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Ishizaka A, Koga M, Mizutani T, Suzuki Y, Matano T, Yotsuyanagi H. Sustained gut dysbiosis and intestinal inflammation show correlation with weight gain in person with chronic HIV infection on antiretroviral therapy. BMC Microbiol 2024; 24:274. [PMID: 39044127 PMCID: PMC11267850 DOI: 10.1186/s12866-024-03431-0] [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: 02/16/2024] [Accepted: 07/18/2024] [Indexed: 07/25/2024] Open
Abstract
BACKGROUND Person with human immunodeficiency virus type-1 (PWH) are prone to chronic inflammation due to residual viral production, even with antiretroviral therapy (ART), which increases the risk of age-related diseases. There is also limited information on changes in the intestinal environment of PWH during ART. In this longitudinal study, we investigated changes in the gut microbiota, persistence of chronic inflammation, interactions between the gut environment and inflammation, and metabolic changes in PWH using long-term ART. RESULTS We analyzed changes in clinical parameters and gut microbiota in 46 PWH over a mean period of 4 years to understand the influence of gut dysbiosis on inflammation. Overall, changes in the gut microbiota included a decrease in some bacteria, mainly involved in short-chain fatty acid (SCFA) production, and an increase in certain opportunistic bacteria. Throughout the study period, an increase in bacterial-specific metabolic activity was observed in the intestinal environment. Continued decline in certain bacteria belonging to the Clostridia class and metabolic changes in gut bacteria involved in glucose metabolism. Additionally, patients with a low abundance of Parabacteroides exhibited low bacterial alpha diversity and a significant increase in body mass index (BMI) during the study period. Monocyte chemoattractant protein 1, a marker of macrophage activation in the plasma, continued to increase from baseline (first stool collection timepoint) to follow-up (second stool collection timepoint), demonstrating a mild correlation with BMI. Elevated BMI was mild to moderately correlated with elevated levels of plasma interleukin 16 and chemokine ligand 13, both of which may play a role in intestinal inflammation and bacterial translocation within the gut microbiota. The rate of BMI increase correlated with the rate of decrease in certain SCFA-producing bacteria, such as Anaerostipes and Coprococcus 3. CONCLUSION Our data suggest that despite effective ART, PWH with chronic inflammation exhibit persistent dysbiosis associated with gut inflammation, resulting in a transition to an intestinal environment with metabolic consequences. Moreover, the loss of certain bacteria such as Parabacteroides in PWH correlates with weight gain and may contribute to the development of metabolic diseases.
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Affiliation(s)
- Aya Ishizaka
- Division of Infectious Diseases, Advanced Clinical Research Center, the Institute of Medical Science, the University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo, 108-8639, Japan
| | - Michiko Koga
- Division of Infectious Diseases, Advanced Clinical Research Center, the Institute of Medical Science, the University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo, 108-8639, Japan
| | - Taketoshi Mizutani
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, the University of Tokyo, 6-2-3 Kashiwanoha, Chiba, Kashiwa-shi, 277-0882, Japan.
| | - Yutaka Suzuki
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, the University of Tokyo, 6-2-3 Kashiwanoha, Chiba, Kashiwa-shi, 277-0882, Japan
| | - Tetsuro Matano
- AIDS Research Center, National Institute of Infectious Diseases, Tokyo, Japan
- Department of AIDS Vaccine Development, The Institute of Medical Science, the University of Tokyo, Tokyo, Japan
| | - Hiroshi Yotsuyanagi
- Division of Infectious Diseases, Advanced Clinical Research Center, the Institute of Medical Science, the University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo, 108-8639, Japan.
- Department of Infectious Diseases and Applied Immunology, IMSUT Hospital of Institute of Medical Science, the University of Tokyo, Tokyo, Japan.
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Saborido-Alconchel A, Serna-Gallego A, Trujillo-Rodriguez M, Muñoz-Muela E, Álvarez-Ríos AI, Lozano C, Llaves-Flores S, Espinosa N, Roca-Oporto C, Herrero M, Sotomayor C, Gutierrez-Valencia A, Lopez-Cortes LF. Long-term effects on immunological, inflammatory markers, and HIV-1 reservoir after switching to a two-drug versus maintaining a three-drug regimen based on integrase inhibitors. Front Immunol 2024; 15:1423734. [PMID: 39055703 PMCID: PMC11269217 DOI: 10.3389/fimmu.2024.1423734] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2024] [Accepted: 06/24/2024] [Indexed: 07/27/2024] Open
Abstract
Objective To compare the long-term effects on immune parameters, inflammation, and HIV-1 reservoir after switching to a two-drug (2DR) versus maintaining an integrase inhibitor (InSTI)-based three-drug regimen (3DR). Methods Cross-sectional study in which HIV-1 treatment-naïve people started and maintained an InSTI-based 3DR or, at different times, switched to 2DR (dolutegravir or darunavir/cobicistat + lamivudine). CD4+ and CD8+ T-cell activation and exhaustion, plasma concentrations of hs-CRP, D-dimer, P-selectin, IL-1β, IL-6, TNF-α, IFN-γ, IP-10, sTNFR-I/II, MIP-1α/β, I-FABP, LBP, sCD14, sCD163, MCP-1, and cellular-associated HIV-1-DNA and -RNA were quantified by flow cytometry, different immunoassays, and droplet digital PCR, respectively. The U de Mann-Whitney test evaluated differences between 3DR and 2DR. Immune recovery was evaluated using a general linear model for repeated measures adjusted for different co-variables. Results Fifty participants per group were included. The median time on 3DR was 82 months for the 3DR group and 30 months for the 2DR group, after which it switched to 2DR for a median of 57 months. We did not find differences between both groups in any of the parameters analyzed. Specifically, some values in 3DR and 2DR were hs-CRP, 0.92 mg/L (0.45-2.23) vs. 1.23 (0.61-2.38); D-dimer, 190.0 µg/L (150.0-370.0) vs. 190.0 (150.0-397.5); IL-6, 2.8 pg/mL (1.3-5.3) vs. 3.2 (2.1-4.7); sCD14, 4.5 ng/mL (3.3-6.2) vs. 5.0 (3.6-6.1), respectively, all p ≥ 0.399. Conclusion In the long term, switching to 2DR does not negatively affect immunologic parameters, inflammatory markers, or HIV-1 reservoir. Clinical trial registration identifier NCT04076423.
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Affiliation(s)
- Abraham Saborido-Alconchel
- Clinical Unit of Infectious Diseases, Microbiology and Parasitology, Institute of Biomedicine of Seville/Virgen del Rocio University Hospital/The Spanish National Research Council (CSIC)/University of Seville, Seville, Spain
| | - Ana Serna-Gallego
- Clinical Unit of Infectious Diseases, Microbiology and Parasitology, Institute of Biomedicine of Seville/Virgen del Rocio University Hospital/The Spanish National Research Council (CSIC)/University of Seville, Seville, Spain
| | - María Trujillo-Rodriguez
- Clinical Unit of Infectious Diseases, Microbiology and Parasitology, Institute of Biomedicine of Seville/Virgen del Rocio University Hospital/The Spanish National Research Council (CSIC)/University of Seville, Seville, Spain
| | - Esperanza Muñoz-Muela
- Clinical Unit of Infectious Diseases, Microbiology and Parasitology, Institute of Biomedicine of Seville/Virgen del Rocio University Hospital/The Spanish National Research Council (CSIC)/University of Seville, Seville, Spain
| | - Ana I. Álvarez-Ríos
- Department of Clinical Biochemistry, Institute of Biomedicine of Seville/Virgen del Rocio University Hospital/The Spanish National Research Council (CSIC)/University of Seville, Seville, Spain
| | - Carmen Lozano
- Clinical Unit of Infectious Diseases, Microbiology and Parasitology, Institute of Biomedicine of Seville/Virgen del Rocio University Hospital/The Spanish National Research Council (CSIC)/University of Seville, Seville, Spain
| | - Silvia Llaves-Flores
- Clinical Unit of Infectious Diseases, Microbiology and Parasitology, Institute of Biomedicine of Seville/Virgen del Rocio University Hospital/The Spanish National Research Council (CSIC)/University of Seville, Seville, Spain
| | - Nuria Espinosa
- Clinical Unit of Infectious Diseases, Microbiology and Parasitology, Institute of Biomedicine of Seville/Virgen del Rocio University Hospital/The Spanish National Research Council (CSIC)/University of Seville, Seville, Spain
| | - Cristina Roca-Oporto
- Clinical Unit of Infectious Diseases, Microbiology and Parasitology, Institute of Biomedicine of Seville/Virgen del Rocio University Hospital/The Spanish National Research Council (CSIC)/University of Seville, Seville, Spain
| | - Marta Herrero
- Clinical Unit of Infectious Diseases, Microbiology and Parasitology, Institute of Biomedicine of Seville/Virgen del Rocio University Hospital/The Spanish National Research Council (CSIC)/University of Seville, Seville, Spain
| | - Cesar Sotomayor
- Clinical Unit of Infectious Diseases, Microbiology and Parasitology, Institute of Biomedicine of Seville/Virgen del Rocio University Hospital/The Spanish National Research Council (CSIC)/University of Seville, Seville, Spain
| | - Alicia Gutierrez-Valencia
- Clinical Unit of Infectious Diseases, Microbiology and Parasitology, Institute of Biomedicine of Seville/Virgen del Rocio University Hospital/The Spanish National Research Council (CSIC)/University of Seville, Seville, Spain
- Primary Care Pharmacist Service, Sevilla Primary Care District, Seville, Spain
| | - Luis F. Lopez-Cortes
- Clinical Unit of Infectious Diseases, Microbiology and Parasitology, Institute of Biomedicine of Seville/Virgen del Rocio University Hospital/The Spanish National Research Council (CSIC)/University of Seville, Seville, Spain
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Semenova L, Wang Y, Falcinelli S, Archin N, Cooper-Volkheimer AD, Margolis DM, Goonetilleke N, Murdoch DM, Rudin CD, Browne EP. Machine learning approaches identify immunologic signatures of total and intact HIV DNA during long-term antiretroviral therapy. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.11.16.567386. [PMID: 38014340 PMCID: PMC10680759 DOI: 10.1101/2023.11.16.567386] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/29/2023]
Abstract
Understanding the interplay between the HIV reservoir and the host immune system may yield insights into HIV persistence during antiretroviral therapy (ART) and inform strategies for a cure. Here, we applied machine learning approaches to cross-sectional high-parameter HIV reservoir and immunology data in order to characterize host-reservoir associations and generate new hypotheses about HIV reservoir biology. High-dimensional immunophenotyping, quantification of HIV-specific T cell responses, and measurement of genetically intact and total HIV proviral DNA frequencies were performed on peripheral blood samples from 115 people with HIV (PWH) on long-term ART. Analysis demonstrated that both intact and total proviral DNA frequencies were positively correlated with T cell activation and exhaustion. Years of ART and select bifunctional HIV-specific CD4 T cell responses were negatively correlated with the percentage of intact proviruses. A Leave-One-Covariate-Out (LOCO) inference approach identified specific HIV reservoir and clinical-demographic parameters, such as age and biological sex, that were particularly important in predicting immunophenotypes. Overall, immune parameters were more strongly associated with total HIV proviral frequencies than intact proviral frequencies. Uniquely, however, expression of the IL-7 receptor alpha chain (CD127) on CD4 T cells was more strongly correlated with the intact reservoir. Unsupervised dimension reduction analysis identified two main clusters of PWH with distinct immune and reservoir characteristics. Using reservoir correlates identified in these initial analyses, decision tree methods were employed to visualize relationships among multiple immune and clinical-demographic parameters and the HIV reservoir. Finally, using random splits of our data as training-test sets, machine learning algorithms predicted with approximately 70% accuracy whether a given participant had qualitatively high or low levels of total or intact HIV DNA. The techniques described here may be useful for assessing global patterns within the increasingly high-dimensional data used in HIV reservoir and other studies of complex biology.
