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Sabour S, Li JF, Lipscomb JT, Santos Tino AP, Johnson JA. Immunocapture of cell surface proteins embedded in HIV envelopes uncovers considerable virion genetic diversity associated with different source cell types. PLoS One 2024; 19:e0296891. [PMID: 38412143 PMCID: PMC10898758 DOI: 10.1371/journal.pone.0296891] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2023] [Accepted: 12/18/2023] [Indexed: 02/29/2024] Open
Abstract
HIV particles in the blood largely originate from activated lymphocytes and can overshadow variants which may be expressed from other cell types. Investigations of virus persistence must be able to distinguish cells refractory to viral clearance that serve as reservoirs. To investigate additional cell types that may be associated with in vivo HIV expression we developed a virus particle immunomagnetic capture method targeting several markers of cellular origin that become embedded within virion envelopes during budding. We evaluated the ability of markers to better distinguish cell lineage source subpopulations by assessing combinations of different antibodies with cell-sorted in vitro culture and clinical specimens. Various deductive algorithms were designed to discriminate source cell lineages and subsets. From the particle capture algorithms, we identified distinct variants expressed within individuals that were associated with disparate cellular markers. Among the variants uncovered were minority-level viruses with drug resistance mutations undetected by sequencing and often were associated with markers indicative of myeloid lineage (CD3-/CD10-/CD16+ or /CD14+, and CD3-/CD16-/CD14-/CD11c+ or /HLA-DR+) cell sources. The diverse HIV genetic sequences expressed from different cell types within individuals, further supported by the appearance of distinct drug-resistant variants, highlights the complexity of HIV reservoirs in vivo which must be considered for HIV cure strategies. This approach could also be helpful in examining in vivo host cell origins and genetic diversity in infections involving other families of budding viruses.
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Affiliation(s)
- Sarah Sabour
- ORISE Fellowship Program, Oak Ridge, Tennessee, United States of America
- Division of HIV Prevention, CDC, Atlanta, Georgia, United States of America
| | - Jin-Fen Li
- Division of HIV Prevention, CDC, Atlanta, Georgia, United States of America
| | | | | | - Jeffrey A Johnson
- Division of HIV Prevention, CDC, Atlanta, Georgia, United States of America
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Anderson JL, Khoury G, Fromentin R, Solomon A, Chomont N, Sinclair E, Milush JM, Hartogensis W, Bacchetti P, Roche M, Tumpach C, Gartner M, Pitman MC, Epling CL, Hoh R, Hecht FM, Somsouk M, Cameron PU, Deeks SG, Lewin SR. Human Immunodeficiency Virus (HIV)-Infected CCR6+ Rectal CD4+ T Cells and HIV Persistence On Antiretroviral Therapy. J Infect Dis 2020; 221:744-755. [PMID: 31796951 PMCID: PMC7026892 DOI: 10.1093/infdis/jiz509] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2019] [Accepted: 12/02/2019] [Indexed: 02/07/2023] Open
Abstract
Background Identifying where human immunodeficiency virus (HIV) persists in people living with HIV and receiving antiretroviral therapy is critical to develop cure strategies. We assessed the relationship of HIV persistence to expression of chemokine receptors and their chemokines in blood (n = 48) and in rectal (n = 20) and lymph node (LN; n = 8) tissue collected from people living with HIV who were receiving suppressive antiretroviral therapy. Methods Cell-associated integrated HIV DNA, unspliced HIV RNA, and chemokine messenger RNA were quantified by quantitative polymerase chain reaction. Chemokine receptor expression on CD4+ T cells was determined using flow cytometry. Results Integrated HIV DNA levels in CD4+ T cells, CCR6+CXCR3+ memory CD4+ T-cell frequency, and CCL20 expression (ligand for CCR6) were highest in rectal tissue, where HIV-infected CCR6+ T cells accounted for nearly all infected cells (median, 89.7%). Conversely in LN tissue, CCR6+ T cells were infrequent, and there was a statistically significant association of cell-associated HIV DNA and RNA with CCL19, CCL21, and CXCL13 chemokines. Conclusions HIV-infected CCR6+ CD4+ T cells accounted for the majority of infected cells in rectal tissue. The different relationships between HIV persistence and T-cell subsets and chemokines in rectal and LN tissue suggest that different tissue-specific strategies may be required to eliminate HIV persistence and that assessment of biomarkers for HIV persistence may not be generalizable between blood and other tissues.
