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Shahid A, Jones BR, Duncan MC, MacLennan S, Dapp MJ, Kuniholm MH, Aouizerat B, Archin NM, Gange S, Ofotokun I, Fischl MA, Kassaye S, Goldstein H, Anastos K, Joy JB, Brumme ZL. A simple phylogenetic approach to analyze hypermutated HIV proviruses reveals insights into their dynamics and persistence during antiretroviral therapy. RESEARCH SQUARE 2024:rs.3.rs-4549934. [PMID: 38947061 PMCID: PMC11213167 DOI: 10.21203/rs.3.rs-4549934/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/02/2024]
Abstract
Hypermutated proviruses, which arise in a single HIV replication cycle when host antiviral APOBEC3 proteins introduce extensive G-to-A mutations throughout the viral genome, persist in all people living with HIV receiving antiretroviral therapy (ART). But, the within-host evolutionary origins of hypermutated sequences are incompletely understood because phylogenetic inference algorithms, which assume that mutations gradually accumulate over generations, incorrectly reconstruct their ancestor-descendant relationships. Using >1400 longitudinal single-genome-amplified HIV env-gp120 sequences isolated from six women over a median 18 years of follow-up - including plasma HIV RNA sequences collected over a median 9 years between seroconversion and ART initiation, and >500 proviruses isolated over a median 9 years on ART - we evaluated three approaches for removing hypermutation from nucleotide alignments. Our goals were to 1) reconstruct accurate phylogenies that can be used for molecular dating and 2) phylogenetically infer the integration dates of hypermutated proviruses persisting during ART. Two of the tested approaches (stripping all positions containing putative APOBEC3 mutations from the alignment, or replacing individual putative APOBEC3 mutations in hypermutated sequences with the ambiguous base R) consistently normalized tree topologies, eliminated erroneous clustering of hypermutated proviruses, and brought env -intact and hypermutated proviruses into comparable ranges with respect to multiple tree-based metrics. Importantly, these corrected trees produced integration date estimates for env -intact proviruses that were highly concordant with those from benchmark trees that excluded hypermutated sequences, indicating that the corrected trees can be used for molecular dating. Use of these trees to infer the integration dates of hypermutated proviruses persisting during ART revealed that these spanned a wide age range, with the oldest ones dating to shortly after infection. This indicates that hypermutated proviruses, like other provirus types, begin to be seeded into the proviral pool immediately following infection, and can persist for decades. In two of the six participants, hypermutated proviruses differed from env -intact ones in terms of their age distributions, suggesting that different provirus types decay at heterogeneous rates in some hosts. These simple approaches to reconstruct hypermutated provirus' evolutionary histories, allow insights into their in vivo origins and longevity, towards a more comprehensive understanding of HIV persistence during ART.
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Reddy K, Lee GQ, Reddy N, Chikowore TJB, Baisley K, Dong KL, Walker BD, Yu XG, Lichterfeld M, Ndung'u T. Differences in HIV-1 reservoir size, landscape characteristics and decay dynamics in acute and chronic treated HIV-1 Clade C infection. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2024:2024.02.16.24302713. [PMID: 38947072 PMCID: PMC11213047 DOI: 10.1101/2024.02.16.24302713] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/02/2024]
Abstract
Background Persisting HIV reservoir viruses in resting CD4 T cells and other cellular subsets are the main barrier to cure efforts. Antiretroviral therapy (ART) intensification by early initiation has been shown to enable post-treatment viral control in some cases but the underlying mechanisms are not fully understood. We hypothesized that ART initiated during the hyperacute phase of infection before peak will affect the size, decay dynamics and landscape characteristics of HIV-1 subtype C viral reservoirs. Methods We studied 35 women at high risk of infection from Durban, South Africa identified with hyperacute HIV infection by twice weekly testing for plasma HIV-1 RNA. Study participants included 11 who started ART at a median of 456 (297-1203) days post onset of viremia (DPOV), and 24 who started ART at a median of 1 (1-3) DPOV. We used peripheral blood mononuclear cells (PBMC) to measure total HIV-1 DNA by ddPCR and to sequence reservoir viral genomes by full length individual proviral sequencing (FLIP-seq) from onset of detection of HIV up to 1 year post treatment initiation. Results Whereas ART in hyperacute infection blunted peak viremia compared to untreated individuals (p<0.0001), there was no difference in total HIV-1 DNA measured contemporaneously (p=0.104). There was a steady decline of total HIV DNA in early treated persons over 1 year of ART (p=0.0004), with no significant change observed in the late treated group. Total HIV-1 DNA after one year of treatment was lower in the early treated compared to the late treated group (p=0.02). Generation of 697 single viral genome sequences revealed a difference in the longitudinal proviral genetic landscape over one year between untreated, late treated, and early treated infection: the relative contribution of intact genomes to the total pool of HIV-1 DNA after 1 year was higher in untreated infection (31%) compared to late treated (14%) and early treated infection (0%). Treatment initiated in both late and early infection resulted in a more rapid decay of intact (13% and 51% per month) versus defective (2% and 35% per month) viral genomes. However, intact genomes were still observed one year post chronic treatment initiation in contrast to early treatment where intact genomes were no longer detectable. