1
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Barbehenn A, Shi L, Shao J, Hoh R, Hartig HM, Pae V, Sarvadhavabhatla S, Donaire S, Sheikhzadeh C, Milush J, Laird GM, Mathias M, Ritter K, Peluso MJ, Martin J, Hecht F, Pilcher C, Cohen SE, Buchbinder S, Havlir D, Gandhi M, Henrich TJ, Hatano H, Wang J, Deeks SG, Lee SA. Rapid Biphasic Decay of Intact and Defective HIV DNA Reservoir During Acute Treated HIV Disease. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2024:2024.03.27.24304867. [PMID: 38585951 PMCID: PMC10996734 DOI: 10.1101/2024.03.27.24304867] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/09/2024]
Abstract
Despite antiretroviral therapy (ART), HIV persists in latently-infected cells ("the reservoir") which decay slowly over time. Here, leveraging >500 longitudinal samples from 67 people with HIV (PWH) treated during acute infection, we developed a novel mathematical model to predict reservoir decay from peripheral CD4+ T cells. Nonlinear generalized additive models demonstrated rapid biphasic decay of intact DNA (week 0-5: t 1/2 ∼2.83 weeks; week 5-24: t 1/2 ∼15.4 weeks) that extended out to 1 year. These estimates were ∼5-fold faster than prior decay estimates among chronic treated PWH. Defective DNA had a similar biphasic pattern, but data were more variable. Predicted intact and defective decay rates were faster for PWH with earlier timing of ART initiation, higher initial CD4+ T cell count, and lower pre-ART viral load. These data add to our limited understanding of HIV reservoir decay at the time of ART initiation, informing future curative strategies targeting this critical time.
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2
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Banga R, Perreau M. The multifaceted nature of HIV tissue reservoirs. Curr Opin HIV AIDS 2024; 19:116-123. [PMID: 38547340 PMCID: PMC10990014 DOI: 10.1097/coh.0000000000000851] [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] [Indexed: 04/04/2024]
Abstract
PURPOSE OF REVIEW To underline the complexity and the heterogeneity of the HIV reservoir. RECENT FINDINGS While lymphoid tissues (spleen, lymph nodes, gut-associated lymphoid tissue) harbor specific subsets of specialized CD4 + T cells enriched in HIV-infected cells, non-CD4 + T cell reservoirs such as tissue-resident macrophages and dendritic cells have also been implicated to contribute to viral persistence. Moreover, studies have applied highly sensitive tools to detect transcriptional activity within HIV-infected cells during prolonged ART and revealed a broader spectrum of transcriptional activity for proviruses than previously thought. Finally, while a combination of factors might be involved in the regulation of HIV persistence within different tissues and remains to be fully elucidated, recent results from autopsy samples of HIV-infected ART suppressed individuals indicate extensive clonality of HIV reservoirs in multiple tissues and suggest that the recirculation of HIV-infected cells and their local expansions in tissues may also contribute to the complexity of the HIV reservoirs in humans. SUMMARY HIV persistence in blood and multiple tissues despite long-standing and potent therapy is one of the major barriers to a cure. Given that the HIV reservoir is established early and is highly complex based on its composition, viral diversity, tissue distribution, transcriptional activity, replication competence, migration dynamics and proliferative potential across the human body and possible compartmentalization in specific tissues, combinatorial therapeutic approaches are needed that may synergize to target multiple viral reservoirs to achieve a cure for HIV infection.
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Affiliation(s)
- Riddhima Banga
- Divisions of Immunology and Allergy, Lausanne University Hospital, University of Lausanne, Lausanne, Switzerland
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3
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Hasler MF, Speck RF, Kadzioch NP. Humanized mice for studying HIV latency and potentially its eradication. Curr Opin HIV AIDS 2024; 19:157-167. [PMID: 38547338 DOI: 10.1097/coh.0000000000000855] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
PURPOSE OF THE REVIEW The quest for an HIV cure faces a formidable challenge: the persistent presence of latent viral infections within the cells and tissues of infected individuals. This review provides a thorough examination of discussions surrounding HIV latency, the use of humanized mouse models, and strategies aimed at eliminating the latent HIV reservoir. It explores the hurdles and advancements in understanding HIV pathogenesis, mainly focusing on establishing latent reservoirs in CD4 + T cells and macrophages. Introducing the concepts of functional and sterile cures, the review underscores the indispensable role of humanized mouse models in HIV research, offering crucial insights into the efficacy of cART and the ongoing pursuit of an HIV cure. RECENT FINDINGS Here, we highlight studies investigating molecular mechanisms and pathogenesis related to HIV latency in humanized mice and discuss novel strategies for eradicating latent HIV. Emphasizing the importance of analytical cART interruption in humanized mouse studies to gauge its impact on the latent reservoir accurately, the review underlines the ongoing progress and challenges in harnessing humanized mouse models for HIV research. SUMMARY This review suggests that humanized mice models provide valuable insights into HIV latency and potential eradication strategies, contributing significantly to the quest for an HIV cure.
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Affiliation(s)
- Moa F Hasler
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital of Zurich, University of Zurich, Zurich, Switzerland
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4
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van Paassen PM, van Pul L, van der Straten K, Buchholtz NV, Grobben M, van Nuenen AC, van Dort KA, Boeser-Nunnink BD, van den Essenburg MD, Burger JA, van Luin M, Jurriaans S, Sanders RW, Swelsen WT, Symons J, Klouwens MJ, Nijhuis M, van Gils MJ, Prins JM, de Bree GJ, Kootstra NA. Virological and immunological correlates of HIV posttreatment control after temporal antiretroviral therapy during acute HIV infection. AIDS 2023; 37:2297-2304. [PMID: 37702421 PMCID: PMC10653294 DOI: 10.1097/qad.0000000000003722] [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: 05/26/2023] [Revised: 09/03/2023] [Accepted: 09/07/2023] [Indexed: 09/14/2023]
Abstract
OBJECTIVE People with HIV rarely control viral replication after cessation of antiretroviral therapy (ART). We present a person with HIV with extraordinary posttreatment control (PTC) for over 23 years after temporary ART during acute HIV infection (AHI) leading to a new insight in factors contributing to PTC. DESIGN/METHODS Viral reservoir was determined by HIV qPCR, Intact Proviral DNA Assay, and quantitative viral outgrowth assay. Viral replication kinetics were determined in autologous and donor PBMC. IgG levels directed against HIV envelope and neutralizing antibodies were measured. Immune phenotyping of T cells and HIV-specific T-cell responses were analyzed by flow cytometry. RESULTS The case presented with AHI and a plasma viral load of 2.7 million copies/ml. ART was initiated 2 weeks after diagnosis and interrupted after 26 months. Replicating virus was isolated shortly after start ART. At 18 years after treatment interruption, HIV-DNA in CD4 + T cells and low levels of HIV-RNA in plasma (<5 copies/ml) were detectable. Stable HIV envelope glycoprotein-directed IgG was present during follow-up, but lacked neutralizing activity. Strong antiviral CD8 + T-cell responses, in particular targeting HIV-gag, were detected during 25 years follow-up. Moreover, we found a P255A mutation in an HLA-B∗44 : 02 restricted gag-epitope, which was associated with decreased replication. CONCLUSION We describe an exceptional case of PTC, which is likely associated with sustained potent gag-specific CD8 + T-cell responses in combination with a replication attenuating escape mutation in gag. Understanding the initiation and preservation of the HIV-specific T-cell responses could guide the development of strategies to induce HIV control.
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Affiliation(s)
- Pien M. van Paassen
- Amsterdam UMC location University of Amsterdam, Experimental Immunology, Meibergdreef 9
- Amsterdam Institute for Infection and Immunity, Infectious Diseases
| | - Lisa van Pul
- Amsterdam UMC location University of Amsterdam, Experimental Immunology, Meibergdreef 9
- Amsterdam Institute for Infection and Immunity, Infectious Diseases
| | - Karlijn van der Straten
- Amsterdam Institute for Infection and Immunity, Infectious Diseases
- Department of Medical Microbiology and Infection Prevention, Laboratory of Experimental Virology, Amsterdam UMC, Amsterdam
| | - Ninée V.J.E. Buchholtz
- Department of Medical Microbiology, Translational Virology, University Medical Center Utrecht
| | - Marloes Grobben
- Amsterdam Institute for Infection and Immunity, Infectious Diseases
- Department of Medical Microbiology and Infection Prevention, Laboratory of Experimental Virology, Amsterdam UMC, Amsterdam
| | - Ad C. van Nuenen
- Amsterdam UMC location University of Amsterdam, Experimental Immunology, Meibergdreef 9
- Amsterdam Institute for Infection and Immunity, Infectious Diseases
| | - Karel A. van Dort
- Amsterdam UMC location University of Amsterdam, Experimental Immunology, Meibergdreef 9
- Amsterdam Institute for Infection and Immunity, Infectious Diseases
| | - Brigitte D. Boeser-Nunnink
- Amsterdam UMC location University of Amsterdam, Experimental Immunology, Meibergdreef 9
- Amsterdam Institute for Infection and Immunity, Infectious Diseases
| | | | - Judith A. Burger
- Amsterdam Institute for Infection and Immunity, Infectious Diseases
- Department of Medical Microbiology and Infection Prevention, Laboratory of Experimental Virology, Amsterdam UMC, Amsterdam
| | - Matthijs van Luin
- Department of Clinical Pharmacy, Division Laboratories, Pharmacy and Biomedical Genetics, University Medical Center Utrecht, Utrecht University, Utrecht
| | - Suzanne Jurriaans
- Amsterdam Institute for Infection and Immunity, Infectious Diseases
- Department of Medical Microbiology and Infection Prevention, Laboratory of Experimental Virology, Amsterdam UMC, Amsterdam
| | - Rogier W. Sanders
- Amsterdam Institute for Infection and Immunity, Infectious Diseases
- Department of Medical Microbiology and Infection Prevention, Laboratory of Experimental Virology, Amsterdam UMC, Amsterdam
| | - Wendy T. Swelsen
- Department of Immunogenetics, Sanquin Diagnostic Services, Amsterdam, the Netherlands
| | - Jori Symons
- Department of Medical Microbiology, Translational Virology, University Medical Center Utrecht
| | - Michelle J. Klouwens
- Amsterdam Institute for Infection and Immunity, Infectious Diseases
- Department of Internal Medicine, Division of Infectious Diseases, Amsterdam UMC, Amsterdam, The Netherlands
| | - Monique Nijhuis
- Department of Medical Microbiology, Translational Virology, University Medical Center Utrecht
| | - Marit J. van Gils
- Amsterdam Institute for Infection and Immunity, Infectious Diseases
- Department of Medical Microbiology and Infection Prevention, Laboratory of Experimental Virology, Amsterdam UMC, Amsterdam
| | - Jan M. Prins
- Amsterdam Institute for Infection and Immunity, Infectious Diseases
- Department of Internal Medicine, Division of Infectious Diseases, Amsterdam UMC, Amsterdam, The Netherlands
| | - Godelieve J. de Bree
- Amsterdam Institute for Infection and Immunity, Infectious Diseases
- Department of Internal Medicine, Division of Infectious Diseases, Amsterdam UMC, Amsterdam, The Netherlands
| | - Neeltje A. Kootstra
- Amsterdam UMC location University of Amsterdam, Experimental Immunology, Meibergdreef 9
- Amsterdam Institute for Infection and Immunity, Infectious Diseases
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5
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Kuse N, Gatanaga H, Zhang Y, Chikata T, Oka S, Takiguchi M. Epitope-dependent effect of long-term cART on maintenance and recovery of HIV-1-specific CD8 + T cells. J Virol 2023; 97:e0102423. [PMID: 37877716 PMCID: PMC10688310 DOI: 10.1128/jvi.01024-23] [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: 07/09/2023] [Accepted: 09/26/2023] [Indexed: 10/26/2023] Open
Abstract
IMPORTANCE HIV-1-specific CD8+ T cells are anticipated to become effector cells for curative treatment using the "shock and kill" approach in people living with HIV-1 (PLWH) under combined antiretroviral therapy (cART). Previous studies demonstrated that the frequency of HIV-1-specific CD8+ T cells is reduced under cART and their functional ability remains impaired. These studies analyzed T-cell responses to a small number of HIV-1 epitopes or overlapping HIV-1 peptides. Therefore, the features of CD8+ T cells specific for HIV-1 epitopes under cART remain only partially clarified. Here, we analyzed CD8+ T cells specific for 63 well-characterized epitopes in 90 PLWH. We demonstrated that CD8+ T cells specific for large numbers of HIV-1 epitopes were maintained in an epitope-dependent fashion under long-term cART and that long-term cART enhanced or restored the ability of HIV-1-specific T cells to proliferate in vitro. This study implies that some HIV-1-specific T cells would be useful as effector cells for curative treatment.
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Affiliation(s)
- Nozomi Kuse
- Division of International Collaboration Research and Tokyo Joint Laboratory, Department of Frontier Research, Joint Research Center for Human Retrovirus Infection, Kumamoto University, Kumamoto, Japan
- AIDS Research Center, National Institute of Infectious Diseases, Shinjuku-ku, Tokyo, Japan
| | - Hiroyuki Gatanaga
- AIDS Clinical Center, National Center for Global Health and Medicine, Shinjuku-ku, Tokyo, Japan
| | - Yu Zhang
- Division of International Collaboration Research and Tokyo Joint Laboratory, Department of Frontier Research, Joint Research Center for Human Retrovirus Infection, Kumamoto University, Kumamoto, Japan
| | - Takayuki Chikata
- Division of International Collaboration Research and Tokyo Joint Laboratory, Department of Frontier Research, Joint Research Center for Human Retrovirus Infection, Kumamoto University, Kumamoto, Japan
| | - Shinichi Oka
- AIDS Clinical Center, National Center for Global Health and Medicine, Shinjuku-ku, Tokyo, Japan
| | - Masafumi Takiguchi
- Division of International Collaboration Research and Tokyo Joint Laboratory, Department of Frontier Research, Joint Research Center for Human Retrovirus Infection, Kumamoto University, Kumamoto, Japan
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6
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Dwivedi AK, Gornalusse GG, Siegel DA, Barbehenn A, Thanh C, Hoh R, Hobbs KS, Pan T, Gibson EA, Martin J, Hecht F, Pilcher C, Milush J, Busch MP, Stone M, Huang ML, Reppetti J, Vo PM, Levy CN, Roychoudhury P, Jerome KR, Hladik F, Henrich TJ, Deeks SG, Lee SA. A cohort-based study of host gene expression: tumor suppressor and innate immune/inflammatory pathways associated with the HIV reservoir size. PLoS Pathog 2023; 19:e1011114. [PMID: 38019897 PMCID: PMC10712869 DOI: 10.1371/journal.ppat.1011114] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Revised: 12/11/2023] [Accepted: 11/01/2023] [Indexed: 12/01/2023] Open
Abstract
The major barrier to an HIV cure is the HIV reservoir: latently-infected cells that persist despite effective antiretroviral therapy (ART). There have been few cohort-based studies evaluating host genomic or transcriptomic predictors of the HIV reservoir. We performed host RNA sequencing and HIV reservoir quantification (total DNA [tDNA], unspliced RNA [usRNA], intact DNA) from peripheral CD4+ T cells from 191 ART-suppressed people with HIV (PWH). After adjusting for nadir CD4+ count, timing of ART initiation, and genetic ancestry, we identified two host genes for which higher expression was significantly associated with smaller total DNA viral reservoir size, P3H3 and NBL1, both known tumor suppressor genes. We then identified 17 host genes for which lower expression was associated with higher residual transcription (HIV usRNA). These included novel associations with membrane channel (KCNJ2, GJB2), inflammasome (IL1A, CSF3, TNFAIP5, TNFAIP6, TNFAIP9, CXCL3, CXCL10), and innate immunity (TLR7) genes (FDR-adjusted q<0.05). Gene set enrichment analyses further identified significant associations of HIV usRNA with TLR4/microbial translocation (q = 0.006), IL-1/NRLP3 inflammasome (q = 0.008), and IL-10 (q = 0.037) signaling. Protein validation assays using ELISA and multiplex cytokine assays supported these observed inverse host gene correlations, with P3H3, IL-10, and TNF-α protein associations achieving statistical significance (p<0.05). Plasma IL-10 was also significantly inversely associated with HIV DNA (p = 0.016). HIV intact DNA was not associated with differential host gene expression, although this may have been due to a large number of undetectable values in our study. To our knowledge, this is the largest host transcriptomic study of the HIV reservoir. Our findings suggest that host gene expression may vary in response to the transcriptionally active reservoir and that changes in cellular proliferation genes may influence the size of the HIV reservoir. These findings add important data to the limited host genetic HIV reservoir studies to date.