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Kilroy JM, Leal AA, Henderson AJ. Chronic HIV Transcription, Translation, and Persistent Inflammation. Viruses 2024; 16:751. [PMID: 38793632 PMCID: PMC11125830 DOI: 10.3390/v16050751] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2024] [Revised: 05/02/2024] [Accepted: 05/07/2024] [Indexed: 05/26/2024] Open
Abstract
People with HIV exhibit persistent inflammation that correlates with HIV-associated comorbidities including accelerated aging, increased risk of cardiovascular disease, and neuroinflammation. Mechanisms that perpetuate chronic inflammation in people with HIV undergoing antiretroviral treatments are poorly understood. One hypothesis is that the persistent low-level expression of HIV proviruses, including RNAs generated from defective proviral genomes, drives the immune dysfunction that is responsible for chronic HIV pathogenesis. We explore factors during HIV infection that contribute to the generation of a pool of defective proviruses as well as how HIV-1 mRNA and proteins alter immune function in people living with HIV.
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Affiliation(s)
- Jonathan M. Kilroy
- Department of Virology, Immunology, Microbiology, Boston University Chobanian and Avedisian School of Medicine, Boston, MA 02118, USA; (J.M.K.); (A.A.L.)
| | - Andrew A. Leal
- Department of Virology, Immunology, Microbiology, Boston University Chobanian and Avedisian School of Medicine, Boston, MA 02118, USA; (J.M.K.); (A.A.L.)
| | - Andrew J. Henderson
- Department of Virology, Immunology, Microbiology, Boston University Chobanian and Avedisian School of Medicine, Boston, MA 02118, USA; (J.M.K.); (A.A.L.)
- Department of Medicine and Virology, Immunology, Microbiology, Boston University Chobanian and Avedisian School of Medicine, Boston, MA 02118, USA
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Mbonye U, Karn J. The cell biology of HIV-1 latency and rebound. Retrovirology 2024; 21:6. [PMID: 38580979 PMCID: PMC10996279 DOI: 10.1186/s12977-024-00639-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/07/2024] Open
Abstract
Transcriptionally latent forms of replication-competent proviruses, present primarily in a small subset of memory CD4+ T cells, pose the primary barrier to a cure for HIV-1 infection because they are the source of the viral rebound that almost inevitably follows the interruption of antiretroviral therapy. Over the last 30 years, many of the factors essential for initiating HIV-1 transcription have been identified in studies performed using transformed cell lines, such as the Jurkat T-cell model. However, as highlighted in this review, several poorly understood mechanisms still need to be elucidated, including the molecular basis for promoter-proximal pausing of the transcribing complex and the detailed mechanism of the delivery of P-TEFb from 7SK snRNP. Furthermore, the central paradox of HIV-1 transcription remains unsolved: how are the initial rounds of transcription achieved in the absence of Tat? A critical limitation of the transformed cell models is that they do not recapitulate the transitions between active effector cells and quiescent memory T cells. Therefore, investigation of the molecular mechanisms of HIV-1 latency reversal and LRA efficacy in a proper physiological context requires the utilization of primary cell models. Recent mechanistic studies of HIV-1 transcription using latently infected cells recovered from donors and ex vivo cellular models of viral latency have demonstrated that the primary blocks to HIV-1 transcription in memory CD4+ T cells are restrictive epigenetic features at the proviral promoter, the cytoplasmic sequestration of key transcription initiation factors such as NFAT and NF-κB, and the vanishingly low expression of the cellular transcription elongation factor P-TEFb. One of the foremost schemes to eliminate the residual reservoir is to deliberately reactivate latent HIV-1 proviruses to enable clearance of persisting latently infected cells-the "Shock and Kill" strategy. For "Shock and Kill" to become efficient, effective, non-toxic latency-reversing agents (LRAs) must be discovered. Since multiple restrictions limit viral reactivation in primary cells, understanding the T-cell signaling mechanisms that are essential for stimulating P-TEFb biogenesis, initiation factor activation, and reversing the proviral epigenetic restrictions have become a prerequisite for the development of more effective LRAs.
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Affiliation(s)
- Uri Mbonye
- Department of Molecular Biology and Microbiology, Case Western Reserve University School of Medicine, Cleveland, OH, 44106, USA.
| | - Jonathan Karn
- Department of Molecular Biology and Microbiology, Case Western Reserve University School of Medicine, Cleveland, OH, 44106, USA.
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Zhang X, Qazi AA, Deshmukh S, Lobato Ventura R, Mukim A, Beliakova-Bethell N. Single-cell RNA sequencing reveals common and unique gene expression profiles in primary CD4+ T cells latently infected with HIV under different conditions. Front Cell Infect Microbiol 2023; 13:1286168. [PMID: 38156317 PMCID: PMC10754520 DOI: 10.3389/fcimb.2023.1286168] [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] [Received: 08/31/2023] [Accepted: 11/20/2023] [Indexed: 12/30/2023] Open
Abstract
Background The latent HIV reservoir represents the major barrier to a cure. One curative strategy is targeting diseased cells for elimination based on biomarkers that uniquely define these cells. Single-cell RNA sequencing (scRNA-seq) has enabled the identification of gene expression profiles associated with disease at the single-cell level. Because HIV provirus in many cells during latency is not entirely silent, it became possible to determine gene expression patterns in a subset of cells latently infected with HIV. Objective The primary objective of this study was the identification of the gene expression profiles of single latently infected CD4+ T cells using scRNA-seq. Different conditions of latency establishment were considered. The identified profiles were then explored to prioritize the identified genes for future experimental validation. Methods To facilitate gene prioritization, three approaches were used. First, we characterized and compared the gene expression profiles of HIV latency established in different environments: in cells that encountered an activation stimulus and then returned to quiescence, and in resting cells that were infected directly via cell-to-cell viral transmission from autologous activated, productively infected cells. Second, we characterized and compared the gene expression profiles of HIV latency established with viruses of different tropisms, using an isogenic pair of CXCR4- and CCR5-tropic viruses. Lastly, we used proviral expression patterns in cells from people with HIV to more accurately define the latently infected cells in vitro. Results Our analyses demonstrated that a subset of genes is expressed differentially between latently infected and uninfected cells consistently under most conditions tested, including cells from people with HIV. Our second important observation was the presence of latency signatures, associated with variable conditions when latency was established, including cellular exposure and responsiveness to a T cell receptor stimulus and the tropism of the infecting virus. Conclusion Common signatures, specifically genes that encode proteins localized to the cell surface, should be prioritized for further testing at the protein level as biomarkers for the ability to enrich or target latently infected cells. Cell- and tropism-dependent biomarkers may need to be considered in developing targeting strategies to ensure that all the different reservoir subsets are eliminated.
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Affiliation(s)
- Xinlian Zhang
- Herbert Wertheim School of Public Health and Human Longevity Science, University of California, San Diego, CA, United States
| | - Andrew A. Qazi
- Veterans Affairs (VA), San Diego Healthcare System and Veterans Medical Research Foundation, San Diego, CA, United States
| | - Savitha Deshmukh
- Veterans Affairs (VA), San Diego Healthcare System and Veterans Medical Research Foundation, San Diego, CA, United States
| | - Roni Lobato Ventura
- Veterans Affairs (VA), San Diego Healthcare System and Veterans Medical Research Foundation, San Diego, CA, United States
| | - Amey Mukim
- Veterans Affairs (VA), San Diego Healthcare System and Veterans Medical Research Foundation, San Diego, CA, United States
| | - Nadejda Beliakova-Bethell
- Veterans Affairs (VA), San Diego Healthcare System and Veterans Medical Research Foundation, San Diego, CA, United States
- Department of Medicine, University of California, San Diego, CA, United States
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Nabatanzi R, Ssekamatte P, Castelnuovo B, Kambugu A, Nakanjako D. Increased Levels of Caspase-1 and IL-1β Among Adults With Persistent Immune Activation After 12 Years of Suppressive Antiretroviral Therapy in the Infectious Diseases Institute HIV Treatment Cohort. Open Forum Infect Dis 2023; 10:ofad539. [PMID: 37953818 PMCID: PMC10638490 DOI: 10.1093/ofid/ofad539] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2023] [Indexed: 11/14/2023] Open
Abstract
Background We sought evidence of activated pyroptosis and the inflammasome pathways among human immunodeficiency virus (HIV)-infected adults after 12 years of suppressive antiretroviral therapy (ART) and persistent immune activation in the Infectious Diseases Institute HIV treatment cohort in Uganda. Methods In a cross-sectional study, using peripheral blood mononuclear cells of HIV-infected individuals with high and low immune activation (CD4/CD8+CD38+HLA-DR+ cells) relative to HIV-negative reference group, caspase-1 expression was measured using flow cytometry and plasma interleukin 18 and interleukin 1β (IL-1β) levels using enzyme-linked immunosorbent assay. Results There was higher expression of caspase-1 by CD4 T cells of ART-treated individuals with high immune activation relative to those with lower immune activation (P = .04). Similarly, plasma levels of IL-1β were higher among ART-treated individuals with high immune activation levels relative to those with low immune activation levels (P = .009). We observed a low positive correlation between caspase-1 expression by CD4/CD8 T cells and immune activation levels (r= 0.497 and r= 0.329, respectively). Conclusions Caspase-1 and IL-1β were high among individuals with high immune activation despite 12 years of suppressive ART. There is a need to further understand the role of persistent abortive infection and the latent HIV reservoir characteristics as drivers of persistent activation and inflammation and to subsequently intervene to prevent the complications of chronic immune activation during long-term ART.
