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Duncan MC, Omondi FH, Kinloch NN, Lapointe HR, Speckmaier S, Moran-Garcia N, Lawson T, DeMarco ML, Simons J, Holmes DT, Lowe CF, Bacani N, Sereda P, Barrios R, Harris M, Romney MG, Montaner JS, Brumme CJ, Brockman MA, Brumme ZL. Effects of COVID-19 mRNA vaccination on HIV viremia and reservoir size. AIDS 2024; 38:1120-1130. [PMID: 38224350 PMCID: PMC11139238 DOI: 10.1097/qad.0000000000003841] [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: 10/08/2023] [Revised: 01/03/2024] [Accepted: 01/07/2024] [Indexed: 01/16/2024]
Abstract
OBJECTIVE The immunogenic nature of coronavirus disease 2019 (COVID-19) mRNA vaccines led to some initial concern that these could stimulate the HIV reservoir. We analyzed changes in plasma HIV loads (pVL) and reservoir size following COVID-19 mRNA vaccination in 62 people with HIV (PWH) receiving antiretroviral therapy (ART), and analyzed province-wide trends in pVL before and after the mass vaccination campaign. DESIGN Longitudinal observational cohort and province-wide analysis. METHODS Sixty-two participants were sampled prevaccination, and one month after their first and second COVID-19 immunizations. Vaccine-induced anti-SARS-CoV-2-Spike antibodies in serum were measured using the Roche Elecsys Anti-S assay. HIV reservoirs were quantified using the intact proviral DNA assay; pVL were measured using the cobas 6800 (lower limit of quantification: 20 copies/ml). The province-wide analysis included all 290 401 pVL performed in British Columbia, Canada between 2012 and 2022. RESULTS Prevaccination, the median intact reservoir size was 77 [interquartile range (IQR): 20-204] HIV copies/million CD4 + T-cells, compared to 74 (IQR: 27-212) and 65 (IQR: 22-174) postfirst and -second dose, respectively (all comparisons P > 0.07). Prevaccination, 82% of participants had pVL <20 copies/ml (max: 110 copies/ml), compared to 79% postfirst dose (max: 183 copies/ml) and 85% postsecond dose (max: 79 copies/ml) ( P > 0.4). There was no evidence that the magnitude of the vaccine-elicited anti-SARS-CoV-2-Spike immune response influenced pVL nor changes in reservoir size ( P > 0.6). We found no evidence linking the COVID-19 mass vaccination campaign to population-level increases in detectable pVL frequency among all PWH in the province, nor among those who maintained pVL suppression on ART. CONCLUSION We found no evidence that COVID-19 mRNA vaccines induced changes in HIV reservoir size nor plasma viremia.
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Affiliation(s)
- Maggie C. Duncan
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, Canada
- Faculty of Health Sciences, Simon Fraser University, Burnaby, Canada
| | - F. Harrison Omondi
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, Canada
- Faculty of Health Sciences, Simon Fraser University, Burnaby, Canada
| | - Natalie N. Kinloch
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, Canada
- Faculty of Health Sciences, Simon Fraser University, Burnaby, Canada
| | - Hope R. Lapointe
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, Canada
| | - Sarah Speckmaier
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, Canada
| | | | - Tanya Lawson
- Division of Medical Microbiology and Virology, St. Paul's Hospital, Vancouver, Canada
| | - Mari L. DeMarco
- Department of Pathology and Laboratory Medicine, Providence Healthcare, Vancouver, Canada
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, Canada
| | - Janet Simons
- Department of Pathology and Laboratory Medicine, Providence Healthcare, Vancouver, Canada
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, Canada
| | - Daniel T. Holmes
- Department of Pathology and Laboratory Medicine, Providence Healthcare, Vancouver, Canada
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, Canada
| | - Christopher F. Lowe
- Division of Medical Microbiology and Virology, St. Paul's Hospital, Vancouver, Canada
- Department of Pathology and Laboratory Medicine, Providence Healthcare, Vancouver, Canada
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, Canada
| | - Nic Bacani
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, Canada
| | - Paul Sereda
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, Canada
| | - Rolando Barrios
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, Canada
- School of Population and Public Health, University of British Columbia, Vancouver, Canada
| | - Marianne Harris
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, Canada
- Department of Family Practice, Faculty of Medicine, University of British Columbia, Vancouver, Canada
| | - Marc G. Romney
- Division of Medical Microbiology and Virology, St. Paul's Hospital, Vancouver, Canada
- Department of Pathology and Laboratory Medicine, Providence Healthcare, Vancouver, Canada
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, Canada
| | - Julio S.G. Montaner
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, Canada
- Department of Medicine, University of British Columbia, Vancouver, Canada
| | - Chanson J. Brumme
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, Canada
- Department of Medicine, University of British Columbia, Vancouver, Canada
| | - Mark A. Brockman
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, Canada
- Faculty of Health Sciences, Simon Fraser University, Burnaby, Canada
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, Canada
| | - Zabrina L. Brumme
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, Canada
- Faculty of Health Sciences, Simon Fraser University, Burnaby, Canada
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Mudd JC. Quantitative and Qualitative Distinctions between HIV-1 and SIV Reservoirs: Implications for HIV-1 Cure-Related Studies. Viruses 2024; 16:514. [PMID: 38675857 PMCID: PMC11054464 DOI: 10.3390/v16040514] [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: 02/02/2024] [Revised: 03/07/2024] [Accepted: 03/16/2024] [Indexed: 04/28/2024] Open
Abstract
The persistence of the latent viral reservoir is the main hurdle to curing HIV-1 infection. SIV infection of non-human primates (NHPs), namely Indian-origin rhesus macaques, is the most relevant and widely used animal model to evaluate therapies that seek to eradicate HIV-1. The utility of a model ultimately rests on how accurately it can recapitulate human disease, and while reservoirs in the NHP model behave quantitatively very similar to those of long-term suppressed persons with HIV-1 (PWH) in the most salient aspects, recent studies have uncovered key nuances at the clonotypic level that differentiate the two in qualitative terms. In this review, we will highlight differences relating to proviral intactness, clonotypic structure, and decay rate during ART between HIV-1 and SIV reservoirs and discuss the relevance of these distinctions in the interpretation of HIV-1 cure strategies. While these, to some degree, may reflect a unique biology of the virus or host, distinctions among the proviral landscape in SIV are likely to be shaped significantly by the condensed timeframe of NHP studies. ART is generally initiated earlier in the disease course, and animals are virologically suppressed for shorter periods before receiving interventions. Because these are experimental variables dictated by the investigator, we offer guidance on study design for cure-related studies performed in the NHP model. Finally, we highlight the case of GS-9620 (Vesatolimod), an antiviral TLR7 agonist tested in multiple independent pre-clinical studies in which virological outcomes may have been influenced by study-related variables.
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Affiliation(s)
- Joseph C. Mudd
- Tulane National Primate Research Center, Covington, LA 70433, USA;
- Department of Microbiology and Immunology, Tulane University School of Medicine, New Orleans, LA 70112, USA
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3
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Vanegas-Torres CA, Schindler M. HIV-1 Vpr Functions in Primary CD4 + T Cells. Viruses 2024; 16:420. [PMID: 38543785 PMCID: PMC10975730 DOI: 10.3390/v16030420] [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: 01/31/2024] [Revised: 03/05/2024] [Accepted: 03/05/2024] [Indexed: 05/23/2024] Open
Abstract
HIV-1 encodes four accesory proteins in addition to its structural and regulatory genes. Uniquely amongst them, Vpr is abundantly present within virions, meaning it is poised to exert various biological effects on the host cell upon delivery. In this way, Vpr contributes towards the establishment of a successful infection, as evidenced by the extent to which HIV-1 depends on this factor to achieve full pathogenicity in vivo. Although HIV infects various cell types in the host organism, CD4+ T cells are preferentially targeted since they are highly permissive towards productive infection, concomitantly bringing about the hallmark immune dysfunction that accompanies HIV-1 spread. The last several decades have seen unprecedented progress in unraveling the activities Vpr possesses in the host cell at the molecular scale, increasingly underscoring the importance of this viral component. Nevertheless, it remains controversial whether some of these advances bear in vivo relevance, since commonly employed cellular models significantly differ from primary T lymphocytes. One prominent example is the "established" ability of Vpr to induce G2 cell cycle arrest, with enigmatic physiological relevance in infected primary T lymphocytes. The objective of this review is to present these discoveries in their biological context to illustrate the mechanisms whereby Vpr supports HIV-1 infection in CD4+ T cells, whilst identifying findings that require validation in physiologically relevant models.
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Affiliation(s)
| | - Michael Schindler
- Institute for Medical Virology and Epidemiology of Viral Diseases, University Hospital Tuebingen, 72076 Tuebingen, Germany;
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4
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Cannon L, Fehrman S, Pinzone M, Weissman S, O'Doherty U. Machine Learning Bolsters Evidence That D1, Nef, and Tat Influence HIV Reservoir Dynamics. Pathog Immun 2024; 8:37-58. [PMID: 38292079 PMCID: PMC10827039 DOI: 10.20411/pai.v8i2.621] [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: 09/07/2023] [Accepted: 12/04/2023] [Indexed: 02/01/2024] Open
Abstract
Background The primary hurdle to curing HIV is due to the establishment of a reservoir early in infection. In an effort to find new treatment strategies, we and others have focused on understanding the selection pressures exerted on the reservoir by studying how proviral sequences change over time. Methods To gain insights into the dynamics of the HIV reservoir we analyzed longitudinal near full-length sequences from 7 people living with HIV between 1 and 20 years following the initiation of antiretroviral treatment. We used this data to employ Bayesian mixed effects models to characterize the decay of the reservoir using single-phase and multiphasic decay models based on near full-length sequencing. In addition, we developed a machine-learning approach utilizing logistic regression to identify elements within the HIV genome most associated with proviral decay and persistence. By systematically analyzing proviruses that are deleted for a specific element, we gain insights into their role in reservoir contraction and expansion. Results Our analyses indicate that biphasic decay models of intact reservoir dynamics were better than single-phase models with a stronger statistical fit. Based on the biphasic decay pattern of the intact reservoir, we estimated the half-lives of the first and second phases of decay to be 18.2 (17.3 to 19.2, 95%CI) and 433 (227 to 6400, 95%CI) months, respectively.In contrast, the dynamics of defective proviruses differed favoring neither model definitively, with an estimated half-life of 87.3 (78.1 to 98.8, 95% CI) months during the first phase of the biphasic model. Machine-learning analysis of HIV genomes at the nucleotide level revealed that the presence of the splice donor site D1 was the principal genomic element associated with contraction. This role of D1 was then validated in an in vitro system. Using the same approach, we additionally found supporting evidence that HIV nef may confer a protective advantage for latently infected T cells while tat was associated with clonal expansion. Conclusions The nature of intact reservoir decay suggests that the long-lived HIV reservoir contains at least 2 distinct compartments. The first compartment decays faster than the second compartment. Our machine-learning analysis of HIV proviral sequences reveals specific genomic elements are associated with contraction while others are associated with persistence and expansion. Together, these opposing forces shape the reservoir over time.
