Biochemistry, Erasmus University Medical Center, Ee622 PO Box 2040, 3000CA Rotterdam, The Netherlands.,Department of Pathology, Erasmus University Medical Center, The Netherlands.,Department of Urology, Erasmus University Medical Center, The Netherlands
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17
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Astorga-Gamaza A, Grau-Expósito J, Burgos J, Navarro J, Curran A, Planas B, Suanzes P, Falcó V, Genescà M, Buzon M. Identification of HIV-reservoir cells with reduced susceptibility to antibody-dependent immune response. eLife 2022; 11:78294. [PMID: 35616530 PMCID: PMC9177146 DOI: 10.7554/elife.78294] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Accepted: 05/23/2022] [Indexed: 11/13/2022] Open
Abstract
HIV establishes a persistent infection in heterogeneous cell reservoirs, which can be maintained by different mechanisms including cellular proliferation, and represent the main obstacle to curing the infection. The expression of the Fcγ receptor CD32 has been identified as a marker of the active cell reservoirs in people on antiretroviral therapy, but if its expression has any role in conferring advantage for viral persistence is unknown. Here, we report that HIV-infected cells expressing CD32 have reduced susceptibility to natural killer (NK) antibody-dependent cell cytotoxicity (ADCC) by a mechanism compatible with the suboptimal binding of HIV-specific antibodies. Infected CD32 cells have increased proliferative capacity in the presence of immune complexes, and are more resistant to strategies directed to potentiate NK function. Remarkably, reactivation of the latent reservoir from antiretroviral-treated people living with HIV increases the pool of infected CD32 cells, which are largely resistant to the ADCC immune mechanism. Thus, we report the existence of reservoir cells that evade part of the NK immune response through the expression of CD32.
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Affiliation(s)
| | | | - Joaquín Burgos
- Infectious Disease Department, Vall d'Hebron Research Institute (VHIR)
| | - Jordi Navarro
- Infectious Disease Department, Vall d'Hebron Research Institute (VHIR)
| | - Adrià Curran
- Infectious Disease Department, Vall d'Hebron Research Institute (VHIR)
| | - Bibiana Planas
- Infectious Disease Department, Vall d'Hebron Research Institute (VHIR)
| | - Paula Suanzes
- Infectious Disease Department, Vall d'Hebron Research Institute (VHIR)
| | - Vicenç Falcó
- Infectious Disease Department, Vall d'Hebron Research Institute (VHIR)
| | - Meritxell Genescà
- Infectious Disease Department, Vall d'Hebron Research Institute (VHIR)
| | - Maria Buzon
- Infectious Disease Department, Vall d'Hebron Research Institute (VHIR)
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18
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Duette G, Hiener B, Morgan H, Mazur FG, Mathivanan V, Horsburgh BA, Fisher K, Tong O, Lee E, Ahn H, Shaik A, Fromentin R, Hoh R, Bacchus-Souffan C, Nasr N, Cunningham AL, Hunt PW, Chomont N, Turville SG, Deeks SG, Kelleher AD, Schlub TE, Palmer S. The HIV-1 proviral landscape reveals that Nef contributes to HIV-1 persistence in effector memory CD4+ T cells. J Clin Invest 2022; 132:154422. [PMID: 35133986 PMCID: PMC8970682 DOI: 10.1172/jci154422] [Citation(s) in RCA: 44] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2021] [Accepted: 02/02/2022] [Indexed: 11/17/2022] Open
Abstract
Despite long-term antiretroviral therapy (ART), HIV-1 persists within a reservoir of CD4+ T cells that contribute to viral rebound if treatment is interrupted. Identifying the cellular populations that contribute to the HIV-1 reservoir and understanding the mechanisms of viral persistence are necessary to achieve an effective cure. In this regard, through Full-Length Individual Proviral Sequencing, we observed that the HIV-1 proviral landscape was different and changed with time on ART across naive and memory CD4+ T cell subsets isolated from 24 participants. We found that the proportion of genetically intact HIV-1 proviruses was higher and persisted over time in effector memory CD4+ T cells when compared with naive, central, and transitional memory CD4+ T cells. Interestingly, we found that escape mutations remained stable over time within effector memory T cells during therapy. Finally, we provided evidence that Nef plays a role in the persistence of genetically intact HIV-1. These findings posit effector memory T cells as a key component of the HIV-1 reservoir and suggest Nef as an attractive therapeutic target.
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Affiliation(s)
- Gabriel Duette
- Centre for Virus Research, The Westmead Institute for Medical Research, Westmead, New South Wales, Australia.,Faculty of Medicine and Health, The University of Sydney, Sydney, New South Wales, Australia
| | - Bonnie Hiener
- Centre for Virus Research, The Westmead Institute for Medical Research, Westmead, New South Wales, Australia.,Faculty of Medicine and Health, The University of Sydney, Sydney, New South Wales, Australia
| | - Hannah Morgan
- Faculty of Medicine and Health, The University of Sydney, Sydney, New South Wales, Australia
| | - Fernando G. Mazur
- Post-graduation Program of Evolutionary Genetics and Molecular Biology, Federal University of São Carlos, São Carlos, Brazil
| | - Vennila Mathivanan
- The Kirby Institute, University of New South Wales, Sydney, New South Wales, Australia
| | - Bethany A. Horsburgh
- Centre for Virus Research, The Westmead Institute for Medical Research, Westmead, New South Wales, Australia
| | - Katie Fisher
- Centre for Virus Research, The Westmead Institute for Medical Research, Westmead, New South Wales, Australia.,Faculty of Medicine and Health, The University of Sydney, Sydney, New South Wales, Australia
| | - Orion Tong
- Centre for Virus Research, The Westmead Institute for Medical Research, Westmead, New South Wales, Australia
| | - Eunok Lee
- Centre for Virus Research, The Westmead Institute for Medical Research, Westmead, New South Wales, Australia.,Faculty of Medicine and Health, The University of Sydney, Sydney, New South Wales, Australia
| | - Haelee Ahn
- Division of Experimental Medicine, University of California, San Francisco, San Francisco, California, USA
| | - Ansari Shaik
- The Kirby Institute, University of New South Wales, Sydney, New South Wales, Australia
| | - Rémi Fromentin
- Centre de Recherche du Centre Hospitalier de l’Université de Montréal, Montreal, Quebec, Canada
| | - Rebecca Hoh
- Department of Medicine, University of California, San Francisco, San Francisco, California, USA
| | - Charline Bacchus-Souffan
- Division of Experimental Medicine, University of California, San Francisco, San Francisco, California, USA
| | - Najla Nasr
- Centre for Virus Research, The Westmead Institute for Medical Research, Westmead, New South Wales, Australia.,Faculty of Medicine and Health, The University of Sydney, Sydney, New South Wales, Australia
| | - Anthony L. Cunningham
- Centre for Virus Research, The Westmead Institute for Medical Research, Westmead, New South Wales, Australia.,Faculty of Medicine and Health, The University of Sydney, Sydney, New South Wales, Australia
| | - Peter W. Hunt
- Division of Experimental Medicine, University of California, San Francisco, San Francisco, California, USA
| | - Nicolas Chomont
- Centre de Recherche du Centre Hospitalier de l’Université de Montréal, Montreal, Quebec, Canada.,Department of Microbiology, Infectiology and Immunology, Université de Montréal, Montreal, Quebec, Canada
| | - Stuart G. Turville
- The Kirby Institute, University of New South Wales, Sydney, New South Wales, Australia
| | - Steven G. Deeks
- Department of Medicine, University of California, San Francisco, San Francisco, California, USA
| | - Anthony D. Kelleher
- The Kirby Institute, University of New South Wales, Sydney, New South Wales, Australia
| | - Timothy E. Schlub
- Faculty of Medicine and Health, The University of Sydney, Sydney, New South Wales, Australia
| | - Sarah Palmer
- Centre for Virus Research, The Westmead Institute for Medical Research, Westmead, New South Wales, Australia.,Faculty of Medicine and Health, The University of Sydney, Sydney, New South Wales, Australia
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19
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Salido J, Czernikier A, Trifone C, Polo ML, Figueroa MI, Urioste A, Cahn P, Sued O, Salomon H, Laufer N, Ghiglione Y, Turk G. Pre-cART Immune Parameters in People Living With HIV Might Help Predict CD8+ T-Cell Characteristics, Inflammation Levels, and Reservoir Composition After Effective cART. Pathog Immun 2022; 6:60-89. [PMID: 34988339 PMCID: PMC8714178 DOI: 10.20411/pai.v6i2.447] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Accepted: 08/22/2021] [Indexed: 01/09/2023] Open
Abstract
Background Combined antiretroviral treatment (cART) for HIV infection is highly effective in controlling viral replication. However, it cannot achieve a sterilizing cure. Several strategies have been proposed to achieve a functional cure, some of them based on immune-mediated clearing of persistently infected cells. Here, we aimed at identifying factors related to CD8TC and CD4TC quality before cART initiation that associate with the persistence of CD8TC antiviral response after cART, inflammation levels, and the size of the viral reservoir. Methods Samples from 25 persons living with HIV were obtained before and after (15 months) cART initiation. Phenotype and functionality of bulk and HIV-specific T cells were assayed by flow cytometry ex vivo or after expansion in pre-cART or post-cART samples, respectively. Cell-Associated (CA) HIV DNA (total and integrated) and RNA (unspliced [US] and multiple spliced [MS]) were quantitated by real-time PCR on post-cART samples. Post-cART plasma levels of CXCL10 (IP-10), soluble CD14 (sCD14) and soluble CD163 (sCD163) were measured by ELISA. Results Pre-cART phenotype of CD8TCs and magnitude and phenotype of HIV-specific response correlated with the phenotype and functionality of CD8TCs post-cART. Moreover, the phenotype of the CD8TCs pre-cART correlated with markers of HIV persistence and inflammation post-cART. Finally, exhaustion and differentiation of CD4TCs pre-cART were associated with the composition of the HIV reservoir post-cART and the level of inflammation. Conclusions Overall, this work provides data to help understand and identify parameters that could be used as markers in the development of immune-based functional HIV cure strategies.