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Affiliation(s)
- Rose Nabatanzi
- Department of Immunology and Molecular Biology, Makerere University College of Health Sciences, Kampala, Uganda
- Infectious Diseases Institute, Makerere University College of Health Sciences, Kampala, Uganda
| | - Phillip Ssekamatte
- Department of Immunology and Molecular Biology, Makerere University College of Health Sciences, Kampala, Uganda
| | - Barbara Castelnuovo
- Infectious Diseases Institute, Makerere University College of Health Sciences, Kampala, Uganda
- Department of Medicine, School of Medicine, Makerere University College of Health Sciences, Kampala, Uganda
| | - Andrew Kambugu
- Infectious Diseases Institute, Makerere University College of Health Sciences, Kampala, Uganda
- Department of Medicine, School of Medicine, Makerere University College of Health Sciences, Kampala, Uganda
| | - Damalie Nakanjako
- Infectious Diseases Institute, Makerere University College of Health Sciences, Kampala, Uganda
- Department of Medicine, School of Medicine, Makerere University College of Health Sciences, Kampala, Uganda
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Dubé M, Tastet O, Dufour C, Sannier G, Brassard N, Delgado GG, Pagliuzza A, Richard C, Nayrac M, Routy JP, Prat A, Estes JD, Fromentin R, Chomont N, Kaufmann DE. Spontaneous HIV expression during suppressive ART is associated with the magnitude and function of HIV-specific CD4 + and CD8 + T cells. Cell Host Microbe 2023; 31:1507-1522.e5. [PMID: 37708853 PMCID: PMC10542967 DOI: 10.1016/j.chom.2023.08.006] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2023] [Revised: 06/01/2023] [Accepted: 08/11/2023] [Indexed: 09/16/2023]
Abstract
Spontaneous transcription and translation of HIV can persist during suppressive antiretroviral therapy (ART). The quantity, phenotype, and biological relevance of this spontaneously "active" reservoir remain unclear. Using multiplexed single-cell RNAflow-fluorescence in situ hybridization (FISH), we detect active HIV transcription in 14/18 people with HIV on suppressive ART, with a median of 28/million CD4+ T cells. While these cells predominantly exhibit abortive transcription, p24-expressing cells are evident in 39% of participants. Phenotypically diverse, active reservoirs are enriched in central memory T cells and CCR6- and activation-marker-expressing cells. The magnitude of the active reservoir positively correlates with total HIV-specific CD4+ and CD8+ T cell responses and with multiple HIV-specific T cell clusters identified by unsupervised analysis. These associations are particularly strong with p24-expressing active reservoir cells. Single-cell vDNA sequencing shows that active reservoirs are largely dominated by defective proviruses. Our data suggest that these reservoirs maintain HIV-specific CD4+ and CD8+ T responses during suppressive ART.
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Affiliation(s)
- Mathieu Dubé
- Department of Immunopathology, Research Centre of the Centre Hospitalier de l'Université de Montréal (CRCHUM), Montreal, QC H2X 0A9, Canada.
| | - Olivier Tastet
- Department of Immunopathology, Research Centre of the Centre Hospitalier de l'Université de Montréal (CRCHUM), Montreal, QC H2X 0A9, Canada
| | - Caroline Dufour
- Department of Immunopathology, Research Centre of the Centre Hospitalier de l'Université de Montréal (CRCHUM), Montreal, QC H2X 0A9, Canada; Department of Microbiology, Infectious Diseases and Immunology, Faculty of Medicine, Université de Montréal, Montreal, QC H3C 3J7, Canada
| | - Gérémy Sannier
- Department of Immunopathology, Research Centre of the Centre Hospitalier de l'Université de Montréal (CRCHUM), Montreal, QC H2X 0A9, Canada; Department of Microbiology, Infectious Diseases and Immunology, Faculty of Medicine, Université de Montréal, Montreal, QC H3C 3J7, Canada
| | - Nathalie Brassard
- Department of Immunopathology, Research Centre of the Centre Hospitalier de l'Université de Montréal (CRCHUM), Montreal, QC H2X 0A9, Canada
| | - Gloria-Gabrielle Delgado
- Department of Immunopathology, Research Centre of the Centre Hospitalier de l'Université de Montréal (CRCHUM), Montreal, QC H2X 0A9, Canada
| | - Amélie Pagliuzza
- Department of Immunopathology, Research Centre of the Centre Hospitalier de l'Université de Montréal (CRCHUM), Montreal, QC H2X 0A9, Canada
| | - Corentin Richard
- Department of Immunopathology, Research Centre of the Centre Hospitalier de l'Université de Montréal (CRCHUM), Montreal, QC H2X 0A9, Canada
| | - Manon Nayrac
- Department of Immunopathology, Research Centre of the Centre Hospitalier de l'Université de Montréal (CRCHUM), Montreal, QC H2X 0A9, Canada
| | - Jean-Pierre Routy
- Chronic Viral Illnesses Service and Division of Hematology, McGill University Health Centre (CUSM), Montreal, QC H4A 3J1, Canada; Infectious Diseases and Immunity in Global Health Program, Research Institute, McGill University Health Centre, Montreal, QC H4A 3J1, Canada
| | - Alexandre Prat
- Department of Immunopathology, Research Centre of the Centre Hospitalier de l'Université de Montréal (CRCHUM), Montreal, QC H2X 0A9, Canada; Department of Neurosciences, Faculty of Medicine, Université de Montréal, Montréal, QC H3C 3J7, Canada
| | - Jacob D Estes
- Vaccine and Gene Therapy Institute, Oregon Health & Science University, Beaverton, OR 97006, USA; Oregon National Primate Research Center, Oregon Health & Science University, Beaverton, OR 97006, USA
| | - Rémi Fromentin
- Department of Immunopathology, Research Centre of the Centre Hospitalier de l'Université de Montréal (CRCHUM), Montreal, QC H2X 0A9, Canada
| | - Nicolas Chomont
- Department of Immunopathology, Research Centre of the Centre Hospitalier de l'Université de Montréal (CRCHUM), Montreal, QC H2X 0A9, Canada; Department of Microbiology, Infectious Diseases and Immunology, Faculty of Medicine, Université de Montréal, Montreal, QC H3C 3J7, Canada
| | - Daniel E Kaufmann
- Department of Immunopathology, Research Centre of the Centre Hospitalier de l'Université de Montréal (CRCHUM), Montreal, QC H2X 0A9, Canada; Department of Microbiology, Infectious Diseases and Immunology, Faculty of Medicine, Université de Montréal, Montreal, QC H3C 3J7, Canada; Division of Infectious Diseases, Department of Medicine, Lausanne University Hospital and University of Lausanne, 1011 Lausanne, Switzerland.
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9
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Ramirez PW, Pantoja C, Beliakova-Bethell N. An Evaluation on the Role of Non-Coding RNA in HIV Transcription and Latency: A Review. HIV AIDS (Auckl) 2023; 15:115-134. [PMID: 36942082 PMCID: PMC10024501 DOI: 10.2147/hiv.s383347] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Accepted: 02/24/2023] [Indexed: 03/16/2023] Open
Abstract
The existence of latent cellular reservoirs is recognized as the major barrier to an HIV cure. Reactivating and eliminating "shock and kill" or permanently silencing "block and lock" the latent HIV reservoir, as well as gene editing, remain promising approaches, but so far have proven to be only partially successful. Moreover, using latency reversing agents or "block and lock" drugs pose additional considerations, including the ability to cause cellular toxicity, a potential lack of specificity for HIV, or low potency when each agent is used alone. RNA molecules, such as microRNAs (miRNAs) and long non-coding RNAs (lncRNAs) are becoming increasingly recognized as important regulators of gene expression. RNA-based approaches for combatting HIV latency represent a promising strategy since both miRNAs and lncRNAs are more cell-type and tissue specific than protein coding genes. Thus, a higher specificity of targeting the latent HIV reservoir with less overall cellular toxicity can likely be achieved. In this review, we summarize current knowledge about HIV gene expression regulation by miRNAs and lncRNAs encoded in the human genome, as well as regulatory molecules encoded in the HIV genome. We discuss both the transcriptional and post-transcriptional regulation of HIV gene expression to align with the current definition of latency, and describe RNA molecules that either promote HIV latency or have anti-latency properties. Finally, we provide perspectives on using each class of RNAs as potential targets for combatting HIV latency, and describe the complexity of the interactions between different RNA molecules, their protein targets, and HIV.
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Affiliation(s)
- Peter W Ramirez
- Department of Biological Sciences, California State University, Long Beach, CA, USA
| | - Christina Pantoja
- Department of Biological Sciences, California State University, Long Beach, CA, USA
| | - Nadejda Beliakova-Bethell
- VA San Diego Healthcare System and Veterans Medical Research Foundation, San Diego, CA, USA
- Department of Medicine, University of California, San Diego, CA, USA
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10
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Mukim A, Smith DM, Deshmukh S, Qazi AA, Beliakova-Bethell N. A Camptothetin Analog, Topotecan, Promotes HIV Latency via Interference with HIV Transcription and RNA Splicing. J Virol 2023; 97:e0163022. [PMID: 36719238 PMCID: PMC9973035 DOI: 10.1128/jvi.01630-22] [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: 10/18/2022] [Accepted: 01/11/2023] [Indexed: 02/01/2023] Open
Abstract
Low level HIV transcription during modern antiretroviral therapy (ART) in persons with HIV is linked to residual inflammation and associated diseases, like cardiovascular disease and cancer. The "block and lock" approach to hold HIV in a state of deep latency may help decrease residual inflammation in a person with HIV on ART and thus improve health. A camptothecin analog topotecan (TPT) was previously implicated as an inhibitor of active HIV replication. Using an in vitro primary T cell model of HIV latency, we demonstrated that (i) TPT reduces HIV transcriptional activity in latently infected cells; (ii) downregulation of HIV RNA by TPT cannot be reversed by latency reversing agents; (iii) several primary and secondary mechanism of action of TPT may be involved in control of HIV replication; (iv) regulation of HIV RNA by TPT is dependent on splicing complexity; (v) increase in proportion of unspliced HIV transcripts was facilitated by intron retention and upregulation of splicing factors, specifically SRSF6, by TPT. Although high TPT dosing (10 μM) was needed to achieve the observed effects, viability of primary CD4+ T cells was not greatly affected. Because toxicity can be observed with TPT in persons with cancer, TPT is unlikely to be used as an anti-HIV agent in clinic, but our study provides proof that camptothetin has "block and lock" activity. Other camptothetin analogs, which are less toxic than TPT, should be designed and tested as HIV "block and lock" agents. IMPORTANCE HIV survives in a state of very low activity, called latency, for long periods in persons with HIV on antiretroviral therapy. This low activity of HIV is linked to residual inflammation and associated diseases, such as heart disease and cancer. New strategies are being explored to further silence the HIV provirus and suppress residual inflammation. This study provides strong evidence that the camptothetin analog, Topotecan, can reduce residual activity of HIV in an experimental model of HIV latency. While Topotecan itself is likely not suitable for use in the clinic due to its toxicity, other camptothetin analogs should be designed and investigated as "block and lock" agents.