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Affiliation(s)
- LaMont Cannon
- Center for Biological Data Science, Virginia Commonwealth University, Richmond, Virginia
| | - Sophia Fehrman
- Center for Biological Data Science, Virginia Commonwealth University, Richmond, Virginia
| | - Marilia Pinzone
- Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Sam Weissman
- Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Una O'Doherty
- Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
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5
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Cossarini F, Aberg JA, Chen BK, Mehandru S. Viral Persistence in the Gut-Associated Lymphoid Tissue and Barriers to HIV Cure. AIDS Res Hum Retroviruses 2023; 40:54-65. [PMID: 37450338 PMCID: PMC10790554 DOI: 10.1089/aid.2022.0180] [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] [Indexed: 07/18/2023] Open
Abstract
More than 40 years after the first reported cases of what then became known as acquired immunodeficiency syndrome (AIDS), tremendous progress has been achieved in transforming the disease from almost universally fatal to a chronic manageable condition. Nonetheless, the efforts to find a preventative vaccine or a cure for the underlying infection with Human Immunodeficiency Virus (HIV) remain largely unsuccessful. Many challenges intrinsic to the virus characteristics and host response need to be overcome for either goal to be achieved. This article will review the obstacles to an effective HIV cure, specifically the steps involved in the generation of HIV latency, focusing on the role of the gut-associated lymphoid tissue, which has received less attention compared with the peripheral blood, despite being the largest repository of lymphoid tissue in the human body, and a large site for HIV persistence.
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Affiliation(s)
- Francesca Cossarini
- Division of Infectious Diseases, Department of Medicine, Icahn School at Mount Sinai, New York, New York, USA
- Precision Immunology Institute, Icahn School at Mount Sinai, New York, New York, USA
| | - Judith A. Aberg
- Division of Infectious Diseases, Department of Medicine, Icahn School at Mount Sinai, New York, New York, USA
| | - Benjamin K. Chen
- Division of Infectious Diseases, Department of Medicine, Icahn School at Mount Sinai, New York, New York, USA
- Precision Immunology Institute, Icahn School at Mount Sinai, New York, New York, USA
| | - Saurabh Mehandru
- Precision Immunology Institute, Icahn School at Mount Sinai, New York, New York, USA
- Division of Gastroenterology, Department of Medicine, Icahn School at Mount Sinai, New York, New York, USA
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6
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Okpaise D, Sluis-Cremer N, Rappocciolo G, Rinaldo CR. Cholesterol Metabolism in Antigen-Presenting Cells and HIV-1 Trans-Infection of CD4 + T Cells. Viruses 2023; 15:2347. [PMID: 38140588 PMCID: PMC10747884 DOI: 10.3390/v15122347] [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: 10/25/2023] [Revised: 11/28/2023] [Accepted: 11/28/2023] [Indexed: 12/24/2023] Open
Abstract
Antiretroviral therapy (ART) provides an effective method for managing HIV-1 infection and preventing the onset of AIDS; however, it is ineffective against the reservoir of latent HIV-1 that persists predominantly in resting CD4+ T cells. Understanding the mechanisms that facilitate the persistence of the latent reservoir is key to developing an effective cure for HIV-1. Of particular importance in the establishment and maintenance of the latent viral reservoir is the intercellular transfer of HIV-1 from professional antigen-presenting cells (APCs-monocytes/macrophages, myeloid dendritic cells, and B lymphocytes) to CD4+ T cells, termed trans-infection. Whereas virus-to-cell HIV-1 cis infection is sensitive to ART, trans-infection is impervious to antiviral therapy. APCs from HIV-1-positive non-progressors (NPs) who control their HIV-1 infection in the absence of ART do not trans-infect CD4+ T cells. In this review, we focus on this unique property of NPs that we propose is driven by a genetically inherited, altered cholesterol metabolism in their APCs. We focus on cellular cholesterol homeostasis and the role of cholesterol metabolism in HIV-1 trans-infection, and notably, the link between cholesterol efflux and HIV-1 trans-infection in NPs.
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Affiliation(s)
| | | | | | - Charles R. Rinaldo
- Department of Medicine, Division of Infectious Diseases, University of Pittsburgh School of Medicine, Pittsburgh, PA 15261, USA; (D.O.); (N.S.-C.); (G.R.)
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7
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Ikeogu N, Ajibola O, Zayats R, Murooka TT. Identifying physiological tissue niches that support the HIV reservoir in T cells. mBio 2023; 14:e0205323. [PMID: 37747190 PMCID: PMC10653859 DOI: 10.1128/mbio.02053-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/26/2023] Open
Abstract
Successful antiretroviral therapy (ART) can efficiently suppress Human Immunodeficiency Virus-1 (HIV-1) replication to undetectable levels, but rare populations of infected memory CD4+ T cells continue to persist, complicating viral eradication efforts. Memory T cells utilize distinct homing and adhesion molecules to enter, exit, or establish residence at diverse tissue sites, integrating cellular and environmental cues that maintain homeostasis and life-long protection against pathogens. Critical roles for T cell receptor and cytokine signals driving clonal expansion and memory generation during immunity generation are well established, but whether HIV-infected T cells can utilize similar mechanisms for their own long-term survival is unclear. How infected, but transcriptionally silent T cells maintain their recirculation potential through blood and peripheral tissues, or whether they acquire new capabilities to establish unique peripheral tissue niches, is also not well understood. In this review, we will discuss the cellular and molecular cues that are important for memory T cell homeostasis and highlight opportunities for HIV to hijack normal immunological processes to establish long-term viral persistence.
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Affiliation(s)
- Nnamdi Ikeogu
- Department of Immunology, Rady Faculty of Health Sciences, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Oluwaseun Ajibola
- Department of Immunology, Rady Faculty of Health Sciences, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Romaniya Zayats
- Department of Immunology, Rady Faculty of Health Sciences, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Thomas T. Murooka
- Department of Immunology, Rady Faculty of Health Sciences, University of Manitoba, Winnipeg, Manitoba, Canada
- Department of Medical Microbiology and Infectious Diseases, Rady Faculty of Health Sciences, University of Manitoba, Winnipeg, Manitoba, Canada
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8
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Reeves DB, Bacchus-Souffan C, Fitch M, Abdel-Mohsen M, Hoh R, Ahn H, Stone M, Hecht F, Martin J, Deeks SG, Hellerstein MK, McCune JM, Schiffer JT, Hunt PW. Estimating the contribution of CD4 T cell subset proliferation and differentiation to HIV persistence. Nat Commun 2023; 14:6145. [PMID: 37783718 PMCID: PMC10545742 DOI: 10.1038/s41467-023-41521-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Accepted: 09/04/2023] [Indexed: 10/04/2023] Open
Abstract
Persistence of HIV in people living with HIV (PWH) on suppressive antiretroviral therapy (ART) has been linked to physiological mechanisms of CD4+ T cells. Here, in the same 37 male PWH on ART we measure longitudinal kinetics of HIV DNA and cell turnover rates in five CD4 cell subsets: naïve (TN), stem-cell- (TSCM), central- (TCM), transitional- (TTM), and effector-memory (TEM). HIV decreases in TTM and TEM but not in less-differentiated subsets. Cell turnover is ~10 times faster than HIV clearance in memory subsets, implying that cellular proliferation consistently creates HIV DNA. The optimal mathematical model for these integrated data sets posits HIV DNA also passages between CD4 cell subsets via cellular differentiation. Estimates are heterogeneous, but in an average participant's year ~10 (in TN and TSCM) and ~104 (in TCM, TTM, TEM) proviruses are generated by proliferation while ~103 proviruses passage via cell differentiation (per million CD4). In simulations, therapies blocking proliferation and/or enhancing differentiation could reduce HIV DNA by 1-2 logs over 3 years. In summary, HIV exploits cellular proliferation and differentiation to persist during ART but clears faster in more proliferative/differentiated CD4 cell subsets and the same physiological mechanisms sustaining HIV might be temporarily modified to reduce it.
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Affiliation(s)
- Daniel B Reeves
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, 1100 Fairview Ave N, Seattle, WA, 98109, USA.
- Department of Global Health, University of Washington, 1959 NE Pacific St, Seattle, WA, 98195, USA.
| | | | - Mark Fitch
- Department of Nutritional Sciences and Toxicology, University of California, University Avenue and Oxford St, Berkeley, CA, 94720, USA
| | | | - Rebecca Hoh
- Department of Medicine, Zuckerberg San Francisco General Hospital, University of California, 1001 Potrero Ave, San Francisco, CA, 94100, USA
| | - Haelee Ahn
- Division of Experimental Medicine, Department of Medicine, University of California San Francisco, 1001 Potrero Ave, San Francisco, CA, 94100, USA
| | - Mars Stone
- Vitalant Research Institute, 360 Spear St Suite 200, San Francisco, CA, 94105, USA
| | - Frederick Hecht
- Division of Experimental Medicine, Department of Medicine, University of California San Francisco, 1001 Potrero Ave, San Francisco, CA, 94100, USA
| | - Jeffrey Martin
- Epidemiology & Biostatistics, University of California San Francisco School of Medicine, 550 16th Street, San Francisco, CA, 94158, USA
| | - Steven G Deeks
- Department of Medicine, Zuckerberg San Francisco General Hospital, University of California, 1001 Potrero Ave, San Francisco, CA, 94100, USA
| | - Marc K Hellerstein
- Department of Nutritional Sciences and Toxicology, University of California, University Avenue and Oxford St, Berkeley, CA, 94720, USA
| | - Joseph M McCune
- HIV Frontiers, Global Health Accelerator, Bill & Melinda Gates Foundation, 500 5th Ave N, Seattle, WA, 98109, USA
| | - Joshua T Schiffer
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, 1100 Fairview Ave N, Seattle, WA, 98109, USA
- Clinical Research Division, Fred Hutchinson Cancer Center, 1100 Fairview Ave N, Seattle, WA, 98109, USA
- Department of Allergy and Infectious Diseases, School of Medicine, University of Washington, 1959 NE Pacific St, Seattle, WA, 98195, USA
| | - Peter W Hunt
- Division of Experimental Medicine, Department of Medicine, University of California San Francisco, 1001 Potrero Ave, San Francisco, CA, 94100, USA
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9
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Arandjelovic P, Kim Y, Cooney JP, Preston SP, Doerflinger M, McMahon JH, Garner SE, Zerbato JM, Roche M, Tumpach C, Ong J, Sheerin D, Smyth GK, Anderson JL, Allison CC, Lewin SR, Pellegrini M. Venetoclax, alone and in combination with the BH3 mimetic S63845, depletes HIV-1 latently infected cells and delays rebound in humanized mice. Cell Rep Med 2023; 4:101178. [PMID: 37652018 PMCID: PMC10518630 DOI: 10.1016/j.xcrm.2023.101178] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Revised: 06/29/2023] [Accepted: 08/09/2023] [Indexed: 09/02/2023]
Abstract
HIV-1 persists indefinitely in people living with HIV (PLWH) on antiretroviral therapy (ART). If ART is stopped, the virus rapidly rebounds from long-lived latently infected cells. Using a humanized mouse model of HIV-1 infection and CD4+ T cells from PLWH on ART, we investigate whether antagonizing host pro-survival proteins can prime latent cells to die and facilitate HIV-1 clearance. Venetoclax, a pro-apoptotic inhibitor of Bcl-2, depletes total and intact HIV-1 DNA in CD4+ T cells from PLWH ex vivo. This venetoclax-sensitive population is enriched for cells with transcriptionally higher levels of pro-apoptotic BH3-only proteins. Furthermore, venetoclax delays viral rebound in a mouse model of persistent HIV-1 infection, and the combination of venetoclax with the Mcl-1 inhibitor S63845 achieves a longer delay in rebound compared with either intervention alone. Thus, selective inhibition of pro-survival proteins can induce death of HIV-1-infected cells that persist on ART, extending time to viral rebound.