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Affiliation(s)
- Jimena Salido
- Universidad de Buenos Aires, Facultad de Medicina, Departamento de Microbiología, Parasitología e Inmunología, Buenos Aires, Argentina.,CONICET - Universidad de Buenos Aires, Instituto de Investigaciones Biomédicas en Retrovirus y SIDA (INBIRS), Buenos Aires, Argentina
| | - Alejandro Czernikier
- CONICET - Universidad de Buenos Aires, Instituto de Investigaciones Biomédicas en Retrovirus y SIDA (INBIRS), Buenos Aires, Argentina.,Universidad de Buenos Aires, Facultad de Medicina, Buenos Aires, Argentina
| | - César Trifone
- CONICET - Universidad de Buenos Aires, Instituto de Investigaciones Biomédicas en Retrovirus y SIDA (INBIRS), Buenos Aires, Argentina.,Universidad de Buenos Aires, Facultad de Medicina, Buenos Aires, Argentina
| | - María Laura Polo
- CONICET - Universidad de Buenos Aires, Instituto de Investigaciones Biomédicas en Retrovirus y SIDA (INBIRS), Buenos Aires, Argentina.,Universidad de Buenos Aires, Facultad de Medicina, Buenos Aires, Argentina
| | | | - Alejandra Urioste
- CONICET - Universidad de Buenos Aires, Instituto de Investigaciones Biomédicas en Retrovirus y SIDA (INBIRS), Buenos Aires, Argentina.,Universidad de Buenos Aires, Facultad de Medicina, Buenos Aires, Argentina
| | - Pedro Cahn
- Fundación Huésped, Buenos Aires, Argentina
| | - Omar Sued
- Fundación Huésped, Buenos Aires, Argentina
| | - Horacio Salomon
- Universidad de Buenos Aires, Facultad de Medicina, Departamento de Microbiología, Parasitología e Inmunología, Buenos Aires, Argentina.,CONICET - Universidad de Buenos Aires, Instituto de Investigaciones Biomédicas en Retrovirus y SIDA (INBIRS), Buenos Aires, Argentina
| | - Natalia Laufer
- Universidad de Buenos Aires, Facultad de Medicina, Departamento de Microbiología, Parasitología e Inmunología, Buenos Aires, Argentina.,CONICET - Universidad de Buenos Aires, Instituto de Investigaciones Biomédicas en Retrovirus y SIDA (INBIRS), Buenos Aires, Argentina.,Hospital General de Agudos "Dr. JA Fernández" Buenos Aires, Argentina
| | - Yanina Ghiglione
- CONICET - Universidad de Buenos Aires, Instituto de Investigaciones Biomédicas en Retrovirus y SIDA (INBIRS), Buenos Aires, Argentina.,Universidad de Buenos Aires, Facultad de Medicina, Buenos Aires, Argentina
| | - Gabriela Turk
- Universidad de Buenos Aires, Facultad de Medicina, Departamento de Microbiología, Parasitología e Inmunología, Buenos Aires, Argentina.,CONICET - Universidad de Buenos Aires, Instituto de Investigaciones Biomédicas en Retrovirus y SIDA (INBIRS), Buenos Aires, Argentina
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20
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Dubé M, Kaufmann DE. Single-Cell Multiparametric Analysis of Rare HIV-Infected Cells Identified by Duplexed RNAflow-FISH. Methods Mol Biol 2022; 2407:291-313. [PMID: 34985672 DOI: 10.1007/978-1-0716-1871-4_20] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
HIV-infected cells are difficult to characterize in vivo because of their great paucity and their diversity. This chapter describes a duplexed flow cytometry method that enables detection, quantification and phenotyping of these rare cells at single-cell resolution. Primary CD4+ T cells are enriched from PBMCs, stained for surface and intracellular proteins and then subjected to fluorescent in situ hybridization to label viral RNA before acquisition on a flow cytometer. Technical and analytical advices are provided to improve the quality of the data. This flow cytometric RNA fluorescent in situ hybridization (RNAflow-FISH) procedure can be applied to the characterization of both HIV-infected cells from viremic people living with HIV and reactivated viral reservoirs from virally suppressed individuals on therapy.
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Affiliation(s)
- Mathieu Dubé
- Research Centre of the Centre Hospitalier de l'Université de Montréal (CRCHUM), Montréal, QC, Canada
| | - Daniel E Kaufmann
- Research Centre of the Centre Hospitalier de l'Université de Montréal (CRCHUM), Montréal, QC, Canada.
- Université de Montréal, Montreal, QC, Canada.
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21
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Atlas of the HIV-1 Reservoir in Peripheral CD4 T Cells of Individuals on Successful Antiretroviral Therapy. mBio 2021; 12:e0307821. [PMID: 34844430 PMCID: PMC8630536 DOI: 10.1128/mbio.03078-21] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Knowing the mechanisms that govern the persistence of infected CD4+ subpopulations could help us to design new therapies to cure HIV-1 infection. We evaluated the simultaneous distribution of the HIV-1 reservoir in 13 CD4+ subpopulations from 14 HIV-1-infected individuals on antiretroviral therapy to analyze its relationship with HIV-1 transcription, immune activation, and cell proliferation. A unique large blood donation was used to isolate CD4, CD4 resting (CD4r), CD4 activated (CD4a), T naive (TN), T stem cell memory (TSCM), T central memory (TCM), T transitional memory (TTM), T effector memory (TEM), circulating T follicular helper (cTFH), TCD20, TCD32, and resting memory TCD2high (rmTCD2high) cells. HIV-1 DNA measured by droplet digital PCR ranged from 3,636 copies/106 in TTM to 244 in peripheral blood mononuclear cells (PBMCs), with no subpopulation standing out for provirus enrichment. Importantly, all the subpopulations harbored intact provirus by intact provirus DNA assay (IPDA). TCD32, cTFH, and TTM had the highest levels of HIV-1 transcription measured by fluorescent in situ hybridization with flow cytometry (FISH/flow), but without reaching statistical differences. The subpopulations more enriched in provirus had a memory phenotype, were less activated (measured by CD38+/HLA-DR+), and expressed more programmed cell death 1 (PD-1). Conversely, subpopulations transcribing more HIV-1 RNA were not necessarily enriched in provirus and were more activated (measured by CD38+/HLA-DR+) and more proliferative (measured by Ki-67). In conclusion, the HIV reservoir is composed of a mosaic of subpopulations contributing to the HIV-1 persistence through different mechanisms such as susceptibility to infection, provirus intactness, or transcriptional status. The narrow range of reservoir differences between the different blood cell subsets tested suggests limited efficacy in targeting only specific cell subpopulations during HIV-1 cure strategies. IMPORTANCE The main barrier for HIV-1 cure is the presence of latently infected CD4+ T cells. Although various cell subpopulations have been identified as major HIV-1 reservoir cells, the relative contribution of infected CD4 subpopulations in the HIV-1 reservoir remains largely unknown. Here, we evaluated the simultaneous distribution of the HIV-1 reservoir in 13 CD4+ T-cell subpopulations in peripheral blood from HIV-1-infected individuals under suppressive antiretroviral therapy. We found that the HIV-1 reservoir is composed of a mosaic of cell subpopulations, with heterogeneous proviral DNA, HIV-1 transcription, and activation status. Hence, each cell subpopulation contributes to the HIV-1 persistence through different mechanisms such as susceptibility to infection, rates of intact provirus, transcriptional status or half-life. This research provides new insights into the composition of the HIV-1 reservoir, suggesting that, to be effective, eradication strategies must simultaneously target multiple cell subpopulations.
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22
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Lau CY, Adan MA, Maldarelli F. Why the HIV Reservoir Never Runs Dry: Clonal Expansion and the Characteristics of HIV-Infected Cells Challenge Strategies to Cure and Control HIV Infection. Viruses 2021; 13:2512. [PMID: 34960781 PMCID: PMC8708047 DOI: 10.3390/v13122512] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Revised: 11/22/2021] [Accepted: 11/27/2021] [Indexed: 12/13/2022] Open
Abstract
Antiretroviral therapy (ART) effectively reduces cycles of viral replication but does not target proviral populations in cells that persist for prolonged periods and that can undergo clonal expansion. Consequently, chronic human immunodeficiency virus (HIV) infection is sustained during ART by a reservoir of long-lived latently infected cells and their progeny. This proviral landscape undergoes change over time on ART. One of the forces driving change in the landscape is the clonal expansion of infected CD4 T cells, which presents a key obstacle to HIV eradication. Potential mechanisms of clonal expansion include general immune activation, antigenic stimulation, homeostatic proliferation, and provirus-driven clonal expansion, each of which likely contributes in varying, and largely unmeasured, amounts to maintaining the reservoir. The role of clinical events, such as infections or neoplasms, in driving these mechanisms remains uncertain, but characterizing these forces may shed light on approaches to effectively eradicate HIV. A limited number of individuals have been cured of HIV infection in the setting of bone marrow transplant; information from these and other studies may identify the means to eradicate or control the virus without ART. In this review, we describe the mechanisms of HIV-1 persistence and clonal expansion, along with the attempts to modify these factors as part of reservoir reduction and cure strategies.
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Affiliation(s)
- Chuen-Yen Lau
- HIV Dynamics and Replication Program, NCI, NIH, Bethesda, MD 20892, USA; (C.-Y.L.); (M.A.A.)
| | - Matthew A. Adan
- HIV Dynamics and Replication Program, NCI, NIH, Bethesda, MD 20892, USA; (C.-Y.L.); (M.A.A.)
- Vagelos College of Physicians & Surgeons, Columbia University, New York, NY 10032, USA
| | - Frank Maldarelli
- HIV Dynamics and Replication Program, NCI, NIH, Bethesda, MD 20892, USA; (C.-Y.L.); (M.A.A.)
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23
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Freen-van Heeren JJ. Flow-FISH as a Tool for Studying Bacteria, Fungi and Viruses. BIOTECH 2021; 10:21. [PMID: 35822795 PMCID: PMC9245478 DOI: 10.3390/biotech10040021] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2021] [Revised: 10/03/2021] [Accepted: 10/08/2021] [Indexed: 12/20/2022] Open
Abstract
Many techniques are currently in use to study microbes. These can be aimed at detecting, identifying, and characterizing bacterial, fungal, and viral species. One technique that is suitable for high-throughput analysis is flow cytometry-based fluorescence in situ hybridization, or Flow-FISH. This technique employs (fluorescently labeled) probes directed against DNA or (m)RNA, for instance targeting a gene or microorganism of interest and provides information on a single-cell level. Furthermore, by combining Flow-FISH with antibody-based protein detection, proteins of interest can be measured simultaneously with genetic material. Additionally, depending on the type of Flow-FISH assay, Flow-FISH can also be multiplexed, allowing for the simultaneous measurement of multiple gene targets and/or microorganisms. Together, this allows for, e.g., single-cell gene expression analysis or identification of (sub)strains in mixed cultures. Flow-FISH has been used in mammalian cells but has also been extensively employed to study diverse microbial species. Here, the use of Flow-FISH for studying microorganisms is reviewed. Specifically, the detection of (intracellular) pathogens, studying microorganism biology and disease pathogenesis, and identification of bacterial, fungal, and viral strains in mixed cultures is discussed, with a particular focus on the viruses EBV, HIV-1, and SARS-CoV-2.
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24
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Simonetti FR, Zhang H, Soroosh GP, Duan J, Rhodehouse K, Hill AL, Beg SA, McCormick K, Raymond HE, Nobles CL, Everett JK, Kwon KJ, White JA, Lai J, Margolick JB, Hoh R, Deeks SG, Bushman FD, Siliciano JD, Siliciano RF. Antigen-driven clonal selection shapes the persistence of HIV-1-infected CD4+ T cells in vivo. J Clin Invest 2021; 131:145254. [PMID: 33301425 DOI: 10.1172/jci145254] [Citation(s) in RCA: 103] [Impact Index Per Article: 34.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2020] [Accepted: 12/01/2020] [Indexed: 12/23/2022] Open
Abstract
Clonal expansion of infected CD4+ T cells is a major mechanism of HIV-1 persistence and a barrier to achieving a cure. Potential causes are homeostatic proliferation, effects of HIV-1 integration, and interaction with antigens. Here, we show that it is possible to link antigen responsiveness, the full proviral sequence, the integration site, and the T cell receptor β-chain (TCRβ) sequence to examine the role of recurrent antigenic exposure in maintaining the HIV-1 reservoir. We isolated CMV- and Gag-responding CD4+ T cells from 10 treated individuals. Proviral populations in CMV-responding cells were dominated by large clones, including clones harboring replication-competent proviruses. TCRβ repertoires showed high clonality driven by converging adaptive responses. Although some proviruses were in genes linked to HIV-1 persistence (BACH2, STAT5B, MKL1), the proliferation of infected cells under antigenic stimulation occurred regardless of the site of integration. Paired TCRβ and integration site analysis showed that infection could occur early or late in the course of a clone's response to antigen and could generate infected cell populations too large to be explained solely by homeostatic proliferation. Together, these findings implicate antigen-driven clonal selection as a major factor in HIV-1 persistence, a finding that will be a difficult challenge to eradication efforts.