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Affiliation(s)
- Ashok K. Dwivedi
- Department of Medicine, Division of HIV, Infectious Diseases & Global Medicine, University of California, San Francisco, California, United States of America
| | - Germán G. Gornalusse
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, Washington, United States of America
- Department of Obstetrics and Gynecology, University of Washington, Seattle, Washington, United States of America
| | - David A. Siegel
- Department of Medicine, Division of HIV, Infectious Diseases & Global Medicine, University of California, San Francisco, California, United States of America
| | - Alton Barbehenn
- Department of Medicine, Division of HIV, Infectious Diseases & Global Medicine, University of California, San Francisco, California, United States of America
| | - Cassandra Thanh
- Department of Medicine, Division of Experimental Medicine, University of California San Francisco, California, United States of America
| | - Rebecca Hoh
- Department of Medicine, Division of HIV, Infectious Diseases & Global Medicine, University of California, San Francisco, California, United States of America
| | - Kristen S. Hobbs
- Department of Medicine, Division of Experimental Medicine, University of California San Francisco, California, United States of America
| | - Tony Pan
- Department of Medicine, Division of Experimental Medicine, University of California San Francisco, California, United States of America
| | - Erica A. Gibson
- Department of Medicine, Division of Experimental Medicine, University of California San Francisco, California, United States of America
| | - Jeffrey Martin
- Department of Biostatistics & Epidemiology, University of California San Francisco, California, United States of America
| | - Frederick Hecht
- Department of Medicine, Division of HIV, Infectious Diseases & Global Medicine, University of California, San Francisco, California, United States of America
| | - Christopher Pilcher
- Department of Medicine, Division of HIV, Infectious Diseases & Global Medicine, University of California, San Francisco, California, United States of America
| | - Jeffrey Milush
- Department of Medicine, Division of Experimental Medicine, University of California San Francisco, California, United States of America
| | - Michael P. Busch
- Vitalant Blood Bank, San Francisco, California, United States of America
| | - Mars Stone
- Vitalant Blood Bank, San Francisco, California, United States of America
| | - Meei-Li Huang
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, Washington, United States of America
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, Washington, United States of America
| | - Julieta Reppetti
- Department of Obstetrics and Gynecology, University of Washington, Seattle, Washington, United States of America
- Universidad de Buenos Aires (UBA), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Instituto de Fisiología y Biofísica Bernardo Houssay (IFIBIO- Houssay), Buenos Aires, Argentina
| | - Phuong M. Vo
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, Washington, United States of America
- Department of Obstetrics and Gynecology, University of Washington, Seattle, Washington, United States of America
| | - Claire N. Levy
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, Washington, United States of America
- Department of Obstetrics and Gynecology, University of Washington, Seattle, Washington, United States of America
| | - Pavitra Roychoudhury
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, Washington, United States of America
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, Washington, United States of America
| | - Keith R. Jerome
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, Washington, United States of America
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, Washington, United States of America
| | - Florian Hladik
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, Washington, United States of America
- Department of Obstetrics and Gynecology, University of Washington, Seattle, Washington, United States of America
- Department of Medicine, Division of Allergy and Infectious Diseases, University of Washington, Seattle, Washington, United States of America
| | - Timothy J. Henrich
- Department of Obstetrics and Gynecology, University of Washington, Seattle, Washington, United States of America
| | - Steven G. Deeks
- Department of Medicine, Division of HIV, Infectious Diseases & Global Medicine, University of California, San Francisco, California, United States of America
| | - Sulggi A. Lee
- Department of Medicine, Division of HIV, Infectious Diseases & Global Medicine, University of California, San Francisco, California, United States of America
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7
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Banga R, Procopio FA, Lana E, Gladkov GT, Roseto I, Parsons EM, Lian X, Armani-Tourret M, Bellefroid M, Gao C, Kauzlaric A, Foglierini M, Alfageme-Abello O, Sluka SHM, Munoz O, Mastrangelo A, Fenwick C, Muller Y, Mkindi CG, Daubenberger C, Cavassini M, Trunfio R, Déglise S, Corpataux JM, Delorenzi M, Lichterfeld M, Pantaleo G, Perreau M. Lymph node dendritic cells harbor inducible replication-competent HIV despite years of suppressive ART. Cell Host Microbe 2023; 31:1714-1731.e9. [PMID: 37751747 PMCID: PMC11068440 DOI: 10.1016/j.chom.2023.08.020] [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: 02/13/2023] [Revised: 06/02/2023] [Accepted: 08/30/2023] [Indexed: 09/28/2023]
Abstract
Although gut and lymph node (LN) memory CD4 T cells represent major HIV and simian immunodeficiency virus (SIV) tissue reservoirs, the study of the role of dendritic cells (DCs) in HIV persistence has long been limited to the blood due to difficulties to access lymphoid tissue samples. In this study, we show that LN migratory and resident DC subpopulations harbor distinct phenotypic and transcriptomic profiles. Interestingly, both LN DC subpopulations contain HIV intact provirus and inducible replication-competent HIV despite the expression of the antiviral restriction factor SAMHD1. Notably, LN DC subpopulations isolated from HIV-infected individuals treated for up to 14 years are transcriptionally silent but harbor replication-competent virus that can be induced upon TLR7/8 stimulation. Taken together, these results uncover a potential important contribution of LN DCs to HIV infection in the presence of ART.
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Affiliation(s)
- Riddhima Banga
- Services of Immunology and Allergy, Lausanne University Hospital, University of Lausanne, 1011 Lausanne, Switzerland
| | - Francesco Andrea Procopio
- Services of Immunology and Allergy, Lausanne University Hospital, University of Lausanne, 1011 Lausanne, Switzerland
| | - Erica Lana
- Services of Immunology and Allergy, Lausanne University Hospital, University of Lausanne, 1011 Lausanne, Switzerland
| | | | | | - Elizabeth M Parsons
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, USA; Infectious Disease Division, Brigham and Women's Hospital, Boston, MA, USA
| | - Xiaodong Lian
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, USA; Infectious Disease Division, Brigham and Women's Hospital, Boston, MA, USA
| | | | | | - Ce Gao
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, USA
| | - Annamaria Kauzlaric
- Translational Bioinformatics and Statistics Department of Oncology, University of Lausanne Swiss Cancer Center, Lausanne, Switzerland
| | - Mathilde Foglierini
- Services of Immunology and Allergy, Lausanne University Hospital, University of Lausanne, 1011 Lausanne, Switzerland
| | - Oscar Alfageme-Abello
- Services of Immunology and Allergy, Lausanne University Hospital, University of Lausanne, 1011 Lausanne, Switzerland
| | - Susanna H M Sluka
- Newborn Screening Switzerland, University Children's Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Olivia Munoz
- Services of Immunology and Allergy, Lausanne University Hospital, University of Lausanne, 1011 Lausanne, Switzerland
| | - Andrea Mastrangelo
- Services of Immunology and Allergy, Lausanne University Hospital, University of Lausanne, 1011 Lausanne, Switzerland
| | - Craig Fenwick
- Services of Immunology and Allergy, Lausanne University Hospital, University of Lausanne, 1011 Lausanne, Switzerland
| | - Yannick Muller
- Services of Immunology and Allergy, Lausanne University Hospital, University of Lausanne, 1011 Lausanne, Switzerland
| | - Catherine Gerald Mkindi
- Ifakara Health Institute, Bagamoyo, United Republic of Tanzania; Department of Medical Parasitology and Infection Biology, Clinical Immunology Unit, Swiss Tropical and Public Health Institute, Basel, Switzerland
| | - Claudia Daubenberger
- Department of Medical Parasitology and Infection Biology, Clinical Immunology Unit, Swiss Tropical and Public Health Institute, Basel, Switzerland; University of Basel, 4001 Basel, Switzerland
| | - Matthias Cavassini
- Services of Infectious Diseases, Lausanne University Hospital, University of Lausanne, 1011 Lausanne, Switzerland
| | - Rafael Trunfio
- Services of Vascular Surgery, Lausanne University Hospital, University of Lausanne, 1011 Lausanne, Switzerland
| | - Sébastien Déglise
- Services of Vascular Surgery, Lausanne University Hospital, University of Lausanne, 1011 Lausanne, Switzerland
| | - Jean-Marc Corpataux
- Services of Vascular Surgery, Lausanne University Hospital, University of Lausanne, 1011 Lausanne, Switzerland
| | - Mauro Delorenzi
- Translational Bioinformatics and Statistics Department of Oncology, University of Lausanne Swiss Cancer Center, Lausanne, Switzerland
| | - Mathias Lichterfeld
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, USA; Infectious Disease Division, Brigham and Women's Hospital, Boston, MA, USA
| | - Giuseppe Pantaleo
- Services of Immunology and Allergy, Lausanne University Hospital, University of Lausanne, 1011 Lausanne, Switzerland; Swiss Vaccine Research Institute, Lausanne University Hospital, University of Lausanne, 1011 Lausanne, Switzerland
| | - Matthieu Perreau
- Services of Immunology and Allergy, Lausanne University Hospital, University of Lausanne, 1011 Lausanne, Switzerland.
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8
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He Y, Wu C, Liu Z, Zhang Y, Feng F, Lin Z, Wang C, Yang Q, Wen Z, Liu Y, Zhang F, Lin Y, Zhang H, Qu L, Li L, Cai W, Sun C, Chen L, Li P. Arsenic trioxide-induced apoptosis contributes to suppression of viral reservoir in SIV-infected rhesus macaques. Microbiol Spectr 2023; 11:e0052523. [PMID: 37695104 PMCID: PMC10581169 DOI: 10.1128/spectrum.00525-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Accepted: 07/07/2023] [Indexed: 09/12/2023] Open
Abstract
Latent viral reservoir is recognized as the major obstacle to achieving a functional cure for HIV infection. We previously reported that arsenic trioxide (As2O3) combined with antiretroviral therapy (ART) can reactivate the viral reservoir and delay viral rebound after ART interruption in chronically simian immunodeficiency virus (SIV)-infected macaques. In this study, we further investigated the effect of As2O3 independent of ART in chronically SIV-infected macaques. We found that As2O3-only treatment significantly increased the CD4/CD8 ratio, improved SIV-specific T cell responses, and reactivated viral latency in chronically SIVmac239-infected macaques. RNA-sequencing analysis revealed that As2O3 treatment downregulated the expression levels of genes related to HIV entry and infection, while the expression levels of genes related to transcription initiation, cell apoptosis, and host restriction factors were significantly upregulated. Importantly, we found that As2O3 treatment specifically induced apoptosis of SIV-infected CD4+ T cells. These findings revealed that As2O3 might not only impact viral latency, but also induce the apoptosis of HIV-infected cells and thus block the secondary infection of bystanders. Moreover, we investigated the therapeutic potential of this regimen in acutely SIVmac239-infected macaques and found that As2O3 + ART treatment effectively restored the CD4+ T cell count, delayed disease progression, and improved survival in acutely SIV-infected macaques. In sum, this work provides new insights to develop As2O3 as a component of the "shock-and-kill" strategy toward HIV functional cure. IMPORTANCE Although antiretroviral therapy (ART) can effectively suppress the viral load of AIDS patients, it cannot functionally cure HIV infection due to the existence of HIV reservoir. Strategies toward HIV functional cure are still highly anticipated to ultimately end the pandemic of AIDS. Herein, we investigated the direct role of As2O3 independent of ART in chronically SIV-infected macaques and explored the underlying mechanisms of the potential of As2O3 in the treatment of HIV/SIV infection. Meanwhile, we investigated the therapeutic effects of ART+As2O3 in acutely SIVmac239-infected macaques. This study showed that As2O3 has the potential to be launched into the "shock-and-kill" strategy to suppress HIV/SIV reservoir due to its latency-reversing and apoptosis-inducing properties.
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Affiliation(s)
- Yizi He
- Guangdong Laboratory of Computational Biomedicine, Center for Infection and Immunity, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Chunxiu Wu
- Guangdong Laboratory of Computational Biomedicine, Center for Infection and Immunity, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Zijian Liu
- Guangdong Laboratory of Computational Biomedicine, Center for Infection and Immunity, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Yudi Zhang
- Guangdong Laboratory of Computational Biomedicine, Center for Infection and Immunity, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Fengling Feng
- School of Public Health (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Shenzhen, China
| | - Zihan Lin
- Guangdong Laboratory of Computational Biomedicine, Center for Infection and Immunity, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Congcong Wang
- School of Public Health (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Shenzhen, China
| | - Qing Yang
- Guangdong Laboratory of Computational Biomedicine, Center for Infection and Immunity, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
| | - Ziyu Wen
- School of Public Health (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Shenzhen, China
| | - Yichu Liu
- Guangdong Laboratory of Computational Biomedicine, Center for Infection and Immunity, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
| | - Fan Zhang
- Guangdong Laboratory of Computational Biomedicine, Center for Infection and Immunity, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
| | - Yanqin Lin
- Guangdong Laboratory of Computational Biomedicine, Center for Infection and Immunity, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
| | - Hao Zhang
- Guangdong Laboratory of Computational Biomedicine, Center for Infection and Immunity, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
| | - Linbing Qu
- Guangdong Laboratory of Computational Biomedicine, Center for Infection and Immunity, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
| | - Linghua Li
- Guangzhou Eighth People’s Hospital, Guangzhou Medical University, Guangzhou, China
| | - Weiping Cai
- Guangzhou Eighth People’s Hospital, Guangzhou Medical University, Guangzhou, China
| | - Caijun Sun
- School of Public Health (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Shenzhen, China
| | - Ling Chen
- Guangdong Laboratory of Computational Biomedicine, Center for Infection and Immunity, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
- Guangzhou Eighth People’s Hospital, Guangzhou Medical University, Guangzhou, China
| | - Pingchao Li
- Guangdong Laboratory of Computational Biomedicine, Center for Infection and Immunity, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
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9
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Williams E, Moso M, Lim C, Chibo D, Nicholson S, Jackson K, Williamson DA. Laboratory diagnosis of HIV: a contemporary overview in the Australian context. Pathology 2023:S0031-3025(23)00125-3. [PMID: 37302942 DOI: 10.1016/j.pathol.2023.04.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2022] [Revised: 03/02/2023] [Accepted: 04/19/2023] [Indexed: 06/13/2023]
Abstract
Over the past decade there have been technical advances in human immunodeficiency virus (HIV) assays and updates to testing regulations that have substantially changed the landscape of laboratory testing for HIV. In addition, there have been significant changes in the epidemiology of HIV in Australia in the context of highly effective contemporary biomedical treatment and prevention strategies. Here, we provide an update on contemporary issues for the laboratory detection and confirmation of HIV in Australia. These include (1) the impact of early treatment and biological prevention strategies on the serological and virological detection of HIV; (2) the updated national HIV laboratory case definition and its interaction with testing regulations, public health and clinical guidelines; and (3) novel strategies for the laboratory detection of HIV, including the incorporation of HIV nucleic acid amplification tests (NAATs) into testing algorithms. These developments present an opportunity to develop a nationally consistent contemporary HIV testing algorithm that would result in optimisation and standardisation of HIV testing in Australia.
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Affiliation(s)
- Eloise Williams
- Victorian Infectious Diseases Reference Laboratory, Royal Melbourne Hospital at the Peter Doherty Institute for Infection and Immunity, Melbourne, Vic, Australia; Department of Infectious Diseases, University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Vic, Australia.
| | - Michael Moso
- Victorian Infectious Diseases Reference Laboratory, Royal Melbourne Hospital at the Peter Doherty Institute for Infection and Immunity, Melbourne, Vic, Australia; Department of Infectious Diseases, University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Vic, Australia; Department of Microbiology, The Royal Melbourne Hospital, Melbourne, Vic, Australia
| | - Chuan Lim
- Victorian Infectious Diseases Reference Laboratory, Royal Melbourne Hospital at the Peter Doherty Institute for Infection and Immunity, Melbourne, Vic, Australia
| | - Doris Chibo
- Victorian Infectious Diseases Reference Laboratory, Royal Melbourne Hospital at the Peter Doherty Institute for Infection and Immunity, Melbourne, Vic, Australia
| | - Suellen Nicholson
- Victorian Infectious Diseases Reference Laboratory, Royal Melbourne Hospital at the Peter Doherty Institute for Infection and Immunity, Melbourne, Vic, Australia
| | - Kathy Jackson
- Victorian Infectious Diseases Reference Laboratory, Royal Melbourne Hospital at the Peter Doherty Institute for Infection and Immunity, Melbourne, Vic, Australia
| | - Deborah Anne Williamson
- Victorian Infectious Diseases Reference Laboratory, Royal Melbourne Hospital at the Peter Doherty Institute for Infection and Immunity, Melbourne, Vic, Australia; Department of Infectious Diseases, University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Vic, Australia
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10
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George AF, Roan NR. Advances in HIV Research Using Mass Cytometry. Curr HIV/AIDS Rep 2023; 20:76-85. [PMID: 36689119 PMCID: PMC9869313 DOI: 10.1007/s11904-023-00649-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/09/2023] [Indexed: 01/24/2023]
Abstract
PURPOSE OF REVIEW This review describes how advances in CyTOF and high-dimensional analysis methods have furthered our understanding of HIV transmission, pathogenesis, persistence, and immunity. RECENT FINDINGS CyTOF has generated important insight on several aspects of HIV biology: (1) the differences between cells permissive to productive vs. latent HIV infection, and the HIV-induced remodeling of infected cells; (2) factors that contribute to the persistence of the long-term HIV reservoir, in both blood and tissues; and (3) the impact of HIV on the immune system, in the context of both uncontrolled and controlled infection. CyTOF and high-dimensional analysis tools have enabled in-depth assessment of specific host antigens remodeled by HIV, and have revealed insights into the features of HIV-infected cells enabling them to survive and persist, and of the immune cells that can respond to and potentially control HIV replication. CyTOF and other related high-dimensional phenotyping approaches remain powerful tools for translational research, and applied HIV to cohort studies can inform on mechanisms of HIV pathogenesis and persistence, and potentially identify biomarkers for viral eradication or control.
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Affiliation(s)
- Ashley F George
- Gladstone Institute of Virology, Gladstone Institutes, San Francisco, CA, 94158, USA
- Department of Urology, University of California at San Francisco, San Francisco, CA, 94143, USA
| | - Nadia R Roan
- Gladstone Institute of Virology, Gladstone Institutes, San Francisco, CA, 94158, USA.
- Department of Urology, University of California at San Francisco, San Francisco, CA, 94143, USA.
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11
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Wu VH, Nordin JML, Nguyen S, Joy J, Mampe F, Del Rio Estrada PM, Torres-Ruiz F, González-Navarro M, Luna-Villalobos YA, Ávila-Ríos S, Reyes-Terán G, Tebas P, Montaner LJ, Bar KJ, Vella LA, Betts MR. Profound phenotypic and epigenetic heterogeneity of the HIV-1-infected CD4 + T cell reservoir. Nat Immunol 2023; 24:359-370. [PMID: 36536105 PMCID: PMC9892009 DOI: 10.1038/s41590-022-01371-3] [Citation(s) in RCA: 29] [Impact Index Per Article: 29.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Accepted: 10/24/2022] [Indexed: 12/24/2022]
Abstract
Understanding the complexity of the long-lived HIV reservoir during antiretroviral therapy (ART) remains a considerable impediment in research towards a cure for HIV. To address this, we developed a single-cell strategy to precisely define the unperturbed peripheral blood HIV-infected memory CD4+ T cell reservoir from ART-treated people living with HIV (ART-PLWH) via the presence of integrated accessible proviral DNA in concert with epigenetic and cell surface protein profiling. We identified profound reservoir heterogeneity within and between ART-PLWH, characterized by new and known surface markers within total and individual memory CD4+ T cell subsets. We further uncovered new epigenetic profiles and transcription factor motifs enriched in HIV-infected cells that suggest infected cells with accessible provirus, irrespective of reservoir distribution, are poised for reactivation during ART treatment. Together, our findings reveal the extensive inter- and intrapersonal cellular heterogeneity of the HIV reservoir, and establish an initial multiomic atlas to develop targeted reservoir elimination strategies.