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Affiliation(s)
- Philip Arandjelovic
- Division of Infectious Disease and Immune Defence, The Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, Australia; Department of Medical Biology, The University of Melbourne, Melbourne, VIC, Australia
| | - Youry Kim
- Department of Infectious Diseases, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
| | - James P Cooney
- Division of Infectious Disease and Immune Defence, The Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, Australia; Department of Medical Biology, The University of Melbourne, Melbourne, VIC, Australia
| | - Simon P Preston
- Division of Infectious Disease and Immune Defence, The Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, Australia; Department of Medical Biology, The University of Melbourne, Melbourne, VIC, Australia
| | - Marcel Doerflinger
- Division of Infectious Disease and Immune Defence, The Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, Australia; Department of Medical Biology, The University of Melbourne, Melbourne, VIC, Australia
| | - James H McMahon
- Department of Infectious Diseases, Alfred Hospital and Monash University, Melbourne, VIC, Australia
| | - Sarah E Garner
- Division of Infectious Disease and Immune Defence, The Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, Australia; Department of Medical Biology, The University of Melbourne, Melbourne, VIC, Australia
| | - Jennifer M Zerbato
- Department of Infectious Diseases, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
| | - Michael Roche
- Department of Infectious Diseases, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia; Emerging Infections Program, School of Health and Biomedical Sciences, RMIT University, Melbourne, VIC, Australia
| | - Carolin Tumpach
- Department of Infectious Diseases, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
| | - Jesslyn Ong
- Department of Infectious Diseases, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
| | - Dylan Sheerin
- Division of Infectious Disease and Immune Defence, The Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, Australia; Department of Medical Biology, The University of Melbourne, Melbourne, VIC, Australia
| | - Gordon K Smyth
- Bioinformatics Division, The Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, Australia; School of Mathematics and Statistics, The University of Melbourne, Parkville, VIC, Australia
| | - Jenny L Anderson
- Department of Infectious Diseases, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
| | - Cody C Allison
- Division of Infectious Disease and Immune Defence, The Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, Australia; Department of Medical Biology, The University of Melbourne, Melbourne, VIC, Australia
| | - Sharon R Lewin
- Department of Infectious Diseases, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia; Department of Infectious Diseases, Alfred Hospital and Monash University, Melbourne, VIC, Australia; Victorian Infectious Diseases Service, The Royal Melbourne Hospital at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
| | - Marc Pellegrini
- Division of Infectious Disease and Immune Defence, The Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, Australia; Department of Medical Biology, The University of Melbourne, Melbourne, VIC, Australia.
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10
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Pasternak AO, Berkhout B. HIV persistence: silence or resistance? Curr Opin Virol 2023; 59:101301. [PMID: 36805974 DOI: 10.1016/j.coviro.2023.101301] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2022] [Revised: 12/05/2022] [Accepted: 12/19/2022] [Indexed: 02/19/2023]
Abstract
Despite decades of suppressive antiretroviral therapy, human immunodeficiency virus (HIV) reservoirs in infected individuals persist and fuel viral rebound once therapy is interrupted. The persistence of viral reservoirs is the main obstacle to achieving HIV eradication or a long-term remission. The last decade has seen a profound change in our understanding of the mechanisms behind HIV persistence, which appears to be much more complex than originally assumed. In addition to the persistence of transcriptionally silent proviruses in a stable latent reservoir that is invisible to the immune system, HIV is increasingly recognized to persist by resistance to the immune clearance, which appears to play a surprisingly prominent role in shaping the reservoir. In this review, we discuss some emerging insights into the mechanisms of HIV persistence, as well as their implications for the development of strategies towards an HIV cure.
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Affiliation(s)
- Alexander O Pasternak
- Laboratory of Experimental Virology, Department of Medical Microbiology, Amsterdam UMC, University of Amsterdam, 1105 AZ Amsterdam, the Netherlands.
| | - Ben Berkhout
- Laboratory of Experimental Virology, Department of Medical Microbiology, Amsterdam UMC, University of Amsterdam, 1105 AZ Amsterdam, the Netherlands
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11
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Huang Y, Dhummakupt A, Khetan P, Nilles T, Zhou W, Mudvari P, Szewczyk J, Chen YH, Boritz E, Ji H, Agwu A, Persaud D. Immune activation and exhaustion marker expression on T-cell subsets in ART-treated adolescents and young adults with perinatal HIV-1 infection as correlates of viral persistence. Front Immunol 2023; 14:1007626. [PMID: 37033916 PMCID: PMC10076634 DOI: 10.3389/fimmu.2023.1007626] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2022] [Accepted: 03/06/2023] [Indexed: 04/11/2023] Open
Abstract
HIV-1 infection in memory CD4+ T cells forms a latent reservoir that is a barrier to cure. Identification of immune biomarkers that correlate with HIV-1 reservoir size may aid with evaluating efficacy of HIV-1 eradication strategies, towards ART-free remission and cure. In adults living with non-perinatal HIV-1, the immune exhaustion marker PD-1 on central memory CD4+ T cells (Tcm) correlates with measures of HIV-1 reservoir size. Immune correlates of HIV-1 are less defined in adolescents and young adults with perinatal HIV-1. With multi-parameter flow cytometry, we examined immune activation (CD69, CD25, HLA-DR), and exhaustion (PD-1, TIGIT, TIM-3 and LAG-3) markers on CD4+ T cell subsets (naïve (Tn), central memory (Tcm), and the combination (Ttem) of transitional (Ttm) and effector memory (Tem) cells, in 10 adolescents and young adults living with perinatal HIV-1 (median age 15.9 years; median duration of virologic suppression 7.0 years), in whom HIV-1 reservoir size was measured with the Intact Proviral HIV-1 DNA Assay (IPDA) and an enhanced Tat/Rev limiting dilution assay (TILDA). RNA-seq was also performed on the unstimulated CD4+ T cells. The median total HIV-1 DNA concentration in memory CD4+ T cells was 211.90 copies per million CD4+ T cells. In the 7 participants with subtype B HIV-1 infection, the median intact proviral DNA load was 7.96 copies per million CD4+ T cells. Levels of HLA-DR and TIGIT on the Ttem were correlated with total HIV-1 DNA (r=0.76, p=0.015) and (r=0.72, p=0.023), respectively, but not with intact proviral load or induced reservoir size. HIV-1 DNA load was also positively correlated with transcriptional clusters associated with HLA-DR expression by RNA-seq. In contrast, PD-1 expression on Tcm was inversely correlated with total HIV-1 DNA (r=-0.67, p=0.039). Reservoir size by IPDA and TILDA were correlated (r=0.81, p=0.036). Thus, in this cohort of youths with long-standing treated perinatal infection, HLA-DR and TIGIT on Ttem were the key correlates of HIV-1 infected cell frequencies by total HIV-1 DNA, and not PD-1. Total HIV-1 DNA was negatively correlated with PD-1 expressing Tcm. These differences in longstanding perinatal HIV-1 infection compared with adult infection requires further study in larger cohorts.
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Affiliation(s)
- Yuyang Huang
- Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD, United States
| | - Adit Dhummakupt
- Department of Pediatric Infectious Disease, Johns Hopkins University School of Medicine, Baltimore, MD, United States
| | - Priya Khetan
- Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD, United States
| | - Tricia Nilles
- Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD, United States
| | - Weiqiang Zhou
- Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD, United States
| | - Prakriti Mudvari
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institute of Health, Bethesda, MD, United States
| | - Joseph Szewczyk
- Department of Pediatric Infectious Disease, Johns Hopkins University School of Medicine, Baltimore, MD, United States
| | - Ya Hui Chen
- Department of Pediatric Infectious Disease, Johns Hopkins University School of Medicine, Baltimore, MD, United States
| | - Eli Boritz
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institute of Health, Bethesda, MD, United States
| | - Hongkai Ji
- Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD, United States
| | - Allison Agwu
- Department of Pediatric Infectious Disease, Johns Hopkins University School of Medicine, Baltimore, MD, United States
| | - Deborah Persaud
- Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD, United States
- Department of Pediatric Infectious Disease, Johns Hopkins University School of Medicine, Baltimore, MD, United States
- *Correspondence: Deborah Persaud,
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12
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Facciolà A, D’Amato S, Calimeri S, Giudice DL, Micali C, Russotto Y, Venanzi Rullo E, Nunnari G, Squeri R, Pellicanò GF. Efficacy of COVID-19 Vaccination in People Living with HIV: A Public Health Fundamental Tool for the Protection of Patients and the Correct Management of Infection. Infect Dis Rep 2022; 14:784-793. [PMID: 36286201 PMCID: PMC9602118 DOI: 10.3390/idr14050080] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Revised: 10/07/2022] [Accepted: 10/12/2022] [Indexed: 09/22/2023] Open
Abstract
HIV/AIDS is considered a risk factor for increased mortality due to COVID-19. For this reason, it is essential to include this population in vaccination campaigns. Studies found that antibodies are lower in HIV+ patients than in healthy individuals. The aim of this study was to assess the immune response in a cohort of people living with HIV/AIDS (PLWH) vaccinated with COVID-19 vaccination in order to evaluate the role played by the HIV infection in the efficacy of this vaccine. We carried out a cross-sectional study in the period April-September 2021, involving a cohort of PLWH and a cohort of HIV-uninfected people as the control group. The efficacy of vaccination was high in both groups despite a slight and not significant difference between them. However, important differences were found according to the intensity of the immune response. Specifically, while in the HIV+ group almost a quarter of people had a low response, it is important to remark that the control group had only a high or intermediate response after vaccination. Our results suggest the high efficacy of the mRNA COVID-19 vaccine in PLWH and the importance to vaccinate against COVID-19 in these patients in order to increase their protection.