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Affiliation(s)
- Jenny L Anderson
- The Peter Doherty Institute for Infection and Immunity, The University of Melbourne and Royal Melbourne Hospital, Melbourne, Victoria, Australia
| | - Gabriela Khoury
- The Peter Doherty Institute for Infection and Immunity, The University of Melbourne and Royal Melbourne Hospital, Melbourne, Victoria, Australia
| | - Rémi Fromentin
- Centre de Recherche du CHUM and Department of Microbiology, Infectiology and Immunology, Université de Montréal, Montreal, Quebec, Canada
| | - Ajantha Solomon
- The Peter Doherty Institute for Infection and Immunity, The University of Melbourne and Royal Melbourne Hospital, Melbourne, Victoria, Australia
| | - Nicolas Chomont
- Centre de Recherche du CHUM and Department of Microbiology, Infectiology and Immunology, Université de Montréal, Montreal, Quebec, Canada
| | - Elizabeth Sinclair
- Department of Medicine, University of California San Francisco, San Francisco, California, USA
| | - Jeffrey M Milush
- Department of Medicine, University of California San Francisco, San Francisco, California, USA
| | - Wendy Hartogensis
- Department of Medicine, University of California San Francisco, San Francisco, California, USA
| | - Peter Bacchetti
- Department of Epidemiology and Biostatistics, University of California, San Francisco, California, USA
| | - Michael Roche
- The Peter Doherty Institute for Infection and Immunity, The University of Melbourne and Royal Melbourne Hospital, Melbourne, Victoria, Australia.,School of Health and Biomedical Sciences, RMIT University, Melbourne, Victoria, Australia
| | - Carolin Tumpach
- The Peter Doherty Institute for Infection and Immunity, The University of Melbourne and Royal Melbourne Hospital, Melbourne, Victoria, Australia.,School of Health and Biomedical Sciences, RMIT University, Melbourne, Victoria, Australia
| | - Matthew Gartner
- School of Health and Biomedical Sciences, RMIT University, Melbourne, Victoria, Australia
| | - Matthew C Pitman
- The Peter Doherty Institute for Infection and Immunity, The University of Melbourne and Royal Melbourne Hospital, Melbourne, Victoria, Australia
| | - Christine Lorrie Epling
- Department of Medicine, University of California San Francisco, San Francisco, California, USA
| | - Rebecca Hoh
- Department of Medicine, University of California San Francisco, San Francisco, California, USA
| | - Frederick M Hecht
- Department of Medicine, University of California San Francisco, San Francisco, California, USA
| | - Ma Somsouk
- Department of Medicine, University of California San Francisco, San Francisco, California, USA
| | - Paul U Cameron
- The Peter Doherty Institute for Infection and Immunity, The University of Melbourne and Royal Melbourne Hospital, Melbourne, Victoria, Australia.,Department of Infectious Diseases, Alfred Hospital and Monash University, Melbourne, Victoria, Australia
| | - Steven G Deeks
- Department of Medicine, University of California San Francisco, San Francisco, California, USA
| | - Sharon R Lewin
- The Peter Doherty Institute for Infection and Immunity, The University of Melbourne and Royal Melbourne Hospital, Melbourne, Victoria, Australia.,Department of Infectious Diseases, Alfred Hospital and Monash University, Melbourne, Victoria, Australia
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Hiransuthikul A, Wongkanya R, Sirivichayakul S, Trachunthong D, Sungsing T, Pankam T, Phanuphak P, Phanuphak N. Short Communication: Discordance in Drug Resistance Mutations Between Blood Plasma and Semen or Rectal Secretions Among Newly Diagnosed HIV-1-Infected Thai Men Who Have Sex with Men. AIDS Res Hum Retroviruses 2018; 34:626-628. [PMID: 29756454 DOI: 10.1089/aid.2018.0029] [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
Human immunodeficiency virus 1 (HIV-1) infection is most commonly transmitted by sexual contact across mucosal surfaces. Information on concordance in drug resistance profile between blood plasma and anogenital compartments in resource-limited settings is limited. We aimed to determine discordances in genotypic drug resistance-associated mutations (DRAMs) between blood plasma and semen or rectal secretions among newly diagnosed, antiretroviral therapy (ART)-naive, HIV-1-infected Thai men who have sex with men (MSM). Blood plasma, semen, and rectal secretions of HIV-1-infected Thai MSM enrolled from the Test and Treat cohort were tested for genotypic mutations in the reverse transcriptase and protease genes. Seven participants with baseline DRAMs in blood plasma were included in this analysis. In anogenital samples, HIV-1 RNA could be fully amplified for DRAMs assessment in semen from three participants and in rectal secretions from four participants. DRAMs were identified in semen from two of three participants and in rectal secretions from four of four participants. Three participants had DRAMs in anogenital compartments that were not detected in blood plasma-one had DRAMs in semen that was not detected in blood plasma (I54FI) and two had DRAMs in rectal secretions that was not detected in blood plasma (I47IM; K70N, L74I, Y115F, M184V, K103N, V108I, and H221Y). Discordance in DRAMs between blood plasma and anogenital compartments is not uncommon among newly diagnosed, ART-naive, HIV-1-infected Thai MSM. Monitoring of drug-resistant virus in these vector compartments is warranted particularly as pre-exposure prophylaxis and treatment as prevention are increasingly used as the mainstay strategies to end the AIDS epidemic.