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Grants
- K08 AI136660 NIAID NIH HHS
- T32 AI007632 NIAID NIH HHS
- R21 AI172629 NIAID NIH HHS
- UM1 AI164570 NIAID NIH HHS
- P30 AI045008 NIAID NIH HHS
- R01 AI031338 NIAID NIH HHS
- U.S. Department of Health & Human Services | NIH | National Institute of Allergy and Infectious Diseases (NIAID)
- Support for this study was provided by the following NIH grants: U19-A1-149680-02 (MRB), P01-AI31338 (MRB, KJB), K08-AI136660 (LAV), T32-AI007632 (VW), P30-AI045008 (Penn Center for AIDS Research) (MRB, LAV, KJB, PT, LJM), UM-1AI164570 (BEAT-HIV Collaboratory) which is co-supported by the National Institute of Allergies and Infectious Diseases (NIAID), the National Institute of Mental Health (NIMH), the National Institute of Neurological Disorders and Stroke (NINDS), the National Institute on Drug Abuse (NIDA), and the Robert I. Jacobs Fund of The Philadelphia Foundation (MRB, KJB, PT, LJM). LJM is also supported by the Herbert Kean, M.D., Family Professorship. CIENI-INER is supported by the Mexican Government (Programa Presupuestal P016; Anexo 13 del Decreto del Presupuesto de Egresos de la Federación).
- CIENI-INER is supported by the Mexican Government (Programa Presupuestal P016; Anexo 13 del Decreto del Presupuesto de Egresos de la Federación).
- LJM is also supported by the Herbert Kean, M.D., Family Professorship.
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Affiliation(s)
- Vincent H Wu
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Center for AIDS Research, University of Pennsylvania, Philadelphia, PA, USA
| | - Jayme M L Nordin
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Center for AIDS Research, University of Pennsylvania, Philadelphia, PA, USA
| | - Son Nguyen
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Institute for Medical Engineering and Science, Department of Chemistry, and Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Jaimy Joy
- Center for AIDS Research, University of Pennsylvania, Philadelphia, PA, USA
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Felicity Mampe
- Center for AIDS Research, University of Pennsylvania, Philadelphia, PA, USA
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Perla M Del Rio Estrada
- Centro de Investigación en Enfermedades Infecciosas, Instituto Nacional de Enfermedades Respiratorias, Mexico City, Mexico
| | - Fernanda Torres-Ruiz
- Centro de Investigación en Enfermedades Infecciosas, Instituto Nacional de Enfermedades Respiratorias, Mexico City, Mexico
| | - Mauricio González-Navarro
- Centro de Investigación en Enfermedades Infecciosas, Instituto Nacional de Enfermedades Respiratorias, Mexico City, Mexico
| | - Yara Andrea Luna-Villalobos
- Centro de Investigación en Enfermedades Infecciosas, Instituto Nacional de Enfermedades Respiratorias, Mexico City, Mexico
| | - Santiago Ávila-Ríos
- Centro de Investigación en Enfermedades Infecciosas, Instituto Nacional de Enfermedades Respiratorias, Mexico City, Mexico
| | - Gustavo Reyes-Terán
- Institutos Nacionales de Salud y Hospitales de Alta Especialidad, Secretaría de Salud de México, Mexico City, Mexico
| | - Pablo Tebas
- Center for AIDS Research, University of Pennsylvania, Philadelphia, PA, USA
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Luis J Montaner
- Center for AIDS Research, University of Pennsylvania, Philadelphia, PA, USA
- The Wistar Institute, Philadelphia, PA, USA
| | - Katharine J Bar
- Center for AIDS Research, University of Pennsylvania, Philadelphia, PA, USA
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Laura A Vella
- Center for AIDS Research, University of Pennsylvania, Philadelphia, PA, USA.
- Division of Infectious Diseases, Children's Hospital of Philadelphia, Philadelphia, PA, USA.
| | - Michael R Betts
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
- Center for AIDS Research, University of Pennsylvania, Philadelphia, PA, USA.
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12
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Dwivedi AK, Siegel DA, Thanh C, Hoh R, Hobbs KS, Pan T, Gibson EA, Martin J, Hecht F, Pilcher C, Milush J, Busch MP, Stone M, Huang ML, Levy CN, Roychoudhury P, Hladik F, Jerome KR, Henrich TJ, Deeks SG, Lee SA. Differences in expression of tumor suppressor, innate immune, inflammasome, and potassium/gap junction channel host genes significantly predict viral reservoir size during treated HIV infection. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.01.10.523535. [PMID: 36712077 PMCID: PMC9882059 DOI: 10.1101/2023.01.10.523535] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
The major barrier to an HIV cure is the persistence of infected cells that evade host immune surveillance despite effective antiretroviral therapy (ART). Most prior host genetic HIV studies have focused on identifying DNA polymorphisms (e.g., CCR5Δ32 , MHC class I alleles) associated with viral load among untreated "elite controllers" (~1% of HIV+ individuals who are able to control virus without ART). However, there have been few studies evaluating host genetic predictors of viral control for the majority of people living with HIV (PLWH) on ART. We performed host RNA sequencing and HIV reservoir quantification (total DNA, unspliced RNA, intact DNA) from peripheral CD4+ T cells from 191 HIV+ ART-suppressed non-controllers. Multivariate models included covariates for timing of ART initiation, nadir CD4+ count, age, sex, and ancestry. Lower HIV total DNA (an estimate of the total reservoir) was associated with upregulation of tumor suppressor genes NBL1 (q=0.012) and P3H3 (q=0.012). Higher HIV unspliced RNA (an estimate of residual HIV transcription) was associated with downregulation of several host genes involving inflammasome ( IL1A, CSF3, TNFAIP5, TNFAIP6, TNFAIP9 , CXCL3, CXCL10 ) and innate immune ( TLR7 ) signaling, as well as novel associations with potassium ( KCNJ2 ) and gap junction ( GJB2 ) channels, all q<0.05. Gene set enrichment analyses identified significant associations with TLR4/microbial translocation (q=0.006), IL-1β/NRLP3 inflammasome (q=0.008), and IL-10 (q=0.037) signaling. HIV intact DNA (an estimate of the "replication-competent" reservoir) demonstrated trends with thrombin degradation ( PLGLB1 ) and glucose metabolism ( AGL ) genes, but data were (HIV intact DNA detected in only 42% of participants). Our findings demonstrate that among treated PLWH, that inflammation, innate immune responses, bacterial translocation, and tumor suppression/cell proliferation host signaling play a key role in the maintenance of the HIV reservoir during ART. Further data are needed to validate these findings, including functional genomic studies, and expanded epidemiologic studies in female, non-European cohorts. Author Summary Although lifelong HIV antiretroviral therapy (ART) suppresses virus, the major barrier to an HIV cure is the persistence of infected cells that evade host immune surveillance despite effective ART, "the HIV reservoir." HIV eradication strategies have focused on eliminating residual virus to allow for HIV remission, but HIV cure trials to date have thus far failed to show a clinically meaningful reduction in the HIV reservoir. There is an urgent need for a better understanding of the host-viral dynamics during ART suppression to identify potential novel therapeutic targets for HIV cure. This is the first epidemiologic host gene expression study to demonstrate a significant link between HIV reservoir size and several well-known immunologic pathways (e.g., IL-1β, TLR7, TNF-α signaling pathways), as well as novel associations with potassium and gap junction channels (Kir2.1, connexin 26). Further data are needed to validate these findings, including functional genomic studies and expanded epidemiologic studies in female, non-European cohorts.
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13
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Shao Y, Xun J, Chen J, Lu H. Significance of initiating antiretroviral therapy in the early stage of HIV infection. Zhejiang Da Xue Xue Bao Yi Xue Ban 2022; 51:373-379. [PMID: 36207834 PMCID: PMC9511487 DOI: 10.3724/zdxbyxb-2022-0052] [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: 02/21/2022] [Accepted: 04/15/2022] [Indexed: 06/16/2023]
Abstract
A growing number of guidelines now recommend that human immunodeficiency virus (HIV) infected patients should be given early antiretroviral therapy (ART), especially in acute HIV infection. ART during early infection can limit viral reservoirs and improve immune cell function. From a societal prospect, early-infected individuals who achieve a state of viral suppression through ART can reduce the chance of HIV transmission and reduce the acquired immunodeficiency syndrome (AIDS)-related disease burden. However, there are many problems in the early diagnosis and treatment of HIV infection, including personal and social factors, which hinder the implementation and development of early treatment. It is recommended that initiating ART in the early stage of HIV infection, combined with other treatment strategies, so as to achieve functional cure.
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Affiliation(s)
- Yueming Shao
- Department of Infectious Diseases and Immunology, Shanghai Public Health Clinical Center, Fudan University, Shanghai 201508, China
| | - Jingna Xun
- Department of Infectious Diseases and Immunology, Shanghai Public Health Clinical Center, Fudan University, Shanghai 201508, China
| | - Jun Chen
- Department of Infectious Diseases and Immunology, Shanghai Public Health Clinical Center, Fudan University, Shanghai 201508, China
| | - Hongzhou Lu
- Department of Infectious Diseases, National Clinical Research Center for Infectious Diseases, the Third People's Hospital of Shenzhen, the Second Affiliated Hospital of Southern University of Science and Technology, Shenzhen 518112, Guangdong Province, China
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14
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Mori L, Valente ST. Cure and Long-Term Remission Strategies. METHODS IN MOLECULAR BIOLOGY (CLIFTON, N.J.) 2022; 2407:391-428. [PMID: 34985678 DOI: 10.1007/978-1-0716-1871-4_26] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
The majority of virally suppressed individuals will experience rapid viral rebound upon antiretroviral therapy (ART) interruption, providing a strong rationale for the development of cure strategies. Moreover, despite ART virological control, HIV infection is still associated with chronic immune activation, inflammation, comorbidities, and accelerated aging. These effects are believed to be due, in part, to low-grade persistent transcription and trickling production of viral proteins from the pool of latent proviruses constituting the viral reservoir. In recent years there has been an increasing interest in developing what has been termed a functional cure for HIV. This approach entails the long-term, durable control of viral expression in the absence of therapy, preventing disease progression and transmission, despite the presence of detectable integrated proviruses. One such strategy, the block-and-lock approach for a functional cure, proposes the epigenetic silencing of proviral expression, locking the virus in a profound latent state, from which reactivation is very unlikely. The proof-of-concept for this approach was demonstrated with the use of a specific small molecule targeting HIV transcription. Here we review the principles behind the block-and-lock approach and some of the additional strategies proposed to silence HIV expression.
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Affiliation(s)
- Luisa Mori
- Department of Immunology and Microbiology, The Scripps Research Institute, Jupiter, FL, USA
| | - Susana T Valente
- Department of Immunology and Microbiology, The Scripps Research Institute, Jupiter, FL, USA.
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15
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George AF, Luo X, Neidleman J, Hoh R, Vohra P, Thomas R, Shin MG, Lee MJ, Blish CA, Deeks S, Greene WC, Lee SA, Roan NR. Deep Phenotypic Analysis of Blood and Lymphoid T and NK Cells From HIV+ Controllers and ART-Suppressed Individuals. Front Immunol 2022; 13:803417. [PMID: 35154118 PMCID: PMC8829545 DOI: 10.3389/fimmu.2022.803417] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2021] [Accepted: 01/04/2022] [Indexed: 12/03/2022] Open
Abstract
T and natural killer (NK) cells are effector cells with key roles in anti-HIV immunity, including in lymphoid tissues, the major site of HIV persistence. However, little is known about the features of these effector cells from people living with HIV (PLWH), particularly from those who initiated antiretroviral therapy (ART) during acute infection. Our study design was to use 42-parameter CyTOF to conduct deep phenotyping of paired blood- and lymph node (LN)-derived T and NK cells from three groups of HIV+ aviremic individuals: elite controllers (N = 5), and ART-suppressed individuals who had started therapy during chronic (N = 6) vs. acute infection (N = 8), the latter of which is associated with better outcomes. We found that acute-treated individuals are enriched for specific subsets of T and NK cells, including blood-derived CD56-CD16+ NK cells previously associated with HIV control, and LN-derived CD4+ T follicular helper cells with heightened expansion potential. An in-depth comparison of the features of the cells from blood vs. LNs of individuals from our cohort revealed that T cells from blood were more activated than those from LNs. By contrast, LNs were enriched for follicle-homing CXCR5+ CD8+ T cells, which expressed increased levels of inhibitory receptors and markers of survival and proliferation as compared to their CXCR5- counterparts. In addition, a subset of memory-like CD56brightTCF1+ NK cells was enriched in LNs relative to blood. These results together suggest unique T and NK cell features in acute-treated individuals, and highlight the importance of examining effector cells not only in blood but also the lymphoid tissue compartment, where the reservoir mostly persists, and where these cells take on distinct phenotypic features.
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Affiliation(s)
- Ashley F. George
- Gladstone Institute of Virology, San Francisco, CA, United States,Department of Urology, University of California San Francisco, San Francisco, CA, United States
| | - Xiaoyu Luo
- Gladstone Institute of Virology, San Francisco, CA, United States
| | - Jason Neidleman
- Gladstone Institute of Virology, San Francisco, CA, United States,Department of Urology, University of California San Francisco, San Francisco, CA, United States
| | - Rebecca Hoh
- Division of HIV, Infectious Diseases and Global Medicine, University of California San Francisco, San Francisco, CA, United States
| | - Poonam Vohra
- Department of Pathology, University of California San Francisco, San Francisco, CA, United States
| | - Reuben Thomas
- Gladstone Institutes, San Francisco, CA, United States
| | | | - Madeline J. Lee
- Department of Medicine, Stanford University School of Medicine, Stanford, CA, United States,Program in Immunology, Stanford School of Medicine, Stanford, CA, United States
| | - Catherine A. Blish
- Department of Medicine, Stanford University School of Medicine, Stanford, CA, United States,Program in Immunology, Stanford School of Medicine, Stanford, CA, United States
| | - Steven G. Deeks
- Division of HIV, Infectious Diseases and Global Medicine, University of California San Francisco, San Francisco, CA, United States
| | - Warner C. Greene
- Gladstone Institute of Virology, San Francisco, CA, United States,Departments of Medicine, and Microbiology & Immunology, University of California San Francisco, San Francisco, CA, United States
| | - Sulggi A. Lee
- Zuckerberg San Francisco General Hospital and the University of California San Francisco, San Francisco, CA, United States,*Correspondence: Sulggi A. Lee, ; Nadia R. Roan,
| | - Nadia R. Roan
- Gladstone Institute of Virology, San Francisco, CA, United States,Department of Urology, University of California San Francisco, San Francisco, CA, United States,*Correspondence: Sulggi A. Lee, ; Nadia R. Roan,
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16
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Kleinman AJ, Pandrea I, Apetrei C. So Pathogenic or So What?-A Brief Overview of SIV Pathogenesis with an Emphasis on Cure Research. Viruses 2022; 14:135. [PMID: 35062339 PMCID: PMC8781889 DOI: 10.3390/v14010135] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2021] [Revised: 12/10/2021] [Accepted: 12/25/2021] [Indexed: 02/07/2023] Open
Abstract
HIV infection requires lifelong antiretroviral therapy (ART) to control disease progression. Although ART has greatly extended the life expectancy of persons living with HIV (PWH), PWH nonetheless suffer from an increase in AIDS-related and non-AIDS related comorbidities resulting from HIV pathogenesis. Thus, an HIV cure is imperative to improve the quality of life of PWH. In this review, we discuss the origins of various SIV strains utilized in cure and comorbidity research as well as their respective animal species used. We briefly detail the life cycle of HIV and describe the pathogenesis of HIV/SIV and the integral role of chronic immune activation and inflammation on disease progression and comorbidities, with comparisons between pathogenic infections and nonpathogenic infections that occur in natural hosts of SIVs. We further discuss the various HIV cure strategies being explored with an emphasis on immunological therapies and "shock and kill".
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Affiliation(s)
- Adam J. Kleinman
- Division of Infectious Diseases, DOM, School of Medicine, University of Pittsburgh, Pittsburgh, PA 15261, USA;
| | - Ivona Pandrea
- Department of Infectious Diseases and Immunology, School of Public Health, University of Pittsburgh, Pittsburgh, PA 15261, USA;
- Department of Pathology, School of Medicine, University of Pittsburgh, Pittsburgh, PA 15261, USA
| | - Cristian Apetrei
- Division of Infectious Diseases, DOM, School of Medicine, University of Pittsburgh, Pittsburgh, PA 15261, USA;
- Department of Infectious Diseases and Immunology, School of Public Health, University of Pittsburgh, Pittsburgh, PA 15261, USA;
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17
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Dijkstra M, Prins H, Prins JM, Reiss P, Boucher C, Verbon A, Rokx C, de Bree G. Cohort profile: the Netherlands Cohort Study on Acute HIV infection (NOVA), a prospective cohort study of people with acute or early HIV infection who immediately initiate HIV treatment. BMJ Open 2021; 11:e048582. [PMID: 34845066 PMCID: PMC8634014 DOI: 10.1136/bmjopen-2020-048582] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/03/2021] [Accepted: 10/14/2021] [Indexed: 11/03/2022] Open
Abstract
PURPOSE Initiation of combination antiretroviral therapy (cART) during acute or early HIV-infection (AEHI) limits the size of the viral reservoir and preserves immune function. This renders individuals who started cART during AEHI promising participants in HIV-cure trials. Therefore, we established a multicentre prospective cohort study in the Netherlands that enrols people with AEHI. In anticipation of future cure trials, we will longitudinally investigate the properties of the viral reservoir size and HIV-specific immune responses among cohort participants. PARTICIPANTS Participants immediately initiate intensified cART: dolutegravir, emtricitabine/tenofovir and darunavir/ritonavir (DRV/r). After 4 weeks, once baseline resistance data are available, DRV/r is discontinued. Three study groups are assembled based on the preparedness of individuals to participate in the extensiveness of sampling. Participants accepting immediate treatment and follow-up but declining additional sampling are included in study group 1 ('standard') and routine diagnostic procedures are performed. Participants willing to undergo blood, leukapheresis and semen sampling are included in study group 2 ('less invasive'). In study group 3 ('extended'), additional tissue (gut-associated lymphoid tissue, peripheral lymph node) and cerebrospinal fluid sampling are performed. FINDINGS TO DATE Between 2015 and 2020, 140 individuals with AEHI have been enrolled at nine study sites. At enrolment, median age was 36 (IQR 28-47) years, and 134 (95.7%) participants were men. Distribution of Fiebig stages was as follows: Fiebig I, 3 (2.1%); II, 20 (14.3%); III, 7 (5.0%); IV, 49 (35.0%); V, 39 (27.9%); VI, 22 (15.7%). Median plasma HIV RNA was 5.9 (IQR 4.7-6.7) log10 copies/mL and CD4 count 510 (IQR 370-700) cells/mm3. Median time from cART initiation to viral suppression was 8.0 (IQR 4.0-16.0) weeks. FUTURE PLANS The Netherlands Cohort Study on Acute HIV infection remains open for participant enrolment and for additional sites to join the network. This cohort provides a unique nationwide platform for conducting future in-depth virological, immunological, host genetic and interventional studies investigating HIV-cure strategies.