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Affiliation(s)
- Francesco R Simonetti
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Hao Zhang
- Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA
| | - Garshasb P Soroosh
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Jiayi Duan
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Kyle Rhodehouse
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Alison L Hill
- Institute for Computational Medicine, Johns Hopkins University, Baltimore, Maryland, USA
| | - Subul A Beg
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Kevin McCormick
- Department of Microbiology, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, USA
| | - Hayley E Raymond
- Department of Microbiology, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, USA
| | - Christopher L Nobles
- Department of Microbiology, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, USA
| | - John K Everett
- Department of Microbiology, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, USA
| | - Kyungyoon J Kwon
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Jennifer A White
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Jun Lai
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Joseph B Margolick
- Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA
| | - Rebecca Hoh
- Division of HIV, Infectious Diseases, and Global Medicine, UCSF, San Francisco, California, USA
| | - Steven G Deeks
- Division of HIV, Infectious Diseases, and Global Medicine, UCSF, San Francisco, California, USA
| | - Frederic D Bushman
- Department of Microbiology, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, USA
| | - Janet D Siliciano
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Robert F Siliciano
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA.,Howard Hughes Medical Institute, Baltimore, Maryland, USA
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25
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Combined single-cell transcriptional, translational, and genomic profiling reveals HIV-1 reservoir diversity. Cell Rep 2021; 36:109643. [PMID: 34469719 DOI: 10.1016/j.celrep.2021.109643] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Revised: 06/11/2021] [Accepted: 08/09/2021] [Indexed: 11/24/2022] Open
Abstract
Although understanding the diversity of HIV-1 reservoirs is key to achieving a cure, their study at the single-cell level in primary samples remains challenging. We combine flow cytometric multiplexed fluorescent in situ RNA hybridization for different viral genes with HIV-1 p24 protein detection, cell phenotyping, and downstream near-full-length single-cell vDNA sequencing. Stimulation-induced viral RNA-positive (vRNA+) cells from viremic and antiretroviral-therapy (ART)-suppressed individuals differ in their ability to produce p24. In participants on ART, latency-reversing agents (LRAs) induce a wide variety of viral gene transcription and translation patterns with LRA class-specific differences in reactivation potency. Reactivated proviruses, including in p24+ cells, are mostly defective. Although LRAs efficiently induce transcription in all memory cell subsets, we observe induction of translation mostly in effector memory cells, rather than in the long-lived central memory pool. We identify HIV-1 clones with diverse transcriptional and translational patterns between individual cells, and this finding suggests that cell-intrinsic factors influence reservoir persistence and heterogeneity.
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26
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The active human immunodeficiency virus reservoir during antiretroviral therapy: emerging players in viral persistence. Curr Opin HIV AIDS 2021; 16:193-199. [PMID: 33973900 DOI: 10.1097/coh.0000000000000685] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
PURPOSE OF REVIEW To discuss the role of CD4+ T cells with active Human immunodeficiency virus (HIV), meaning infected cells with transcriptional and/or translational viral activity during antiretroviral therapy (ART), focusing on new technologies for its detection, potential cell markers for its characterization, and evidences on the contribution of the active HIV reservoir to long-term viral persistence. RECENT FINDINGS HIV-infected cells expressing viral ribonucleic acid are systematically detected in subjects on long-term ART. In recent years, powerful new tools have provided significant insights into the nature, quantification, and identification of cells with active HIV, including the identification of new cell markers, and the presence of viral activity in specific cell populations located in different cellular and anatomical compartments. Moreover, studies on viral sequence integrity have identified cell clones with intact viral genomes and active viral transcription that could potentially persist for years. Together, new investigations support the notion that the active reservoir could represent a relevant fraction of long-term infected cells, and therefore, the study of its cell sources and mechanisms of maintenance could represent a significant advance in our understanding of viral persistence and the development of new curative strategies. SUMMARY The presence of HIV-infected cells with viral expression during ART has been traditionally overlooked for years. Based on recent investigations, this active viral reservoir could play an important role in HIV persistence.
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Ismail SD, Pankrac J, Ndashimye E, Prodger JL, Abrahams MR, Mann JFS, Redd AD, Arts EJ. Addressing an HIV cure in LMIC. Retrovirology 2021; 18:21. [PMID: 34344423 PMCID: PMC8330180 DOI: 10.1186/s12977-021-00565-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2021] [Accepted: 07/19/2021] [Indexed: 12/15/2022] Open
Abstract
HIV-1 persists in infected individuals despite years of antiretroviral therapy (ART), due to the formation of a stable and long-lived latent viral reservoir. Early ART can reduce the latent reservoir and is associated with post-treatment control in people living with HIV (PLWH). However, even in post-treatment controllers, ART cessation after a period of time inevitably results in rebound of plasma viraemia, thus lifelong treatment for viral suppression is indicated. Due to the difficulties of sustained life-long treatment in the millions of PLWH worldwide, a cure is undeniably necessary. This requires an in-depth understanding of reservoir formation and dynamics. Differences exist in treatment guidelines and accessibility to treatment as well as social stigma between low- and-middle income countries (LMICs) and high-income countries. In addition, demographic differences exist in PLWH from different geographical regions such as infecting viral subtype and host genetics, which can contribute to differences in the viral reservoir between different populations. Here, we review topics relevant to HIV-1 cure research in LMICs, with a focus on sub-Saharan Africa, the region of the world bearing the greatest burden of HIV-1. We present a summary of ART in LMICs, highlighting challenges that may be experienced in implementing a HIV-1 cure therapeutic. Furthermore, we discuss current research on the HIV-1 latent reservoir in different populations, highlighting research in LMIC and gaps in the research that may facilitate a global cure. Finally, we discuss current experimental cure strategies in the context of their potential application in LMICs.
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Affiliation(s)
- Sherazaan D Ismail
- Division of Medical Virology, Department of Pathology, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, 7925, South Africa
| | - Joshua Pankrac
- Department of Microbiology and Immunology, Schulich School of Medicine and Dentistry, University of Western Ontario, London, ON, N6A5C1, Canada
| | - Emmanuel Ndashimye
- Department of Microbiology and Immunology, Schulich School of Medicine and Dentistry, University of Western Ontario, London, ON, N6A5C1, Canada
- Center for AIDS Research Uganda Laboratories, Joint Clinical Research Centre, Kampala, Uganda
| | - Jessica L Prodger
- Department of Microbiology and Immunology, Schulich School of Medicine and Dentistry, University of Western Ontario, London, ON, N6A5C1, Canada
- Department of Epidemiology and Biostatistics, Schulich School of Medicine and Dentistry, University of Western Ontario, London, ON, N6A 5C1, Canada
- Division of Infectious Diseases, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Melissa-Rose Abrahams
- Division of Medical Virology, Department of Pathology, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, 7925, South Africa
| | - Jamie F S Mann
- Department of Microbiology and Immunology, Schulich School of Medicine and Dentistry, University of Western Ontario, London, ON, N6A5C1, Canada
- Bristol Veterinary School, University of Bristol, Langford House, Langford, Bristol, BS40 5DU, UK
| | - Andrew D Redd
- Division of Medical Virology, Department of Pathology, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, 7925, South Africa
- Division of Infectious Diseases, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Laboratory of Immunoregulation, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD, USA
| | - Eric J Arts
- Department of Microbiology and Immunology, Schulich School of Medicine and Dentistry, University of Western Ontario, London, ON, N6A5C1, Canada.
- Division of Infectious Diseases, Department of Medicine, Case Western Reserve University, Cleveland, OH, 44106, USA.
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28
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Brandt L, Cristinelli S, Ciuffi A. Single-Cell Analysis Reveals Heterogeneity of Virus Infection, Pathogenicity, and Host Responses: HIV as a Pioneering Example. Annu Rev Virol 2021; 7:333-350. [PMID: 32991268 DOI: 10.1146/annurev-virology-021820-102458] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
While analyses of cell populations provide averaged information about viral infections, single-cell analyses offer individual consideration, thereby revealing a broad spectrum of diversity as well as identifying extreme phenotypes that can be exploited to further understand the complex virus-host interplay. Single-cell technologies applied in the context of human immunodeficiency virus (HIV) infection proved to be valuable tools to help uncover specific biomarkers as well as novel candidate players in virus-host interactions. This review aims at providing an updated overview of single-cell analyses in the field of HIV and acquired knowledge on HIV infection, latency, and host response. Although HIV is a pioneering example, similar single-cell approaches have proven to be valuable for elucidating the behavior and virus-host interplay in a range of other viruses.
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Affiliation(s)
- Ludivine Brandt
- Institute of Microbiology, Lausanne University Hospital, University of Lausanne, 1011 Lausanne, Switzerland;
| | - Sara Cristinelli
- Institute of Microbiology, Lausanne University Hospital, University of Lausanne, 1011 Lausanne, Switzerland;
| | - Angela Ciuffi
- Institute of Microbiology, Lausanne University Hospital, University of Lausanne, 1011 Lausanne, Switzerland;
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29
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Cole B, Lambrechts L, Gantner P, Noppe Y, Bonine N, Witkowski W, Chen L, Palmer S, Mullins JI, Chomont N, Pardons M, Vandekerckhove L. In-depth single-cell analysis of translation-competent HIV-1 reservoirs identifies cellular sources of plasma viremia. Nat Commun 2021; 12:3727. [PMID: 34140517 PMCID: PMC8211655 DOI: 10.1038/s41467-021-24080-1] [Citation(s) in RCA: 39] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2021] [Accepted: 05/22/2021] [Indexed: 02/07/2023] Open
Abstract
Clonal expansion of HIV-infected cells contributes to the long-term persistence of the HIV reservoir in ART-suppressed individuals. However, the contribution from cell clones that harbor inducible proviruses to plasma viremia is poorly understood. Here, we describe a single-cell approach to simultaneously sequence the TCR, integration sites and proviral genomes from translation-competent reservoir cells, called STIP-Seq. By applying this approach to blood samples from eight participants, we show that the translation-competent reservoir mainly consists of proviruses with short deletions at the 5'-end of the genome, often involving the major splice donor site. TCR and integration site sequencing reveal that cell clones with predicted pathogen-specificity can harbor inducible proviruses integrated into cancer-related genes. Furthermore, we find several matches between proviruses retrieved with STIP-Seq and plasma viruses obtained during ART and upon treatment interruption, suggesting that STIP-Seq can capture clones that are responsible for low-level viremia or viral rebound.