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Affiliation(s)
- Alessio Facciolà
- Department of Biomedical and Dental Sciences and Morphofunctional Imaging, University of Messina, 98124 Messina, Italy
| | - Smeralda D’Amato
- Department of Biomedical and Dental Sciences and Morphofunctional Imaging, University of Messina, 98124 Messina, Italy
| | - Sebastiano Calimeri
- Department of Biomedical and Dental Sciences and Morphofunctional Imaging, University of Messina, 98124 Messina, Italy
| | - Daniela Lo Giudice
- Department of Biomedical and Dental Sciences and Morphofunctional Imaging, University of Messina, 98124 Messina, Italy
| | - Cristina Micali
- Department of Clinical and Experimental Medicine, University of Messina, 98124 Messina, Italy
| | - Ylenia Russotto
- Department of Clinical and Experimental Medicine, University of Messina, 98124 Messina, Italy
| | - Emmanuele Venanzi Rullo
- Department of Clinical and Experimental Medicine, University of Messina, 98124 Messina, Italy
| | - Giuseppe Nunnari
- Department of Clinical and Experimental Medicine, University of Messina, 98124 Messina, Italy
| | - Raffaele Squeri
- Department of Biomedical and Dental Sciences and Morphofunctional Imaging, University of Messina, 98124 Messina, Italy
| | - Giovanni Francesco Pellicanò
- Department of Human Pathology of the Adult and the Developmental Age “G. Barresi”, University of Messina, 98124 Messina, Italy
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13
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Russotto Y, Micali C, Pellicanò GF, Nunnari G, Venanzi Rullo E. HIV and Mediterranean Zoonoses: A Review of the Literature. Infect Dis Rep 2022; 14:694-709. [PMID: 36136825 PMCID: PMC9498920 DOI: 10.3390/idr14050075] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Revised: 08/21/2022] [Accepted: 09/14/2022] [Indexed: 11/16/2022] Open
Abstract
A zoonosis is an infectious disease that has jumped from a non-human animal to humans. Some zoonoses are very common in the Mediterranean area and endemic in specific regions, so they represent an important problem for public health. Human Immunodeficiency Virus (HIV) is a virus that has originated as a zoonosis and is now diffused globally, with the most significant numbers of infected people among the infectious diseases. Since the introduction of antiretroviral therapy (ART), the history for people living with HIV (PLWH) has changed drastically, and many diseases are now no different in epidemiology and prognosis as they are in not-HIV-infected people. Still, the underlying inflammatory state that is correlated with HIV and other alterations related to the infection itself can be a risk factor when infected with other bacteria, parasites or viruses. We reviewed the literature for infection by the most common Mediterranean zoonoses, such as Campylobacter, Salmonella, Brucella, Rickettsia, Borrelia, Listeria and Echinococcus, and a possible correlation with HIV. We included Monkeypox, since the outbreak of cases is becoming a concern lately. We found that HIV may be related with alterations of the microbiome, as for campylobacteriosis, and that there are some zoonoses with a significant prevalence in PLWH, as for salmonellosis.
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Affiliation(s)
- Ylenia Russotto
- Unit of Infectious Diseases, Department of Clinical and Experimental Medicine, University of Messina, 98124 Messina, Italy
| | - Cristina Micali
- Unit of Infectious Diseases, Department of Clinical and Experimental Medicine, University of Messina, 98124 Messina, Italy
- Correspondence: ; Tel.: +39-09-0221-2032
| | - Giovanni Francesco Pellicanò
- Department of Human Pathology of the Adult and the Developmental Age “G. Barresi”, University of Messina, 98124 Messina, Italy
| | - Giuseppe Nunnari
- Unit of Infectious Diseases, Department of Clinical and Experimental Medicine, University of Messina, 98124 Messina, Italy
| | - Emmanuele Venanzi Rullo
- Unit of Infectious Diseases, Department of Clinical and Experimental Medicine, University of Messina, 98124 Messina, Italy
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14
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Micali C, Russotto Y, Celesia BM, Santoro L, Marino A, Pellicanò GF, Nunnari G, Venanzi Rullo E. Thyroid Diseases and Thyroid Asymptomatic Dysfunction in People Living With HIV. Infect Dis Rep 2022; 14:655-667. [PMID: 36136821 PMCID: PMC9498502 DOI: 10.3390/idr14050071] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Revised: 08/26/2022] [Accepted: 08/30/2022] [Indexed: 11/16/2022] Open
Abstract
Thyroid diseases (TDs) and thyroid asymptomatic dysfunctions (TADs) are correlated with Human Immunodeficiency virus (HIV) infection and Acquired ImmunoDeficiency Syndrome (AIDS) as well as many endocrine dysfunctions and dysregulation of hormonal axes. To date, available studies on People Living With HIV (PLWH) affected by thyroid diseases and asymptomatic dysfunctions are few and rather controversial. The purpose of the present non-systematic literature review is to recap the current knowledge on the main features of thyroid dysfunctions and disorders in PLWH. Large cohort studies are needed for a better comprehension of the impact, evolution and treatment of thyroid pathologies in the HIV-infected population.
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Affiliation(s)
- Cristina Micali
- Unit of Infectious Diseases, Department of Clinical and Experimental Medicine, University of Messina, 98124 Messina, Italy
| | - Ylenia Russotto
- Unit of Infectious Diseases, Department of Clinical and Experimental Medicine, University of Messina, 98124 Messina, Italy
- Correspondence: ; Tel.: +39-090-221-2032
| | - Benedetto Maurizio Celesia
- Unit of Infectious Diseases, Department of Clinical and Experimental Medicine, University of Catania, 95131 Catania, Italy
| | - Laura Santoro
- Unit of Infectious Diseases, Department of Clinical and Experimental Medicine, University of Messina, 98124 Messina, Italy
| | - Andrea Marino
- Biomedical and Biotechnological Sciences Department, University of Catania, 95131 Catania, Italy
| | - Giovanni Francesco Pellicanò
- Department of Human Pathology of the Adult and the Developmental Age “G. Barresi”, University of Messina, 98124 Messina, Italy
| | - Giuseppe Nunnari
- Unit of Infectious Diseases, Department of Clinical and Experimental Medicine, University of Messina, 98124 Messina, Italy
| | - Emmanuele Venanzi Rullo
- Unit of Infectious Diseases, Department of Clinical and Experimental Medicine, University of Messina, 98124 Messina, Italy
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15
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Soto PC, Terry VH, Lewinski MK, Deshmukh S, Beliakova-Bethell N, Spina CA. HIV-1 latency is established preferentially in minimally activated and non-dividing cells during productive infection of primary CD4 T cells. PLoS One 2022; 17:e0271674. [PMID: 35895672 PMCID: PMC9328514 DOI: 10.1371/journal.pone.0271674] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2021] [Accepted: 07/05/2022] [Indexed: 11/19/2022] Open
Abstract
Latently infected CD4 T cells form a stable reservoir of HIV that leads to life-long viral persistence; the mechanisms involved in establishment of this latency are not well understood. Three scenarios have been proposed: 1) an activated, proliferating cell becomes infected and reverts back to a resting state; 2) an activated cell becomes infected during its return to resting; or 3) infection is established directly in a resting cell. The aim of this study was, therefore, to investigate the relationship between T cell activation and proliferation and the establishment of HIV latency. Isolated primary CD4 cells were infected at different time points before or after TCR-induced stimulation. Cell proliferation within acutely infected cultures was tracked using CFSE viable dye over 14 days; and cell subsets that underwent varying degrees of proliferation were isolated at end of culture by flow cytometric sorting. Recovered cell subpopulations were analyzed for the amount of integrated HIV DNA, and the ability to produce virus, upon a second round of cell stimulation. We show that cell cultures exposed to virus, prior to stimulus addition, contained the highest levels of integrated and replication-competent provirus after returning to quiescence; whereas, cells infected during the height of cell proliferation retained the least. Cells that did not divide or exhibited limited division, following virus exposure and stimulation contained greater amounts of integrated and inducible HIV than did cells that had divided many times. Based on these results, co-culture experiments were conducted to demonstrate that latent infection could be established directly in non-dividing cells via cell-to-cell transmission from autologous productively infected cells. Together, the findings from our studies implicate the likely importance of direct infection of sub-optimally activated T cells in establishment of latently infected reservoirs in vivo, especially in CD4 lymphocytes that surround productive viral foci within immune tissue microenvironments.
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Affiliation(s)
- Paula C. Soto
- Veterans Affairs San Diego Healthcare System, San Diego, California, United States of America
- Department of Pathology, University of California San Diego, La Jolla, California, United States of America
| | - Valeri H. Terry
- Veterans Affairs San Diego Healthcare System, San Diego, California, United States of America
| | - Mary K. Lewinski
- Department of Medicine, University of California San Diego, La Jolla, California, United States of America
| | - Savitha Deshmukh
- Veterans Medical Research Foundation, San Diego, California, United States of America
| | - Nadejda Beliakova-Bethell
- Veterans Affairs San Diego Healthcare System, San Diego, California, United States of America
- Department of Medicine, University of California San Diego, La Jolla, California, United States of America
| | - Celsa A. Spina
- Veterans Affairs San Diego Healthcare System, San Diego, California, United States of America
- Department of Pathology, University of California San Diego, La Jolla, California, United States of America
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16
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Kim EH, Manganaro L, Schotsaert M, Brown BD, Mulder LC, Simon V. Development of an HIV reporter virus that identifies latently infected CD4 + T cells. CELL REPORTS METHODS 2022; 2:100238. [PMID: 35784650 PMCID: PMC9243624 DOI: 10.1016/j.crmeth.2022.100238] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 01/26/2022] [Revised: 03/26/2022] [Accepted: 05/24/2022] [Indexed: 04/23/2023]
Abstract
There is no cure for HIV infection, as the virus establishes a latent reservoir, which escapes highly active antiretroviral treatments. One major obstacle is the difficulty identifying cells that harbor latent proviruses. We devised a single-round viral vector that carries a series of versatile reporter molecules that are expressed in an LTR-dependent or LTR-independent manner and make it possible to accurately distinguish productive from latent infection. Using primary human CD4+ T cells, we show that transcriptionally silent proviruses are found in more than 50% of infected cells. The latently infected cells harbor proviruses but lack evidence for multiple spliced transcripts. LTR-silent integrations occurred to variable degrees in all CD4+ T subsets examined, with CD4+ TEM and CD4+ TREG displaying the highest frequency of latent infections. This viral vector permits the interrogation of HIV latency at single-cell resolution, revealing mechanisms of latency establishment and allowing the characterization of effective latency-reversing agents.