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Affiliation(s)
- Maartje Dijkstra
- Department of Infectious Diseases, Public Health Service of Amsterdam, Amsterdam, Netherlands
- Department of Internal Medicine, Division of Infectious Diseases, Amsterdam Institute for Infection and Immunity (AII), Amsterdam UMC, University of Amsterdam, Amsterdam, Netherlands
| | - Henrieke Prins
- Department of Internal Medicine, Division of Infectious Diseases, Erasmus University Medical Center, Rotterdam, Netherlands
| | - Jan M Prins
- Department of Internal Medicine, Division of Infectious Diseases, Amsterdam Institute for Infection and Immunity (AII), Amsterdam UMC, University of Amsterdam, Amsterdam, Netherlands
| | - Peter Reiss
- Department of Internal Medicine, Division of Infectious Diseases, Amsterdam Institute for Infection and Immunity (AII), Amsterdam UMC, University of Amsterdam, Amsterdam, Netherlands
- HIV Monitoring Foundation, Amsterdam, Noord-Holland, Netherlands
- Department of Global Health, Amsterdam Institute for Global Health and Development, Amsterdam UMC, University of Amsterdam, Amsterdam, the Netherlands
| | - Charles Boucher
- Department of Viroscience, Erasmus University Medical Center, Rotterdam, Netherlands
| | - Annelies Verbon
- Department of Internal Medicine, Division of Infectious Diseases, Erasmus University Medical Center, Rotterdam, Netherlands
| | - Casper Rokx
- Department of Internal Medicine, Division of Infectious Diseases, Erasmus University Medical Center, Rotterdam, Netherlands
| | - Godelieve de Bree
- Department of Internal Medicine, Amsterdam University Medical Centre, Amsterdam, Netherlands
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18
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Cohn LB, Chomont N, Deeks SG. The Biology of the HIV-1 Latent Reservoir and Implications for Cure Strategies. Cell Host Microbe 2020; 27:519-530. [PMID: 32272077 DOI: 10.1016/j.chom.2020.03.014] [Citation(s) in RCA: 163] [Impact Index Per Article: 40.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
Antiretroviral therapy (ART) inhibits HIV replication but is not curative. During ART, the integrated HIV genome persists indefinitely within CD4+ T cells and perhaps other cells. Here, we describe the mechanisms thought to contribute to its persistence during treatment and highlight findings from numerous recent studies describing the importance of cell proliferation in that process. Continued progress elucidating the biology will enhance our ability to develop effective curative interventions.
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Affiliation(s)
- Lillian B Cohn
- Chan Zuckerberg Biohub, San Francisco, CA; Department of Medicine, University of California, San Francisco, CA
| | - Nicolas Chomont
- Centre de recherche du CHUM and Department of Microbiology, Infectiology and Immunology, Université de Montréal, Montreal, QC, Canada
| | - Steven G Deeks
- Department of Medicine, University of California, San Francisco, CA.
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19
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Thorball CW, Borghesi A, Bachmann N, Von Siebenthal C, Vongrad V, Turk T, Neumann K, Beerenwinkel N, Bogojeska J, Roth V, Kok YL, Parbhoo S, Wieser M, Böni J, Perreau M, Klimkait T, Yerly S, Battegay M, Rauch A, Schmid P, Bernasconi E, Cavassini M, Kouyos RD, Günthard HF, Metzner KJ, Fellay J. Host Genomics of the HIV-1 Reservoir Size and Its Decay Rate During Suppressive Antiretroviral Treatment. J Acquir Immune Defic Syndr 2020; 85:517-524. [PMID: 33136754 DOI: 10.1097/qai.0000000000002473] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
BACKGROUND The primary hurdle for the eradication of HIV-1 is the establishment of a latent viral reservoir early after primary infection. Here, we investigated the potential influence of human genetic variation on the HIV-1 reservoir size and its decay rate during suppressive antiretroviral treatment. SETTING Genome-wide association study and exome sequencing study to look for host genetic determinants of HIV-1 reservoir measurements in patients enrolled in the Swiss HIV Cohort Study, a nation-wide prospective observational study. METHODS We measured total HIV-1 DNA in peripheral blood mononuclear cells from study participants, as a proxy for the reservoir size at 3 time points over a median of 5.4 years, and searched for associations between human genetic variation and 2 phenotypic readouts: the reservoir size at the first time point and its decay rate over the study period. We assessed the contribution of common genetic variants using genome-wide genotyping data from 797 patients with European ancestry enrolled in the Swiss HIV Cohort Study and searched for a potential impact of rare variants and exonic copy number variants using exome sequencing data generated in a subset of 194 study participants. RESULTS Genome-wide and exome-wide analyses did not reveal any significant association with the size of the HIV-1 reservoir or its decay rate on suppressive antiretroviral treatment. CONCLUSIONS Our results point to a limited influence of human genetics on the size of the HIV-1 reservoir and its long-term dynamics in successfully treated individuals.
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Affiliation(s)
- Christian W Thorball
- School of Life Sciences, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Alessandro Borghesi
- School of Life Sciences, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
- Neonatal Intensive Care Unit, Fondazione IRCCS Policlinico San Matteo, Pavia, Italy
| | - Nadine Bachmann
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, Zurich, Switzerland
- Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | - Chantal Von Siebenthal
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, Zurich, Switzerland
- Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | - Valentina Vongrad
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, Zurich, Switzerland
- Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | - Teja Turk
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, Zurich, Switzerland
- Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | - Kathrin Neumann
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, Zurich, Switzerland
- Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | - Niko Beerenwinkel
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
- SIB Swiss Institute of Bioinformatics, Basel, Switzerland
| | | | - Volker Roth
- Department of Mathematics and Computer Science, University of Basel, Basel, Switzerland
| | - Yik Lim Kok
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, Zurich, Switzerland
- Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | - Sonali Parbhoo
- Department of Mathematics and Computer Science, University of Basel, Basel, Switzerland
- Harvard John A. Paulson School of Engineering and Applied Sciences, Harvard University, Cambridge, MA
| | - Mario Wieser
- Department of Mathematics and Computer Science, University of Basel, Basel, Switzerland
| | - Jürg Böni
- Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | - Matthieu Perreau
- Division of Immunology and Allergy, Lausanne University Hospital (CHUV) and University of Lausanne, Lausanne, Switzerland
| | - Thomas Klimkait
- Division Infection Diagnostics, Department Biomedicine-Petersplatz, University of Basel, Basel, Switzerland
| | - Sabine Yerly
- Division of Infectious Diseases and Laboratory of Virology, University Hospital Geneva, University of Geneva, Geneva, Switzerland
| | - Manuel Battegay
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Basel, Basel, Switzerland
| | - Andri Rauch
- Department of Infectious Diseases, University Hospital Bern, Bern, Switzerland
| | - Patrick Schmid
- Division of Infectious Diseases, Cantonal Hospital of St. Gallen, St. Gallen, Switzerland
| | - Enos Bernasconi
- Infectious Diseases Service, Regional Hospital of Lugano, Lugano, Switzerland
| | - Matthias Cavassini
- Division of Infectious Diseases, Centre Hospitalier Universitaire Vaudois, University of Lausanne, Lausanne, Switzerland; and
| | - Roger D Kouyos
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, Zurich, Switzerland
- Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | - Huldrych F Günthard
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, Zurich, Switzerland
- Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | - Karin J Metzner
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, Zurich, Switzerland
- Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | - Jacques Fellay
- School of Life Sciences, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
- Precision Medicine Unit, Lausanne University Hospital (CHUV) and University of Lausanne, Lausanne, Switzerland
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20
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Gardner MR. Promise and Progress of an HIV-1 Cure by Adeno-Associated Virus Vector Delivery of Anti-HIV-1 Biologics. Front Cell Infect Microbiol 2020; 10:176. [PMID: 32391289 PMCID: PMC7190809 DOI: 10.3389/fcimb.2020.00176] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2020] [Accepted: 04/02/2020] [Indexed: 12/13/2022] Open
Abstract
Despite the success of antiretroviral therapy (ART) at suppressing HIV-1 infection, a cure that eradicates all HIV-1-infected cells has been elusive. The latent viral reservoir remains intact in tissue compartments that are not readily targeted by the host immune response that could accelerate the rate of reservoir decline during ART. However, over the past decade, numerous broadly neutralizing antibodies (bNAbs) have been discovered and characterized. These bNAbs have also given rise to engineered antibody-like inhibitors that are just as or more potent than bNAbs themselves. The question remains whether bNAbs and HIV-1 inhibitors will be the effective “kill” to a shock-and-kill approach to eliminate the viral reservoir. Additional research over the past few years has sought to develop recombinant adeno-associated virus (rAAV) vectors to circumvent the need for continual administration of bNAbs and maintain persistent expression in a host. This review discusses the advancements made in using rAAV vectors for the delivery of HIV-1 bNAbs and inhibitors and the future of this technology in HIV-1 cure research. Numerous groups have demonstrated with great efficacy that rAAV vectors can successfully express protective concentrations of bNAbs and HIV-1 inhibitors. Yet, therapeutic concentrations, especially in non-human primate (NHP) models, are not routinely achieved. As new studies have been reported, more challenges have been identified for utilizing rAAV vectors, specifically how the host immune response limits the attainable concentrations of bNAbs and inhibitors. The next few years should provide improvements to rAAV vector delivery that will ultimately show whether they can be used for expressing bNAbs and HIV-1 inhibitors to eliminate the HIV-1 viral reservoir.
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Affiliation(s)
- Matthew R Gardner
- Department of Immunology and Microbiology, The Scripps Research Institute, Jupiter, FL, United States
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21
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Peluso MJ, Bacchetti P, Ritter KD, Beg S, Lai J, Martin JN, Hunt PW, Henrich TJ, Siliciano JD, Siliciano RF, Laird GM, Deeks SG. Differential decay of intact and defective proviral DNA in HIV-1-infected individuals on suppressive antiretroviral therapy. JCI Insight 2020; 5:132997. [PMID: 32045386 PMCID: PMC7101154 DOI: 10.1172/jci.insight.132997] [Citation(s) in RCA: 132] [Impact Index Per Article: 33.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2019] [Accepted: 01/29/2020] [Indexed: 12/24/2022] Open
Abstract
BACKGROUNDThe relative stabilities of the intact and defective HIV genomes over time during effective antiretroviral therapy (ART) have not been fully characterized.METHODSWe used the intact proviral DNA assay (IPDA) to estimate the rate of change of intact and defective proviruses in HIV-infected adults on ART. We used linear spline models with a knot at seven years and a random intercept and slope up to the knot. We estimated the influence of covariates on rates of change.RESULTSWe studied 81 individuals for a median of 7.3 (IQR 5.9-9.6) years. Intact genomes declined more rapidly from initial suppression through seven years (15.7% per year decline; 95% CI -22.8%, -8.0%) and more slowly after seven years (3.6% per year; 95% CI -8.1%, +1.1%). The estimated half-life of the reservoir was 4.0 years (95% CI 2.7-8.3) until year seven and 18.7 years (95% CI 8.2-infinite) thereafter. There was substantial variability between individuals in the rate of decline until year seven. Intact provirus declined more rapidly than defective provirus (P < 0.001) and showed a faster decline in individuals with higher CD4+ T cell nadirs.CONCLUSIONThe biology of the replication-competent (intact) reservoir differs from that of the replication-incompetent (non-intact) pool of proviruses. The IPDA will likely be informative when investigating the impact of interventions targeting the reservoir.FUNDINGDelaney AIDS Research Enterprise, UCSF/Gladstone Institute of Virology & Immunology CFAR, CFAR Network of Integrated Systems, amfAR Institute for HIV Cure Research, I4C and Beat-HIV Collaboratories, Howard Hughes Medical Institute, Gilead Sciences, Bill and Melinda Gates Foundation.
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Affiliation(s)
- Michael J. Peluso
- Division of HIV, Infectious Diseases, and Global Medicine, Department of Medicine, and
| | - Peter Bacchetti
- Department of Epidemiology and Biostatistics, UCSF, San Francisco, California, USA
| | | | - Subul Beg
- Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Jun Lai
- Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Jeffrey N. Martin
- Department of Epidemiology and Biostatistics, UCSF, San Francisco, California, USA
| | - Peter W. Hunt
- Division of Experimental Medicine, Department of Medicine, UCSF, San Francisco, California, USA
| | - Timothy J. Henrich
- Division of Experimental Medicine, Department of Medicine, UCSF, San Francisco, California, USA
| | | | - Robert F. Siliciano
- Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
- Howard Hughes Medical Institute, Chevy Chase, Maryland, USA
| | | | - Steven G. Deeks
- Division of HIV, Infectious Diseases, and Global Medicine, Department of Medicine, and
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22
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Masters MC, Krueger KM, Williams JL, Morrison L, Cohn SE. Beyond one pill, once daily: current challenges of antiretroviral therapy management in the United States. Expert Rev Clin Pharmacol 2019; 12:1129-1143. [PMID: 31774001 DOI: 10.1080/17512433.2019.1698946] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Introduction: Modern antiretroviral therapy (ART) has revolutionized HIV treatment. ART regimens are now highly efficacious, well-tolerated, safe, often with one multi-drug pill, once-daily regimens available. However, clinical challenges persist in managing ART in persons with HIV (PWH), such as drug-drug interactions, side effects, pregnancy, co-morbidities, and adherence.Areas Covered: In this review, we discuss the ongoing challenges of ART for adults in the United States. We review the difficulties of initiating ART and maintaining therapy throughout adulthood and discuss new agents and strategies under investigation to address these issues. A PubMed search was utilized to identify relevant publications and guidelines through July 2019.Expert Opinion: Challenges persist in initiation and maintenance of ART. An individual's coexisting medical, social and personal factors must be considered in selecting and continuing ART to ensure safety, tolerability, and efficacy throughout adulthood. Continued development of new therapeutics and novel approaches to ART, such as long acting drugs or dual therapy, are needed to respond to many of these challenges. In addition, future research must address therapeutic disparities for populations historically underrepresented in clinical trials, including women, people aging with HIV, and those with complex comorbidities.
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Affiliation(s)
- Mary Clare Masters
- Division of Infectious Diseases, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Karen M Krueger
- Division of Infectious Diseases, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Janna L Williams
- Division of Infectious Diseases, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Lindsay Morrison
- Division of Infectious Diseases, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Susan E Cohn
- Division of Infectious Diseases, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
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23
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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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24
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Bachmann N, von Siebenthal C, Vongrad V, Turk T, Neumann K, Beerenwinkel N, Bogojeska J, Fellay J, Roth V, Kok YL, Thorball CW, Borghesi A, Parbhoo S, Wieser M, Böni J, Perreau M, Klimkait T, Yerly S, Battegay M, Rauch A, Hoffmann M, Bernasconi E, Cavassini M, Kouyos RD, Günthard HF, Metzner KJ. Determinants of HIV-1 reservoir size and long-term dynamics during suppressive ART. Nat Commun 2019; 10:3193. [PMID: 31324762 PMCID: PMC6642170 DOI: 10.1038/s41467-019-10884-9] [Citation(s) in RCA: 108] [Impact Index Per Article: 21.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2019] [Accepted: 06/05/2019] [Indexed: 12/20/2022] Open
Abstract
The HIV-1 reservoir is the major hurdle to a cure. We here evaluate viral and host characteristics associated with reservoir size and long-term dynamics in 1,057 individuals on suppressive antiretroviral therapy for a median of 5.4 years. At the population level, the reservoir decreases with diminishing differences over time, but increases in 26.6% of individuals. Viral blips and low-level viremia are significantly associated with slower reservoir decay. Initiation of ART within the first year of infection, pretreatment viral load, and ethnicity affect reservoir size, but less so long-term dynamics. Viral blips and low-level viremia are thus relevant for reservoir and cure studies. Here, Bachmann et al. provide data on long-term dynamics of the HIV-1 reservoir in 1,057 individuals on suppressive antiretroviral therapy and show that in 26.6% of individuals the reservoir increases. Viral blips and low-level viremia are significantly associated with a slower reservoir decay.