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Affiliation(s)
| | | | - Sunee Sirivichayakul
- Vaccine and Cellular Immunology Laboratory, Chulalongkorn Medical Research Center (ChulaMRC), Chulalongkorn University, Bangkok, Thailand
- Department of Medicine, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
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Khan S, Telwatte S, Trapecar M, Yukl S, Sanjabi S. Differentiating Immune Cell Targets in Gut-Associated Lymphoid Tissue for HIV Cure. AIDS Res Hum Retroviruses 2017; 33:S40-S58. [PMID: 28882067 PMCID: PMC5685216 DOI: 10.1089/aid.2017.0153] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
The single greatest challenge to an HIV cure is the persistence of latently infected cells containing inducible, replication-competent proviral genomes, which constitute only a small fraction of total or infected cells in the body. Although resting CD4+ T cells in the blood are a well-known source of viral rebound, more than 90% of the body's lymphocytes reside elsewhere. Many are in gut tissue, where HIV DNA levels per million CD4+ T cells are considerably higher than in the blood. Despite the significant contribution of gut tissue to viral replication and persistence, little is known about the cell types that support persistence of HIV in the gut; importantly, T cells in the gut have phenotypic, functional, and survival properties that are distinct from T cells in other tissues. The mechanisms by which latency is established and maintained will likely depend on the location and cytokine milieu surrounding the latently infected cells in each compartment. Therefore, successful HIV cure strategies require identification and characterization of the exact cell types that support viral persistence, particularly in the gut. In this review, we describe the seeding of the latent HIV reservoir in the gut mucosa; highlight the evidence for compartmentalization and depletion of T cells; summarize the immunologic consequences of HIV infection within the gut milieu; propose how the damaged gut environment may promote the latent HIV reservoir; and explore several immune cell targets in the gut and their place on the path toward HIV cure.
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Affiliation(s)
- Shahzada Khan
- Gladstone Institute of Virology and Immunology, Gladstone Institutes, San Francisco, California
| | - Sushama Telwatte
- San Francisco VA Health Care System and University of California, San Francisco (UCSF), San Francisco, California
| | - Martin Trapecar
- Gladstone Institute of Virology and Immunology, Gladstone Institutes, San Francisco, California
| | - Steven Yukl
- San Francisco VA Health Care System and University of California, San Francisco (UCSF), San Francisco, California
| | - Shomyseh Sanjabi
- Gladstone Institute of Virology and Immunology, Gladstone Institutes, San Francisco, California
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, California
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Abstract
PURPOSE OF REVIEW Tissue reservoirs of HIV may promote the persistent immunopathology responsible for non-AIDS morbidity and data support multifocal reactivation from tissues as the source of viral rebound during antiretroviral therapy (ART) interruption. The heterogeneity of tissue reservoirs and incomplete knowledge about their composition are obstacles to an HIV cure. RECENT FINDINGS In addition to the higher concentration of infected CD4 T cells found in both central lymphoid tissues and gut, specific subsets of CD4 T cells appear to play a disproportionate role in HIV persistence. Recently, a subset of central memory T cells enriched in lymph node germinal centers called T-follicular helper cells has been identified that expresses more viral RNA and occupies an anatomic niche inaccessible to cytotoxic T lymphocyte killing. Additional observations suggest that antiretroviral drug (ARV) concentrations may be lower in some tissues, raising the possibility for localized, low-level viral replication. Finally, some recent data implicate the persistence of infected, non-CD4 T-cell types in tissues during ART. SUMMARY The retention of infected cells in a wide variety of tissues, often with distinct viral and cellular characteristics, underscores the importance of studying tissue reservoirs in the development and assessment of cure strategies. Both inhibitory ARVs and latency-reversing drugs must reach these sites, and novel strategies may be needed to attack virus in cells as variable as T-follicular helper cells and macrophages.