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Affiliation(s)
- Eun Hye Kim
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- The Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Center for Vaccine Research and Pandemic Preparedness, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Lara Manganaro
- INGM, Istituto Nazionale di Genetica Molecolare, ‘Romeo ed Enrica Invernizzi’, Milan, Italy
- Department of Pharmacological and Biomolecular Sciences (DiSFeB), University of Milan, Milan, Italy
| | - Michael Schotsaert
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- The Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Brian D. Brown
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Icahn Genomics Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Lubbertus C.F. Mulder
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- The Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Center for Vaccine Research and Pandemic Preparedness, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Viviana Simon
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Division of Infectious Disease, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- The Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Pathology, Molecular and Cell Based Medicine at Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Center for Vaccine Research and Pandemic Preparedness, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
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17
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Single-cell multiomics reveals persistence of HIV-1 in expanded cytotoxic T cell clones. Immunity 2022; 55:1013-1031.e7. [PMID: 35320704 PMCID: PMC9203927 DOI: 10.1016/j.immuni.2022.03.004] [Citation(s) in RCA: 55] [Impact Index Per Article: 27.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Revised: 02/19/2022] [Accepted: 03/08/2022] [Indexed: 02/02/2023]
Abstract
Understanding the drivers and markers of clonally expanding HIV-1-infected CD4+ T cells is essential for HIV-1 eradication. We used single-cell ECCITE-seq, which captures surface protein expression, cellular transcriptome, HIV-1 RNA, and TCR sequences within the same single cell to track clonal expansion dynamics in longitudinally archived samples from six HIV-1-infected individuals (during viremia and after suppressive antiretroviral therapy) and two uninfected individuals, in unstimulated conditions and after CMV and HIV-1 antigen stimulation. Despite antiretroviral therapy, persistent antigen and TNF responses shaped T cell clonal expansion. HIV-1 resided in Th1-polarized, antigen-responding T cells expressing BCL2 and SERPINB9 that may resist cell death. HIV-1 RNA+ T cell clones were larger in clone size, established during viremia, persistent after viral suppression, and enriched in GZMB+ cytotoxic effector memory Th1 cells. Targeting HIV-1-infected cytotoxic CD4+ T cells and drivers of clonal expansion provides another direction for HIV-1 eradication.
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18
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HIV Latency in Myeloid Cells: Challenges for a Cure. Pathogens 2022; 11:pathogens11060611. [PMID: 35745465 PMCID: PMC9230125 DOI: 10.3390/pathogens11060611] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Revised: 05/10/2022] [Accepted: 05/21/2022] [Indexed: 01/27/2023] Open
Abstract
The use of antiretroviral therapy (ART) for Human Immunodeficiency Virus (HIV) treatment has been highly successful in controlling plasma viremia to undetectable levels. However, a complete cure for HIV is hindered by the presence of replication-competent HIV, integrated in the host genome, that can persist long term in a resting state called viral latency. Resting memory CD4+ T cells are considered the biggest reservoir of persistent HIV infection and are often studied exclusively as the main target for an HIV cure. However, other cell types, such as circulating monocytes and tissue-resident macrophages, can harbor integrated, replication-competent HIV. To develop a cure for HIV, focus is needed not only on the T cell compartment, but also on these myeloid reservoirs of persistent HIV infection. In this review, we summarize their importance when designing HIV cure strategies and challenges associated to their identification and specific targeting by the “shock and kill” approach.
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19
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Heterogeneity of Latency Establishment in the Different Human CD4
+
T Cell Subsets Stimulated with IL-15. J Virol 2022; 96:e0037922. [PMID: 35499323 PMCID: PMC9131862 DOI: 10.1128/jvi.00379-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
HIV integrates into the host genome, creating a viral reservoir of latently infected cells that persists despite effective antiretroviral treatment. CD4-positive (CD4+) T cells are the main contributors to the HIV reservoir. CD4+ T cells are a heterogeneous population, and the mechanisms of latency establishment in the different subsets, as well as their contribution to the reservoir, are still unclear. In this study, we analyzed HIV latency establishment in different CD4+ T cell subsets stimulated with interleukin 15 (IL-15), a cytokine that increases both susceptibility to infection and reactivation from latency. Using a dual-reporter virus that allows discrimination between latent and productive infection at the single-cell level, we found that IL-15-treated primary human CD4+ T naive and CD4+ T stem cell memory (TSCM) cells are less susceptible to HIV infection than CD4+ central memory (TCM), effector memory (TEM), and transitional memory (TTM) cells but are also more likely to harbor transcriptionally silent provirus. The propensity of these subsets to harbor latent provirus compared to the more differentiated memory subsets was independent of differential expression of pTEFb components. Microscopy analysis of NF-κB suggested that CD4+ T naive cells express smaller amounts of nuclear NF-κB than the other subsets, partially explaining the inefficient long terminal repeat (LTR)-driven transcription. On the other hand, CD4+ TSCM cells display similar levels of nuclear NF-κB to CD4+ TCM, CD4+ TEM, and CD4+ TTM cells, indicating the availability of transcription initiation and elongation factors is not solely responsible for the inefficient HIV gene expression in the CD4+ TSCM subset. IMPORTANCE The formation of a latent reservoir is the main barrier to HIV cure. Here, we investigated how HIV latency is established in different CD4+ T cell subsets in the presence of IL-15, a cytokine that has been shown to efficiently induce latency reversal. We observed that, even in the presence of IL-15, the less differentiated subsets display lower levels of productive HIV infection than the more differentiated subsets. These differences were not related to different expression of pTEFb, and modest differences in NF-κB were observed for CD4+ T naive cells only, implying the involvement of other mechanisms. Understanding the molecular basis of latency establishment in different CD4+ T cell subsets might be important for tailoring specific strategies to reactivate HIV transcription in all the CD4+ T subsets that compose the latent reservoir.
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20
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Svensson Akusjärvi S, Krishnan S, Jütte BB, Ambikan AT, Gupta S, Rodriguez JE, Végvári Á, Sperk M, Nowak P, Vesterbacka J, Svensson JP, Sönnerborg A, Neogi U. Peripheral blood CD4 +CCR6 + compartment differentiates HIV-1 infected or seropositive elite controllers from long-term successfully treated individuals. Commun Biol 2022; 5:357. [PMID: 35418589 PMCID: PMC9008025 DOI: 10.1038/s42003-022-03315-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Accepted: 03/24/2022] [Indexed: 11/09/2022] Open
Abstract
HIV-1 infection induces a chronic inflammatory environment not restored by suppressive antiretroviral therapy (ART). As of today, the effect of viral suppression and immune reconstitution in people living with HIV-1 (PLWH) has been well described but not completely understood. Herein, we show how PLWH who naturally control the virus (PLWHEC) have a reduced proportion of CD4+CCR6+ and CD8+CCR6+ cells compared to PLWH on suppressive ART (PLWHART) and HIV-1 negative controls (HC). Expression of CCR2 was reduced on both CD4+, CD8+ and classical monocytes in PLWHEC compared to PLWHART and HC. Longer suppressive therapy, measured in the same patients, decreased number of cells expressing CCR2 on all monocytic cell populations while expression on CD8+ T cells increased. Furthermore, the CD4+CCR6+/CCR6- cells exhibited a unique proteomic profile with a modulated energy metabolism in PLWHEC compared to PLWHART independent of CCR6 status. The CD4+CCR6+ cells also showed an enrichment in proteins involved in apoptosis and p53 signalling in PLWHEC compared to PLWHART, indicative of increased sensitivity towards cell death mechanisms. Collectively, this data shows how PLWHEC have a unique chemokine receptor profile that may aid in facilitating natural control of HIV-1 infection.
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Affiliation(s)
- Sara Svensson Akusjärvi
- Division of Clinical Microbiology, Department of Laboratory Medicine, Karolinska Institutet, ANA Futura, Campus Flemingsberg, 141 52, Stockholm, Sweden.
| | - Shuba Krishnan
- Division of Clinical Microbiology, Department of Laboratory Medicine, Karolinska Institutet, ANA Futura, Campus Flemingsberg, 141 52, Stockholm, Sweden
| | - Bianca B Jütte
- Department of Biosciences and Nutrition, Karolinska Institutet, Neo, Campus Flemingsberg, 141 83, Stockholm, Sweden
| | - Anoop T Ambikan
- Division of Clinical Microbiology, Department of Laboratory Medicine, Karolinska Institutet, ANA Futura, Campus Flemingsberg, 141 52, Stockholm, Sweden
| | - Soham Gupta
- Division of Clinical Microbiology, Department of Laboratory Medicine, Karolinska Institutet, ANA Futura, Campus Flemingsberg, 141 52, Stockholm, Sweden
| | - Jimmy Esneider Rodriguez
- Division of Chemistry I, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Campus Solna, 171 65, Stockholm, Sweden
| | - Ákos Végvári
- Division of Chemistry I, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Campus Solna, 171 65, Stockholm, Sweden
| | - Maike Sperk
- Division of Clinical Microbiology, Department of Laboratory Medicine, Karolinska Institutet, ANA Futura, Campus Flemingsberg, 141 52, Stockholm, Sweden
| | - Piotr Nowak
- Division of Infectious Disease, Department of Medicine Huddinge, Karolinska Institutet, I73, Karolinska University Hospital, 141 86, Stockholm, Sweden
| | - Jan Vesterbacka
- Division of Infectious Disease, Department of Medicine Huddinge, Karolinska Institutet, I73, Karolinska University Hospital, 141 86, Stockholm, Sweden
| | - J Peter Svensson
- Department of Biosciences and Nutrition, Karolinska Institutet, Neo, Campus Flemingsberg, 141 83, Stockholm, Sweden
| | - Anders Sönnerborg
- Division of Clinical Microbiology, Department of Laboratory Medicine, Karolinska Institutet, ANA Futura, Campus Flemingsberg, 141 52, Stockholm, Sweden.,Division of Infectious Disease, Department of Medicine Huddinge, Karolinska Institutet, I73, Karolinska University Hospital, 141 86, Stockholm, Sweden
| | - Ujjwal Neogi
- Division of Clinical Microbiology, Department of Laboratory Medicine, Karolinska Institutet, ANA Futura, Campus Flemingsberg, 141 52, Stockholm, Sweden. .,Christopher S. Bond Life Sciences Centre, University of Missouri, Columbia, MO, 65211, USA. .,Manipal Institute of Virology (MIV), Manipal Academy of Higher Education, Manipal, Karnataka, India.
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21
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Leyre L, Jones RB. Hide and seek: for HIV-infected CD4+ T cells, playing well comes with maturity. J Clin Invest 2022; 132:1-4. [PMID: 35362485 PMCID: PMC8976498 DOI: 10.1172/jci158872] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Antiretroviral therapy suppresses HIV replication but leaves a population of infected CD4+ T cells with integrated proviruses. While most of these proviruses contain defects, such as deletions, some intact proviruses persist and can reinitiate viral replication. In this issue of the JCI, Duette, Hiener, and colleagues performed a tour de force proviral landscape analysis on clinical samples collected over many years with in vitro functional assays. The researchers showed that effector memory CD4+ T cells provide partial sanctuary to intact proviruses from CD8+ T cells and this was associated with superior Nef-mediated MHC-I downregulation relative to less mature CD4+ T cell populations. This finding implicates differential immunoevasion as a cell-intrinsic property, influencing proviral persistence, and highlights Nef as a therapeutic target.