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Affiliation(s)
- Nadine Bachmann
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, 8091, Zurich, Switzerland.,Institute of Medical Virology, University of Zurich, 8057, Zurich, Switzerland
| | - Chantal von Siebenthal
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, 8091, Zurich, Switzerland.,Institute of Medical Virology, University of Zurich, 8057, Zurich, Switzerland
| | - Valentina Vongrad
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, 8091, Zurich, Switzerland.,Institute of Medical Virology, University of Zurich, 8057, Zurich, Switzerland
| | - Teja Turk
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, 8091, Zurich, Switzerland.,Institute of Medical Virology, University of Zurich, 8057, Zurich, Switzerland
| | - Kathrin Neumann
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, 8091, Zurich, Switzerland.,Institute of Medical Virology, University of Zurich, 8057, Zurich, Switzerland
| | - Niko Beerenwinkel
- Department of Biosystems Science and Engineering, ETH Zurich, 4058, Basel, Switzerland.,SIB Swiss Institute of Bioinformatics, 4057 Basel, Switzerland
| | | | - Jaques Fellay
- School of Life Sciences, EPFL, 1015, Lausanne, Switzerland.,Precision Medicine Unit, Lausanne University Hospital, 1011, Lausanne, Switzerland
| | - Volker Roth
- Department of Mathematics and Computer Science, University of Basel, 4001, Basel, Switzerland
| | - Yik Lim Kok
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, 8091, Zurich, Switzerland.,Institute of Medical Virology, University of Zurich, 8057, Zurich, Switzerland
| | | | - Alessandro Borghesi
- School of Life Sciences, EPFL, 1015, Lausanne, Switzerland.,Neonatal Intensive Care Unit, Fondazione IRCCS Policlinico San Matteo, Pavia, 27100, Italy
| | - Sonali Parbhoo
- Department of Mathematics and Computer Science, University of Basel, 4001, Basel, Switzerland
| | - Mario Wieser
- Department of Mathematics and Computer Science, University of Basel, 4001, Basel, Switzerland
| | - Jürg Böni
- Institute of Medical Virology, University of Zurich, 8057, Zurich, Switzerland
| | - Matthieu Perreau
- Division of Immunology and Allergy, Centre Hospitalier Universitaire Vaudois, University of Lausanne, 1015, Lausanne, Switzerland
| | - Thomas Klimkait
- Division Infection Diagnostics, Department Biomedicine-Petersplatz, University of Basel, 4001, Basel, Switzerland
| | - Sabine Yerly
- Division of Infectious Diseases and Laboratory of Virology, University Hospital Geneva, University of Geneva, 1211, Geneva, Switzerland
| | - Manuel Battegay
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Basel, 4031, Basel, Switzerland
| | - Andri Rauch
- Department of Infectious Diseases, University Hospital Bern, 3010, Bern, Switzerland
| | - Matthias Hoffmann
- Division of Infectious Diseases, Cantonal Hospital of St. Gallen, 9007, St. Gallen, Switzerland
| | - Enos Bernasconi
- Infectious Diseases Service, Regional Hospital, 6900, Lugano, Switzerland
| | - Matthias Cavassini
- Division of Infectious Diseases, Centre Hospitalier Universitaire Vaudois, University of Lausanne, 1015, Lausanne, Switzerland
| | - Roger D Kouyos
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, 8091, Zurich, Switzerland.,Institute of Medical Virology, University of Zurich, 8057, Zurich, Switzerland
| | - Huldrych F Günthard
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, 8091, Zurich, Switzerland. .,Institute of Medical Virology, University of Zurich, 8057, Zurich, Switzerland.
| | - Karin J Metzner
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, 8091, Zurich, Switzerland.,Institute of Medical Virology, University of Zurich, 8057, Zurich, Switzerland
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25
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Cao S, Woodrow KA. Nanotechnology approaches to eradicating HIV reservoirs. Eur J Pharm Biopharm 2019; 138:48-63. [PMID: 29879528 PMCID: PMC6279622 DOI: 10.1016/j.ejpb.2018.06.002] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2018] [Revised: 05/29/2018] [Accepted: 06/02/2018] [Indexed: 02/06/2023]
Abstract
The advent of combination antiretroviral therapy (cART) has transformed HIV-1 infection into a controllable chronic disease, but these therapies are incapable of eradicating the virus to bring about an HIV cure. Multiple strategies have been proposed and investigated to eradicate latent viral reservoirs from various biological sanctuaries. However, due to the complexity of HIV infection and latency maintenance, a single drug is unlikely to eliminate all HIV reservoirs and novel strategies may be needed to achieve better efficacy while limiting systemic toxicity. In this review, we describe HIV latency in cellular and anatomical reservoirs, and present an overview of current strategies for HIV cure with a focus on their challenges for clinical translation. Then we provide a summary of nanotechnology solutions that have been used to address challenges in HIV cure by delivering physicochemically diverse agents for combination therapy or targeting HIV reservoir sites. We also review nanocarrier-based gene delivery and immunotherapy used in cancer treatment but may have potential applications in HIV cure.
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Affiliation(s)
- Shijie Cao
- Department of Bioengineering, University of Washington, Seattle, WA 98105, USA
| | - Kim A Woodrow
- Department of Bioengineering, University of Washington, Seattle, WA 98105, USA.
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26
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Bon I, Calza L, Musumeci G, Longo S, Bertoldi A, D'Urbano V, Gibellini D, Magistrelli E, Viale PL, Re MC. Impact of Different Antiretroviral Strategies on Total HIV-DNA Level in Virologically Suppressed HIV-1 Infected Patients. Curr HIV Res 2019; 15:448-455. [PMID: 29210661 PMCID: PMC5876918 DOI: 10.2174/1570162x16666171206121026] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2017] [Revised: 11/02/2017] [Accepted: 11/28/2017] [Indexed: 01/11/2023]
Abstract
Background: Total HIV-DNA load in peripheral blood cell (PBMCs) reflects the global viral reservoir that seems not to be affected by antiretroviral treatment. However, some studies report-ed a different permeability of different drugs in cellular compartments. Objective: To investigate the relation between the amount of total HIV-1 DNA and different treatment strategies. Methods: Total HIV-1 DNA was quantified by real time PCR in PBMCs collected from 161 patients with long-term undetectable HIV-RNA receiving different therapy schedules (3-drug regimens or 2-drug regimen containing Raltegravir as integrase inhibitor). Results: Overall, HIV patients who started therapy with a median pre-ART CD4+ cell count >400 cells/mm3 and HIV viral load of 3 log10 copies/ml, achieved a lower amount of HIV total DNA. No significant correlation was found in DNA size when patients were stratified on the basis of different therapeutic protocols. However, HIV DNA load analysis, when only performed in HIV patients with a median pre-ART CD4+ cell count >200 cells/mm3 and HIV viral load < 3 log10 copies/ml, showed a significative DNA decrease in Raltegravir treated group with respect to the NNRTIs-treated group. Conclusion: The data emphasize that HIV-DNA level represents a predictive factor in long-term sup-pressive therapy patients. In addition, the diminished reservoir, only observed in patients treated with the NRTI-sparing regimen RAL plus PI/r before immunological and virological derangement, sug-gests that latest generation drugs, such as integrase inhibitors, might represent an optimal chance in the management of HIV infection.
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Affiliation(s)
- Isabella Bon
- Microbiology Section of the Department of Experimental, Diagnostic and Specialty Medicine, School of Medicine, University of Bologna, Via Massarenti, 9, Bologna, Italy
| | - Leonardo Calza
- Unit of Infectious Diseases, Department of Medical and Surgical Sciences, School of Medicine, University of Bologna, Via Massarenti, 9, Bologna, Italy
| | - Giuseppina Musumeci
- Microbiology Section of the Department of Experimental, Diagnostic and Specialty Medicine, School of Medicine, University of Bologna, Via Massarenti, 9, Bologna, Italy
| | - Serena Longo
- Microbiology Section of the Department of Experimental, Diagnostic and Specialty Medicine, School of Medicine, University of Bologna, Via Massarenti, 9, Bologna, Italy
| | - Alessia Bertoldi
- Microbiology Section of the Department of Experimental, Diagnostic and Specialty Medicine, School of Medicine, University of Bologna, Via Massarenti, 9, Bologna, Italy
| | - Vanessa D'Urbano
- Microbiology Section of the Department of Experimental, Diagnostic and Specialty Medicine, School of Medicine, University of Bologna, Via Massarenti, 9, Bologna, Italy
| | - Davide Gibellini
- Unit of Microbiology Department of Diagnostic and Public Health, University of Verona, Verona, Italy
| | - Eleonora Magistrelli
- Unit of Infectious Diseases, Department of Medical and Surgical Sciences, School of Medicine, University of Bologna, Via Massarenti, 9, Bologna, Italy
| | - Pier Luigi Viale
- Unit of Infectious Diseases, Department of Medical and Surgical Sciences, School of Medicine, University of Bologna, Via Massarenti, 9, Bologna, Italy
| | - Maria Carla Re
- Microbiology Section of the Department of Experimental, Diagnostic and Specialty Medicine, School of Medicine, University of Bologna, Via Massarenti, 9, Bologna, Italy.,Interuniversity Consortium, National Institute of Biostructures and Biosystems (INBB), Rome, Italy
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27
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HIV Subtype and Nef-Mediated Immune Evasion Function Correlate with Viral Reservoir Size in Early-Treated Individuals. J Virol 2019; 93:JVI.01832-18. [PMID: 30602611 DOI: 10.1128/jvi.01832-18] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2018] [Accepted: 11/30/2018] [Indexed: 11/20/2022] Open
Abstract
The HIV accessory protein Nef modulates key immune evasion and pathogenic functions, and its encoding gene region exhibits high sequence diversity. Given the recent identification of early HIV-specific adaptive immune responses as novel correlates of HIV reservoir size, we hypothesized that viral factors that facilitate the evasion of such responses-namely, Nef genetic and functional diversity-might also influence reservoir establishment and/or persistence. We isolated baseline plasma HIV RNA-derived nef clones from 30 acute/early-infected individuals who participated in a clinical trial of early combination antiretroviral therapy (cART) (<6 months following infection) and assessed each Nef clone's ability to downregulate CD4 and human leukocyte antigen (HLA) class I in vitro We then explored the relationships between baseline clinical, immunological, and virological characteristics and the HIV reservoir size measured 48 weeks following initiation of suppressive cART (where the reservoir size was quantified in terms of the proviral DNA loads as well as the levels of replication-competent HIV in CD4+ T cells). Maximal within-host Nef-mediated downregulation of HLA, but not CD4, correlated positively with post-cART proviral DNA levels (Spearman's R = 0.61, P = 0.0004) and replication-competent reservoir sizes (Spearman's R = 0.36, P = 0.056) in univariable analyses. Furthermore, the Nef-mediated HLA downregulation function was retained in final multivariable models adjusting for established clinical and immunological correlates of reservoir size. Finally, HIV subtype B-infected persons (n = 25) harbored significantly larger viral reservoirs than non-subtype B-infected persons (2 infected with subtype CRF01_AE and 3 infected with subtype G). Our results highlight a potentially important role of viral factors-in particular, HIV subtype and accessory protein function-in modulating viral reservoir establishment and persistence.IMPORTANCE While combination antiretroviral therapies (cART) have transformed HIV infection into a chronic manageable condition, they do not act upon the latent HIV reservoir and are therefore not curative. As HIV cure or remission should be more readily achievable in individuals with smaller HIV reservoirs, achieving a deeper understanding of the clinical, immunological, and virological determinants of reservoir size is critical to eradication efforts. We performed a post hoc analysis of 30 participants of a clinical trial of early cART who had previously been assessed in detail for their clinical, immunological, and reservoir size characteristics. We observed that the HIV subtype and autologous Nef-mediated HLA downregulation function correlated with the viral reservoir size measured approximately 1 year post-cART initiation. Our findings highlight virological characteristics-both genetic and functional-as possible novel determinants of HIV reservoir establishment and persistence.
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Pezzi HM, Guckenberger DJ, Schehr JL, Rothbauer J, Stahlfeld C, Singh A, Horn S, Schultz ZD, Bade RM, Sperger JM, Berry SM, Lang JM, Beebe DJ. Versatile exclusion-based sample preparation platform for integrated rare cell isolation and analyte extraction. LAB ON A CHIP 2018; 18:3446-3458. [PMID: 30334061 PMCID: PMC6402328 DOI: 10.1039/c8lc00620b] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
Rare cell populations provide a patient-centric tool to monitor disease treatment, response, and resistance. However, understanding rare cells is a complex problem, which requires cell isolation/purification and downstream molecular interrogation - processes challenged by non-target populations, which vary patient-to-patient and change with disease. As such, cell isolation platforms must be amenable to a range of sample types while maintaining high efficiency and purity. The multiplexed technology for automated extraction (mTAE) is a versatile magnetic bead-based isolation platform that facilitates positive, negative, and combinatorial selection with integrated protein staining and nucleic acid isolation. mTAE is validated by isolating circulating tumor cells (CTCs) - a model rare cell population - from breast and prostate cancer patient samples. Negative selection yielded high efficiency capture of CTCs while positive selection yielded higher purity with an average of only 95 contaminant cells captured per milliliter of processed whole blood. With combinatorial selection, an overall increase in capture efficiency was observed, highlighting the potential significance of integrating multiple capture approaches on a single platform. Following capture (and staining), on platform nucleic acid extraction enabled the detection of androgen receptor-related transcripts from CTCs isolated from prostate cancer patients. The flexibility (e.g. negative, positive, combinatorial selection) and capabilities (e.g. isolation, protein staining, and nucleic acid extraction) of mTAE enable users to freely interrogate specific cell populations, a capability required to understand the potential of emerging rare cell populations and readily adapt to the heterogeneity presented across clinical samples.
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Affiliation(s)
- Hannah M Pezzi
- Department of Biomedical Engineering, Wisconsin Institutes for Medical Research, University of Wisconsin-Madison, 1111 Highland Avenue, Madison, Wisconsin 53705, USA
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Bermejo M, Ambrosioni J, Bautista G, Climent N, Mateos E, Rovira C, Rodríguez-Mora S, López-Huertas MR, García-Gutiérrez V, Steegmann JL, Duarte R, Cervantes F, Plana M, Miró JM, Alcamí J, Coiras M. Evaluation of resistance to HIV-1 infection ex vivo of PBMCs isolated from patients with chronic myeloid leukemia treated with different tyrosine kinase inhibitors. Biochem Pharmacol 2018; 156:248-264. [PMID: 30142322 DOI: 10.1016/j.bcp.2018.08.031] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2018] [Accepted: 08/20/2018] [Indexed: 12/12/2022]
Abstract
Current antiretroviral treatment (ART) may control HIV-1 replication but it cannot cure the infection due to the formation of a reservoir of latently infected cells. CD4+ T cell activation during HIV-1 infection eliminates the antiviral function of the restriction factor SAMHD1, allowing proviral integration and the reservoir establishment. The role of tyrosine kinases during T-cell activation is essential for these processes. Therefore, the inhibition of tyrosine kinases could control HIV-1 infection and restrict the formation of the reservoir. A family of tyrosine kinase inhibitors (TKIs) is successfully used in clinic for treating chronic myeloid leukemia (CML). The safety and efficacy against HIV-1 infection of five TKIs was assayed in PBMCs isolated from CML patients on prolonged treatment with these drugs that were infected ex vivo with HIV-1. We determined that the most potent and safe TKI against HIV-1 infection was dasatinib, which preserved SAMHD1 antiviral function and avoid T-cell activation through TCR engagement and homeostatic cytokines. Imatinib and nilotinib showed lower potency and bosutinib was quite toxic in vitro. Ponatinib presented similar profile to dasatinib but as it has been associated with higher incidence of arterial ischemic events, dasatinib would be the better choice of TKI to be used as adjuvant of ART in order to avoid the establishment and replenishment of HIV-1 reservoir and move forward towards an HIV cure.
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Affiliation(s)
- Mercedes Bermejo
- AIDS Immunopathology Unit, National Center of Microbiology, Instituto de Salud Carlos III, Madrid, Spain
| | - Juan Ambrosioni
- Infectious Diseases Service, AIDS Research Group, Institut d́Investigacions Biomèdiques August Pi I Sunyer (IDIBAPS), Hospital Clínic, University of Barcelona, Barcelona, Spain
| | - Guiomar Bautista
- Clinical Hematology Service, Hospital Universitario Puerta de Hierro Majadahonda, Madrid, Spain
| | - Núria Climent
- Retrovirology and Viral Immunopathology Laboratory, AIDS Research Group, IDIBAPS, Hospital Clínic, University of Barcelona, Barcelona, Spain
| | - Elena Mateos
- AIDS Immunopathology Unit, National Center of Microbiology, Instituto de Salud Carlos III, Madrid, Spain
| | - Cristina Rovira
- Retrovirology and Viral Immunopathology Laboratory, AIDS Research Group, IDIBAPS, Hospital Clínic, University of Barcelona, Barcelona, Spain
| | - Sara Rodríguez-Mora
- AIDS Immunopathology Unit, National Center of Microbiology, Instituto de Salud Carlos III, Madrid, Spain; Division of Infection and Immunity, University College of London, UK
| | - María Rosa López-Huertas
- AIDS Immunopathology Unit, National Center of Microbiology, Instituto de Salud Carlos III, Madrid, Spain; Infectious Diseases Service, Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS) - Hospital Universitario Ramón y Cajal, Madrid, Spain
| | | | - Juan Luis Steegmann
- Hematology Department, Instituto de Investigación Sanitaria Hospital Universitario de La Princesa (IIS-IP), Madrid, Spain
| | - Rafael Duarte
- Clinical Hematology Service, Hospital Universitario Puerta de Hierro Majadahonda, Madrid, Spain
| | - Francisco Cervantes
- Hematology Department, IDIBAPS, Hospital Clínic, University of Barcelona, Barcelona, Spain
| | - Montserrat Plana
- Retrovirology and Viral Immunopathology Laboratory, AIDS Research Group, IDIBAPS, Hospital Clínic, University of Barcelona, Barcelona, Spain
| | - José M Miró
- Infectious Diseases Service, AIDS Research Group, Institut d́Investigacions Biomèdiques August Pi I Sunyer (IDIBAPS), Hospital Clínic, University of Barcelona, Barcelona, Spain
| | - José Alcamí
- AIDS Immunopathology Unit, National Center of Microbiology, Instituto de Salud Carlos III, Madrid, Spain
| | - Mayte Coiras
- AIDS Immunopathology Unit, National Center of Microbiology, Instituto de Salud Carlos III, Madrid, Spain.