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Affiliation(s)
- Amey Mukim
- Veterans Medical Research Foundation, San Diego, California, USA
| | - Davey M. Smith
- Department of Medicine, University of California, San Diego, California, USA
| | - Savitha Deshmukh
- Veterans Medical Research Foundation, San Diego, California, USA
| | - Andrew A. Qazi
- Veterans Medical Research Foundation, San Diego, California, USA
| | - Nadejda Beliakova-Bethell
- Veterans Medical Research Foundation, San Diego, California, USA
- Department of Medicine, University of California, San Diego, California, USA
- VA San Diego Healthcare System, San Diego, California, USA
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11
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Mbonye U, Kizito F, Karn J. New insights into transcription elongation control of HIV-1 latency and rebound. Trends Immunol 2023; 44:60-71. [PMID: 36503686 DOI: 10.1016/j.it.2022.11.003] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2022] [Revised: 11/07/2022] [Accepted: 11/09/2022] [Indexed: 12/13/2022]
Abstract
Antiretroviral therapy reduces circulating HIV-1 to undetectable amounts but does not eliminate the virus due to the persistence of a stable reservoir of latently infected cells. The reservoir is maintained both by proliferation of latently infected cells and by reseeding from reactivated cells. A major challenge for the field is to find safe and effective methods to eliminate this source of rebounding HIV-1. Studies on the molecular mechanisms leading to HIV-1 latency and reactivation are being transformed using latency models in primary and patient CD4+ T cells. These studies have revealed the central role played by the biogenesis of the transcription elongation factor P-TEFb (Positive Transcription Elongation Factor b) and its recruitment to proviral HIV-1, for the maintenance of viral latency and the control of viral reactivation.
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Affiliation(s)
- Uri Mbonye
- Department of Molecular Biology and Microbiology, Case Western Reserve University, Cleveland, OH, USA
| | - Fredrick Kizito
- Department of Molecular Biology and Microbiology, Case Western Reserve University, Cleveland, OH, USA
| | - Jonathan Karn
- Department of Molecular Biology and Microbiology, Case Western Reserve University, Cleveland, OH, USA.
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12
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Rozera G, Sberna G, Berno G, Gruber CEM, Giombini E, Spezia PG, Orchi N, Puro V, Mondi A, Girardi E, Vaia F, Antinori A, Maggi F, Abbate I. Intact provirus and integration sites analysis in acute HIV-1 infection and changes after one year of early antiviral therapy. J Virus Erad 2022; 8:100306. [PMID: 36582472 PMCID: PMC9792883 DOI: 10.1016/j.jve.2022.100306] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Accepted: 12/07/2022] [Indexed: 12/14/2022] Open
Abstract
Background and objectives HIV-1 provirus integration in host genomes provides a lifelong reservoir of virally infected cells. Although not able to generate viral progeny, the expression of defective proviruses has been associated with activation. Provirus integration may influence host gene transcription and shifts may occur during disease progression or antiretroviral therapy (ART). The study aimed to analyze intact/defective provirus and sites of provirus integration in acute infections: changes after 48 weeks of early therapy were also evaluated. Methods DNA from peripheral blood lymphomonocytes of 8 acute HIV-1 infections at serodiagnosis (T0) and after 48 weeks of therapy (T1) was used to quantify intact and defective provirus by digital-droplet PCR and to analyze provirus integration sites, by next-generation sequencing of libraries derived from ligation-mediated PCR. Results A high variability in the amount of intact proviral DNA was observed at both T0 and T1, in the different subjects. Although the ratio of intact/total proviral HIV-1 DNA did not dramatically change between T0 (8.05%) and T1 (9.34%), after early therapy both intact and total HIV-1 DNA declined significantly, p = 0.047 and p = 0.008, respectively. The median number of different (IQR) integration sites in human chromosomes/subject was 5 (2.25-13.00) at T0 and 4 (3.00-6.75) at T1. Of all the integration sites observed at T1, 64% were already present at T0. Provirus integration was observed in introns of transcriptionally active genes. Some sites of integration, among which the most represented was in the neuregulin 2 gene, were shared by different patients, together with the orientation of the insertion. Provirus integration was also observed in intergenic regions, with median (IQR) % of 15.13 (6.81-21.40) at T0 and 18.46 (8.98-22.18) at T1 of all read matches. Conclusions In acute HIV-1 infection, the amount of intact proviral DNA in peripheral lymphomonocytes did not exceed 10% of total HIV-1 DNA, a percentage that was not substantially changed by early administrated ART. Provirus displayed a relatively small number of recurrent integration sites in introns of transcriptionally active genes, mainly related to cell-cycle control. Consideration should be given to therapeutic strategies able to target the cells harboring defective proviruses, that are not reached by conventional antiviral drugs, these potentially also impacting on replicative competent integrated provirus.
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Affiliation(s)
- Gabriella Rozera
- Laboratory of Virology, National Institute for Infectious Diseases Lazzaro Spallanzani IRCCS, Rome, Italy
| | - Giuseppe Sberna
- Laboratory of Virology, National Institute for Infectious Diseases Lazzaro Spallanzani IRCCS, Rome, Italy
| | - Giulia Berno
- Laboratory of Virology, National Institute for Infectious Diseases Lazzaro Spallanzani IRCCS, Rome, Italy
| | | | - Emanuela Giombini
- Laboratory of Virology, National Institute for Infectious Diseases Lazzaro Spallanzani IRCCS, Rome, Italy
| | - Pietro Giorgio Spezia
- Department of Translational Research, Retrovirus Center, University of Pisa, Pisa, Italy
| | - Nicoletta Orchi
- AIDS Referral Center, National Institute for Infectious Diseases Lazzaro Spallanzani IRCCS, Rome, Italy
| | - Vincenzo Puro
- AIDS Referral Center, National Institute for Infectious Diseases Lazzaro Spallanzani IRCCS, Rome, Italy
| | - Annalisa Mondi
- Clinical and Research Infectious Department, National Institute for Infectious Diseases Lazzaro Spallanzani IRCCS, Rome, Italy
| | - Enrico Girardi
- Scientific Direction, National Institute for Infectious Diseases Lazzaro Spallanzani IRCCS, Rome, Italy
| | - Francesco Vaia
- General Direction, National Institute for Infectious Diseases Lazzaro Spallanzani IRCCS, Rome, Italy
| | - Andrea Antinori
- Clinical and Research Infectious Department, National Institute for Infectious Diseases Lazzaro Spallanzani IRCCS, Rome, Italy
| | - Fabrizio Maggi
- Laboratory of Virology, National Institute for Infectious Diseases Lazzaro Spallanzani IRCCS, Rome, Italy
| | - Isabella Abbate
- Laboratory of Virology, National Institute for Infectious Diseases Lazzaro Spallanzani IRCCS, Rome, Italy,Corresponding author.
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Zerbato JM, Avihingsanon A, Singh KP, Zhao W, Deleage C, Rosen E, Cottrell ML, Rhodes A, Dantanarayana A, Tumpach C, Tennakoon S, Crane M, Price DJ, Braat S, Mason H, Roche M, Kashuba AD, Revill PA, Audsley J, Lewin SR. HIV DNA persists in hepatocytes in people with HIV-hepatitis B co-infection on antiretroviral therapy. EBioMedicine 2022; 87:104391. [PMID: 36502576 PMCID: PMC9763386 DOI: 10.1016/j.ebiom.2022.104391] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Revised: 11/04/2022] [Accepted: 11/17/2022] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND HIV can infect multiple cells in the liver including hepatocytes, Kupffer cells and infiltrating T cells, but whether HIV can persist in the liver in people with HIV (PWH) on suppressive antiretroviral therapy (ART) remains unknown. METHODS In a prospective longitudinal cohort of PWH and hepatitis B virus (HBV) co-infection living in Bangkok, Thailand, we collected blood and liver biopsies from 18 participants prior to and following ART and quantified HIV and HBV persistence using quantitative (q)PCR and RNA/DNAscope. Antiretroviral (ARV) drug levels were quantified using mass spectroscopy. FINDINGS In liver biopsies taken prior to ART, HIV DNA and HIV RNA were detected by qPCR in 53% (9/17) and 47% (8/17) of participants respectively. Following a median ART duration of 3.4 years, HIV DNA was detected in liver in 61% (11/18) of participants by either qPCR, DNAscope or both, but only at very low and non-quantifiable levels. Using immunohistochemistry, HIV DNA was observed in both hepatocytes and liver infiltrating CD4+ T cells on ART. HIV RNA was not detected in liver biopsies collected on ART, by either qPCR or RNAscope. All ARVs were clearly detected in liver tissue. INTERPRETATION Persistence of HIV DNA in liver in PWH on ART represents an additional reservoir that warrants further investigation. FUNDING National Health and Medical Research Council of Australia (Project Grant APP1101836, 1149990, and 1135851); This project has been funded in part with federal funds from the National Cancer Institute, National Institutes of Health, under Contract No. 75N91019D00024.