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Affiliation(s)
- Basiel Cole
- HIV Cure Research Center, Department of Internal Medicine and Pediatrics, Ghent University Hospital, Ghent University, Ghent, Belgium
| | - Laurens Lambrechts
- HIV Cure Research Center, Department of Internal Medicine and Pediatrics, Ghent University Hospital, Ghent University, Ghent, Belgium
- BioBix, Department of Data Analysis and Mathematical Modelling, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium
| | - Pierre Gantner
- Department of Microbiology, Infectiology and Immunology, Université de Montréal, Montreal, QC, Canada
| | - Ytse Noppe
- HIV Cure Research Center, Department of Internal Medicine and Pediatrics, Ghent University Hospital, Ghent University, Ghent, Belgium
| | - Noah Bonine
- HIV Cure Research Center, Department of Internal Medicine and Pediatrics, Ghent University Hospital, Ghent University, Ghent, Belgium
- BioBix, Department of Data Analysis and Mathematical Modelling, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium
| | - Wojciech Witkowski
- HIV Cure Research Center, Department of Internal Medicine and Pediatrics, Ghent University Hospital, Ghent University, Ghent, Belgium
| | - Lennie Chen
- Department of Microbiology, University of Washington, Seattle, WA, USA
| | - Sarah Palmer
- Centre for Virus Research, The Westmead Institute for Medical Research, The University of Sydney, Sydney, NSW, Australia
| | - James I Mullins
- Department of Microbiology, University of Washington, Seattle, WA, USA
- Department of Medicine, University of Washington, Seattle, WA, USA
- Department of Global Health, University of Washington, Seattle, WA, USA
| | - Nicolas Chomont
- Department of Microbiology, Infectiology and Immunology, Université de Montréal, Montreal, QC, Canada
- Centre de Recherche du Centre Hospitalier de l'Université de Montréal, Montreal, QC, Canada
| | - Marion Pardons
- HIV Cure Research Center, Department of Internal Medicine and Pediatrics, Ghent University Hospital, Ghent University, Ghent, Belgium
| | - Linos Vandekerckhove
- HIV Cure Research Center, Department of Internal Medicine and Pediatrics, Ghent University Hospital, Ghent University, Ghent, Belgium.
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30
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Freen-van Heeren JJ. Addressing HIV-1 latency with Flow-FISH: Finding, characterizing and targeting HIV-1 infected cells. Cytometry A 2021; 99:861-865. [PMID: 34018663 DOI: 10.1002/cyto.a.24462] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2021] [Revised: 04/28/2021] [Accepted: 05/11/2021] [Indexed: 11/11/2022]
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Selective cell death in HIV-1-infected cells by DDX3 inhibitors leads to depletion of the inducible reservoir. Nat Commun 2021; 12:2475. [PMID: 33931637 PMCID: PMC8087668 DOI: 10.1038/s41467-021-22608-z] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2020] [Accepted: 03/15/2021] [Indexed: 02/02/2023] Open
Abstract
An innovative approach to eliminate HIV-1-infected cells emerging out of latency, the major hurdle to HIV-1 cure, is to pharmacologically reactivate viral expression and concomitantly trigger intracellular pro-apoptotic pathways in order to selectively induce cell death (ICD) of infected cells, without reliance on the extracellular immune system. In this work, we demonstrate the effect of DDX3 inhibitors on selectively inducing cell death in latent HIV-1-infected cell lines, primary CD4+ T cells and in CD4+ T cells from cART-suppressed people living with HIV-1 (PLWHIV). We used single-cell FISH-Flow technology to characterise the contribution of viral RNA to inducing cell death. The pharmacological targeting of DDX3 induced HIV-1 RNA expression, resulting in phosphorylation of IRF3 and upregulation of IFNβ. DDX3 inhibition also resulted in the downregulation of BIRC5, critical to cell survival during HIV-1 infection, and selectively induced apoptosis in viral RNA-expressing CD4+ T cells but not bystander cells. DDX3 inhibitor treatment of CD4+ T cells from PLWHIV resulted in an approximately 50% reduction of the inducible latent HIV-1 reservoir by quantitation of HIV-1 RNA, by FISH-Flow, RT-qPCR and TILDA. This study provides proof of concept for pharmacological reversal of latency coupled to induction of apoptosis towards the elimination of the inducible reservoir.
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32
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Rossi A, Pacella I, Piconese S. RNA Flow Cytometry for the Study of T Cell Metabolism. Int J Mol Sci 2021; 22:ijms22083906. [PMID: 33918901 PMCID: PMC8069477 DOI: 10.3390/ijms22083906] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2021] [Revised: 04/06/2021] [Accepted: 04/07/2021] [Indexed: 12/30/2022] Open
Abstract
T cells undergo activation and differentiation programs along a continuum of states that can be tracked through flow cytometry using a combination of surface and intracellular markers. Such dynamic behavior is the result of transcriptional and post-transcriptional events, initiated and sustained by the activation of specific transcription factors and by epigenetic remodeling. These signaling pathways are tightly integrated with metabolic routes in a bidirectional manner: on the one hand, T cell receptors and costimulatory molecules activate metabolic reprogramming; on the other hand, metabolites modify T cell transcriptional programs and functions. Flow cytometry represents an invaluable tool to analyze the integration of phenotypical, functional, metabolic and transcriptional features, at the single cell level in heterogeneous T cell populations, and from complex microenvironments, with potential clinical application in monitoring the efficacy of cancer immunotherapy. Here, we review the most recent advances in flow cytometry-based analysis of gene expression, in combination with indicators of mitochondrial activity, with the aim of revealing and characterizing major metabolic pathways in T cells.
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Affiliation(s)
- Alessandra Rossi
- Department of Internal Clinical Sciences, Anaesthesiology and Cardiovascular Sciences, Sapienza University of Rome, 00161 Roma, Italy; (A.R.); (I.P.)
| | - Ilenia Pacella
- Department of Internal Clinical Sciences, Anaesthesiology and Cardiovascular Sciences, Sapienza University of Rome, 00161 Roma, Italy; (A.R.); (I.P.)
| | - Silvia Piconese
- Department of Internal Clinical Sciences, Anaesthesiology and Cardiovascular Sciences, Sapienza University of Rome, 00161 Roma, Italy; (A.R.); (I.P.)
- Istituto Pasteur Italia-Fondazione Cenci Bolognetti, 00161 Roma, Italy
- Correspondence:
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33
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Darcis G, Kootstra NA, Hooibrink B, van Montfort T, Maurer I, Groen K, Jurriaans S, Bakker M, van Lint C, Berkhout B, Pasternak AO. CD32 +CD4 + T Cells Are Highly Enriched for HIV DNA and Can Support Transcriptional Latency. Cell Rep 2021; 30:2284-2296.e3. [PMID: 32075737 PMCID: PMC7050565 DOI: 10.1016/j.celrep.2020.01.071] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2019] [Revised: 11/25/2019] [Accepted: 01/21/2020] [Indexed: 02/07/2023] Open
Abstract
The HIV latent reservoir forms the major hurdle to an HIV cure. The discovery of CD32 as marker of this reservoir has aroused much interest, but subsequent reports have challenged this finding. Here, we observe a positive correlation between the percentages of CD32+ cells among CD4+ T cells of aviremic cART-treated, HIV-infected individuals and their HIV DNA loads in peripheral blood. Moreover, optimization of the CD32+CD4+ T cell purification protocol reveals prominent enrichment for HIV DNA (mean, 292-fold) in these cells. However, no enrichment for HIV RNA is observed in CD32+CD4+ cells, yielding significantly reduced HIV RNA/DNA ratios. Furthermore, HIV proviruses in CD32+CD4+ cells can be reactivated ex vivo to produce virus, strongly suggesting that these cells support HIV transcriptional latency. Our results underscore the importance of isolating pure, bona fide CD32+CD4+ T cells for future studies and indicate that CD32 remains a promising candidate marker of the HIV reservoir.
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Affiliation(s)
- Gilles Darcis
- Laboratory of Experimental Virology, Department of Medical Microbiology, Amsterdam UMC, University of Amsterdam, Amsterdam, the Netherlands; Infectious Diseases Department, Liège University Hospital, Liège, Belgium.
| | - Neeltje A Kootstra
- Laboratory of Viral Immune Pathogenesis, Department of Experimental Immunology, Amsterdam UMC, University of Amsterdam, Amsterdam, the Netherlands
| | - Berend Hooibrink
- Department of Cell Biology, Amsterdam UMC, University of Amsterdam, Amsterdam, the Netherlands
| | - Thijs van Montfort
- Laboratory of Experimental Virology, Department of Medical Microbiology, Amsterdam UMC, University of Amsterdam, Amsterdam, the Netherlands
| | - Irma Maurer
- Laboratory of Viral Immune Pathogenesis, Department of Experimental Immunology, Amsterdam UMC, University of Amsterdam, Amsterdam, the Netherlands
| | - Kevin Groen
- Laboratory of Experimental Virology, Department of Medical Microbiology, Amsterdam UMC, University of Amsterdam, Amsterdam, the Netherlands
| | - Suzanne Jurriaans
- Laboratory of Clinical Virology, Department of Medical Microbiology, Amsterdam UMC, University of Amsterdam, Amsterdam, the Netherlands
| | - Margreet Bakker
- Laboratory of Experimental Virology, Department of Medical Microbiology, Amsterdam UMC, University of Amsterdam, Amsterdam, the Netherlands
| | - Carine van Lint
- Service of Molecular Virology, Département de Biologie Moléculaire (DBM), Université Libre de Bruxelles (ULB), Gosselies, Belgium
| | - Ben Berkhout
- Laboratory of Experimental Virology, Department of Medical Microbiology, Amsterdam UMC, University of Amsterdam, Amsterdam, the Netherlands
| | - Alexander O Pasternak
- Laboratory of Experimental Virology, Department of Medical Microbiology, Amsterdam UMC, University of Amsterdam, Amsterdam, the Netherlands.
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34
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Fromentin R, Chomont N. HIV persistence in subsets of CD4+ T cells: 50 shades of reservoirs. Semin Immunol 2021; 51:101438. [PMID: 33272901 PMCID: PMC8164644 DOI: 10.1016/j.smim.2020.101438] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/18/2020] [Accepted: 11/19/2020] [Indexed: 12/16/2022]
Abstract
Antiretroviral therapy controls HIV replication but does not eliminate the virus from the infected host. The persistence of a small pool of cells harboring integrated and replication-competent HIV genomes impedes viral eradication efforts. The HIV reservoir was originally described as a relatively homogeneous pool of resting memory CD4+ T cells. Over the past 20 years, the identification of multiple cellular subsets of CD4+ T cells endowed with distinct biological properties shed new lights on the heterogeneity of HIV reservoirs. It is now clear that HIV persists in a large variety of CD4+ T cells, which contribute to HIV persistence through different mechanisms. In this review, we summarize recent findings indicating that specific biological features of well-characterized subsets of CD4+ T cells individually contribute to the persistence of HIV. These include an increased sensitivity to HIV infection, specific tissue locations, enhanced survival and heightened capacity to proliferate. We also discuss the relative abilities of these cellular reservoirs to contribute to viral rebound upon ART interruption. Together, these findings reveal that the HIV reservoir is not homogeneous and should be viewed as a mosaic of multiple cell types that all contribute to HIV persistence through different mechanisms.
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Affiliation(s)
- Rémi Fromentin
- Centre de Recherche du Centre Hospitalier de l'Université de Montréal, Montreal, Quebec, Canada
| | - Nicolas Chomont
- Centre de Recherche du Centre Hospitalier de l'Université de Montréal, Montreal, Quebec, Canada; Department of Microbiology, Infectiology and Immunology, Université de Montréal, Montreal, Quebec, Canada.