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Duwal S, Dickinson L, Khoo S, von Kleist M. Hybrid stochastic framework predicts efficacy of prophylaxis against HIV: An example with different dolutegravir prophylaxis schemes. PLoS Comput Biol 2018; 14:e1006155. [PMID: 29902179 PMCID: PMC6001963 DOI: 10.1371/journal.pcbi.1006155] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2017] [Accepted: 04/21/2018] [Indexed: 01/02/2023] Open
Abstract
To achieve the 90-90-90 goals set by UNAIDS, the number of new HIV infections needs to decrease to approximately 500,000 by 2020. One of the 'five pillars' to achieve this goal is pre-exposure prophylaxis (PrEP). Truvada (emtricitabine-tenofovir) is currently the only medication approved for PrEP. Despite its advantages, Truvada is costly and requires individuals to adhere to the once-daily regimen. To improve PrEP, many next-generation regimen, including long-acting formulations, are currently investigated. However, pre-clinical testing may not guide candidate selection, since it often fails to translate into clinical efficacy. On the other hand, quantifying prophylactic efficacy in the clinic is ethically problematic and requires to conduct long (years) and large (N>1000 individuals) trials, precluding systematic evaluation of candidates and deployment strategies. To prioritize- and help design PrEP regimen, tools are urgently needed that integrate pharmacological-, viral- and host factors determining prophylactic efficacy. Integrating the aforementioned factors, we developed an efficient and exact stochastic simulation approach to predict prophylactic efficacy, as an example for dolutegravir (DTG). Combining the population pharmacokinetics of DTG with the stochastic framework, we predicted that plasma concentrations of 145.18 and 722.23nM prevent 50- and 90% sexual transmissions respectively. We then predicted the reduction in HIV infection when DTG was used in PrEP, PrEP 'on demand' and post-exposure prophylaxis (PEP) before/after virus exposure. Once daily PrEP with 50mg oral DTG prevented 99-100% infections, and 85% of infections when 50% of dosing events were missed. PrEP 'on demand' prevented 79-84% infections and PEP >80% when initiated within 6 hours after virus exposure and continued for as long as possible. While the simulation framework can easily be adapted to other PrEP candidates, our simulations indicated that oral 50mg DTG is non-inferior to Truvada. Moreover, the predicted 90% preventive concentrations can guide release kinetics of currently developed DTG nano-formulations.
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Affiliation(s)
- Sulav Duwal
- Department of Mathematics & Computer Science, Freie Universität Berlin, Berlin, Germany
| | - Laura Dickinson
- Institute of Translational Medicine, University of Liverpool, Liverpool, United Kingdom
| | - Saye Khoo
- Institute of Translational Medicine, University of Liverpool, Liverpool, United Kingdom
| | - Max von Kleist
- Department of Mathematics & Computer Science, Freie Universität Berlin, Berlin, Germany
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Ophinni Y, Inoue M, Kotaki T, Kameoka M. CRISPR/Cas9 system targeting regulatory genes of HIV-1 inhibits viral replication in infected T-cell cultures. Sci Rep 2018; 8:7784. [PMID: 29773895 PMCID: PMC5958087 DOI: 10.1038/s41598-018-26190-1] [Citation(s) in RCA: 61] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2017] [Accepted: 05/08/2018] [Indexed: 01/06/2023] Open
Abstract
The CRISPR/Cas9 system provides a novel and promising tool for editing the HIV-1 proviral genome. We designed RNA-guided CRISPR/Cas9 targeting the HIV-1 regulatory genes tat and rev with guide RNAs (gRNA) selected from each gene based on CRISPR specificity and sequence conservation across six major HIV-1 subtypes. Each gRNA was cloned into lentiCRISPRv2 before co-transfection to create a lentiviral vector and transduction into target cells. CRISPR/Cas9 transduction into 293 T and HeLa cells stably expressing Tat and Rev proteins successfully abolished the expression of each protein relative to that in non-transduced and gRNA-absent vector-transduced cells. Tat functional assays showed significantly reduced HIV-1 promoter-driven luciferase expression after tat-CRISPR transduction, while Rev functional assays revealed abolished gp120 expression after rev-CRISPR transduction. The target gene was mutated at the Cas9 cleavage site with high frequency and various indel mutations. Conversely, no mutations were detected at off-target sites and Cas9 expression had no effect on cell viability. CRISPR/Cas9 was further tested in persistently and latently HIV-1-infected T-cell lines, in which p24 levels were significantly suppressed even after cytokine reactivation, and multiplexing all six gRNAs further increased efficiency. Thus, the CRISPR/Cas9 system targeting HIV-1 regulatory genes may serve as a favorable means to achieve functional cures.
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Affiliation(s)
- Youdiil Ophinni
- Center for Infectious Diseases, Kobe University Graduate School of Medicine, Hyogo, 650-0017, Japan
| | - Mari Inoue
- Department of International Health, Kobe University Graduate School of Health Sciences, Hyogo, 654-0142, Japan
| | - Tomohiro Kotaki
- Department of International Health, Kobe University Graduate School of Health Sciences, Hyogo, 654-0142, Japan
| | - Masanori Kameoka
- Center for Infectious Diseases, Kobe University Graduate School of Medicine, Hyogo, 650-0017, Japan. .,Department of International Health, Kobe University Graduate School of Health Sciences, Hyogo, 654-0142, Japan.
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CHOMONT N, OKOYE AA, FAVRE D, TRAUTMANN L. Wake me up before you go: a strategy to reduce the latent HIV reservoir. AIDS 2018; 32:293-298. [PMID: 29135580 PMCID: PMC5758429 DOI: 10.1097/qad.0000000000001695] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
In the quest to eliminate or reduce the HIV reservoir, shock and kill strategies require the combined administration of a latency reversing agent (LRA) to reactivate the latent reservoir and an intervention to boost effector functions to clear this reservoir. Both parts of this strategy are quite inefficient when LRAs are administered to HIV-infected individuals on suppressive ART for several years, possibly due to low levels of induced antigen expression, negative impact of LRAs on clearance mechanisms, and very low number of effective cytotoxic T cells (CTLs). Here we provide rationale for an approach that would require only the administration of an LRA at the time of ART initiation to significantly reduce the HIV reservoir. The advantage of this strategy is an efficient reactivation of the latent HIV reservoir when high numbers of HIV-specific CD8+ T cells are present. This strategy may also potentiate more effective CTL responses and the establishment of a longer period of immune surveillance. This “window of opportunity” has been validated in silico , can be tested in preclinical non-human primate (NHP) models and translated rapidly in the clinic.
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Affiliation(s)
- Nicolas CHOMONT
- Research Centre of the Centre Hospitalier de l’Université de Montréal (CRCHUM), Montreal, Quebec, Canada
- Department of microbiology, infectiology and immunology, Faculty of Medicine. Université de Montréal, Montreal, Quebec, Canada
| | - Afam A. OKOYE
- Vaccine and Gene Therapy Institute, Oregon Health & Science University, Beaverton, Oregon, USA
- Oregon National Primate Research Center, Oregon Health & Science University, Beaverton, Oregon, USA
| | - David FAVRE
- GlaxoSmithKline, Durham, North Carolina, USA
| | - Lydie TRAUTMANN
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, Maryland, USA
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, Maryland, USA
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White DAE, Giordano TP, Pasalar S, Jacobson KR, Glick NR, Sha BE, Mammen PE, Hunt BR, Todorovic T, Moreno-Walton L, Adomolga V, Feaster DJ, Branson BM. Acute HIV Discovered During Routine HIV Screening With HIV Antigen-Antibody Combination Tests in 9 US Emergency Departments. Ann Emerg Med 2018; 72:29-40.e2. [PMID: 29310870 DOI: 10.1016/j.annemergmed.2017.11.027] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2017] [Revised: 11/09/2017] [Accepted: 11/22/2017] [Indexed: 11/16/2022]
Abstract
STUDY OBJECTIVE Newer combination HIV antigen-antibody tests allow detection of HIV sooner after infection than previous antibody-only immunoassays because, in addition to HIV-1 and -2 antibodies, they detect the HIV-1 p24 antigen, which appears before antibodies develop. We determine the yield of screening with HIV antigen-antibody tests and clinical presentations for new diagnoses of acute and established HIV infection across US emergency departments (EDs). METHODS This was a retrospective study of 9 EDs in 6 cities with HIV screening programs that integrated laboratory-based antigen-antibody tests between November 1, 2012, and December 31, 2015. Unique patients with newly diagnosed HIV infection were identified and classified as having either acute HIV infection or established HIV infection. Acute HIV infection was defined as a repeatedly reactive antigen-antibody test result, a negative HIV-1/HIV-2 antibody differentiation assay, or Western blot result, but detectable HIV ribonucleic acid (RNA); established HIV infection was defined as a repeatedly reactive antigen-antibody test result and a positive HIV-1/HIV-2 antibody differentiation assay or Western blot result. The primary outcomes were the number of new HIV diagnoses and proportion of patients with laboratory-defined acute HIV infection. Secondary outcomes compared reason for visit and the clinical presentation of acute HIV infection. RESULTS In total, 214,524 patients were screened for HIV and 839 (0.4%) received a new diagnosis, of which 122 (14.5%) were acute HIV infection and 717 (85.5%) were established HIV infection. Compared with patients with established HIV infection, those with acute HIV infection were younger, had higher RNA and CD4 counts, and were more likely to have viral syndrome (41.8% versus 6.5%) or fever (14.3% versus 3.4%) as their reason for visit. Most patients with acute HIV infection displayed symptoms attributable to acute infection (median symptom count 5 [interquartile range 3 to 6]), with fever often accompanied by greater than or equal to 3 other symptoms (60.7%). CONCLUSION ED screening using antigen-antibody tests identifies previously undiagnosed HIV infection at proportions that exceed the Centers for Disease Control and Prevention's screening threshold, with the added yield of identifying acute HIV infection in approximately 15% of patients with a new diagnosis. Patients with acute HIV infection often seek ED care for symptoms related to seroconversion.
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Affiliation(s)
- Douglas A E White
- Department of Emergency Medicine, Alameda Health System, Highland Hospital, Oakland, CA.
| | - Thomas P Giordano
- Department of Medicine, Section of Infectious Diseases, Baylor College of Medicine, Houston, TX
| | | | - Kathleen R Jacobson
- Clinical Family Medicine, University of Southern California, Keck School of Medicine, Los Angeles, CA
| | - Nancy R Glick
- Department of Medicine, Division of Infectious Diseases, Sinai Health System, Chicago, IL
| | - Beverly E Sha
- Department of Medicine, Division of Infectious Diseases, Rush University Medical Center, Chicago, IL
| | - Priya E Mammen
- Department of Emergency Medicine, Thomas Jefferson University Hospital, Philadelphia, PA
| | - Bijou R Hunt
- Sinai Urban Health Institute, Sinai Health System, Chicago, IL
| | - Tamara Todorovic
- Department of Emergency Medicine, Alameda Health System, Highland Hospital, Oakland, CA
| | - Lisa Moreno-Walton
- Department of Medicine, Section of Emergency Medicine, Louisiana State University Health Science Center, New Orleans, LA
| | - Vincent Adomolga
- Department of Emergency Medicine, Thomas Jefferson University Hospital, Philadelphia, PA
| | - Daniel J Feaster
- Department of Public Health Sciences, University of Miami, Miami, FL
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Murray JM, Zaunders J, Emery S, Cooper DA, Hey-Nguyen WJ, Koelsch KK, Kelleher AD. HIV dynamics linked to memory CD4+ T cell homeostasis. PLoS One 2017; 12:e0186101. [PMID: 29049331 PMCID: PMC5648138 DOI: 10.1371/journal.pone.0186101] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2017] [Accepted: 09/25/2017] [Indexed: 11/18/2022] Open
Abstract
The dynamics of latent HIV is linked to infection and clearance of resting memory CD4+ T cells. Infection also resides within activated, non-dividing memory cells and can be impacted by antigen-driven and homeostatic proliferation despite suppressive antiretroviral therapy (ART). We investigated whether plasma viral level (pVL) and HIV DNA dynamics could be explained by HIV’s impact on memory CD4+ T cell homeostasis. Median total, 2-LTR and integrated HIV DNA levels per μL of peripheral blood, for 8 primary (PHI) and 8 chronic HIV infected (CHI) individuals enrolled on a raltegravir (RAL) based regimen, exhibited greatest changes over the 1st year of ART. Dynamics slowed over the following 2 years so that total HIV DNA levels were equivalent to reported values for individuals after 10 years of ART. The mathematical model reproduced the multiphasic dynamics of pVL, and levels of total, 2-LTR and integrated HIV DNA in both PHI and CHI over 3 years of ART. Under these simulations, residual viremia originated from reactivated latently infected cells where most of these cells arose from clonal expansion within the resting phenotype. Since virion production from clonally expanded cells will not be affected by antiretroviral drugs, simulations of ART intensification had little impact on pVL. HIV DNA decay over the first year of ART followed the loss of activated memory cells (120 day half-life) while the 5.9 year half-life of total HIV DNA after this point mirrored the slower decay of resting memory cells. Simulations had difficulty reproducing the fast early HIV DNA dynamics, including 2-LTR levels peaking at week 12, and the later slow loss of total and 2-LTR HIV DNA, suggesting some ongoing infection. In summary, our modelling indicates that much of the dynamical behavior of HIV can be explained by its impact on memory CD4+ T cell homeostasis.
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Affiliation(s)
- John M. Murray
- School of Mathematics and Statistics, UNSW Australia, Sydney, NSW, Australia
- * E-mail:
| | - John Zaunders
- St Vincent's Hospital, Sydney, Centre for Applied Medical Research, Darlinghurst, NSW, Australia
| | - Sean Emery
- The Kirby Institute, University of New South Wales, Sydney, NSW Australia
| | - David A. Cooper
- The Kirby Institute, University of New South Wales, Sydney, NSW Australia
| | | | - Kersten K. Koelsch
- The Kirby Institute, University of New South Wales, Sydney, NSW Australia
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Prodger JL, Lai J, Reynolds SJ, Keruly JC, Moore RD, Kasule J, Kityamuweesi T, Buule P, Serwadda D, Nason M, Capoferri AA, Porcella SF, Siliciano RF, Redd AD, Siliciano JD, Quinn TC. Reduced Frequency of Cells Latently Infected With Replication-Competent Human Immunodeficiency Virus-1 in Virally Suppressed Individuals Living in Rakai, Uganda. Clin Infect Dis 2017; 65:1308-1315. [PMID: 28535179 PMCID: PMC5850010 DOI: 10.1093/cid/cix478] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2017] [Accepted: 05/19/2017] [Indexed: 01/17/2023] Open
Abstract
Background Human immunodeficiency virus type 1 (HIV-1) persists in latently infected resting CD4+ T cells (rCD4 cells), posing a major barrier to curing HIV-1 infection. Previous studies have quantified this pool of latently infected cells in Americans; however, no study has quantified this reservoir in sub-Saharan Africans, who make up the largest population of HIV-1-infected individuals globally. Methods Peripheral blood was collected from 70 virally suppressed HIV-1-infected individuals from Rakai District, Uganda, who had initiated antiretroviral therapy (ART) during chronic infection. The quantitative viral outgrowth assay was used to determine frequency of latently infected rCD4 cells containing replication-competent virus. Multivariate regression was used to identify correlates of reservoir size and to compare reservoir size between this Ugandan cohort and a previously studied cohort of individuals from Baltimore, Maryland. Results The median frequency of latently infected rCD4 cells in this Ugandan cohort was 0.36 infectious units per million cells (IUPM; 95% confidence interval, 0.26-0.55 IUPM), 3-fold lower than the frequency observed in the Baltimore cohort (1.08 IUPM; .72-1.49 IUPM; P < .001). Reservoir size in Ugandans was correlated positively with set-point viral load and negatively with duration of viral suppression. Conclusions Virally suppressed Ugandans had a 3-fold lower frequency of rCD4 cells latently infected with replication-competent HIV-1, compared with previous observations in a cohort of American patients, also treated with ART during chronic infection. The biological mechanism driving the observed smaller reservoir in Ugandans is of interest and may be of significance to HIV-1 eradication efforts.
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Affiliation(s)
- Jessica L Prodger
- Laboratory of Immunoregulation, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, and
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health and
| | - Jun Lai
- Division of Infectious Diseases, Johns Hopkins University School of Medicine,Baltimore, Maryland
| | - Steven J Reynolds
- Laboratory of Immunoregulation, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, and
- Division of Infectious Diseases, Johns Hopkins University School of Medicine,Baltimore, Maryland
- Rakai Health Sciences Program, Kalisizo,Uganda
| | - Jeanne C Keruly
- Division of Infectious Diseases, Johns Hopkins University School of Medicine,Baltimore, Maryland
| | - Richard D Moore
- Department of Medicine, Johns Hopkins University, Baltimore, Maryland
| | | | | | - Paul Buule
- Rakai Health Sciences Program, Kalisizo,Uganda
| | - David Serwadda
- Rakai Health Sciences Program, Kalisizo,Uganda
- Makerere University, Kampala, Uganda
| | - Martha Nason
- Biostatistics Research Branch, Division of Clinical Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland
| | - Adam A Capoferri
- Division of Infectious Diseases, Johns Hopkins University School of Medicine,Baltimore, Maryland
| | - Stephen F Porcella
- Genomics Unit, Research Technologies Branch, Rocky Mountain Laboratories, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, Montana; and
| | - Robert F Siliciano
- Division of Infectious Diseases, Johns Hopkins University School of Medicine,Baltimore, Maryland
- Howard Hughes Medical Institute, Baltimore, Maryland
| | - Andrew D Redd
- Laboratory of Immunoregulation, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, and
- Division of Infectious Diseases, Johns Hopkins University School of Medicine,Baltimore, Maryland
| | - Janet D Siliciano
- Department of Medicine, Johns Hopkins University, Baltimore, Maryland
| | - Thomas C Quinn
- Laboratory of Immunoregulation, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, and
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health and
- Division of Infectious Diseases, Johns Hopkins University School of Medicine,Baltimore, Maryland
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Henrich TJ, Hobbs KS, Hanhauser E, Scully E, Hogan LE, Robles YP, Leadabrand KS, Marty FM, Palmer CD, Jost S, Körner C, Li JZ, Gandhi RT, Hamdan A, Abramson J, LaCasce AS, Kuritzkes DR. Human Immunodeficiency Virus Type 1 Persistence Following Systemic Chemotherapy for Malignancy. J Infect Dis 2017; 216:254-262. [PMID: 28838149 DOI: 10.1093/infdis/jix265] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2017] [Accepted: 05/30/2017] [Indexed: 11/13/2022] Open
Abstract
Background Systemic chemotherapies for various malignancies have been shown to significantly, yet transiently, decrease numbers of CD4+ T lymphocytes, a major reservoir for human immunodeficiency virus type 1 (HIV-1) infection. However, little is known about the impact of cytoreductive chemotherapy on HIV-1 reservoir dynamics, persistence, and immune responses. Methods We investigated the changes in peripheral CD4+ T-cell-associated HIV-1 DNA and RNA levels, lymphocyte activation, viral population structure, and virus-specific immune responses in a longitudinal cohort of 15 HIV-1-infected individuals receiving systemic chemotherapy or subsequent autologous stem cell transplantation for treatment of hematological malignancies and solid tumors. Results Despite a transient reduction in CD4+ T cells capable of harboring HIV-1, a 1.7- and 3.3-fold increase in mean CD4+ T-cell-associated HIV-1 RNA and DNA, respectively, were observed months following completion of chemotherapy in individuals on antiretroviral therapy. We also observed changes in CD4+ T-cell population diversity and clonal viral sequence expansion during CD4+ T-cell reconstitution following chemotherapy cessation. Finally, HIV-1 DNA was preferentially, and in some cases exclusively, detected in cytomegalovirus (CMV)- and Epstein-Barr virus (EBV)-responsive CD4+ T cells following chemotherapy. Conclusions Expansion of HIV-infected CMV/EBV-specific CD4 + T cells may contribute to maintenance of the HIV DNA reservoir following chemotherapy.