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Affiliation(s)
- Jennifer M. Zerbato
- Department of Infectious Diseases, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, Australia
| | - Anchalee Avihingsanon
- HIV-NAT, Thai Red Cross AIDS Research Centre and Centre of Excellence in Tuberculosis, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Kasha P. Singh
- Department of Infectious Diseases, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, Australia,Victorian Infectious Diseases Service, Royal Melbourne Hospital at the Peter Doherty Institute for Infection and Immunity, Melbourne, Australia,Department of Infectious Diseases, Alfred Hospital and Monash University, Melbourne, Australia
| | - Wei Zhao
- Department of Infectious Diseases, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, Australia
| | - Claire Deleage
- AIDS and Cancer Virus Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc., Frederick, MD, USA
| | - Elias Rosen
- Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, NC, USA
| | | | - Ajantha Rhodes
- Department of Infectious Diseases, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, Australia
| | - Ashanti Dantanarayana
- Department of Infectious Diseases, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, Australia
| | - Carolin Tumpach
- Department of Infectious Diseases, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, Australia
| | - Surekha Tennakoon
- Department of Infectious Diseases, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, Australia
| | - Megan Crane
- National Centre for Infections in Cancer, Department of Infectious Diseases, Peter MacCallum Cancer Centre, Melbourne, Australia
| | - David J. Price
- Department of Infectious Diseases, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, Australia,Centre for Epidemiology & Biostatistics, Melbourne School of Population & Global Health, University of Melbourne, Melbourne, Australia
| | - Sabine Braat
- Department of Infectious Diseases, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, Australia,Centre for Epidemiology & Biostatistics, Melbourne School of Population & Global Health, University of Melbourne, Melbourne, Australia,MISCH (Methods and Implementation Support for Clinical Health) Research Hub, Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne, Melbourne, Australia
| | - Hugh Mason
- Victorian Infectious Diseases Reference Laboratory, Royal Melbourne Hospital at The Peter Doherty Institute of Infection and Immunity, Melbourne, Australia
| | - Michael Roche
- Department of Infectious Diseases, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, Australia
| | - Angela D.M. Kashuba
- Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, NC, USA
| | - Peter A. Revill
- Victorian Infectious Diseases Reference Laboratory, Royal Melbourne Hospital at The Peter Doherty Institute of Infection and Immunity, Melbourne, Australia
| | - Jennifer Audsley
- Department of Infectious Diseases, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, Australia
| | - Sharon R. Lewin
- Department of Infectious Diseases, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, Australia,Victorian Infectious Diseases Service, Royal Melbourne Hospital at the Peter Doherty Institute for Infection and Immunity, Melbourne, Australia,Department of Infectious Diseases, Alfred Hospital and Monash University, Melbourne, Australia,Corresponding author. Department of Infectious Diseases, University of Melbourne at The Peter Doherty Institute for Infection and Immunity, 786-798 Elizabeth Street, Melbourne, Victoria 3010, Australia.
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14
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Elevation of cell-associated HIV-1 transcripts in CSF CD4+ T cells, despite effective antiretroviral therapy, is linked to brain injury. Proc Natl Acad Sci U S A 2022; 119:e2210584119. [PMID: 36413502 PMCID: PMC9860316 DOI: 10.1073/pnas.2210584119] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Antiretroviral therapy (ART) can attain prolonged undetectable HIV-1 in plasma and cerebrospinal fluid (CSF), but brain injury remains prevalent in people living with HIV-1 infection (PLHIV). We investigated cell-associated (CA)-HIV-1 RNA transcripts in cells in CSF and blood, using the highly sensitive Double-R assay, together with proton Magnetic Resonance Spectroscopy (1H MRS) of major brain metabolites, in sixteen PLHIV. 14/16 CSF cell samples had quantifiable CA-HIV-1 RNA, at levels significantly higher than in their PBMCs (median 9,266 vs 185 copies /106 CD4+ T-cells; p<0.0001). In individual PLHIV, higher levels of HIV-1 transcripts in CSF cells were associated with greater brain injury in the frontal white matter (Std β=-0.73; p=0.007) and posterior cingulate (Std β=-0.61; p=0.03). 18-colour flow cytometry revealed that the CSF cells were 91% memory T-cells, equally CD4+ and CD8+ T-cells, but fewer B cells (0.4 %), and monocytes (3.1%). CXCR3+CD49d+integrin β7-, CCR5+CD4+ T-cells were highly enriched in CSF, compared with PBMC (p <0.001). However, CA-HIV-1 RNA could not be detected in 10/16 preparations of highly purified monocytes from PBMC, and was extremely low in the other six. Our data show that elevated HIV-1 transcripts in CSF cells were associated with brain injury, despite suppressive ART. The cellular source is most likely memory CD4+ T cells from blood, rather than trafficking monocytes. Future research should focus on inhibitors of this transcription to reduce local production of potentially neurotoxic and inflammatory viral products.
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15
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Kuniholm J, Coote C, Henderson AJ. Defective HIV-1 genomes and their potential impact on HIV pathogenesis. Retrovirology 2022; 19:13. [PMID: 35764966 PMCID: PMC9238239 DOI: 10.1186/s12977-022-00601-8] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Accepted: 06/17/2022] [Indexed: 11/28/2022] Open
Abstract
Defective HIV-1 proviruses represent a population of viral genomes that are selected for by immune pressures, and clonally expanded to dominate the persistent HIV-1 proviral genome landscape. There are examples of RNA and protein expression from these compromised genomes which are generated by a variety of mechanisms. Despite the evidence that these proviruses are transcribed and translated, their role in HIV pathogenesis has not been fully explored. The potential for these genomes to participate in immune stimulation is particularly relevant considering the accumulation of cells harboring these defective proviruses over the course of antiretroviral therapy in people living with HIV. The expression of defective proviruses in different cells and tissues could drive innate sensing mechanisms and inflammation. They may also alter antiviral T cell responses and myeloid cell functions that directly contribute to HIV-1 associated chronic comorbidities. Understanding the impact of these defective proviruses needs to be considered as we advance cure strategies that focus on targeting the diverse population of HIV-1 proviral genomes.
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Affiliation(s)
- Jeffrey Kuniholm
- Department of Microbiology, Section of Infectious Diseases, Boston University School of Medicine, Boston, MA, 02116, USA
| | - Carolyn Coote
- Department of Medicine, Section of Infectious Diseases, Boston University School of Medicine, Boston, MA, 02116, USA
| | - Andrew J Henderson
- Department of Microbiology, Section of Infectious Diseases, Boston University School of Medicine, Boston, MA, 02116, USA. .,Department of Medicine, Section of Infectious Diseases, Boston University School of Medicine, Boston, MA, 02116, USA.
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16
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Ishizaka A, Koga M, Mizutani T, Lim LA, Adachi E, Ikeuchi K, Ueda R, Aoyagi H, Tanaka S, Kiyono H, Matano T, Aizaki H, Yoshio S, Mita E, Muramatsu M, Kanto T, Tsutsumi T, Yotsuyanagi H. Prolonged Gut Dysbiosis and Fecal Excretion of Hepatitis A Virus in Patients Infected with Human Immunodeficiency Virus. Viruses 2021; 13:v13102101. [PMID: 34696531 PMCID: PMC8539651 DOI: 10.3390/v13102101] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2021] [Revised: 10/13/2021] [Accepted: 10/14/2021] [Indexed: 12/24/2022] Open
Abstract
Hepatitis A virus (HAV) causes transient acute infection, and little is known of viral shedding via the duodenum and into the intestinal environment, including the gut microbiome, from the period of infection until after the recovery of symptoms. Therefore, in this study, we aimed to comprehensively observe the amount of virus excreted into the intestinal tract, the changes in the intestinal microbiome, and the level of inflammation during the healing process. We used blood and stool specimens from patients with human immunodeficiency virus who were infected with HAV during the HAV outbreak in Japan in 2018. Moreover, we observed changes in fecal HAV RNA and quantified the plasma cytokine level and gut microbiome by 16S rRNA analysis from clinical onset to at least 6 months after healing. HAV was detected from clinical onset up to a period of more than 150 days. Immediately after infection, many pro-inflammatory cytokines were elicited, and some cytokines showed different behaviors. The intestinal microbiome changed significantly after infection (dysbiosis), and the dysbiosis continued for a long time after healing. These observations suggest that the immunocompromised state is associated with prolonged viral shedding into the intestinal tract and delayed recovery of the intestinal environment.
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Affiliation(s)
- Aya Ishizaka
- Division of Infectious Diseases, Advanced Clinical Research Center, The Institute of Medical Science, The University of Tokyo, Tokyo 108-8639, Japan; (A.I.); (M.K.); (T.T.)
- International Research and Development Center for Mucosal Vaccines, The Institute of Medical Science, The University of Tokyo, Tokyo 108-8639, Japan;
- Japan Foundation for AIDS Prevention, Tokyo 101-0064, Japan
| | - Michiko Koga
- Division of Infectious Diseases, Advanced Clinical Research Center, The Institute of Medical Science, The University of Tokyo, Tokyo 108-8639, Japan; (A.I.); (M.K.); (T.T.)
| | - Taketoshi Mizutani
- Division of Infectious Diseases, Advanced Clinical Research Center, The Institute of Medical Science, The University of Tokyo, Tokyo 108-8639, Japan; (A.I.); (M.K.); (T.T.)