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35
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Venanzi Rullo E, Pinzone MR, Cannon L, Weissman S, Ceccarelli M, Zurakowski R, Nunnari G, O'Doherty U. Persistence of an intact HIV reservoir in phenotypically naive T cells. JCI Insight 2020; 5:133157. [PMID: 33055422 PMCID: PMC7605525 DOI: 10.1172/jci.insight.133157] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2019] [Accepted: 09/10/2020] [Indexed: 12/25/2022] Open
Abstract
Despite the efficacy of antiretroviral therapy (ART), HIV persists in a latent form and remains a hurdle to eradication. CD4+ T lymphocytes harbor the majority of the HIV reservoir, but the role of individual subsets remains unclear. CD4+ T cells were sorted into central, transitional, effector memory, and naive T cells. We measured HIV DNA and performed proviral sequencing of more than 1900 proviruses in 2 subjects at 2 and 9 years after ART initiation to estimate the contribution of each subset to the reservoir. Although our study was limited to 2 subjects, we obtained comparable findings with publicly available sequences. While the HIV integration levels were lower in naive compared with memory T cells, naive cells were a major contributor to the intact proviral reservoir. Notably, proviral sequences isolated from naive cells appeared to be unique, while those retrieved from effector memory cells were mainly clonal. The number of clones increased as cells differentiated from a naive to an effector memory phenotype, suggesting naive cells repopulate the effector memory reservoir as previously shown for central memory cells. Naive T cells contribute substantially to the intact HIV reservoir and represent a significant hurdle for HIV eradication.
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Affiliation(s)
- Emmanuele Venanzi Rullo
- Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA.,Department of Clinical and Experimental Medicine, Unit of Infectious Diseases, University of Messina, Messina, Italy
| | - Marilia Rita Pinzone
- Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - LaMont Cannon
- Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA.,Center for the Study of Biological Complexity, Virginia Commonwealth University, Virginia, USA
| | - Sam Weissman
- Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Manuela Ceccarelli
- Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA.,Department of Clinical and Experimental Medicine, Unit of Infectious Diseases, University of Messina, Messina, Italy
| | - Ryan Zurakowski
- Department of Biomedical Engineering, University of Delaware, Newark, Delaware, USA
| | - Giuseppe Nunnari
- Department of Clinical and Experimental Medicine, Unit of Infectious Diseases, University of Messina, Messina, Italy
| | - Una O'Doherty
- Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
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36
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Tuyishime M, Garrido C, Jha S, Moeser M, Mielke D, LaBranche C, Montefiori D, Haynes BF, Joseph S, Margolis DM, Ferrari G. Improved killing of HIV-infected cells using three neutralizing and non-neutralizing antibodies. J Clin Invest 2020; 130:5157-5170. [PMID: 32584790 PMCID: PMC7524508 DOI: 10.1172/jci135557] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2019] [Accepted: 06/24/2020] [Indexed: 02/06/2023] Open
Abstract
The correlation of HIV-specific antibody-dependent cellular cytotoxicity (ADCC) responses with protection from and delayed progression of HIV-1 infection provides a rationale to leverage ADCC-mediating antibodies for treatment purposes. We evaluated ADCC mediated by different combinations of 2 to 6 neutralizing and non-neutralizing anti-HIV-1 Envelope (Env) mAbs, using concentrations ≤ 1 μg/mL, to identify combinations effective at targeting latent reservoir HIV-1 viruses from 10 individuals. We found that within 2 hours, combinations of 3 mAbs mediated more than 30% killing of HIV-infected primary CD4+ T cells in the presence of autologous NK cells, with the combination of A32 (C1C2), DH511.2K3 (MPER), and PGT121 (V3) mAbs being the most effective. Increasing the incubation of target and effector cells in the presence of mAb combinations from 2 to 24 hours resulted in increased specific killing of infected cells, even with neutralization-resistant viruses. The same combination eliminated reactivated latently HIV-1-infected cells in an ex vivo quantitative viral outgrowth assay. Therefore, administration of a combination of 3 mAbs should be considered in planning in vivo studies seeking to eliminate persistently HIV-1-infected cells.
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Affiliation(s)
- Marina Tuyishime
- Department of Surgery, Duke University Medical Center, Durham, North Carolina, USA
| | | | - Shalini Jha
- Department of Surgery, Duke University Medical Center, Durham, North Carolina, USA
| | - Matt Moeser
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Dieter Mielke
- Department of Surgery, Duke University Medical Center, Durham, North Carolina, USA
| | - Celia LaBranche
- Department of Surgery, Duke University Medical Center, Durham, North Carolina, USA
| | - David Montefiori
- Department of Surgery, Duke University Medical Center, Durham, North Carolina, USA
| | - Barton F. Haynes
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, North Carolina, USA
- Department of Medicine and
- Department of Immunology, Duke University Medical Center, Durham, North Carolina, USA
| | - Sarah Joseph
- UNC HIV Cure Center and
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
- Department of Microbiology and Immunology and
| | - David M. Margolis
- UNC HIV Cure Center and
- Department of Microbiology and Immunology and
- Department of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Guido Ferrari
- Department of Surgery, Duke University Medical Center, Durham, North Carolina, USA
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, North Carolina, USA
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37
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Neidleman J, Luo X, Frouard J, Xie G, Hsiao F, Ma T, Morcilla V, Lee A, Telwatte S, Thomas R, Tamaki W, Wheeler B, Hoh R, Somsouk M, Vohra P, Milush J, James KS, Archin NM, Hunt PW, Deeks SG, Yukl SA, Palmer S, Greene WC, Roan NR. Phenotypic analysis of the unstimulated in vivo HIV CD4 T cell reservoir. eLife 2020; 9:e60933. [PMID: 32990219 PMCID: PMC7524554 DOI: 10.7554/elife.60933] [Citation(s) in RCA: 54] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2020] [Accepted: 08/28/2020] [Indexed: 02/07/2023] Open
Abstract
The latent reservoir is a major barrier to HIV cure. As latently infected cells cannot be phenotyped directly, the features of the in vivo reservoir have remained elusive. Here, we describe a method that leverages high-dimensional phenotyping using CyTOF to trace latently infected cells reactivated ex vivo to their original pre-activation states. Our results suggest that, contrary to common assumptions, the reservoir is not randomly distributed among cell subsets, and is remarkably conserved between individuals. However, reservoir composition differs between tissues and blood, as do cells successfully reactivated by different latency reversing agents. By selecting 8-10 of our 39 original CyTOF markers, we were able to isolate highly purified populations of unstimulated in vivo latent cells. These purified populations were highly enriched for replication-competent and intact provirus, transcribed HIV, and displayed clonal expansion. The ability to isolate unstimulated latent cells from infected individuals enables previously impossible studies on HIV persistence.
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Affiliation(s)
- Jason Neidleman
- Gladstone Institutes, San Francisco, United States
- Department of Urology, University of California, San Francisco, San Francisco, United States
| | - Xiaoyu Luo
- Gladstone Institutes, San Francisco, United States
| | - Julie Frouard
- Gladstone Institutes, San Francisco, United States
- Department of Urology, University of California, San Francisco, San Francisco, United States
| | - Guorui Xie
- Gladstone Institutes, San Francisco, United States
- Department of Urology, University of California, San Francisco, San Francisco, United States
| | - Feng Hsiao
- Gladstone Institutes, San Francisco, United States
- Department of Urology, University of California, San Francisco, San Francisco, United States
| | - Tongcui Ma
- Gladstone Institutes, San Francisco, United States
- Department of Urology, University of California, San Francisco, San Francisco, United States
| | - Vincent Morcilla
- Centre for Virus Research, the Westmead Institute for Medical Research, The University of Sydney, Sydney, Australia
| | - Ashley Lee
- Centre for Virus Research, the Westmead Institute for Medical Research, The University of Sydney, Sydney, Australia
| | - Sushama Telwatte
- San Francisco Veterans Affairs (VA) Medical Center and University of California, San Francisco, San Francisco, United States
| | | | - Whitney Tamaki
- Department of Medicine, University of California, San Francisco, San Francisco, United States
| | - Benjamin Wheeler
- Department of Medicine, University of California, San Francisco, San Francisco, United States
| | - Rebecca Hoh
- Division of HIV, Infectious Diseases and Global Medicine, University of California, San Francisco, San Francisco, United States
| | - Ma Somsouk
- Department of Medicine, Division of Gastroenterology, San Francisco General Hospital and University of California, San Francisco, San Francisco, United States
| | - Poonam Vohra
- Department of Pathology, University of California, San Francisco, San Francisco, United States
| | - Jeffrey Milush
- Department of Medicine, University of California, San Francisco, San Francisco, United States
| | - Katherine Sholtis James
- Division of Infectious Diseases, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, United States
| | - Nancie M Archin
- Division of Infectious Diseases, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, United States
| | - Peter W Hunt
- Division of Experimental Medicine, University of California, San Francisco, San Francisco, United States
| | - Steven G Deeks
- Division of HIV, Infectious Diseases and Global Medicine, University of California, San Francisco, San Francisco, United States
| | - Steven A Yukl
- San Francisco Veterans Affairs (VA) Medical Center and University of California, San Francisco, San Francisco, United States
| | - Sarah Palmer
- Centre for Virus Research, the Westmead Institute for Medical Research, The University of Sydney, Sydney, Australia
| | - Warner C Greene
- Gladstone Institutes, San Francisco, United States
- Department of Medicine, University of California, San Francisco, San Francisco, United States
| | - Nadia R Roan
- Gladstone Institutes, San Francisco, United States
- Department of Urology, University of California, San Francisco, San Francisco, United States
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38
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Lungu C, Procopio FA, Overmars RJ, Beerkens RJJ, Voermans JJC, Rao S, Prins HAB, Rokx C, Pantaleo G, van de Vijver DAMC, Mahmoudi T, Boucher CAB, Gruters RA, van Kampen JJA. Inter-Laboratory Reproducibility of Inducible HIV-1 Reservoir Quantification by TILDA. Viruses 2020; 12:v12090973. [PMID: 32887284 PMCID: PMC7552071 DOI: 10.3390/v12090973] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2020] [Revised: 08/29/2020] [Accepted: 08/31/2020] [Indexed: 12/16/2022] Open
Abstract
Substantial efforts to eliminate or reduce latent HIV-1 reservoirs are underway in clinical trials and have created a critical demand for sensitive, accurate, and reproducible tools to evaluate the efficacy of these strategies. Alternative reservoir quantification assays have been developed to circumvent limitations of the quantitative viral outgrowth assay. One such assay is tat/rev induced limiting dilution assay (TILDA), which measures the frequency of CD4+ T cells harboring inducible latent HIV-1 provirus. We modified pre-amplification reagents and conditions (TILDA v2.0) to improve assay execution and first internally validated assay performance using CD4+ T cells obtained from cART-suppressed HIV-1-infected individuals. Detection of tat/rev multiply spliced RNA was not altered by modifying pre-amplification conditions, confirming the robustness of the assay, and supporting the technique’s amenability to limited modifications to ensure better implementation for routine use in clinical studies of latent HIV-1 reservoirs. Furthermore, we cross-validated results of TILDA v2.0 and the original assay performed in two separate laboratories using samples from 15 HIV-1-infected individuals. TILDA and TILDA v2.0 showed a strong correlation (Lin’s Concordance Correlation Coefficient = 0.86). The low inter-laboratory variability between TILDAs performed at different institutes further supports use of TILDA for reservoir quantitation in multi-center interventional HIV-1 Cure trials.
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Affiliation(s)
- Cynthia Lungu
- Department of Viroscience, Erasmus University Medical Center, 3015 GD Rotterdam, The Netherlands; (R.J.O.); (R.J.J.B.); (J.J.C.V.); (D.A.M.C.v.d.V.); (C.A.B.B.); (R.A.G.); (J.J.A.v.K.)