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Affiliation(s)
- Timothy J Henrich
- Division of Experimental Medicine, University of California, San Francisco.,Division of Infectious Diseases, Brigham and Women's Hospital.,Harvard Medical School
| | - Kristen S Hobbs
- Division of Experimental Medicine, University of California, San Francisco.,Division of Infectious Diseases, Brigham and Women's Hospital
| | - Emily Hanhauser
- Division of Experimental Medicine, University of California, San Francisco.,Division of Infectious Diseases, Brigham and Women's Hospital
| | - Eileen Scully
- Division of Infectious Diseases, Brigham and Women's Hospital.,Harvard Medical School.,Dana-Farber Cancer Institute, Boston
| | - Louise E Hogan
- Division of Experimental Medicine, University of California, San Francisco.,Division of Infectious Diseases, Brigham and Women's Hospital.,Harvard Medical School
| | - Yvonne P Robles
- Division of Infectious Diseases, Brigham and Women's Hospital
| | | | - Francisco M Marty
- Division of Infectious Diseases, Brigham and Women's Hospital.,Harvard Medical School.,Dana-Farber Cancer Institute, Boston
| | - Christine D Palmer
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology and Harvard University, Cambridge
| | - Stephanie Jost
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology and Harvard University, Cambridge.,Beth Israel Deaconess Medical Center
| | - Christian Körner
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology and Harvard University, Cambridge
| | - Jonathan Z Li
- Division of Infectious Diseases, Brigham and Women's Hospital.,Harvard Medical School
| | - Rajesh T Gandhi
- Harvard Medical School.,Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology and Harvard University, Cambridge.,Massachusetts General Hospital, Boston
| | - Ayad Hamdan
- Harvard Medical School.,Beth Israel Deaconess Medical Center
| | - Jeremy Abramson
- Harvard Medical School.,Massachusetts General Hospital, Boston
| | - Ann S LaCasce
- Harvard Medical School.,Dana-Farber Cancer Institute, Boston
| | - Daniel R Kuritzkes
- Division of Infectious Diseases, Brigham and Women's Hospital.,Harvard Medical School
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37
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Kwarteng A, Ahuno ST, Kwakye-Nuako G. The therapeutic landscape of HIV-1 via genome editing. AIDS Res Ther 2017; 14:32. [PMID: 28705213 PMCID: PMC5513397 DOI: 10.1186/s12981-017-0157-8] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2017] [Accepted: 05/30/2017] [Indexed: 12/31/2022] Open
Abstract
Current treatment for HIV-1 largely relies on chemotherapy through the administration of antiretroviral drugs. While the search for anti-HIV-1 vaccine remain elusive, the use of highly active antiretroviral therapies (HAART) have been far-reaching and has changed HIV-1 into a manageable chronic infection. There is compelling evidence, including several side-effects of ARTs, suggesting that eradication of HIV-1 cannot depend solely on antiretrovirals. Gene therapy, an expanding treatment strategy, using RNA interference (RNAi) and programmable nucleases such as meganuclease, zinc finger nuclease (ZFN), transcription activator-like effector nuclease (TALEN), and clustered regularly interspaced short palindromic repeats/CRISPR-associated proteins (CRISPR-Cas9) are transforming the therapeutic landscape of HIV-1. TALENS and ZFNS are structurally similar modular systems, which consist of a FokI endonuclease fused to custom-designed effector proteins but have been largely limited, particularly ZFNs, due to their complexity and cost of protein engineering. However, the newly developed CRISPR-Cas9 system, consists of a single guide RNA (sgRNA), which directs a Cas9 endonuclease to complementary target sites, and serves as a superior alternative to the previous protein-based systems. The techniques have been successfully applied to the development of better HIV-1 models, generation of protective mutations in endogenous/host cells, disruption of HIV-1 genomes and even reactivating latent viruses for better detection and clearance by host immune response. Here, we focus on gene editing-based HIV-1 treatment and research in addition to providing perspectives for refining these techniques.
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Affiliation(s)
- Alexander Kwarteng
- Department of Biochemistry and Biotechnology, Kwame Nkrumah University of Science and Technology (KNUST), PMB, Kumasi, Ghana
- Kumasi Centre for Collaborative Research in Tropical Medicine (KCCR), Kumasi, Ghana
| | - Samuel Terkper Ahuno
- Department of Biochemistry and Biotechnology, Kwame Nkrumah University of Science and Technology (KNUST), PMB, Kumasi, Ghana
| | - Godwin Kwakye-Nuako
- Department of Biomedical Sciences, School of Allied Health Sciences, College of Health and Allied Sciences, University of Cape Coast, Cape Coast, Ghana
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38
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Mullins JI, Frenkel LM. Clonal Expansion of Human Immunodeficiency Virus-Infected Cells and Human Immunodeficiency Virus Persistence During Antiretroviral Therapy. J Infect Dis 2017; 215:S119-S127. [PMID: 28520966 DOI: 10.1093/infdis/jiw636] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
The latent HIV-1 reservoir in blood decays very slowly, even during prolonged suppression of viral replication by antiretroviral therapy (ART). Mechanisms for reservoir persistence include replenishment through low-level viral replication, longevity and homeostatic proliferation of memory T cells, and most recently appreciated, clonal expansion of HIV-infected cells. Clonally expanded cells make up a large and increasing fraction of the residual infected cell population on ART, and insertion of HIV proviruses into certain host cellular genes has been associated with this proliferation. That the vast majority of proviruses are defective clouds our assessment of the degree to which clonally expanded cells harbor infectious viruses, and thus the extent to which they contribute to reservoirs relevant to curing infection. This review summarizes past studies that have defined our current understanding and the gaps in our knowledge of the mechanisms by which proviral integration and clonal expansion sustain the HIV reservoir.
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Affiliation(s)
- James I Mullins
- Departments of Microbiology, Medicine, Global Health and Laboratory Medicine, University of Washington, Seattle, WA, US
| | - Lisa M Frenkel
- Departments of Pediatrics, Medicine, Global Health and Laboratory Medicine, University of Washington, Seattle, WA, US.,Center for Global Infectious Disease Research, Seattle Children's Research Institute, Seattle, WA, US
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39
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Dijkstra M, de Bree GJ, Stolte IG, Davidovich U, Sanders EJ, Prins M, Schim van der Loeff MF. Development and validation of a risk score to assist screening for acute HIV-1 infection among men who have sex with men. BMC Infect Dis 2017; 17:425. [PMID: 28615005 PMCID: PMC5471739 DOI: 10.1186/s12879-017-2508-4] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2016] [Accepted: 05/30/2017] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Early treatment of acute HIV-1 infection (AHI) is beneficial for patients and could reduce onward transmission. However, guidelines on whom to test for AHI with HIV-1 RNA testing are lacking. METHODS A risk score for possible AHI based on literature and expert opinion - including symptoms associated with AHI and early HIV-1 - was evaluated using data from the Amsterdam Cohort Studies among men who have sex with men (MSM). Subsequently, we optimized the risk score by constructing two multivariable logistic regression models: one including only symptoms and one combining symptoms with known risk factors for HIV-1 seroconversion, using generalized estimating equations. Several risk scores were generated from these models and the optimal risk score was validated using data from the Multicenter AIDS Cohort Study. RESULTS Using data from 1562 MSM with 175 HIV-1 seroconversion visits and 17,271 seronegative visits in the Amsterdam Cohort Studies, the optimal risk score included four symptoms (oral thrush, fever, lymphadenopathy, weight loss) and three risk factors (self-reported gonorrhea, receptive condomless anal intercourse, more than five sexual partners, all in the preceding six months) and yielded an AUC of 0.82. Sensitivity was 76.3% and specificity 76.3%. Validation in the Multicenter AIDS Cohort Study resulted in an AUC of 0.78, sensitivity of 56.2% and specificity of 88.8%. CONCLUSIONS The optimal risk score had good overall performance in the Amsterdam Cohort Studies and performed comparable (but showed lower sensitivity) in the validation study. Screening for AHI with four symptoms and three risk factors would increase the efficiency of AHI testing and potentially enhance early diagnosis and immediate treatment.
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Affiliation(s)
- Maartje Dijkstra
- Academic Medical Center, Department of Infectious Diseases, University of Amsterdam, P.O. Box 22700, 1100DE, Amsterdam, the Netherlands.,Public Health Service of Amsterdam, Department of Infectious Diseases, Research and Prevention, P.O. Box 2200, 1000CE, Amsterdam, the Netherlands
| | - Godelieve J de Bree
- Academic Medical Center, Department of Infectious Diseases, University of Amsterdam, P.O. Box 22700, 1100DE, Amsterdam, the Netherlands. .,Amsterdam Institute for Global Health and Development, University of Amsterdam, P.O. Box 22700, 1100DE, Amsterdam, the Netherlands.
| | - Ineke G Stolte
- Public Health Service of Amsterdam, Department of Infectious Diseases, Research and Prevention, P.O. Box 2200, 1000CE, Amsterdam, the Netherlands
| | - Udi Davidovich
- Academic Medical Center, Department of Infectious Diseases, University of Amsterdam, P.O. Box 22700, 1100DE, Amsterdam, the Netherlands.,Public Health Service of Amsterdam, Department of Infectious Diseases, Research and Prevention, P.O. Box 2200, 1000CE, Amsterdam, the Netherlands
| | - Eduard J Sanders
- Amsterdam Institute for Global Health and Development, University of Amsterdam, P.O. Box 22700, 1100DE, Amsterdam, the Netherlands.,Kenya Medical Research Institute, Centre for Geographic Medicine Research -Coast, P.O. Box 230, Kilifi, Kenya.,Nuffield Department of Clinical Medicine, University of Oxford, Oxford, OX3 7BN, UK
| | - Maria Prins
- Academic Medical Center, Department of Infectious Diseases, University of Amsterdam, P.O. Box 22700, 1100DE, Amsterdam, the Netherlands.,Public Health Service of Amsterdam, Department of Infectious Diseases, Research and Prevention, P.O. Box 2200, 1000CE, Amsterdam, the Netherlands
| | - Maarten F Schim van der Loeff
- Academic Medical Center, Department of Infectious Diseases, University of Amsterdam, P.O. Box 22700, 1100DE, Amsterdam, the Netherlands.,Public Health Service of Amsterdam, Department of Infectious Diseases, Research and Prevention, P.O. Box 2200, 1000CE, Amsterdam, the Netherlands
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40
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Alshorman A, Samarasinghe C, Lu W, Rong L. An HIV model with age-structured latently infected cells. JOURNAL OF BIOLOGICAL DYNAMICS 2017; 11:192-215. [PMID: 27338168 DOI: 10.1080/17513758.2016.1198835] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
HIV latency remains a major obstacle to viral elimination. The activation rate of latently infected cells may depend on the age of latent infection. In this paper, we develop a model of HIV infection including age-structured latently infected cells. We mathematically analyse the model and use numerical simulations with different activation functions to show that the model can explain the persistence of low-level viremia and the latent reservoir stability in patients on therapy. Sensitivity tests suggest that the model is robust to the changes of most parameters but is sensitive to the relative magnitude of the net generation rate and the long-term activation rate of latently infected cells. To reduce the sensitivity, we extend the model to include homeostatic proliferation of latently infected cells. The new model is robust in reproducing the long-term dynamics of the virus and latently infected cells observed in patients receiving prolonged combination therapy.
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Affiliation(s)
- Areej Alshorman
- a Department of Mathematics and Statistics , Oakland University , Rochester , MI , USA
| | - Chathuri Samarasinghe
- a Department of Mathematics and Statistics , Oakland University , Rochester , MI , USA
| | - Wenlian Lu
- b School of Mathematical Science , Fudan University , Shanghai , People's Republic of China
| | - Libin Rong
- a Department of Mathematics and Statistics , Oakland University , Rochester , MI , USA
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41
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Abstract
Descriptions of individuals who are able to control viral replication in the absence of antiretroviral therapy after receiving short-term therapy early in infection ("post-treatment controllers") has generated excitement and controversy within the field. As with natural or "elite" controllers, these cases provide hope that a long-term remission or "functional cure" might one day be possible. Here, we review what is known and not known about these cases and discuss the immunologic factors that may allow these unique individuals to be maintain viral control and may be important for future curative strategies.
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Affiliation(s)
- Leslie R Cockerham
- Division of Infectious Diseases, Medical College of Wisconsin, 9200 W. Wisconsin Ave, Suite 5100, Milwaukee, WI, 53226, USA.
| | - Hiroyu Hatano
- HIV/AIDS Division, San Francisco General Hospital, University of California, 995 Potrero Avenue, San Francisco, CA, 94110, USA.
| | - Steven G Deeks
- HIV/AIDS Division, San Francisco General Hospital, University of California, 995 Potrero Avenue, San Francisco, CA, 94110, USA.
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42
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Achieving HIV-1 Control through RNA-Directed Gene Regulation. Genes (Basel) 2016; 7:genes7120119. [PMID: 27941595 PMCID: PMC5192495 DOI: 10.3390/genes7120119] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2016] [Revised: 11/28/2016] [Accepted: 11/29/2016] [Indexed: 12/13/2022] Open
Abstract
HIV-1 infection has been transformed by combined anti-retroviral therapy (ART), changing a universally fatal infection into a controllable infection. However, major obstacles for an HIV-1 cure exist. The HIV latent reservoir, which exists in resting CD4+ T cells, is not impacted by ART, and can reactivate when ART is interrupted or ceased. Additionally, multi-drug resistance can arise. One alternate approach to conventional HIV-1 drug treatment that is being explored involves gene therapies utilizing RNA-directed gene regulation. Commonly known as RNA interference (RNAi), short interfering RNA (siRNA) induce gene silencing in conserved biological pathways, which require a high degree of sequence specificity. This review will provide an overview of the silencing pathways, the current RNAi technologies being developed for HIV-1 gene therapy, current clinical trials, and the challenges faced in progressing these treatments into clinical trials.
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43
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The Multifaceted Contributions of Chromatin to HIV-1 Integration, Transcription, and Latency. INTERNATIONAL REVIEW OF CELL AND MOLECULAR BIOLOGY 2016; 328:197-252. [PMID: 28069134 DOI: 10.1016/bs.ircmb.2016.08.006] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
The capacity of the human immunodeficiency virus (HIV-1) to establish latent infections constitutes a major barrier to the development of a cure for HIV-1. In latent infection, replication competent HIV-1 provirus is integrated within the host genome but remains silent, masking the infected cells from the activity of the host immune response. Despite the progress in elucidating the molecular players that regulate HIV-1 gene expression, the mechanisms driving the establishment and maintenance of latency are still not fully understood. Transcription from the HIV-1 genome occurs in the context of chromatin and is subjected to the same regulatory mechanisms that drive cellular gene expression. Much like in eukaryotic genes, the nucleosomal landscape of the HIV-1 promoter and its position within genomic chromatin are determinants of its transcriptional activity. Understanding the multilayered chromatin-mediated mechanisms that underpin HIV-1 integration and expression is of utmost importance for the development of therapeutic strategies aimed at reducing the pool of latently infected cells. In this review, we discuss the impact of chromatin structure on viral integration, transcriptional regulation and latency, and the host factors that influence HIV-1 replication by regulating chromatin organization. Finally, we describe therapeutic strategies under development to target the chromatin-HIV-1 interplay.