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22
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Duette G, Hiener B, Morgan H, Mazur FG, Mathivanan V, Horsburgh BA, Fisher K, Tong O, Lee E, Ahn H, Shaik A, Fromentin R, Hoh R, Bacchus-Souffan C, Nasr N, Cunningham AL, Hunt PW, Chomont N, Turville SG, Deeks SG, Kelleher AD, Schlub TE, Palmer S. The HIV-1 proviral landscape reveals that Nef contributes to HIV-1 persistence in effector memory CD4+ T cells. J Clin Invest 2022; 132:154422. [PMID: 35133986 PMCID: PMC8970682 DOI: 10.1172/jci154422] [Citation(s) in RCA: 44] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2021] [Accepted: 02/02/2022] [Indexed: 11/17/2022] Open
Abstract
Despite long-term antiretroviral therapy (ART), HIV-1 persists within a reservoir of CD4+ T cells that contribute to viral rebound if treatment is interrupted. Identifying the cellular populations that contribute to the HIV-1 reservoir and understanding the mechanisms of viral persistence are necessary to achieve an effective cure. In this regard, through Full-Length Individual Proviral Sequencing, we observed that the HIV-1 proviral landscape was different and changed with time on ART across naive and memory CD4+ T cell subsets isolated from 24 participants. We found that the proportion of genetically intact HIV-1 proviruses was higher and persisted over time in effector memory CD4+ T cells when compared with naive, central, and transitional memory CD4+ T cells. Interestingly, we found that escape mutations remained stable over time within effector memory T cells during therapy. Finally, we provided evidence that Nef plays a role in the persistence of genetically intact HIV-1. These findings posit effector memory T cells as a key component of the HIV-1 reservoir and suggest Nef as an attractive therapeutic target.
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Affiliation(s)
- Gabriel Duette
- Centre for Virus Research, The Westmead Institute for Medical Research, Westmead, New South Wales, Australia.,Faculty of Medicine and Health, The University of Sydney, Sydney, New South Wales, Australia
| | - Bonnie Hiener
- Centre for Virus Research, The Westmead Institute for Medical Research, Westmead, New South Wales, Australia.,Faculty of Medicine and Health, The University of Sydney, Sydney, New South Wales, Australia
| | - Hannah Morgan
- Faculty of Medicine and Health, The University of Sydney, Sydney, New South Wales, Australia
| | - Fernando G. Mazur
- Post-graduation Program of Evolutionary Genetics and Molecular Biology, Federal University of São Carlos, São Carlos, Brazil
| | - Vennila Mathivanan
- The Kirby Institute, University of New South Wales, Sydney, New South Wales, Australia
| | - Bethany A. Horsburgh
- Centre for Virus Research, The Westmead Institute for Medical Research, Westmead, New South Wales, Australia
| | - Katie Fisher
- Centre for Virus Research, The Westmead Institute for Medical Research, Westmead, New South Wales, Australia.,Faculty of Medicine and Health, The University of Sydney, Sydney, New South Wales, Australia
| | - Orion Tong
- Centre for Virus Research, The Westmead Institute for Medical Research, Westmead, New South Wales, Australia
| | - Eunok Lee
- Centre for Virus Research, The Westmead Institute for Medical Research, Westmead, New South Wales, Australia.,Faculty of Medicine and Health, The University of Sydney, Sydney, New South Wales, Australia
| | - Haelee Ahn
- Division of Experimental Medicine, University of California, San Francisco, San Francisco, California, USA
| | - Ansari Shaik
- The Kirby Institute, University of New South Wales, Sydney, New South Wales, Australia
| | - Rémi Fromentin
- Centre de Recherche du Centre Hospitalier de l’Université de Montréal, Montreal, Quebec, Canada
| | - Rebecca Hoh
- Department of Medicine, University of California, San Francisco, San Francisco, California, USA
| | - Charline Bacchus-Souffan
- Division of Experimental Medicine, University of California, San Francisco, San Francisco, California, USA
| | - Najla Nasr
- Centre for Virus Research, The Westmead Institute for Medical Research, Westmead, New South Wales, Australia.,Faculty of Medicine and Health, The University of Sydney, Sydney, New South Wales, Australia
| | - Anthony L. Cunningham
- Centre for Virus Research, The Westmead Institute for Medical Research, Westmead, New South Wales, Australia.,Faculty of Medicine and Health, The University of Sydney, Sydney, New South Wales, Australia
| | - Peter W. Hunt
- Division of Experimental Medicine, University of California, San Francisco, San Francisco, California, USA
| | - Nicolas Chomont
- Centre de Recherche du Centre Hospitalier de l’Université de Montréal, Montreal, Quebec, Canada.,Department of Microbiology, Infectiology and Immunology, Université de Montréal, Montreal, Quebec, Canada
| | - Stuart G. Turville
- The Kirby Institute, University of New South Wales, Sydney, New South Wales, Australia
| | - Steven G. Deeks
- Department of Medicine, University of California, San Francisco, San Francisco, California, USA
| | - Anthony D. Kelleher
- The Kirby Institute, University of New South Wales, Sydney, New South Wales, Australia
| | - Timothy E. Schlub
- Faculty of Medicine and Health, The University of Sydney, Sydney, New South Wales, Australia
| | - Sarah Palmer
- Centre for Virus Research, The Westmead Institute for Medical Research, Westmead, New South Wales, Australia.,Faculty of Medicine and Health, The University of Sydney, Sydney, New South Wales, Australia
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23
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Lentiviral Nef Proteins Differentially Govern the Establishment of Viral Latency. J Virol 2022; 96:e0220621. [PMID: 35266804 DOI: 10.1128/jvi.02206-21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Despite the clinical importance of latent human immunodeficiency virus type 1 (HIV-1) infection, our understanding of the biomolecular processes involved in HIV-1 latency control is still limited. This study was designed to address whether interactions between viral proteins, specifically HIV Nef, and the host cell could affect latency establishment. The study was driven by three reported observations. First, early reports suggested that human immunodeficiency virus type 2 (HIV-2) infection in patients produces a lower viral RNA/DNA ratio than HIV-1 infection, potentially indicating an increased propensity of HIV-2 to produce latent infection. Second, Nef, an early viral gene product, has been shown to alter the activation state of infected cells in a lentiviral lineage-dependent manner. Third, it has been demonstrated that the ability of HIV-1 to establish latent infection is a function of the activation state of the host cell at the time of infection. Based on these observations, we reasoned that HIV-2 Nef may have the ability to promote latency establishment. We demonstrate that HIV-1 latency establishment in T cell lines and primary T cells is indeed differentially modulated by Nef proteins. In the context of an HIV-1 backbone, HIV-1 Nef promoted active HIV-1 infection, while HIV-2 Nef strongly promoted latency establishment. Given that Nef represents the only difference in these HIV-1 vectors and is known to interact with numerous cellular factors, these data add support to the idea that latency establishment is a host cell-virus interaction phenomenon, but they also suggest that the HIV-1 lineage may have evolved mechanisms to counteract host cell suppression. IMPORTANCE Therapeutic attempts to eliminate the latent HIV-1 reservoir have failed, at least in part due to our incomplete biomolecular understanding of how latent HIV-1 infection is established and maintained. We here address the fundamental question of whether all lentiviruses actually possess a similar capacity to establish latent infections or whether there are differences between the lentiviral lineages driving differential latency establishment that could be exploited to develop improved latency reversal agents. Research investigating the viral RNA/DNA ratio in HIV-1 and HIV-2 patients could suggest that HIV-2 indeed has a much higher propensity to establish latent infections, a trait that we found, at least in part, to be attributable to the HIV-2 Nef protein. Reported Nef-mediated effects on host cell activation thus also affect latency establishment, and HIV-1 vectors that carry different lentiviral nef genes should become key tools to develop a better understanding of the biomolecular basis of HIV-1 latency establishment.
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24
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Yeh YHJ, Yang K, Razmi A, Ho YC. The Clonal Expansion Dynamics of the HIV-1 Reservoir: Mechanisms of Integration Site-Dependent Proliferation and HIV-1 Persistence. Viruses 2021; 13:1858. [PMID: 34578439 PMCID: PMC8473165 DOI: 10.3390/v13091858] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2021] [Revised: 09/11/2021] [Accepted: 09/14/2021] [Indexed: 12/16/2022] Open
Abstract
More than 50% of the HIV-1 latent reservoir is maintained by clonal expansion. The clonally expanded HIV-1-infected cells can contribute to persistent nonsuppressible low-level viremia and viral rebound. HIV-1 integration site and proviral genome landscape profiling reveals the clonal expansion dynamics of HIV-1-infected cells. In individuals under long-term suppressive antiretroviral therapy (ART), HIV-1 integration sites are enriched in specific locations in certain cancer-related genes in the same orientation as the host transcription unit. Single-cell transcriptome analysis revealed that HIV-1 drives aberrant cancer-related gene expression through HIV-1-to-host RNA splicing. Furthermore, the HIV-1 promoter dominates over the host gene promoter and drives high levels of cancer-related gene expression. When HIV-1 integrates into cancer-related genes and causes gain of function of oncogenes or loss of function of tumor suppressor genes, HIV-1 insertional mutagenesis drives the proliferation of HIV-1-infected cells and may cause cancer in rare cases. HIV-1-driven aberrant cancer-related gene expression at the integration site can be suppressed by CRISPR-mediated inhibition of the HIV-1 promoter or by HIV-1 suppressing agents. Given that ART does not suppress HIV-1 promoter activity, therapeutic agents that suppress HIV-1 transcription and halt the clonal expansion of HIV-1-infected cells should be explored to block the clonal expansion of the HIV-1 latent reservoir.
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Affiliation(s)
| | | | | | - Ya-Chi Ho
- Department of Microbial Pathogenesis, Yale University School of Medicine, New Haven, CT 06519, USA; (Y.-H.J.Y.); (K.Y.); (A.R.)
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25
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Venanzi Rullo E, Maimone MG, Fiorica F, Ceccarelli M, Guarneri C, Berretta M, Nunnari G. Non-Melanoma Skin Cancer in People Living With HIV: From Epidemiology to Clinical Management. Front Oncol 2021; 11:689789. [PMID: 34422644 PMCID: PMC8371466 DOI: 10.3389/fonc.2021.689789] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Accepted: 07/07/2021] [Indexed: 12/13/2022] Open
Abstract
Skin cancers represent the most common human tumors with a worldwide increasing incidence. They can be divided into melanoma and non-melanoma skin cancers (NMSCs). NMSCs include mainly squamous cell (SCC) and basal cell carcinoma (BCC) with the latest representing the 80% of the diagnosed NMSCs. The pathogenesis of NMSCs is clearly multifactorial. A growing body of literature underlies a crucial correlation between skin cancer, chronic inflammation and immunodeficiency. Intensity and duration of immunodeficiency plays an important role. In immunocompromised patients the incidence of more malignant forms or the development of multiple tumors seems to be higher than among immunocompetent patients. With regards to people living with HIV (PLWH), since the advent of combined antiretroviral therapy (cART), the incidence of non-AIDS-defining cancers (NADCs), such as NMSCs, have been increasing and now these neoplasms represent a leading cause of illness in this particular population. PLWH with NMSCs tend to be younger, to have a higher risk of local recurrence and to have an overall poorer outcome. NMSCs show an indolent clinical course if diagnosed and treated in an early stage. BCC rarely metastasizes, while SCC presents a 4% annual incidence of metastasis. Nevertheless, metastatic forms lead to poor patient outcome. NMSCs are often treated with full thickness treatments (surgical excision, Mohs micro-graphic surgery and radiotherapy) or superficial ablative techniques (such as cryotherapy, electrodesiccation and curettage). Advances in genetic landscape understanding of NMSCs have favored the establishment of novel therapeutic strategies. Concerning the therapeutic evaluation of PLWH, it’s mandatory to evaluate the risk of interactions between cART and other treatments, particularly antiblastic chemotherapy, targeted therapy and immunotherapy. Development of further treatment options for NMSCs in PLWH seems needed. We reviewed the literature after searching for clinical trials, case series, clinical cases and available databases in Embase and Pubmed. We review the incidence of NMSCs among PLWH, focusing our attention on any differences in clinicopathological features of BCC and SCC between PLWH and HIV negative persons, as well as on any differences in efficacy and safety of treatments and response to immunomodulators and finally on any differences in rates of metastatic disease and outcomes.