- International Research and Development Center for Mucosal Vaccines, The Institute of Medical Science, The University of Tokyo, Tokyo 108-8639, Japan;
- Correspondence: (T.M.); (H.Y.)
| | - Lay Ahyoung Lim
- Department of Infectious Diseases and Applied Immunology, IMSUT Hospital of Institute of Medical Science, The University of Tokyo, Tokyo 108-8639, Japan; (L.A.L.); (E.A.); (K.I.)
| | - Eisuke Adachi
- Department of Infectious Diseases and Applied Immunology, IMSUT Hospital of Institute of Medical Science, The University of Tokyo, Tokyo 108-8639, Japan; (L.A.L.); (E.A.); (K.I.)
| | - Kazuhiko Ikeuchi
- Department of Infectious Diseases and Applied Immunology, IMSUT Hospital of Institute of Medical Science, The University of Tokyo, Tokyo 108-8639, Japan; (L.A.L.); (E.A.); (K.I.)
| | - Ryuta Ueda
- Department of Virology II, National Institute of Infectious Diseases, Tokyo 162-8640, Japan; (R.U.); (H.A.); (H.A.); (M.M.)
| | - Haruyo Aoyagi
- Department of Virology II, National Institute of Infectious Diseases, Tokyo 162-8640, Japan; (R.U.); (H.A.); (H.A.); (M.M.)
| | - Satoshi Tanaka
- Department of Gastroenterology and Hepatology, National Hospital Organization Osaka National Hospital, Osaka 540-0006, Japan; (S.T.); (E.M.)
| | - Hiroshi Kiyono
- International Research and Development Center for Mucosal Vaccines, The Institute of Medical Science, The University of Tokyo, Tokyo 108-8639, Japan;
- CU-UCSD Center for Mucosal Immunology, Allergy and Vaccines (cMAV), Department of Medicine, University of California San Diego, San Diego, CA 92093, USA
| | - Tetsuro Matano
- AIDS Research Center, National Institute of Infectious Diseases, Tokyo 162-8640, Japan;
- Department of AIDS Vaccine Development, IMSUT Hospital, The Institute of Medical Science, The University of Tokyo, Tokyo 108-8639, Japan
| | - Hideki Aizaki
- Department of Virology II, National Institute of Infectious Diseases, Tokyo 162-8640, Japan; (R.U.); (H.A.); (H.A.); (M.M.)
| | - Sachiyo Yoshio
- The Research Center for Hepatitis and Immunology, National Center for Global Health and Medicine, Chiba 272-8516, Japan; (S.Y.); (T.K.)
| | - Eiji Mita
- Department of Gastroenterology and Hepatology, National Hospital Organization Osaka National Hospital, Osaka 540-0006, Japan; (S.T.); (E.M.)
| | - Masamichi Muramatsu
- Department of Virology II, National Institute of Infectious Diseases, Tokyo 162-8640, Japan; (R.U.); (H.A.); (H.A.); (M.M.)
| | - Tatsuya Kanto
- The Research Center for Hepatitis and Immunology, National Center for Global Health and Medicine, Chiba 272-8516, Japan; (S.Y.); (T.K.)
| | - Takeya Tsutsumi
- Division of Infectious Diseases, Advanced Clinical Research Center, The Institute of Medical Science, The University of Tokyo, Tokyo 108-8639, Japan; (A.I.); (M.K.); (T.T.)
| | - Hiroshi Yotsuyanagi
- Division of Infectious Diseases, Advanced Clinical Research Center, The Institute of Medical Science, The University of Tokyo, Tokyo 108-8639, Japan; (A.I.); (M.K.); (T.T.)
- Department of Infectious Diseases and Applied Immunology, IMSUT Hospital of Institute of Medical Science, The University of Tokyo, Tokyo 108-8639, Japan; (L.A.L.); (E.A.); (K.I.)
- Correspondence: (T.M.); (H.Y.)
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17
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Ishizaka A, Koga M, Mizutani T, Parbie PK, Prawisuda D, Yusa N, Sedohara A, Kikuchi T, Ikeuchi K, Adachi E, Koibuchi T, Furukawa Y, Tojo A, Imoto S, Suzuki Y, Tsutsumi T, Kiyono H, Matano T, Yotsuyanagi H. Unique Gut Microbiome in HIV Patients on Antiretroviral Therapy (ART) Suggests Association with Chronic Inflammation. Microbiol Spectr 2021; 9:e0070821. [PMID: 34378948 PMCID: PMC8552706 DOI: 10.1128/spectrum.00708-21] [Citation(s) in RCA: 41] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2021] [Accepted: 07/13/2021] [Indexed: 02/07/2023] Open
Abstract
Chronic inflammation is a hallmark of human immunodeficiency virus (HIV) infection and a risk factor for the development and progression of age-related comorbidities. Although HIV-associated gut dysbiosis has been suggested to be involved in sustained chronic inflammation, there remains a limited understanding of the association between gut dysbiosis and chronic inflammation during HIV infection. Here, we investigated compositional changes in the gut microbiome and its role in chronic inflammation in patients infected with HIV. We observed that the gut microbiomes of patients with low CD4 counts had reduced alpha diversity compared to those in uninfected controls. Following CD4 recovery, alpha diversity was restored, but intergroup dissimilarity of bacterial composition remained unchanged between patients and uninfected controls. Patients with HIV had higher abundance of the classes Negativicutes, Bacilli, and Coriobacteriia, as well as depletion of the class Clostridia. These relative abundances positively correlated with inflammatory cytokines and negatively correlated with anti-inflammatory cytokines. We found that gut dysbiosis accompanying HIV infection was characterized by a depletion of obligate anaerobic Clostridia and enrichment of facultative anaerobic bacteria, reflecting increased intestinal oxygen levels and intestinal permeability. Furthermore, it is likely that HIV-associated dysbiosis shifts the immunological balance toward inflammatory Th1 responses and encourages proinflammatory cytokine production. Our results suggest that gut dysbiosis contributes to sustaining chronic inflammation in patients with HIV infection despite effective antiretroviral therapy and that correcting gut dysbiosis will be effective in improving long-term outcomes in patients. IMPORTANCE Chronic inflammation is a hallmark of HIV infection and is associated with the development and progression of age-related comorbidities. Although the gastrointestinal tract is a major site of HIV replication and CD4+ T-cell depletion, the role of HIV-associated imbalance of gut microbiome in chronic inflammation is unclear. Here, we aimed to understand the causal relationship between abnormalities in the gut microbiome and chronic inflammation in patients with HIV. Our results suggest HIV-associated gut dysbiosis presents a more aerobic environment than that of healthy individuals, despite prolonged viral suppression. This dysbiosis likely results from a sustained increase in intestinal permeability, which supports sustained bacterial translocation in HIV patients, despite effective therapy. Additionally, we observed that several bacterial taxa enriched in HIV patients were associated with increased expression of inflammatory cytokines. Collectively, these results suggest that gut dysbiosis plays an important role in chronic inflammation in HIV patients.
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Affiliation(s)
- Aya Ishizaka
- Division of Infectious Diseases, Advanced Clinical Research Center, the Institute of Medical Science, The University of Tokyo, Tokyo, Japan
- International Research and Development Center for Mucosal Vaccines, the Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Michiko Koga
- Division of Infectious Diseases, Advanced Clinical Research Center, the Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Taketoshi Mizutani
- Division of Infectious Diseases, Advanced Clinical Research Center, the Institute of Medical Science, The University of Tokyo, Tokyo, Japan
- International Research and Development Center for Mucosal Vaccines, the Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Prince Kofi Parbie
- AIDS Research Center, National Institute of Infectious Diseases, Tokyo, Japan
| | - Diki Prawisuda
- Division of Infectious Diseases, Advanced Clinical Research Center, the Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Nozomi Yusa
- Department of Applied Genomics, Research Hospital, Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Ayako Sedohara
- Division of Infectious Diseases, Advanced Clinical Research Center, the Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Tadashi Kikuchi
- AIDS Research Center, National Institute of Infectious Diseases, Tokyo, Japan
- Department of Infectious Diseases and Applied Immunology, IMSUT Hospital of Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Kazuhiko Ikeuchi
- Department of Infectious Diseases and Applied Immunology, IMSUT Hospital of Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Eisuke Adachi
- Department of Infectious Diseases and Applied Immunology, IMSUT Hospital of Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Tomohiko Koibuchi
- Department of Infectious Diseases and Applied Immunology, IMSUT Hospital of Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Yoichi Furukawa
- Department of Applied Genomics, Research Hospital, Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Arinobu Tojo
- Department of Laboratory Medicine, Research Hospital, Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Seiya Imoto
- Division of Health Medical Data Science, Health Intelligence Center, the Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Yutaka Suzuki
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Chiba, Japan
| | - Takeya Tsutsumi
- Division of Infectious Diseases, Advanced Clinical Research Center, the Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Hiroshi Kiyono
- International Research and Development Center for Mucosal Vaccines, the Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Tetsuro Matano
- AIDS Research Center, National Institute of Infectious Diseases, Tokyo, Japan
- Department of AIDS Vaccine Development, IMSUT Hospital, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Hiroshi Yotsuyanagi
- Division of Infectious Diseases, Advanced Clinical Research Center, the Institute of Medical Science, The University of Tokyo, Tokyo, Japan
- Department of Infectious Diseases and Applied Immunology, IMSUT Hospital of Institute of Medical Science, The University of Tokyo, Tokyo, Japan
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The active human immunodeficiency virus reservoir during antiretroviral therapy: emerging players in viral persistence. Curr Opin HIV AIDS 2021; 16:193-199. [PMID: 33973900 DOI: 10.1097/coh.0000000000000685] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
PURPOSE OF REVIEW To discuss the role of CD4+ T cells with active Human immunodeficiency virus (HIV), meaning infected cells with transcriptional and/or translational viral activity during antiretroviral therapy (ART), focusing on new technologies for its detection, potential cell markers for its characterization, and evidences on the contribution of the active HIV reservoir to long-term viral persistence. RECENT FINDINGS HIV-infected cells expressing viral ribonucleic acid are systematically detected in subjects on long-term ART. In recent years, powerful new tools have provided significant insights into the nature, quantification, and identification of cells with active HIV, including the identification of new cell markers, and the presence of viral activity in specific cell populations located in different cellular and anatomical compartments. Moreover, studies on viral sequence integrity have identified cell clones with intact viral genomes and active viral transcription that could potentially persist for years. Together, new investigations support the notion that the active reservoir could represent a relevant fraction of long-term infected cells, and therefore, the study of its cell sources and mechanisms of maintenance could represent a significant advance in our understanding of viral persistence and the development of new curative strategies. SUMMARY The presence of HIV-infected cells with viral expression during ART has been traditionally overlooked for years. Based on recent investigations, this active viral reservoir could play an important role in HIV persistence.
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Hsieh SM, Pan SC, Huang YS, Chang SC. Reversal of Viral Latency and Induction of Gag-Specific T-Cell Responses in HIV-1-Infected Adults Through Cyclic Treatment Interruption of Rosuvastatin: A Proof-of-Concept Study. J Acquir Immune Defic Syndr 2021; 86:500-508. [PMID: 33620177 DOI: 10.1097/qai.0000000000002577] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2020] [Accepted: 11/02/2020] [Indexed: 11/25/2022]
Abstract
BACKGROUND HIV-1 infection remains incurable through combination antiretroviral therapy. Previous studies have shown statins have immunomodulatory effects, and interruption of statins may cause an immune rebound. METHODS In this proof-of-concept study, we longitudinally assessed the impact of immune rebound by cyclic treatment-interruption (CTI) of rosuvastatin on the reversal of HIV latency. The HIV-1-infected persons with stable viral control were considered to be enrolled for CTI of rosuvastatin with a fixed 12-week interval for 72 weeks (3 treatment-interruption cycles). HIV-1 Gag-specific T-cell responses, cell-associated RNA, and proviral DNA were determined. RESULTS From Feb 2017 to Dec 2019, 10 subjects were enrolled. During the 72-week follow-up, their CD4+ T-cell counts did not significantly change, and plasma HIV RNA remained undetectable. Transient but remarkable increases in levels of cell-associated RNA, Gag-specific interferon-γ production from CD4+ T cells and Gag-specific CD8+ cytotoxic capacity were detected shortly after stopping rosuvastatin in every cycle of CTI of rosuvastatin. Furthermore, there was a 2.63-fold reduction (range, 1.41-4.82) in proviral DNA levels (P = 0.005) during the 72-week follow-up. A significant linear association was demonstrated between their nadir CD4+ T-cell counts and the fold decrease in proviral DNA levels (R = 0.81, P = 0.004). CONCLUSION It may be possible to reverse viral latency in CD4+ T cells, activate Gag-specific T cells, and reduce viral reservoir size through CTI of rosuvastatin in HIV-1-infected subjects with stable combination antiretroviral therapy, especially in those with nadir CD4+ T-cell counts > 350 cells/μL.