- Correspondence:
| | - Francesco A. Procopio
- Service of Immunology and Allergy, Lausanne University Hospital, University of Lausanne, 1011 Lausanne, Switzerland; (F.A.P.); (G.P.)
| | - Ronald J. Overmars
- Department of Viroscience, Erasmus University Medical Center, 3015 GD Rotterdam, The Netherlands; (R.J.O.); (R.J.J.B.); (J.J.C.V.); (D.A.M.C.v.d.V.); (C.A.B.B.); (R.A.G.); (J.J.A.v.K.)
| | - Rob J. J. Beerkens
- Department of Viroscience, Erasmus University Medical Center, 3015 GD Rotterdam, The Netherlands; (R.J.O.); (R.J.J.B.); (J.J.C.V.); (D.A.M.C.v.d.V.); (C.A.B.B.); (R.A.G.); (J.J.A.v.K.)
| | - Jolanda J. C. Voermans
- Department of Viroscience, Erasmus University Medical Center, 3015 GD Rotterdam, The Netherlands; (R.J.O.); (R.J.J.B.); (J.J.C.V.); (D.A.M.C.v.d.V.); (C.A.B.B.); (R.A.G.); (J.J.A.v.K.)
| | - Shringar Rao
- Department of Biochemistry, Erasmus University Medical Center, 3015 GD Rotterdam, The Netherlands; (S.R.); (T.M.)
| | - Henrieke A. B. Prins
- Department of Internal Medicine, Section of Infectious Diseases, Erasmus University Medical Center, 3015 GD Rotterdam, The Netherlands; (H.A.B.P.); (C.R.)
| | - Casper Rokx
- Department of Internal Medicine, Section of Infectious Diseases, Erasmus University Medical Center, 3015 GD Rotterdam, The Netherlands; (H.A.B.P.); (C.R.)
| | - Giuseppe Pantaleo
- Service of Immunology and Allergy, Lausanne University Hospital, University of Lausanne, 1011 Lausanne, Switzerland; (F.A.P.); (G.P.)
| | - David A. M. C. van de Vijver
- Department of Viroscience, Erasmus University Medical Center, 3015 GD Rotterdam, The Netherlands; (R.J.O.); (R.J.J.B.); (J.J.C.V.); (D.A.M.C.v.d.V.); (C.A.B.B.); (R.A.G.); (J.J.A.v.K.)
| | - Tokameh Mahmoudi
- Department of Biochemistry, Erasmus University Medical Center, 3015 GD Rotterdam, The Netherlands; (S.R.); (T.M.)
| | - Charles A. B. Boucher
- Department of Viroscience, Erasmus University Medical Center, 3015 GD Rotterdam, The Netherlands; (R.J.O.); (R.J.J.B.); (J.J.C.V.); (D.A.M.C.v.d.V.); (C.A.B.B.); (R.A.G.); (J.J.A.v.K.)
| | - Rob A. Gruters
- Department of Viroscience, Erasmus University Medical Center, 3015 GD Rotterdam, The Netherlands; (R.J.O.); (R.J.J.B.); (J.J.C.V.); (D.A.M.C.v.d.V.); (C.A.B.B.); (R.A.G.); (J.J.A.v.K.)
| | - Jeroen J. A. van Kampen
- Department of Viroscience, Erasmus University Medical Center, 3015 GD Rotterdam, The Netherlands; (R.J.O.); (R.J.J.B.); (J.J.C.V.); (D.A.M.C.v.d.V.); (C.A.B.B.); (R.A.G.); (J.J.A.v.K.)
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39
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Abdel-Mohsen M, Richman D, Siliciano RF, Nussenzweig MC, Howell BJ, Martinez-Picado J, Chomont N, Bar KJ, Yu XG, Lichterfeld M, Alcami J, Hazuda D, Bushman F, Siliciano JD, Betts MR, Spivak AM, Planelles V, Hahn BH, Smith DM, Ho YC, Buzon MJ, Gaebler C, Paiardini M, Li Q, Estes JD, Hope TJ, Kostman J, Mounzer K, Caskey M, Fox L, Frank I, Riley JL, Tebas P, Montaner LJ. Recommendations for measuring HIV reservoir size in cure-directed clinical trials. Nat Med 2020; 26:1339-1350. [PMID: 32895573 PMCID: PMC7703694 DOI: 10.1038/s41591-020-1022-1] [Citation(s) in RCA: 83] [Impact Index Per Article: 20.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2020] [Accepted: 07/16/2020] [Indexed: 12/28/2022]
Abstract
Therapeutic strategies are being clinically tested either to eradicate latent HIV reservoirs or to achieve virologic control in the absence of antiretroviral therapy. Attaining this goal will require a consensus on how best to measure the numbers of persistently infected cells with the potential to cause viral rebound after antiretroviral-therapy cessation in assessing the results of cure-directed strategies in vivo. Current measurements assess various aspects of the HIV provirus and its functionality and produce divergent results. Here, we provide recommendations from the BEAT-HIV Martin Delaney Collaboratory on which viral measurements should be prioritized in HIV-cure-directed clinical trials.
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Affiliation(s)
| | - Douglas Richman
- VA San Diego Healthcare System and University of California, San Diego, CA, USA
| | | | | | | | - Javier Martinez-Picado
- IrsiCaixa AIDS Research Institute, Badalona, Spain
- University of Vic-Central University of Catalonia (UVic-UCC), Vic, Spain
- Catalan Institution for Research and Advanced Studies (ICREA), Barcelona, Spain
| | | | | | - Xu G Yu
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, USA
- Brigham and Women's Hospital, Boston, MA, USA
| | - Mathias Lichterfeld
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, USA
- Brigham and Women's Hospital, Boston, MA, USA
| | - Jose Alcami
- AIDS Immunopathogenesis Unit, Instituto de Salud Carlos III, Madrid and Infectious Diseases Unit, IBIDAPS, Hospital Clinic, University of Barcelona, Barcelona, Spain
| | | | | | | | | | | | | | | | - Davey M Smith
- VA San Diego Healthcare System and University of California, San Diego, CA, USA
| | - Ya-Chi Ho
- Yale School of Medicine, New Haven, CT, USA
| | - Maria J Buzon
- AIDS Immunopathogenesis Unit, Instituto de Salud Carlos III, Madrid and Infectious Diseases Unit, IBIDAPS, Hospital Clinic, University of Barcelona, Barcelona, Spain
| | | | - Mirko Paiardini
- Division of Microbiology and Immunology, Yerkes National Primate Research Center, and Emory University, Atlanta, GA, USA
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, GA, USA
| | - Qingsheng Li
- School of Biological Sciences and Nebraska Center for Virology, University of Nebraska-Lincoln, Lincoln, NE, USA
| | - Jacob D Estes
- Vaccine and Gene Therapy Institute and Oregon National Primate Research Center (ONPRC), Oregon Health and Science University (OHSU), Beaverton, OR, USA
| | | | - Jay Kostman
- Jonathan Lax Center, Philadelphia FIGHT, Philadelphia, PA, USA
| | - Karam Mounzer
- Jonathan Lax Center, Philadelphia FIGHT, Philadelphia, PA, USA
| | | | - Lawrence Fox
- Division of AIDS, NIAID, NIH, North Bethesda, MD, USA
| | - Ian Frank
- University of Pennsylvania, Philadelphia, PA, USA
| | | | - Pablo Tebas
- University of Pennsylvania, Philadelphia, PA, USA
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40
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The Role of Single-Cell Technology in the Study and Control of Infectious Diseases. Cells 2020; 9:cells9061440. [PMID: 32531928 PMCID: PMC7348906 DOI: 10.3390/cells9061440] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2020] [Revised: 06/03/2020] [Accepted: 06/05/2020] [Indexed: 02/07/2023] Open
Abstract
The advent of single-cell research in the recent decade has allowed biological studies at an unprecedented resolution and scale. In particular, single-cell analysis techniques such as Next-Generation Sequencing (NGS) and Fluorescence-Activated Cell Sorting (FACS) have helped show substantial links between cellular heterogeneity and infectious disease progression. The extensive characterization of genomic and phenotypic biomarkers, in addition to host-pathogen interactions at the single-cell level, has resulted in the discovery of previously unknown infection mechanisms as well as potential treatment options. In this article, we review the various single-cell technologies and their applications in the ongoing fight against infectious diseases, as well as discuss the potential opportunities for future development.
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41
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Thomas J, Ruggiero A, Paxton WA, Pollakis G. Measuring the Success of HIV-1 Cure Strategies. Front Cell Infect Microbiol 2020; 10:134. [PMID: 32318356 PMCID: PMC7154081 DOI: 10.3389/fcimb.2020.00134] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2020] [Accepted: 03/13/2020] [Indexed: 01/10/2023] Open
Abstract
HIV-1 eradication strategies aim to achieve viral remission in the absence of antiretroviral therapy (ART). The development of an HIV-1 cure remains challenging due to the latent reservoir (LR): long-lived CD4 T cells that harbor transcriptionally silent HIV-1 provirus. The LR is stable despite years of suppressive ART and is the source of rebound viremia following therapy interruption. Cure strategies such as "shock and kill" aim to eliminate or reduce the LR by reversing latency, exposing the infected cells to clearance via the immune response or the viral cytopathic effect. Alternative strategies include therapeutic vaccination, which aims to prime the immune response to facilitate control of the virus in the absence of ART. Despite promising advances, these strategies have been unable to significantly reduce the LR or increase the time to viral rebound but have provided invaluable insight in the field of HIV-1 eradication. The development and assessment of an HIV-1 cure requires robust assays that can measure the LR with sufficient sensitivity to detect changes that may occur following treatment. The viral outgrowth assay (VOA) is considered the gold standard method for LR quantification due to its ability to distinguish intact and defective provirus. However, the VOA is time consuming and resource intensive, therefore several alternative assays have been developed to bridge the gap between practicality and accuracy. Whilst a cure for HIV-1 infection remains elusive, recent advances in our understanding of the LR and methods for its eradication have offered renewed hope regarding achieving ART free viral remission.
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Affiliation(s)
- Jordan Thomas
- Department of Clinical Infection, Microbiology and Immunology, Institute of Infection and Global Health, University of Liverpool, Liverpool, United Kingdom
| | - Alessandra Ruggiero
- Department of Clinical Infection, Microbiology and Immunology, Institute of Infection and Global Health, University of Liverpool, Liverpool, United Kingdom.,Immune and Infectious Disease Division, Academic Department of Pediatrics (DPUO), Bambino Gesù Children's Hospital, Rome, Italy
| | - William A Paxton
- Department of Clinical Infection, Microbiology and Immunology, Institute of Infection and Global Health, University of Liverpool, Liverpool, United Kingdom
| | - Georgios Pollakis
- Department of Clinical Infection, Microbiology and Immunology, Institute of Infection and Global Health, University of Liverpool, Liverpool, United Kingdom
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42
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Real F, Capron C, Sennepin A, Arrigucci R, Zhu A, Sannier G, Zheng J, Xu L, Massé JM, Greffe S, Cazabat M, Donoso M, Delobel P, Izopet J, Eugenin E, Gennaro ML, Rouveix E, Cramer Bordé E, Bomsel M. Platelets from HIV-infected individuals on antiretroviral drug therapy with poor CD4+ T cell recovery can harbor replication-competent HIV despite viral suppression. Sci Transl Med 2020; 12:12/535/eaat6263. [DOI: 10.1126/scitranslmed.aat6263] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2018] [Revised: 07/23/2019] [Accepted: 10/01/2019] [Indexed: 12/24/2022]
Abstract
In addition to hemostasis, human platelets have several immune functions and interact with infectious pathogens including HIV in vitro. Here, we report that platelets from HIV-infected individuals on combined antiretroviral drug therapy (ART) with low blood CD4+ T cell counts (<350 cells/μl) contained replication-competent HIV despite viral suppression. In vitro, human platelets harboring HIV propagated the virus to macrophages, a process that could be prevented with the biologic abciximab, an anti–integrin αIIb/β3 Fab. Furthermore, in our cohort, 88% of HIV-infected individuals on ART with viral suppression and with platelets containing HIV were poor immunological responders with CD4+ T cell counts remaining below <350 cells/μl for more than one year. Our study suggests that platelets may be transient carriers of HIV and may provide an alternative pathway for HIV dissemination in HIV-infected individuals on ART with viral suppression and poor CD4+ T cell recovery.