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44
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Michelini Z, Galluzzo CM, Pirillo MF, Francisci D, Degli Antoni A, Vivarelli A, Ladisa N, Cirioni O, Weimer LE, Fragola V, Cara A, Floridia M, Baroncelli S. HIV-1 DNA dynamics and variations in HIV-1 DNA protease and reverse transcriptase sequences in multidrug-resistant patients during successful raltegravir-based therapy. J Med Virol 2016; 88:2115-2124. [PMID: 27197719 DOI: 10.1002/jmv.24581] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/17/2016] [Indexed: 01/04/2023]
Abstract
There is limited information on the variations of HIV-1 DNA mutation profile in reverse transcriptase (RT) and protease (PR) genes during suppressive antiretroviral treatment (plasma HIV-1 RNA continuously <50 copies/ml) with raltegravir (RAL)-based regimens in patients with baseline RT/PR resistant HIV. Twelve multidrug resistant (RT: 12/12, PR: 8/12) HIV-infected patients were followed during effectively suppressive RAL-based therapy. Total and integrated HIV-1 DNA were assessed by real time PCR at baseline and every 6 months. Ultrasensitive (threshold: 2.5 copies/ml) plasma HIV-1 RNA and genotypic analysis of RT and PR in proviral DNA were performed at baseline and at 24 months. Half of the patients had full viral suppression (plasma HIV-RNA < 2.5 copies/ml) at month 12. Total HIV-1 DNA declined significantly after 12 months of therapy (from 249.2 to 145.7 copies/106 cells, P = 0.023), and remained stable until 24 months, when total HIV-1 DNA levels raised, concomitantly with a less stringent suppression of HIV-1 RNA (81.8% of patients with >2.5 copies/ml). Integrated HIV-1 DNA did not show fluctuations during the study period. Sequencing of the PR and RT regions from HIV-1 DNA revealed changes in the resistance mutation profile in five patients. Total HIV-1 DNA declined after the introduction of RAL-based therapy, with a rebound after 2 years. No changes were observed in levels of integrated DNA, suggesting limited effect on archived HIV. The RT and PR sequence changes in archived HIV-1 DNA suggest that variation of the mutation profile can occur even in the absence of detectable HIV-1 RNA. J. Med. Virol. 88:2115-2124, 2016. © 2016 Wiley Periodicals, Inc.
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Affiliation(s)
- Zuleika Michelini
- Department of Therapeutic Research and Medicines Evaluation, Istituto Superiore di Sanità, Rome, Italy
| | - Clementina Maria Galluzzo
- Department of Therapeutic Research and Medicines Evaluation, Istituto Superiore di Sanità, Rome, Italy
| | - Maria Franca Pirillo
- Department of Therapeutic Research and Medicines Evaluation, Istituto Superiore di Sanità, Rome, Italy
| | - Daniela Francisci
- Division of Infectious Diseases, Department of Medicine, University of Perugia, Perugia, Italy
| | - Anna Degli Antoni
- Department of Infectious Diseases and Hepatology, Azienda Ospedaliera di Parma, Parma, Italy
| | | | | | - Oscar Cirioni
- Clinic of Infectious Diseases, Ospedali Riuniti, Marche Polytechnic University, Ancona, Italy
| | - Liliana Elena Weimer
- Department of Therapeutic Research and Medicines Evaluation, Istituto Superiore di Sanità, Rome, Italy
| | - Vincenzo Fragola
- Department of Therapeutic Research and Medicines Evaluation, Istituto Superiore di Sanità, Rome, Italy
| | - Andrea Cara
- Department of Therapeutic Research and Medicines Evaluation, Istituto Superiore di Sanità, Rome, Italy
| | - Marco Floridia
- Department of Therapeutic Research and Medicines Evaluation, Istituto Superiore di Sanità, Rome, Italy
| | - Silvia Baroncelli
- Department of Therapeutic Research and Medicines Evaluation, Istituto Superiore di Sanità, Rome, Italy.
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45
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Integrated and Total HIV-1 DNA Predict Ex Vivo Viral Outgrowth. PLoS Pathog 2016; 12:e1005472. [PMID: 26938995 PMCID: PMC4777389 DOI: 10.1371/journal.ppat.1005472] [Citation(s) in RCA: 69] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2015] [Accepted: 02/03/2016] [Indexed: 02/06/2023] Open
Abstract
The persistence of a reservoir of latently infected CD4 T cells remains one of the major obstacles to cure HIV. Numerous strategies are being explored to eliminate this reservoir. To translate these efforts into clinical trials, there is a strong need for validated biomarkers that can monitor the reservoir over time in vivo. A comprehensive study was designed to evaluate and compare potential HIV-1 reservoir biomarkers. A cohort of 25 patients, treated with suppressive antiretroviral therapy was sampled at three time points, with median of 2.5 years (IQR: 2.4–2.6) between time point 1 and 2; and median of 31 days (IQR: 28–36) between time point 2 and 3. Patients were median of 6 years (IQR: 3–12) on ART, and plasma viral load (<50 copies/ml) was suppressed for median of 4 years (IQR: 2–8). Total HIV-1 DNA, unspliced (us) and multiply spliced HIV-1 RNA, and 2LTR circles were quantified by digital PCR in peripheral blood, at 3 time points. At the second time point, a viral outgrowth assay (VOA) was performed, and integrated HIV-1 DNA and relative mRNA expression levels of HIV-1 restriction factors were quantified. No significant change was found for long- and short-term dynamics of all HIV-1 markers tested in peripheral blood. Integrated HIV-1 DNA was associated with total HIV-1 DNA (p<0.001, R² = 0.85), us HIV-1 RNA (p = 0.029, R² = 0.40), and VOA (p = 0.041, R2 = 0.44). Replication-competent virus was detected in 80% of patients by the VOA and it correlated with total HIV-1 DNA (p = 0.039, R² = 0.54). The mean quantification difference between Alu-PCR and VOA was 2.88 log10, and 2.23 log10 between total HIV-1 DNA and VOA. The levels of usHIV-1 RNA were inversely correlated with mRNA levels of several HIV-1 restriction factors (TRIM5α, SAMHD1, MX2, SLFN11, pSIP1). Our study reveals important correlations between the viral outgrowth and total and integrated HIV-1 DNA measures, suggesting that the total pool of HIV-1 DNA may predict the size of the replication-competent virus in ART suppressed patients. Current HIV-1 research aims to find a cure for HIV-1, either by pursuing viral eradication or by attempting to attain an immune-mediated functional cure. For the purpose of interpreting the findings of these eradication strategies, a validated representative biomarker of the replication-competent latent HIV-1 reservoir is urgently needed. In this study we have evaluated several cell-associated HIV-1 persistence markers, and we have measured replication-competent reservoir using the viral outgrowth assay (VOA). The results show a correlation between the pool of HIV-1 DNA and the replication-competent reservoir. Our data show that the pool of HIV-1 DNA (total or integrated HIV-1 DNA) can predict the amount of replication-competent latent HIV-1 in patients receiving treatment. Hence, PCR based assays quantifying integrated and/or total HIV-1 DNA can play an important role in future studies aiming at HIV-1 eradication.
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46
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Massanella M, Fromentin R, Chomont N. Residual inflammation and viral reservoirs: alliance against an HIV cure. Curr Opin HIV AIDS 2016; 11:234-41. [PMID: 26575148 PMCID: PMC4743501 DOI: 10.1097/coh.0000000000000230] [Citation(s) in RCA: 99] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
PURPOSE OF REVIEW HIV persists in cellular and anatomical reservoirs during antiretroviral therapy (ART). Viral persistence is ensured by a variety of mechanisms including ongoing viral replication and proliferation of latently infected cells. In this review, we summarize recent findings establishing a link between the unresolved levels of inflammation observed in virally suppressed individuals on ART and the mechanisms responsible for HIV persistence. RECENT FINDINGS Residual levels of viral replication during ART are associated with persistent low levels of immune activation, suggesting that unresolved inflammation can promote the replenishment of the HIV reservoir in tissues. In addition, the recent findings that the latent HIV reservoir is maintained by continuous proliferation of latently infected cells provide another mechanism by which residual inflammation could contribute to HIV persistence. SUMMARY Residual inflammation during ART is likely to be a critical parameter contributing to HIV persistence. Therefore, reducing inflammation may be an efficient way to interfere with the maintenance of the HIV reservoir in virally suppressed individuals on ART.
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Affiliation(s)
- Marta Massanella
- Université de Montréal, Faculté de Médecine, Department of microbiology, infectiology and immunology, Montréal, QC, Canada
- Centre de Recherche du CHUM, Montréal, QC, Canada
| | - Rémi Fromentin
- Université de Montréal, Faculté de Médecine, Department of microbiology, infectiology and immunology, Montréal, QC, Canada
- Centre de Recherche du CHUM, Montréal, QC, Canada
| | - Nicolas Chomont
- Université de Montréal, Faculté de Médecine, Department of microbiology, infectiology and immunology, Montréal, QC, Canada
- Centre de Recherche du CHUM, Montréal, QC, Canada
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47
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Bermejo M, López-Huertas MR, García-Pérez J, Climent N, Descours B, Ambrosioni J, Mateos E, Rodríguez-Mora S, Rus-Bercial L, Benkirane M, Miró JM, Plana M, Alcamí J, Coiras M. Dasatinib inhibits HIV-1 replication through the interference of SAMHD1 phosphorylation in CD4+ T cells. Biochem Pharmacol 2016; 106:30-45. [PMID: 26851491 DOI: 10.1016/j.bcp.2016.02.002] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2015] [Accepted: 02/02/2016] [Indexed: 02/07/2023]
Abstract
Massive activation of infected CD4+ T cells during acute HIV-1 infection leads to reservoir seeding and T-cell destruction. During T-cell activation, the antiviral effect of the innate factor SAMHD1 is neutralized through phosphorylation at T592, allowing HIV-1 infection. Dasatinib, a tyrosine kinase inhibitor currently used for treating chronic myeloid leukemia, has been described to control HIV-1 replication through its negative effect on T-cell proliferation and viral entry. We demonstrate that Dasatinib can actually interfere with SAMHD1 phosphorylation in human peripheral blood lymphocytes, preserving its antiviral activity against HIV-1. Dasatinib prevented SAMHD1 phosphorylation in vitro and ex vivo, impairing HIV-1 reverse transcription and proviral integration. This was the major mechanism of action because the presence of Vpx, which degrades SAMHD1, in HIV-1 virions impeded the inhibitory effect of Dasatinib on HIV-1 replication. In fact, infection with VSV-pseudotyped HIV-1 virions and fusion of BlaM-Vpr-containing HIV-1 viruses with activated PBMCs in the presence of Dasatinib suggested that Dasatinib was not acting at fusion level. Finally, PBMCs from patients on chronic treatment with Dasatinib showed a lower level of SAMHD1 phosphorylation in response to activating stimuli and low susceptibility to HIV-1 infection ex vivo. Consequently, Dasatinib is a compound currently used in clinic that preserves the antiviral function of SAMHD1. Using Dasatinib as adjuvant of antiretroviral therapy during early primary HIV-1 infection would contribute to reduce viral replication and spread, prevent reservoir seeding, and preserve CD4 counts and CTL responses. These events would create a more favorable virologic and immunologic environment for future interventional studies aiming at HIV-1 eradication.
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MESH Headings
- Adult
- Anti-HIV Agents/pharmacology
- Antineoplastic Agents/pharmacology
- CD4-Positive T-Lymphocytes/drug effects
- CD4-Positive T-Lymphocytes/enzymology
- CD4-Positive T-Lymphocytes/virology
- Cell Proliferation/drug effects
- Dasatinib/pharmacology
- Female
- Gene Expression Regulation
- HIV Infections/drug therapy
- HIV Infections/enzymology
- HIV Infections/genetics
- HIV Infections/virology
- HIV-1/drug effects
- HIV-1/genetics
- HIV-1/growth & development
- Host-Pathogen Interactions
- Humans
- Leukemia, Myelogenous, Chronic, BCR-ABL Positive/drug therapy
- Leukemia, Myelogenous, Chronic, BCR-ABL Positive/enzymology
- Leukemia, Myelogenous, Chronic, BCR-ABL Positive/genetics
- Leukemia, Myelogenous, Chronic, BCR-ABL Positive/pathology
- Lymphocyte Activation
- Male
- Monomeric GTP-Binding Proteins/antagonists & inhibitors
- Monomeric GTP-Binding Proteins/genetics
- Monomeric GTP-Binding Proteins/metabolism
- Phosphorylation/drug effects
- Protein Kinase Inhibitors/pharmacology
- SAM Domain and HD Domain-Containing Protein 1
- Signal Transduction
- Vesiculovirus/genetics
- Viral Fusion Proteins/genetics
- Viral Fusion Proteins/metabolism
- Virus Internalization/drug effects
- Virus Replication/drug effects
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Affiliation(s)
- Mercedes Bermejo
- AIDS Immunopathology Unit, National Center of Microbiology, Instituto de Salud Carlos III, Madrid, Spain
| | - María Rosa López-Huertas
- AIDS Immunopathology Unit, National Center of Microbiology, Instituto de Salud Carlos III, Madrid, Spain
| | - Javier García-Pérez
- AIDS Immunopathology Unit, National Center of Microbiology, Instituto de Salud Carlos III, Madrid, Spain
| | - Núria Climent
- Retrovirology and Viral Immunopathology Laboratory, AIDS Research Group, Institut d'Investigacions Biomèdiques August Pi I Sunyer (IDIBAPS), Hospital Clínic, University of Barcelona, Barcelona, Spain
| | - Benjamin Descours
- Laboratory of Molecular Virology, Institute of Human Genetics, Montpellier, France
| | - Juan Ambrosioni
- Infectious Diseases Service, AIDS Research Group, Institut d'Investigacions Biomèdiques August Pi I Sunyer (IDIBAPS), Hospital Clínic, University of Barcelona, Barcelona, Spain
| | - Elena Mateos
- AIDS Immunopathology Unit, National Center of Microbiology, Instituto de Salud Carlos III, Madrid, Spain
| | - Sara Rodríguez-Mora
- AIDS Immunopathology Unit, National Center of Microbiology, Instituto de Salud Carlos III, Madrid, Spain
| | - Lucía Rus-Bercial
- AIDS Immunopathology Unit, National Center of Microbiology, Instituto de Salud Carlos III, Madrid, Spain
| | - Monsef Benkirane
- Laboratory of Molecular Virology, Institute of Human Genetics, Montpellier, France
| | - José M Miró
- Infectious Diseases Service, AIDS Research Group, Institut d'Investigacions Biomèdiques August Pi I Sunyer (IDIBAPS), Hospital Clínic, University of Barcelona, Barcelona, Spain
| | - Montserrat Plana
- Retrovirology and Viral Immunopathology Laboratory, AIDS Research Group, Institut d'Investigacions Biomèdiques August Pi I Sunyer (IDIBAPS), Hospital Clínic, University of Barcelona, Barcelona, Spain
| | - José Alcamí
- AIDS Immunopathology Unit, National Center of Microbiology, Instituto de Salud Carlos III, Madrid, Spain
| | - Mayte Coiras
- AIDS Immunopathology Unit, National Center of Microbiology, Instituto de Salud Carlos III, Madrid, Spain.
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48
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Sarmati L, D'Ettorre G, Parisi SG, Andreoni M. HIV Replication at Low Copy Number and its Correlation with the HIV Reservoir: A Clinical Perspective. Curr HIV Res 2016; 13:250-7. [PMID: 25845389 PMCID: PMC4460281 DOI: 10.2174/1570162x13666150407142539] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2014] [Revised: 01/27/2015] [Accepted: 04/02/2015] [Indexed: 01/01/2023]
Abstract
The efficacy of combination therapy (antiretroviral therapy - ARV) is demonstrated by the high rates of viral suppression achieved in most treated HIV patients. Whereas contemporary
treatments may continuously suppress HIV replication, they do not eliminate the latent reservoir, which can reactivate HIV infection if ARV is discontinued. The persistence of HIV proviral DNA and
infectious viruses in CD4+ T cells and others cells has long been considered a major obstacle in eradicating the HIV virus in treated patients. Moreover, recent studies have demonstrated the
persistence of HIV replication at low copies in most patients on suppressive ARV. The source of this ‘residual viraemia’ and whether it declines over years of therapy remain unknown. Similarly, little is known regarding the biological
relationships between the HIV reservoir and viral replication at low copies. The question of whether this ‘residual viraemia’ represents active replication or the release of non-productive virus from the reservoir has not been adequately
resolved. From a clinical perspective, both the quantification of the HIV reservoir and the detection of low levels of replication in full-responder patients on prolonged ARV may provide important information regarding the effectiveness of treatment
and the eradication of HIV. To date, the monitoring of these two parameters has been conducted only for research purposes; the routine use of standardised tests procedure is lacking.
This review aims to assess the current data regarding the correlation between HIV replication at low copies and the HIV reservoir and to provide useful information for clinicians.
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Affiliation(s)
- Loredana Sarmati
- Clinical Infectious Diseases, Tor Vergata University, V. Montpellier 1, 00133, Roma, Italy.
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49
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Ananworanich J, McSteen B, Robb ML. Broadly neutralizing antibody and the HIV reservoir in acute HIV infection: a strategy toward HIV remission? Curr Opin HIV AIDS 2016; 10:198-206. [PMID: 25700203 DOI: 10.1097/coh.0000000000000144] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
PURPOSE OF REVIEW Infection of long-lived CD4 T cells is a major obstacle to HIV remission, and antiretroviral therapy (ART) instituted during acute HIV infection restricts HIV reservoir establishment. Broadly neutralizing antibodies (bNAbs) may be employed in conjunction with early ART as strategies toward HIV remission. RECENT FINDINGS Proof-of-concept studies in vitro and in animal models demonstrated bNAbs' ability to block viral entry into cells, suppress viremia and reduce cell-associated viral DNA. Combination bNAbs were more effective than single bNAb in suppressing viremia. When bNAb was used with ART with or without combination latency reversing agents, it prevented viral rebound after ART interruption in at least half of the animals. In one study, macaques with low baseline viral load achieved viral remission even after the blood bNAb titer was no longer detected. SUMMARY The acute HIV infection period represents a unique opportunity to explore the use of bNAbs with ART to limit the reservoir seeding that may enhance the chance of HIV remission. This article discusses the effects of early ART and bNAbs on HIV reservoirs and proposes research strategies in acute HIV infection aiming at HIV reservoir reduction and HIV remission.
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Affiliation(s)
- Jintanat Ananworanich
- aU.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring bHenry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, Maryland, USA
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50
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The Effect of Therapeutic HIV Vaccination With ALVAC-HIV With or Without Remune on the Size of the Viral Reservoir (A CTN 173 Substudy). J Acquir Immune Defic Syndr 2015; 70:122-8. [PMID: 26375464 PMCID: PMC4577611 DOI: 10.1097/qai.0000000000000734] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
To assess whether therapeutic vaccination with ALVAC-HIV ± Remune affects viral reservoir size in antiretroviral therapy–treated individuals.
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