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Affiliation(s)
- Emmanuele Venanzi Rullo
- Unit of Infectious Disease, Department of Clinical and Experimental Medicine, University of Messina, Messina, Italy
| | - Maria Grazia Maimone
- Unit of Infectious Disease, Department of Clinical and Experimental Medicine, University of Messina, Messina, Italy
| | - Francesco Fiorica
- Department of Radiation Oncology and Nuclear Medicine, State Hospital "Mater Salutis" Azienda Unità Locale Socio Sanitaria (AULSS) 9, Legnago, Italy
| | - Manuela Ceccarelli
- Unit of Infectious Disease, Department of Clinical and Experimental Medicine, University of Messina, Messina, Italy.,Unit of Infectious Disease, Department of Clinical and Experimental Medicine, University of Catania, Catania, Italy
| | - Claudio Guarneri
- Unit of Dermatology, Department of Biomedical and Dental Sciences and Morphofunctional Imaging, University of Messina, Messina, Italy
| | - Massimiliano Berretta
- Unit of Infectious Disease, Department of Clinical and Experimental Medicine, University of Messina, Messina, Italy
| | - Giuseppe Nunnari
- Unit of Infectious Disease, Department of Clinical and Experimental Medicine, University of Messina, Messina, Italy
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26
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Pinzone MR, Weissman S, Pasternak AO, Zurakowski R, Migueles S, O'Doherty U. Naive infection predicts reservoir diversity and is a formidable hurdle to HIV eradication. JCI Insight 2021; 6:e150794. [PMID: 34228640 PMCID: PMC8409977 DOI: 10.1172/jci.insight.150794] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2021] [Accepted: 06/30/2021] [Indexed: 12/16/2022] Open
Abstract
Historically, naive cells have been considered inconsequential to HIV persistence. Here, we compared the contributions of naive and memory cells to the reservoirs of individuals with a spectrum of reservoir sizes and variable immunological control. We performed proviral sequencing of approximately 6000 proviruses from cellular subsets of 5 elite controllers (ECs) off antiretroviral therapy (ART) and 5 chronic progressors (CPs) on ART. The levels of naive infection were barely detectable in ECs and approximately 300-fold lower compared with those in CPs. Moreover, the ratio of infected naive to memory cells was significantly lower in ECs. Overall, the naive infection level increased as reservoir size increased, such that naive cells were a major contributor to the intact reservoir of CPs, whose reservoirs were generally very diverse. In contrast, the reservoirs of ECs were dominated by proviral clones. Critically, the fraction of proviral clones increased with cell differentiation, with naive infection predicting reservoir diversity. Longitudinal sequencing revealed that the reservoir of ECs was less dynamic compared with that of CPs. Naive cells play a critical role in HIV persistence. Their infection level predicts reservoir size and diversity. Moreover, the diminishing diversity of the reservoir as cellular subsets mature suggests that naive T cells repopulate the memory compartment and that direct infection of naive T cells occurs in vivo.
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Affiliation(s)
- Marilia R Pinzone
- Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Sam Weissman
- Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Alexander O Pasternak
- Department of Medical Microbiology, Amsterdam UMC, University of Amsterdam, Laboratory of Experimental Virology, Amsterdam, Netherlands
| | - Ryan Zurakowski
- Department of Biomedical Engineering, University of Delaware, Newark, Delaware, USA
| | - Stephen Migueles
- HIV-Specific Immunity Section of the Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, Maryland, USA
| | - Una O'Doherty
- Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
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27
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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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28
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Bricker KM, Chahroudi A, Mavigner M. New Latency Reversing Agents for HIV-1 Cure: Insights from Nonhuman Primate Models. Viruses 2021; 13:1560. [PMID: 34452425 PMCID: PMC8402914 DOI: 10.3390/v13081560] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Revised: 07/26/2021] [Accepted: 08/03/2021] [Indexed: 01/30/2023] Open
Abstract
Antiretroviral therapy (ART) controls human immunodeficiency virus 1 (HIV-1) replication and prevents disease progression but does not eradicate HIV-1. The persistence of a reservoir of latently infected cells represents the main barrier to a cure. "Shock and kill" is a promising strategy involving latency reversing agents (LRAs) to reactivate HIV-1 from latently infected cells, thus exposing the infected cells to killing by the immune system or clearance agents. Here, we review advances to the "shock and kill" strategy made through the nonhuman primate (NHP) model, highlighting recently identified latency reversing agents and approaches such as mimetics of the second mitochondrial activator of caspase (SMACm), experimental CD8+ T cell depletion, immune checkpoint blockade (ICI), and toll-like receptor (TLR) agonists. We also discuss the advantages and limits of the NHP model for HIV cure research and methods developed to evaluate the efficacy of in vivo treatment with LRAs in NHPs.
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Affiliation(s)
- Katherine M. Bricker
- Department of Pediatrics, Emory University School of Medicine, Atlanta, GA 30322, USA; (K.M.B.); (A.C.)
| | - Ann Chahroudi
- Department of Pediatrics, Emory University School of Medicine, Atlanta, GA 30322, USA; (K.M.B.); (A.C.)
- Yerkes National Primate Research Center, Emory University, Atlanta, GA 30329, USA
- Emory + Children’s Center for Childhood Infections and Vaccines, Atlanta, GA 30322, USA
| | - Maud Mavigner
- Department of Pediatrics, Emory University School of Medicine, Atlanta, GA 30322, USA; (K.M.B.); (A.C.)
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29
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Pino M, Pereira Ribeiro S, Pagliuzza A, Ghneim K, Khan A, Ryan E, Harper JL, King CT, Welbourn S, Micci L, Aldrete S, Delman KA, Stuart T, Lowe M, Brenchley JM, Derdeyn CA, Easley K, Sekaly RP, Chomont N, Paiardini M, Marconi VC. Increased homeostatic cytokines and stability of HIV-infected memory CD4 T-cells identify individuals with suboptimal CD4 T-cell recovery on-ART. PLoS Pathog 2021; 17:e1009825. [PMID: 34449812 PMCID: PMC8397407 DOI: 10.1371/journal.ppat.1009825] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2021] [Accepted: 07/23/2021] [Indexed: 01/12/2023] Open
Abstract
Clinical outcomes are inferior for individuals with HIV having suboptimal CD4 T-cell recovery during antiretroviral therapy (ART). We investigated if the levels of infection and the response to homeostatic cytokines of CD4 T-cell subsets contributed to divergent CD4 T-cell recovery and HIV reservoir during ART by studying virologically-suppressed immunologic responders (IR, achieving a CD4 cell count >500 cells/μL on or before two years after ART initiation), and virologically-suppressed suboptimal responders (ISR, did not achieve a CD4 cell count >500 cells/μL in the first two years after ART initiation). Compared to IR, ISR demonstrated higher levels of HIV-DNA in naïve, central (CM), transitional (TM), and effector (EM) memory CD4 T-cells in blood, both pre- and on-ART, and specifically in CM CD4 T-cells in LN on-ART. Furthermore, ISR had higher pre-ART plasma levels of IL-7 and IL-15, cytokines regulating T-cell homeostasis. Notably, pre-ART PD-1 and TIGIT expression levels were higher in blood CM and TM CD4 T-cells for ISR; this was associated with a significantly lower fold-changes in HIV-DNA levels between pre- and on-ART time points exclusively on CM and TM T-cell subsets, but not naïve or EM T-cells. Finally, the frequency of CM CD4 T-cells expressing PD-1 or TIGIT pre-ART as well as plasma levels of IL-7 and IL-15 predicted HIV-DNA content on-ART. Our results establish the association between infection, T-cell homeostasis, and expression of PD-1 and TIGIT in long-lived CD4 T-cell subsets prior to ART with CD4 T-cell recovery and HIV persistence on-ART.