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Affiliation(s)
- Fernando Real
- Mucosal Entry of HIV and Mucosal Immunity, Institut Cochin, Université de Paris, Paris, France
- INSERM U1016, Paris, France
- CNRS UMR8104, Paris, France
| | | | - Alexis Sennepin
- Mucosal Entry of HIV and Mucosal Immunity, Institut Cochin, Université de Paris, Paris, France
- INSERM U1016, Paris, France
- CNRS UMR8104, Paris, France
| | - Riccardo Arrigucci
- Public Health Research Institute, New Jersey Medical School, Rutgers, The State University of New Jersey, Newark, NJ, USA
| | - Aiwei Zhu
- Mucosal Entry of HIV and Mucosal Immunity, Institut Cochin, Université de Paris, Paris, France
- INSERM U1016, Paris, France
- CNRS UMR8104, Paris, France
| | - Gérémy Sannier
- Mucosal Entry of HIV and Mucosal Immunity, Institut Cochin, Université de Paris, Paris, France
- INSERM U1016, Paris, France
- CNRS UMR8104, Paris, France
| | - Jonathan Zheng
- Mucosal Entry of HIV and Mucosal Immunity, Institut Cochin, Université de Paris, Paris, France
- INSERM U1016, Paris, France
- CNRS UMR8104, Paris, France
| | - Lin Xu
- Mucosal Entry of HIV and Mucosal Immunity, Institut Cochin, Université de Paris, Paris, France
- INSERM U1016, Paris, France
- CNRS UMR8104, Paris, France
| | - Jean-Marc Massé
- INSERM U1016, Paris, France
- CNRS UMR8104, Paris, France
- Electron Microscopy Platform, Institut Cochin, Université de Paris, Paris, France
| | - Ségolène Greffe
- Department of Internal Medicine, Hôpital Ambroise Paré, Boulogne, France
| | - Michelle Cazabat
- CHU de Toulouse, Hôpital Purpan, Laboratoire de Virologie, Toulouse, France
| | - Maribel Donoso
- Department of Neuroscience, Cell Biology, and Anatomy, University of Texas Medical Branch (UTMB), Galveston, TX, USA
| | - Pierre Delobel
- INSERM U1043, Toulouse, France
- Université Toulouse III Paul-Sabatier, Faculté de Médecine Toulouse-Purpan, Toulouse, France
- CHU de Toulouse, Hôpital Purpan, Service des Maladies Infectieuses et Tropicales, Toulouse, France
| | - Jacques Izopet
- CHU de Toulouse, Hôpital Purpan, Laboratoire de Virologie, Toulouse, France
- INSERM U1043, Toulouse, France
- Université Toulouse III Paul-Sabatier, Faculté de Médecine Toulouse-Purpan, Toulouse, France
| | - Eliseo Eugenin
- Department of Neuroscience, Cell Biology, and Anatomy, University of Texas Medical Branch (UTMB), Galveston, TX, USA
| | - Maria Laura Gennaro
- Public Health Research Institute, New Jersey Medical School, Rutgers, The State University of New Jersey, Newark, NJ, USA
| | - Elisabeth Rouveix
- Department of Internal Medicine, Hôpital Ambroise Paré, Boulogne, France
| | - Elisabeth Cramer Bordé
- Mucosal Entry of HIV and Mucosal Immunity, Institut Cochin, Université de Paris, Paris, France
- INSERM U1016, Paris, France
- Hôpital Ambroise Paré, Boulogne-Billancourt, France
| | - Morgane Bomsel
- Mucosal Entry of HIV and Mucosal Immunity, Institut Cochin, Université de Paris, Paris, France
- INSERM U1016, Paris, France
- CNRS UMR8104, Paris, France
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43
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Sannier G, Dubé M, Kaufmann DE. Single-Cell Technologies Applied to HIV-1 Research: Reaching Maturity. Front Microbiol 2020; 11:297. [PMID: 32194526 PMCID: PMC7064469 DOI: 10.3389/fmicb.2020.00297] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Accepted: 02/10/2020] [Indexed: 12/11/2022] Open
Abstract
The need for definitive answers probably explains our natural tendency to seek simplicity. The reductionist “bulk” approach, in which a mean behavior is attributed to a heterogeneous cell population, fulfills this need by considerably helping the conceptualization of complex biological processes. However, the limits of this methodology are becoming increasingly clear as models seek to explain biological events occurring in vivo, where heterogeneity is the rule. Research in the HIV-1 field is no exception: the challenges encountered in the development of preventive and curative anti-HIV-1 strategies may well originate in part from inadequate assumptions built on bulk technologies, highlighting the need for new perspectives. The emergence of diverse single-cell technologies set the stage for potential breakthrough discoveries, as heterogeneous processes can now be investigated with an unprecedented depth in topics as diverse as HIV-1 tropism, dynamics of the replication cycle, latency, viral reservoirs and immune control. In this review, we summarize recent advances in the HIV-1 field made possible by single-cell technologies, and contextualize their importance.
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Affiliation(s)
- Gérémy Sannier
- Research Centre of the Centre Hospitalier de l'Université de Montréal (CRCHUM), Montreal, QC, Canada.,Department of Microbiology, Infectiology and Immunology, Université de Montréal, Montreal, QC, Canada
| | - Mathieu Dubé
- Research Centre of the Centre Hospitalier de l'Université de Montréal (CRCHUM), Montreal, QC, Canada
| | - Daniel E Kaufmann
- Research Centre of the Centre Hospitalier de l'Université de Montréal (CRCHUM), Montreal, QC, Canada.,Department of Medicine, Université de Montréal, Montreal, QC, Canada.,Consortium for HIV/AIDS Vaccine Development (Scripps CHAVD), La Jolla, CA, United States
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44
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Su H, Sravanam S, Gorantla S, Kaminski R, Khalili K, Poluektova L, Gendelman HE, Dash PK. Amplification of Replication Competent HIV-1 by Adoptive Transfer of Human Cells From Infected Humanized Mice. Front Cell Infect Microbiol 2020; 10:38. [PMID: 32117811 PMCID: PMC7026001 DOI: 10.3389/fcimb.2020.00038] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2019] [Accepted: 01/20/2020] [Indexed: 12/20/2022] Open
Abstract
Detection of latent human immunodeficiency virus type 1 (HIV-1) in "putative" infectious reservoirs is required for determining treatment efficiency and for viral elimination strategies. Such tests require induction of replication competent provirus and quantitative testing of viral load for validation. Recently, humanized mice were employed in the development of such tests by employing a murine viral outgrowth assay (mVOA). Here blood cells were recovered from virus infected antiretroviral therapy suppressed patients. These cells were adoptively transferred to uninfected humanized mice where replication competent virus was recovered. Prior reports supported the notion that an mVOA assay provides greater sensitivity than cell culture-based quantitative VOA tests for detection of latent virus. In the current study, the mVOA assays was adapted using donor human hematopoietic stem cells-reconstituted mice to affirm research into HIV-1 elimination. We simulated an antiretroviral therapy (ART)-treated virus-infected human by maintaining the infected humanized mice under suppressive treatment. This was operative prior to human cell adoptive transfers. Replication-competent HIV-1 was easily detected in recipient animals from donors with undetectable virus in plasma. Moreover, when the assay was used to investigate viral presence in tissue reservoirs, quantitative endpoints were determined in "putative" viral reservoirs not possible in human sample analyses. We conclude that adoptive transfer of cells between humanized mice is a sensitive and specific assay system for detection of replication competent latent HIV-1.
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Affiliation(s)
- Hang Su
- Department of Pharmacology and Experimental Neuroscience, College of Medicine, University of Nebraska Medical Center, Omaha, NE, United States
| | - Sruthi Sravanam
- Department of Pharmacology and Experimental Neuroscience, College of Medicine, University of Nebraska Medical Center, Omaha, NE, United States
| | - Santhi Gorantla
- Department of Pharmacology and Experimental Neuroscience, College of Medicine, University of Nebraska Medical Center, Omaha, NE, United States
| | - Rafal Kaminski
- Department of Neuroscience, Lewis Katz School of Medicine at Temple University, Philadelphia, PA, United States
| | - Kamel Khalili
- Department of Neuroscience, Lewis Katz School of Medicine at Temple University, Philadelphia, PA, United States
| | - Larisa Poluektova
- Department of Pharmacology and Experimental Neuroscience, College of Medicine, University of Nebraska Medical Center, Omaha, NE, United States
| | - Howard E. Gendelman
- Department of Pharmacology and Experimental Neuroscience, College of Medicine, University of Nebraska Medical Center, Omaha, NE, United States
- Department of Pharmaceutical Sciences, Center for Neurovirology, College of Pharmacy, University of Nebraska Medical Center, Omaha, NE, United States
| | - Prasanta K. Dash
- Department of Pharmacology and Experimental Neuroscience, College of Medicine, University of Nebraska Medical Center, Omaha, NE, United States
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45
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Bradley T, Ferrari G, Haynes BF, Margolis DM, Browne EP. Single-Cell Analysis of Quiescent HIV Infection Reveals Host Transcriptional Profiles that Regulate Proviral Latency. Cell Rep 2020; 25:107-117.e3. [PMID: 30282021 DOI: 10.1016/j.celrep.2018.09.020] [Citation(s) in RCA: 64] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2018] [Revised: 06/26/2018] [Accepted: 09/07/2018] [Indexed: 02/04/2023] Open
Abstract
A detailed understanding of the mechanisms that establish or maintain the latent reservoir of HIV will guide approaches to eliminate persistent infection. We used a cell line and primary cell models of HIV latency to investigate viral RNA (vRNA) expression and the role of the host transcriptome using single-cell approaches. Single-cell vRNA quantitation identified distinct populations of cells expressing various levels of vRNA, including completely silent populations. Strikingly, single-cell RNA-seq of latently infected primary cells demonstrated that HIV downregulation occurred in diverse transcriptomic environments but was significantly associated with expression of a specific set of cellular genes. In particular, latency was more frequent in cells expressing a transcriptional signature that included markers of naive and central memory T cells. These data reveal that expression of HIV proviruses within the latent reservoir are influenced by the host cell transcriptional program. Therapeutic modulation of these programs may reverse or enforce HIV latency.