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Affiliation(s)
- Szu-Min Hsieh
- Section of Infectious Diseases, Division of Infectious Diseases, Department of Internal Medicine, National Taiwan University Hospital and College of Medicine, National Taiwan University, Taipei, Taiwan
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Cell-Associated HIV-1 Unspliced-to-Multiply-Spliced RNA Ratio at 12 Weeks of ART Predicts Immune Reconstitution on Therapy. mBio 2021; 12:mBio.00099-21. [PMID: 33688002 PMCID: PMC8092199 DOI: 10.1128/mbio.00099-21] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Human immunodeficiency virus (HIV) infection is currently managed by antiretroviral drugs, which block virus replication and promote immune restoration. However, the latter effect is not universal, with a proportion of infected individuals failing to sufficiently reconstitute their immune function despite a successful virological response to antiretroviral therapy (ART). Incomplete restoration of CD4+ T-cell counts on antiretroviral therapy (ART) is a major predictor of HIV-related morbidity and mortality. To understand the possible mechanisms behind this poor immunological response despite viral suppression, we longitudinally measured more than 50 virological and immunological biomarkers in a cohort of HIV-infected individuals at several time points during the first 96 weeks of virologically suppressive ART. No baseline virological or immunological marker was predictive of the degree of immune reconstitution. However, the cell-associated HIV-1 unspliced-to-multiply-spliced (US/MS) RNA ratio at 12 weeks of ART positively correlated with markers of CD4+ T-cell activation and apoptosis and negatively predicted both the absolute and relative CD4+ T-cell counts at 48 and 96 weeks. A higher US/MS RNA ratio may reflect the higher frequency of productively infected cells that could exert pressure on the immune system, contributing to persistent immune activation and apoptosis and subsequently to a poor immunological response to ART.
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21
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De Pablo-Bernal RS, Jimenez-Leon MR, Tarancon-Diez L, Gutierrez-Valencia A, Serna-Gallego A, Trujillo-Rodriguez M, Alvarez-Rios AI, Milanes-Guisado Y, Espinosa N, Roca-Oporto C, Viciana P, Lopez-Cortes LF, Ruiz-Mateos E. Modulation of Monocyte Activation and Function during Direct Antiviral Agent Treatment in Patients Coinfected with HIV and Hepatitis C Virus. Antimicrob Agents Chemother 2020; 64:e00773-20. [PMID: 32571815 PMCID: PMC7449156 DOI: 10.1128/aac.00773-20] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2020] [Accepted: 06/15/2020] [Indexed: 12/16/2022] Open
Abstract
The activation phenotypes and functional changes in monocyte subsets during hepatitis C virus (HCV) elimination in HIV/HCV-coinfected patients were evaluated. Twenty-two HIV/HCV-coinfected patients on suppressive combination antiretroviral treatment (cART) achieving HCV elimination after direct-acting antiviral (DAA) therapy and 10 HIV-monoinfected patients were included. The activation phenotype (10 markers) and polyfunctionality (intracellular interleukin-1α [IL-1α], IL-1β, IL-6, IL-8, tumor necrosis factor alpha [TNF-α], and IL-10 production) in three monocyte subsets (classical, intermediate, and nonclassical) were evaluated by flow cytometry before and at the end of treatment. Cell-associated HIV DNA levels were assayed by droplet digital PCR. After HCV clearance, there was a significant increase in classical monocyte and decreases in intermediate and nonclassical monocyte levels. The levels of the activation markers CD49d, CD40, and CX3CR1 were decreased after treatment in the monocyte subsets, reaching the levels in HIV-monoinfected patients. After lipopolysaccharide (LPS) stimulation, although polyfunctionality significantly decreased in intermediate and nonclassical monocytes, some combinations, such as the IL-1α- (IL-1α-negative) IL-1β- IL-6+ (IL-6-producing) IL-8- TNF-α- IL-10- combination, were remarkably increased at the end of treatment compared to the control group. Cell-associated HIV DNA levels correlated with activation markers before but not after treatment. HCV clearance after DAA treatment in patients on cART exerts an anti-inflammatory profile on monocyte subsets, activation phenotypes, and polyfunctionality. However, there is not a complete normalization compared with HIV-monoinfected patients.
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Affiliation(s)
- Rebeca S De Pablo-Bernal
- Clinical Unit of Infectious Diseases, Microbiology and Preventive Medicine, Institute of Biomedicine of Seville (IBiS), Virgen del Rocío University Hospital, CSIC, University of Seville, Seville, Spain
| | - M Reyes Jimenez-Leon
- Clinical Unit of Infectious Diseases, Microbiology and Preventive Medicine, Institute of Biomedicine of Seville (IBiS), Virgen del Rocío University Hospital, CSIC, University of Seville, Seville, Spain
| | - Laura Tarancon-Diez
- Clinical Unit of Infectious Diseases, Microbiology and Preventive Medicine, Institute of Biomedicine of Seville (IBiS), Virgen del Rocío University Hospital, CSIC, University of Seville, Seville, Spain
| | - Alicia Gutierrez-Valencia
- Clinical Unit of Infectious Diseases, Microbiology and Preventive Medicine, Institute of Biomedicine of Seville (IBiS), Virgen del Rocío University Hospital, CSIC, University of Seville, Seville, Spain
| | - Ana Serna-Gallego
- Clinical Unit of Infectious Diseases, Microbiology and Preventive Medicine, Institute of Biomedicine of Seville (IBiS), Virgen del Rocío University Hospital, CSIC, University of Seville, Seville, Spain
| | - Maria Trujillo-Rodriguez
- Clinical Unit of Infectious Diseases, Microbiology and Preventive Medicine, Institute of Biomedicine of Seville (IBiS), Virgen del Rocío University Hospital, CSIC, University of Seville, Seville, Spain
| | - Ana I Alvarez-Rios
- Department of Clinical Biochemistry, Virgen del Rocío University Hospital, CSIC, University of Seville, Seville, Spain
| | - Yusnelkis Milanes-Guisado
- Clinical Unit of Infectious Diseases, Microbiology and Preventive Medicine, Institute of Biomedicine of Seville (IBiS), Virgen del Rocío University Hospital, CSIC, University of Seville, Seville, Spain
| | - Nuria Espinosa
- Clinical Unit of Infectious Diseases, Microbiology and Preventive Medicine, Institute of Biomedicine of Seville (IBiS), Virgen del Rocío University Hospital, CSIC, University of Seville, Seville, Spain
| | - Cristina Roca-Oporto
- Clinical Unit of Infectious Diseases, Microbiology and Preventive Medicine, Institute of Biomedicine of Seville (IBiS), Virgen del Rocío University Hospital, CSIC, University of Seville, Seville, Spain
| | - Pompeyo Viciana
- Clinical Unit of Infectious Diseases, Microbiology and Preventive Medicine, Institute of Biomedicine of Seville (IBiS), Virgen del Rocío University Hospital, CSIC, University of Seville, Seville, Spain
| | - Luis F Lopez-Cortes
- Clinical Unit of Infectious Diseases, Microbiology and Preventive Medicine, Institute of Biomedicine of Seville (IBiS), Virgen del Rocío University Hospital, CSIC, University of Seville, Seville, Spain
| | - Ezequiel Ruiz-Mateos
- Clinical Unit of Infectious Diseases, Microbiology and Preventive Medicine, Institute of Biomedicine of Seville (IBiS), Virgen del Rocío University Hospital, CSIC, University of Seville, Seville, Spain
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22
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Chromatin maturation of the HIV-1 provirus in primary resting CD4+ T cells. PLoS Pathog 2020; 16:e1008264. [PMID: 31999790 PMCID: PMC6991963 DOI: 10.1371/journal.ppat.1008264] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2019] [Accepted: 12/09/2019] [Indexed: 12/14/2022] Open
Abstract
Human immunodeficiency virus type 1 (HIV-1) infection is a chronic condition, where viral DNA integrates into the genome. Latently infected cells form a persistent, heterogeneous reservoir that at any time can reactivate the integrated HIV-1. Here we confirmed that latently infected cells from HIV-1 positive study participants exhibited active HIV-1 transcription but without production of mature spliced mRNAs. To elucidate the mechanisms behind this we employed primary HIV-1 latency models to study latency establishment and maintenance. We characterized proviral transcription and chromatin development in cultures of resting primary CD4+ T-cells for four months after ex vivo HIV-1 infection. As heterochromatin (marked with H3K9me3 or H3K27me3) gradually stabilized, the provirus became less accessible with reduced activation potential. In a subset of infected cells, active marks (e.g. H3K27ac) and elongating RNAPII remained detectable at the latent provirus, despite prolonged proviral silencing. In many aspects, latent HIV-1 resembled an active enhancer in a subset of resting cells. The enhancer chromatin actively promoted latency and the enhancer-specific CBP/P300-inhibitor GNE049 was identified as a new latency reversal agent. The division of the latent reservoir according to distinct chromatin compositions with different reactivation potential enforces the notion that even though a relatively large set of cells contains the HIV-1 provirus, only a discrete subset is readily able to reactivate the provirus and spread the infection. HIV infection is a devastating disease affecting 35 million people worldwide. Current anti-retroviral treatment is highly effective and has made the HIV infection chronic. However, despite more effective treatments, the prospects of a cure are distant. The problem for an HIV cure is that, even though the virus particles are eradicated, the infected cells maintain the information of remake the virus. This information is integrated in the host cell as a provirus. The provirus switches between active and inactive states. Thereby, the infected cells evade both the immune system and death associated with massive viral production. We have characterized the composition of proviral chromatin and how it connects with transcription and viral production. In resting primary CD4+ T-cells, we follow the fate of the provirus starting at infection until latency is firmly established. Only in a fraction of intact proviruses were we able to reverse latency and that this was highly regulated by the chromatin composition. Whereas the proviruses encompassed in heterochromatin were refractory to activation, latent proviruses with “enhancer” characteristics were readily activated. Our study provides key insights as to detect the remaining HIV-1 infected cells capable of reseeding the infection, and the mechanisms whereby they are maintained.