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Depincé AE, Dussert E, Vergnon-Miszczycha D, Keita A, Pillet S, Botelho-Nevers E, Frésard A, Gagneux-Brunon A, Lucht FR, Roblin X, Pozzetto B, Paul S, Bourlet T. The Genotyping Resistance Profile of the Pol Gene Detected in Blood of Newly Diagnosed HIV-Positive Men Is Durably Archived in the Gut Whatever the Time of Initiation of cART. Intervirology 2017; 59:256-261. [PMID: 28402970 DOI: 10.1159/000472716] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2017] [Accepted: 03/23/2017] [Indexed: 02/01/2023] Open
Abstract
OBJECTIVE To evaluate the mutational patterns on the pol gene of the main HIV-1 strain archived in cell genome of 10 chronically infected men according to their clinical and therapeutic history. The genotyping resistance profiles were compared between the first blood plasma available at the time of HIV diagnosis and rectal biopsies and PBMC sampled 1-5 years after the initiation of combined antiretroviral therapy (cART). METHODS HIV-1 RNA and cell-associated HIV-1 DNA were quantified by Abbott Real-Time HIV-1 and Generic HIV® DNA cell (Biocentric) assays. The mutations in protease and reverse transcriptase genes were assessed by the Trugene® assay (Siemens). The C2V3 region was amplified to determine the viral tropism. RESULTS In 9 patients, slight or no differences were observed between the 3 resistance profiles. Those mostly detected were related to the resistance to nucleos(t)ide (D67N, L210W, T215A, T69D) and nonnucleoside (K103N, V106I, V179I) inhibitors. In 1 rilpivirine-treated patient, the M230I mutation was detected in PBMC. No change of viral tropism was observed between samples. CONCLUSION These data suggest that resistance mutations harbored by the main HIV strain in plasma at the time of diagnosis are durably archived in DNA cells whatever the delay between infection and initiation of therapy in patients well controlled by cART.
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Affiliation(s)
- Anne Emmanuelle Depincé
- Groupe Immunité des Muqueuses et Agents Pathogènes - GIMAP EA 3064, CIC 1408, Université de Saint-Etienne, Université de Lyon, Saint-Etienne, France
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Svicher V, Ceccherini-Silberstein F, Antinori A, Aquaro S, Perno CF. Understanding HIV compartments and reservoirs. Curr HIV/AIDS Rep 2015; 11:186-94. [PMID: 24729094 DOI: 10.1007/s11904-014-0207-y] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
The spectrum of HIV-1 cellular reservoirs is highly diversified, and their role varies according to the milieu of the anatomical sites in which the virus replicates. In this light, mechanisms underlying HIV-1 persistence in anatomical compartments may be profoundly different from what is observed in peripheral blood. This scenario is further complicated by sub-optimal drug penetration in tissues allowing persistent and cryptic HIV-1 replication in body districts despite undetectable viremia. On this basis, this review aims at providing recent insights regarding the critical role of HIV-1 cellular reservoirs in different anatomical compartments, and their relationship with the pathogenesis of HIV-1 infection. A comprehensive definition of the complex interplay between the virus and its reservoir is critical in order to set up prophylactic and therapeutic strategies aimed at achieving the maximal virological suppression and hopefully in the near future the cure of HIV-1 infection (either functional or biological).
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Affiliation(s)
- Valentina Svicher
- Department of Experimental Medicine and Surgery, University of Rome Tor Vergata, Rome, Italy
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