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Affiliation(s)
- Todd Bradley
- Duke University, Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA
| | - Guido Ferrari
- Duke University, Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA
| | - Barton F Haynes
- Duke University, Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA
| | - David M Margolis
- UNC HIV Cure Center and Department of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Edward P Browne
- UNC HIV Cure Center and Department of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
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46
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Falcinelli SD, Ceriani C, Margolis DM, Archin NM. New Frontiers in Measuring and Characterizing the HIV Reservoir. Front Microbiol 2019; 10:2878. [PMID: 31921056 PMCID: PMC6930150 DOI: 10.3389/fmicb.2019.02878] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2019] [Accepted: 11/28/2019] [Indexed: 12/13/2022] Open
Abstract
A cure for HIV infection remains elusive due to the persistence of replication-competent HIV proviral DNA during suppressive antiretroviral therapy (ART). With the exception of rare elite or post-treatment controllers of viremia, withdrawal of ART invariably results in the rebound of viremia and progression of HIV disease. A thorough understanding of the reservoir is necessary to develop new strategies in order to reduce or eliminate the reservoir. However, there is significant heterogeneity in the sequence composition, genomic location, stability, and expression of the HIV reservoir both within and across individuals, and a majority of proviral sequences are replication-defective. These factors, and the low frequency of persistently infected cells in individuals on suppressive ART, make understanding the reservoir and its response to experimental reservoir reduction interventions challenging. Here, we review the characteristics of the HIV reservoir, state-of-the-art assays to measure and characterize the reservoir, and how these assays can be applied to accurately detect reductions in reservoir during efforts to develop a cure for HIV infection. In particular, we highlight recent advances in the development of direct measures of provirus, including intact proviral DNA assays and full-length HIV DNA sequencing with integration site analysis. We also focus on novel techniques to quantitate persistent and inducible HIV, including RNA sequencing and RNA/gag protein staining techniques, as well as modified viral outgrowth methods that seek to improve upon throughput, sensitivity and dynamic range.
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Affiliation(s)
- Shane D Falcinelli
- UNC HIV Cure Center, The University of North Carolina at Chapel Hill, Chapel Hill, NC, United States.,Department of Microbiology and Immunology, The University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Cristina Ceriani
- UNC HIV Cure Center, The University of North Carolina at Chapel Hill, Chapel Hill, NC, United States.,Department of Medicine, The University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - David M Margolis
- UNC HIV Cure Center, The University of North Carolina at Chapel Hill, Chapel Hill, NC, United States.,Department of Microbiology and Immunology, The University of North Carolina at Chapel Hill, Chapel Hill, NC, United States.,Department of Medicine, The University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Nancie M Archin
- UNC HIV Cure Center, The University of North Carolina at Chapel Hill, Chapel Hill, NC, United States.,Department of Medicine, The University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
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Development of C-TILDA: A modified TILDA method for reservoir quantification in long term treated patients infected with subtype C HIV-1. J Virol Methods 2019; 276:113778. [PMID: 31756409 DOI: 10.1016/j.jviromet.2019.113778] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2019] [Revised: 11/11/2019] [Accepted: 11/18/2019] [Indexed: 12/30/2022]
Abstract
A better characterization of the HIV reservoir is pivotal for the development of effective eradication strategies. Accurate quantification of the latent reservoir remains challenging. Starting from a regular blood draw, the Tat/Rev induced limiting dilution assay (TILDA) combines serial dilution of CD4+ T cells with a PCR-based detection of HIV-1 spliced mRNA produced upon cell stimulation. Here we adapted the original protocol for HIV-1 subtype B to detect tat/rev mRNAs transcribed from reactivated latently infected cells in long term suppressed patients infected with HIV-1 subtype C. Given the heterogeneity of global HIV epidemiology, it is pivotal to develop assays with optimal performances also in patients infected with non-B subtypes. We observed that, in these patients infected with subtype C virus, the HIV reservoir quantified by TILDA correlates with both the time of virological suppression and CD4/CD8 ratio.
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Visualization of Positive and Negative Sense Viral RNA for Probing the Mechanism of Direct-Acting Antivirals against Hepatitis C Virus. Viruses 2019; 11:v11111039. [PMID: 31717338 PMCID: PMC6893808 DOI: 10.3390/v11111039] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2019] [Revised: 11/03/2019] [Accepted: 11/07/2019] [Indexed: 12/14/2022] Open
Abstract
RNA viruses are highly successful pathogens and are the causative agents for many important diseases. To fully understand the replication of these viruses it is necessary to address the roles of both positive-strand RNA ((+)RNA) and negative-strand RNA ((−)RNA), and their interplay with viral and host proteins. Here we used branched DNA (bDNA) fluorescence in situ hybridization (FISH) to stain both the abundant (+)RNA and the far less abundant (−)RNA in both hepatitis C virus (HCV)- and Zika virus-infected cells, and combined these analyses with visualization of viral proteins through confocal imaging. We were able to phenotypically examine HCV-infected cells in the presence of uninfected cells and revealed the effect of direct-acting antivirals on HCV (+)RNA, (−)RNA, and protein, within hours of commencing treatment. Herein, we demonstrate that bDNA FISH is a powerful tool for the study of RNA viruses that can provide insights into drug efficacy and mechanism of action.
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Cantero-Pérez J, Grau-Expósito J, Serra-Peinado C, Rosero DA, Luque-Ballesteros L, Astorga-Gamaza A, Castellví J, Sanhueza T, Tapia G, Lloveras B, Fernández MA, Prado JG, Solé-Sedeno JM, Tarrats A, Lecumberri C, Mañalich-Barrachina L, Centeno-Mediavilla C, Falcó V, Buzon MJ, Genescà M. Resident memory T cells are a cellular reservoir for HIV in the cervical mucosa. Nat Commun 2019; 10:4739. [PMID: 31628331 PMCID: PMC6802119 DOI: 10.1038/s41467-019-12732-2] [Citation(s) in RCA: 68] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2019] [Accepted: 09/30/2019] [Indexed: 11/09/2022] Open
Abstract
HIV viral reservoirs are established very early during infection. Resident memory T cells (TRM) are present in tissues such as the lower female genital tract, but the contribution of this subset of cells to the pathogenesis and persistence of HIV remains unclear. Here, we show that cervical CD4+TRM display a unique repertoire of clusters of differentiation, with enrichment of several molecules associated with HIV infection susceptibility, longevity and self-renewing capacities. These protein profiles are enriched in a fraction of CD4+TRM expressing CD32. Cervical explant models show that CD4+TRM preferentially support HIV infection and harbor more viral DNA and protein than non-TRM. Importantly, cervical tissue from ART-suppressed HIV+ women contain high levels of viral DNA and RNA, being the TRM fraction the principal contributor. These results recognize the lower female genital tract as an HIV sanctuary and identify CD4+TRM as primary targets of HIV infection and viral persistence. Thus, strategies towards an HIV cure will need to consider TRM phenotypes, which are widely distributed in tissues.
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Affiliation(s)
- Jon Cantero-Pérez
- Infectious Diseases Department, Hospital Universitari Vall d'Hebron, Institut de Recerca (VHIR), Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Judith Grau-Expósito
- Infectious Diseases Department, Hospital Universitari Vall d'Hebron, Institut de Recerca (VHIR), Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Carla Serra-Peinado
- Infectious Diseases Department, Hospital Universitari Vall d'Hebron, Institut de Recerca (VHIR), Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Daniela A Rosero
- Infectious Diseases Department, Hospital Universitari Vall d'Hebron, Institut de Recerca (VHIR), Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Laura Luque-Ballesteros
- Infectious Diseases Department, Hospital Universitari Vall d'Hebron, Institut de Recerca (VHIR), Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Antonio Astorga-Gamaza
- Infectious Diseases Department, Hospital Universitari Vall d'Hebron, Institut de Recerca (VHIR), Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Josep Castellví
- Pathology Department, Hospital Universitari Vall d'Hebron, UAB, Barcelona, Spain
| | - Tamara Sanhueza
- Pathology Department, Hospital Universitari Germans Trias i Pujol, Badalona, Barcelona, Spain
| | - Gustavo Tapia
- Pathology Department, Hospital Universitari Germans Trias i Pujol, Badalona, Barcelona, Spain
| | - Belen Lloveras
- Pathology Department, Hospital del Mar, Parc de Salut Mar, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Marco A Fernández
- Flow Cytometry Facility, Institut d'Investigació en Ciències de la Salut Germans Trias i Pujol, Badalona, Spain
| | - Julia G Prado
- AIDS Research Institute IrsiCaixa, Institut d'Investigació en Ciències de la Salut Germans Trias i Pujol, Universitat Autònoma de Barcelona, Badalona, Spain
| | - Josep M Solé-Sedeno
- Obstetrics and Gynecology Department, Hospital del Mar, Parc de Salut Mar, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Antoni Tarrats
- Department of Obstetrics and Gynecology, Hospital Universitari Germans Trias i Pujol, Badalona, Barcelona, Spain
| | - Carla Lecumberri
- Department of Obstetrics and Gynecology, Hospital Universitari Germans Trias i Pujol, Badalona, Barcelona, Spain
| | - Laura Mañalich-Barrachina
- Department of Obstetrics and Gynecology, Hospital Universitari Vall d'Hebron, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Cristina Centeno-Mediavilla
- Department of Obstetrics and Gynecology, Hospital Universitari Vall d'Hebron, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Vicenç Falcó
- Infectious Diseases Department, Hospital Universitari Vall d'Hebron, Institut de Recerca (VHIR), Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Maria J Buzon
- Infectious Diseases Department, Hospital Universitari Vall d'Hebron, Institut de Recerca (VHIR), Universitat Autònoma de Barcelona, Barcelona, Spain.
| | - Meritxell Genescà
- Infectious Diseases Department, Hospital Universitari Vall d'Hebron, Institut de Recerca (VHIR), Universitat Autònoma de Barcelona, Barcelona, Spain.
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Loiseau C, Cooper MM, Doolan DL. Deciphering host immunity to malaria using systems immunology. Immunol Rev 2019; 293:115-143. [PMID: 31608461 DOI: 10.1111/imr.12814] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2019] [Revised: 09/18/2019] [Accepted: 09/20/2019] [Indexed: 12/11/2022]
Abstract
A century of conceptual and technological advances in infectious disease research has changed the face of medicine. However, there remains a lack of effective interventions and a poor understanding of host immunity to the most significant and complex pathogens, including malaria. The development of successful interventions against such intractable diseases requires a comprehensive understanding of host-pathogen immune responses. A major advance of the past decade has been a paradigm switch in thinking from the contemporary reductionist (gene-by-gene or protein-by-protein) view to a more holistic (whole organism) view. Also, a recognition that host-pathogen immunity is composed of complex, dynamic interactions of cellular and molecular components and networks that cannot be represented by any individual component in isolation. Systems immunology integrates the field of immunology with omics technologies and computational sciences to comprehensively interrogate the immune response at a systems level. Herein, we describe the system immunology toolkit and report recent studies deploying systems-level approaches in the context of natural exposure to malaria or controlled human malaria infection. We contribute our perspective on the potential of systems immunity for the rational design and development of effective interventions to improve global public health.
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Affiliation(s)
- Claire Loiseau
- Centre for Molecular Therapeutics, Australian Institute of Tropical Health and Medicine, James Cook University, Cairns, Qld, Australia
| | - Martha M Cooper
- Centre for Molecular Therapeutics, Australian Institute of Tropical Health and Medicine, James Cook University, Cairns, Qld, Australia
| | - Denise L Doolan
- Centre for Molecular Therapeutics, Australian Institute of Tropical Health and Medicine, James Cook University, Cairns, Qld, Australia
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