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Affiliation(s)
- Maria Pino
- Division of Microbiology and Immunology, Yerkes National Primate Research Center, Emory University, Atlanta, Atlanta, Georgia, United States of America
| | - Susan Pereira Ribeiro
- Department of Pathology and Laboratory Medicine, Emory School of Medicine, Emory University, Atlanta, Georgia, United States of America
| | - Amélie Pagliuzza
- Centre de Recherche du CHUM and Department of Microbiology, Infectious Diseases and Immunology, Université de Montréal, QC, Canada
| | - Khader Ghneim
- Department of Pathology and Laboratory Medicine, Emory School of Medicine, Emory University, Atlanta, Georgia, United States of America
| | - Anum Khan
- Department of Biostatistics and Bioinformatics, Rollins School of Public Health, Emory University, Atlanta, Georgia, United States of America
| | - Emily Ryan
- Division of Microbiology and Immunology, Yerkes National Primate Research Center, Emory University, Atlanta, Atlanta, Georgia, United States of America
| | - Justin L. Harper
- Division of Microbiology and Immunology, Yerkes National Primate Research Center, Emory University, Atlanta, Atlanta, Georgia, United States of America
| | - Colin T. King
- Division of Microbiology and Immunology, Yerkes National Primate Research Center, Emory University, Atlanta, Atlanta, Georgia, United States of America
| | - Sarah Welbourn
- Emory Vaccine Center, Yerkes National Primate Research Center, Emory University, Atlanta, Georgia, United States of America
| | - Luca Micci
- Division of Microbiology and Immunology, Yerkes National Primate Research Center, Emory University, Atlanta, Atlanta, Georgia, United States of America
| | - Sol Aldrete
- Division of Infectious Diseases, Emory University School of Medicine, Atlanta, Georgia, United States of America
| | - Keith A. Delman
- Division of Surgical Oncology, Department of Surgery, Winship Cancer Institute, Emory University, Atlanta, Georgia, United States of America
| | - Theron Stuart
- Emory Vaccine Center, Emory University, Hope Clinic, Decatur, Georgia, United States of America
| | - Michael Lowe
- Division of Surgical Oncology, Department of Surgery, Winship Cancer Institute, Emory University, Atlanta, Georgia, United States of America
| | - Jason M. Brenchley
- Barrier Immunity Section, Laboratory of Viral Diseases, National Institutes of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), Bethesda, Maryland, United States of America
| | - Cynthia A. Derdeyn
- Department of Pathology and Laboratory Medicine, Emory School of Medicine, Emory University, Atlanta, Georgia, United States of America
- Emory Vaccine Center, Yerkes National Primate Research Center, Emory University, Atlanta, Georgia, United States of America
| | - Kirk Easley
- Department of Biostatistics and Bioinformatics, Rollins School of Public Health, Emory University, Atlanta, Georgia, United States of America
| | - Rafick P. Sekaly
- Department of Pathology and Laboratory Medicine, Emory School of Medicine, Emory University, Atlanta, Georgia, United States of America
| | - Nicolas Chomont
- Centre de Recherche du CHUM and Department of Microbiology, Infectious Diseases and Immunology, Université de Montréal, QC, Canada
| | - Mirko Paiardini
- Division of Microbiology and Immunology, Yerkes National Primate Research Center, Emory University, Atlanta, Atlanta, Georgia, United States of America
- Department of Pathology and Laboratory Medicine, Emory School of Medicine, Emory University, Atlanta, Georgia, United States of America
| | - Vincent C. Marconi
- Division of Microbiology and Immunology, Yerkes National Primate Research Center, Emory University, Atlanta, Atlanta, Georgia, United States of America
- Emory Vaccine Center, Yerkes National Primate Research Center, Emory University, Atlanta, Georgia, United States of America
- Division of Infectious Diseases, Emory University School of Medicine, Atlanta, Georgia, United States of America
- Atlanta Veterans Affairs Medical Center, Atlanta, Georgia, United States of America
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30
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Zhao S, Tsibris A. Leveraging Novel Integrated Single-Cell Analyses to Define HIV-1 Latency Reversal. Viruses 2021; 13:1197. [PMID: 34206546 PMCID: PMC8310207 DOI: 10.3390/v13071197] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Revised: 06/11/2021] [Accepted: 06/16/2021] [Indexed: 01/24/2023] Open
Abstract
While suppressive antiretroviral therapy can effectively limit HIV-1 replication and evolution, it leaves behind a residual pool of integrated viral genomes that persist in a state of reversible nonproductive infection, referred to as the HIV-1 reservoir. HIV-1 infection models were established to investigate HIV-1 latency and its reversal; recent work began to probe the dynamics of HIV-1 latency reversal at single-cell resolution. Signals that establish HIV-1 latency and govern its reactivation are complex and may not be completely resolved at the cellular and regulatory levels by the aggregated measurements of bulk cellular-sequencing methods. High-throughput single-cell technologies that characterize and quantify changes to the epigenome, transcriptome, and proteome continue to rapidly evolve. Combinations of single-cell techniques, in conjunction with novel computational approaches to analyze these data, were developed and provide an opportunity to improve the resolution of the heterogeneity that may exist in HIV-1 reactivation. In this review, we summarize the published single-cell HIV-1 transcriptomic work and explore how cutting-edge advances in single-cell techniques and integrative data-analysis tools may be leveraged to define the mechanisms that control the reversal of HIV-1 latency.
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Affiliation(s)
| | - Athe Tsibris
- Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02139, USA;
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31
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Horsburgh BA, Hiener B, Fisher K, Lee E, Morgan H, Eden JS, von Stockenstrom S, Odevall L, Milush JM, Hoh R, Fromentin R, Chomont N, Hecht FM, Schlub TE, Deeks SG, Palmer S. Cellular activation, differentiation and proliferation influence the dynamics of genetically-intact proviruses over time. J Infect Dis 2021; 225:1168-1178. [PMID: 34037766 PMCID: PMC8974828 DOI: 10.1093/infdis/jiab291] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2021] [Accepted: 05/24/2021] [Indexed: 11/14/2022] Open
Abstract
Human immunodeficiency virus (HIV) persists in cells despite antiretroviral therapy; however, the influence of cellular mechanisms such as activation, differentiation, and proliferation upon the distribution of proviruses over time is unclear. To address this, we used full-length sequencing to examine proviruses within memory CD4+ T-cell subsets longitudinally in 8 participants. Over time, the odds of identifying a provirus increased in effector and decreased in transitional memory cells. In all subsets, more activated (HLA-DR–expressing) cells contained a higher frequency of intact provirus, as did more differentiated cells such as transitional and effector memory subsets. The proportion of genetically identical proviruses increased over time, indicating that cellular proliferation was maintaining the persistent reservoir; however, the number of genetically identical proviral clusters in each subset was stable. As such, key biological processes of activation, differentiation, and proliferation influence the dynamics of the HIV reservoir and must be considered during the development of any immune intervention.
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Affiliation(s)
- Bethany A Horsburgh
- Centre for Virus Research, The Westmead Institute of Medical Research, The University of Sydney, Sydney, New South Wales, 2145, Australia.,Sydney Medical School, Westmead Clinical School, Faculty of Medicine and Health, The University of Sydney, Sydney, New South Wales, 2006, Australia
| | - Bonnie Hiener
- Centre for Virus Research, The Westmead Institute of Medical Research, The University of Sydney, Sydney, New South Wales, 2145, Australia.,Sydney Medical School, Westmead Clinical School, Faculty of Medicine and Health, The University of Sydney, Sydney, New South Wales, 2006, Australia
| | - Katie Fisher
- Centre for Virus Research, The Westmead Institute of Medical Research, The University of Sydney, Sydney, New South Wales, 2145, Australia.,Sydney Medical School, Westmead Clinical School, Faculty of Medicine and Health, The University of Sydney, Sydney, New South Wales, 2006, Australia
| | - Eunok Lee
- Centre for Virus Research, The Westmead Institute of Medical Research, The University of Sydney, Sydney, New South Wales, 2145, Australia.,Sydney Medical School, Westmead Clinical School, Faculty of Medicine and Health, The University of Sydney, Sydney, New South Wales, 2006, Australia
| | - Hannah Morgan
- Sydney School of Public Health, Faculty of Medicine and Health, The University of Sydney, Sydney, New South Wales, 2006, Australia
| | - John-Sebastian Eden
- Centre for Virus Research, The Westmead Institute of Medical Research, The University of Sydney, Sydney, New South Wales, 2145, Australia.,Sydney Medical School, Westmead Clinical School, Faculty of Medicine and Health, The University of Sydney, Sydney, New South Wales, 2006, Australia
| | - Susanne von Stockenstrom
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, 171 77, Sweden
| | - Lina Odevall
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, 171 77, Sweden
| | - Jeffrey M Milush
- Department of Medicine, University of California San Francisco, California, 94110, United States of America
| | - Rebecca Hoh
- Department of Medicine, University of California San Francisco, California, 94110, United States of America
| | - Rémi Fromentin
- Centre de Recherche du CHUM and Department of Microbiology, Infectiology and Immunology, Université de Montréal, Montreal, H2X 0A9 Canada
| | - Nicolas Chomont
- Centre de Recherche du CHUM and Department of Microbiology, Infectiology and Immunology, Université de Montréal, Montreal, H2X 0A9 Canada
| | - Frederick M Hecht
- Department of Medicine, University of California San Francisco, California, 94110, United States of America
| | - Timothy E Schlub
- Sydney School of Public Health, Faculty of Medicine and Health, The University of Sydney, Sydney, New South Wales, 2006, Australia
| | - Steven G Deeks
- Department of Medicine, University of California San Francisco, California, 94110, United States of America
| | - Sarah Palmer
- Centre for Virus Research, The Westmead Institute of Medical Research, The University of Sydney, Sydney, New South Wales, 2145, Australia.,Sydney Medical School, Westmead Clinical School, Faculty of Medicine and Health, The University of Sydney, Sydney, New South Wales, 2006, Australia
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32
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Triplex digital PCR assays for the quantification of intact proviral HIV-1 DNA. Methods 2021; 201:41-48. [PMID: 33992770 DOI: 10.1016/j.ymeth.2021.05.006] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2021] [Revised: 04/19/2021] [Accepted: 05/04/2021] [Indexed: 01/10/2023] Open
Abstract
The development of an HIV-1 cure is hampered by the existence of a persistent (latent) reservoir that contains a small proportion of replication-competent intact proviruses which refuels viral replication upon treatment discontinuation. Therefore, an accurate evaluation and quantification of these (intact) proviruses is essential to determine the efficacy of HIV-1 cure strategies which aim to eliminate this reservoir. Here, we present two triplex digital PCR assays which resulted from a combination of two existing methods, the IPDA (a 2-colour digital PCR based method) and Q4PCR assays (4 colour qPCR method), and tested the functionality on a three-colour digital PCR platform. In the present paper, we provide a step-by-step experimental protocol for these triplex digital PCR assays and validate their performance on a latently infected Jurkat cell-line model and HIV-1 patient samples. Our data demonstrates the potential and flexibility of increasing the number of subgenomic regions of HIV-1 within the IPDA to acquire sensitive detection of the HIV-1 reservoir while benefitting from the advantages of a dPCR setup.
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33
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Wolf G, Singh NJ. Modular Approaches to Understand the Immunobiology of Human Immunodeficiency Virus Latency. Viral Immunol 2021; 34:365-375. [PMID: 33600238 DOI: 10.1089/vim.2020.0171] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Despite advances in slowing the progression of acquired immunodeficiency syndrome (AIDS), there is no viable cure for human immunodeficiency virus (HIV). The challenge toward a cure is mainly the formation and maintenance of a latent reservoir of cells that harbor the virus in both replication-competent and replication-defective states. This small niche of quiescent cells has been identified to reside primarily in quiescent and memory CD4+ T cells, but parameters that could reliably distinguish an infected T cell from an uninfected one, if any, are not clear. In addition, the migratory properties and specific anatomical reservoirs of latent T cells are difficult to measure at a high resolution in humans. A functional cure of HIV would require targeting this population using innovative new clinical strategies. One constraint toward the empirical development of such approaches is the absence of a native small animal model for AIDS. Since HIV does not efficiently infect murine cells, probing molecular-genetic questions involving latently infected T cells homing to deep tissue sites, interacting with stroma and persisting through different treatment regimens, is challenging. The goal of this article is to discuss how examining the dynamics of T cells in mouse models can provide a framework for effectively studying these questions, even without infecting mice with HIV. The inflammatory and cytokine milieu found in early human HIV infections are being increasingly understood as a result of clinical measurements. Mouse studies that recreate this milieu can potentially be used to subsequently map the fate of T cells activated in this context as well as their migratory routes. In essence, such a framework could allow complementary studies in mice to enhance our understanding of aspects of the biology of HIV latency. This can be the basis of a modular approach to small animal HIV modeling, amenable to preclinical curative strategy development.
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Affiliation(s)
- Gideon Wolf
- Department of Microbiology & Immunology, University of Maryland School of Medicine, Baltimore, Maryland, USA
| | - Nevil J Singh
- Department of Microbiology & Immunology, University of Maryland School of Medicine, Baltimore, Maryland, USA
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