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23
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Zerbato JM, Purves HV, Lewin SR, Rasmussen TA. Between a shock and a hard place: challenges and developments in HIV latency reversal. Curr Opin Virol 2019; 38:1-9. [PMID: 31048093 DOI: 10.1016/j.coviro.2019.03.004] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2019] [Revised: 03/26/2019] [Accepted: 03/27/2019] [Indexed: 02/07/2023]
Abstract
Latently infected cells that persist in HIV-infected individuals on antiretroviral therapy (ART) are a major barrier to cure. One strategy to eliminate latency is by activating viral transcription, commonly called latency reversal. Several small non-randomised clinical trials of latency reversing agents (LRAs) in HIV-infected individuals on ART increased viral production, but disappointingly did not reduce the number of latently infected cells or delay time to viral rebound following cessation of ART. More recent approaches aimed at reversing latency include compounds that both activate virus and also modulate immunity to enhance clearance of infected cells. These immunomodulatory LRAs include toll-like receptor agonists, immune checkpoint inhibitors and some cytokines. Here, we provide a brief review of the rationale for transcription-activating and immunomodulatory LRAs, discuss recent clinical trials and some suggestions for combination approaches and research priorities for the future.
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Affiliation(s)
- Jennifer M Zerbato
- The Peter Doherty Institute for Infection and Immunity, University of Melbourne and the Royal Melbourne Hospital, Melbourne, Australia
| | - Harrison V Purves
- The Peter Doherty Institute for Infection and Immunity, University of Melbourne and the Royal Melbourne Hospital, Melbourne, Australia
| | - Sharon R Lewin
- The Peter Doherty Institute for Infection and Immunity, University of Melbourne and the Royal Melbourne Hospital, Melbourne, Australia; Department of Infectious Diseases, Alfred Hospital and Monash University, Melbourne, Australia.
| | - Thomas A Rasmussen
- The Peter Doherty Institute for Infection and Immunity, University of Melbourne and the Royal Melbourne Hospital, Melbourne, Australia
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24
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Boucau J, Madouasse J, Kourjian G, Carlin CS, Wambua D, Berberich MJ, Le Gall S. The Activation State of CD4 T Cells Alters Cellular Peptidase Activities, HIV Antigen Processing, and MHC Class I Presentation in a Sequence-Dependent Manner. THE JOURNAL OF IMMUNOLOGY 2019; 202:2856-2872. [PMID: 30936293 DOI: 10.4049/jimmunol.1700950] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/03/2017] [Accepted: 03/08/2019] [Indexed: 12/19/2022]
Abstract
CD4 T cell activation is critical to the initiation of adaptive immunity. CD4 T cells are also the main targets of HIV infection, and their activation status contributes to the maintenance and outcome of infection. Although the role of activation in the differentiation and proliferation of CD4 T cells is well studied, its impact on the processing and MHC class I (MHC-I) presentation of epitopes and immune recognition by CD8 T cells are not investigated. In this study, we show that the expression and hydrolytic activities of cellular peptidases are increased upon TCR-dependent and MHC-peptide activation of primary CD4 T cells from healthy or HIV-infected persons. Changes in peptidase activities altered the degradation patterns of HIV Ags analyzed by mass spectrometry, modifying the amount of MHC-I epitopes produced, the antigenicity of the degradation products, and the coverage of Ags by degradation peptides presentable by MHC-I. The computational analysis of 2237 degradation peptides generated during the degradation of various HIV-antigenic fragments in CD4 T cells identified cleavage sites that were predictably enhanced, reduced, or unchanged upon cellular activation. Epitope processing and presentation by CD4 T cells may be modulated by the activation state of cells in a sequence-dependent manner. Accordingly, cellular activation modified endogenous Ag processing and presentation and killing of HIV-infected CD4 T cells by CD8 T cells in a way that mirrored differences in in vitro epitope processing. The clearance of HIV-infected cells may rely on different immune responses according to activation state during HIV infection.
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Affiliation(s)
- Julie Boucau
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139
| | | | | | | | - Daniel Wambua
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139
| | | | - Sylvie Le Gall
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139
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25
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Pasternak AO, Berkhout B. What do we measure when we measure cell-associated HIV RNA. Retrovirology 2018; 15:13. [PMID: 29378657 PMCID: PMC5789533 DOI: 10.1186/s12977-018-0397-2] [Citation(s) in RCA: 62] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2017] [Accepted: 01/16/2018] [Indexed: 12/21/2022] Open
Abstract
Cell-associated (CA) HIV RNA has received much attention in recent years as a surrogate measure of the efficiency of HIV latency reversion and because it may provide an estimate of the viral reservoir size. This review provides an update on some recent insights in the biology and clinical utility of this biomarker. We discuss a number of important considerations to be taken into account when interpreting CA HIV RNA measurements, as well as different methods to measure this biomarker.
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Affiliation(s)
- Alexander O Pasternak
- Laboratory of Experimental Virology, Department of Medical Microbiology, Academic Medical Center of the University of Amsterdam, Meibergdreef 15, 1105 AZ, Amsterdam, The Netherlands.
| | - Ben Berkhout
- Laboratory of Experimental Virology, Department of Medical Microbiology, Academic Medical Center of the University of Amsterdam, Meibergdreef 15, 1105 AZ, Amsterdam, The Netherlands
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26
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Barclay RA, Schwab A, DeMarino C, Akpamagbo Y, Lepene B, Kassaye S, Iordanskiy S, Kashanchi F. Exosomes from uninfected cells activate transcription of latent HIV-1. J Biol Chem 2017; 292:11682-11701. [PMID: 28536264 DOI: 10.1074/jbc.m117.793521] [Citation(s) in RCA: 50] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2017] [Revised: 05/23/2017] [Indexed: 01/24/2023] Open
Abstract
HIV-1 infection causes AIDS, infecting millions worldwide. The virus can persist in a state of chronic infection due to its ability to become latent. We have previously shown a link between HIV-1 infection and exosome production. Specifically, we have reported that exosomes transport viral proteins and RNA from infected cells to neighboring uninfected cells. These viral products could then elicit an innate immune response, leading to activation of the Toll-like receptor and NF-κB pathways. In this study, we asked whether exosomes from uninfected cells could activate latent HIV-1 in infected cells. We observed that irrespective of combination antiretroviral therapy, both short- and long-length viral transcripts were increased in wild-type HIV-1-infected cells exposed to purified exosomes from uninfected cells. A search for a possible mechanism for this finding revealed that the exosomes increase RNA polymerase II loading onto the HIV-1 promoter in the infected cells. These viral transcripts, which include trans-activation response (TAR) RNA and a novel RNA that we termed TAR-gag, can then be packaged into exosomes and potentially be exported to neighboring uninfected cells, leading to increased cellular activation. To better decipher the exosome release pathways involved, we used siRNA to suppress expression of ESCRT (endosomal sorting complex required for transport) proteins and found that ESCRT II and IV significantly control exosome release. Collectively, these results imply that exosomes from uninfected cells activate latent HIV-1 in infected cells and that true transcriptional latency may not be possible in vivo, especially in the presence of combination antiretroviral therapy.
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Affiliation(s)
- Robert A Barclay
- Laboratory of Molecular Virology, George Mason University, Manassas, Virginia 20110
| | - Angela Schwab
- Laboratory of Molecular Virology, George Mason University, Manassas, Virginia 20110
| | - Catherine DeMarino
- Laboratory of Molecular Virology, George Mason University, Manassas, Virginia 20110
| | - Yao Akpamagbo
- Laboratory of Molecular Virology, George Mason University, Manassas, Virginia 20110
| | | | - Seble Kassaye
- Department of Medicine, Women's Inter-Agency HIV Study, Georgetown University Medical Center, Washington, D. C. 20007
| | - Sergey Iordanskiy
- Laboratory of Molecular Virology, George Mason University, Manassas, Virginia 20110; Department of Pharmacology and Molecular Therapeutics, Uniformed Services University of the Health Sciences, Bethesda, Maryland 20814
| | - Fatah Kashanchi
- Laboratory of Molecular Virology, George Mason University, Manassas, Virginia 20110.
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Total HIV-1 DNA, a Marker of Viral Reservoir Dynamics with Clinical Implications. Clin Microbiol Rev 2017; 29:859-80. [PMID: 27559075 DOI: 10.1128/cmr.00015-16] [Citation(s) in RCA: 152] [Impact Index Per Article: 21.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
HIV-1 DNA persists in infected cells despite combined antiretroviral therapy (cART), forming viral reservoirs. Recent trials of strategies targeting latent HIV reservoirs have rekindled hopes of curing HIV infection, and reliable markers are thus needed to evaluate viral reservoirs. Total HIV DNA quantification is simple, standardized, sensitive, and reproducible. Total HIV DNA load influences the course of the infection and is therefore clinically relevant. In particular, it is predictive of progression to AIDS and death, independently of HIV RNA load and the CD4 cell count. Baseline total HIV DNA load is predictive of the response to cART. It declines during cART but remains quantifiable, at a level that reflects both the history of infection (HIV RNA zenith, CD4 cell count nadir) and treatment efficacy (residual viremia, cumulative viremia, immune restoration, immune cell activation). Total HIV DNA load in blood is also predictive of the presence and severity of some HIV-1-associated end-organ disorders. It can be useful to guide individual treatment, notably, therapeutic de-escalation. Although it does not distinguish between replication-competent and -defective latent viruses, the total HIV DNA load in blood, tissues, and cells provides insights into HIV pathogenesis, probably because all viral forms participate in host cell activation and HIV pathogenesis. Total HIV DNA is thus a biomarker of HIV reservoirs, which can be defined as all infected cells and tissues containing all forms of HIV persistence that participate in pathogenesis. This participation may occur through the production of new virions, creating new cycles of infection and disseminating infected cells; maintenance or amplification of reservoirs by homeostatic cell proliferation; and viral transcription and synthesis of viral proteins without new virion production. These proteins can induce immune activation, thus participating in the vicious circle of HIV pathogenesis.
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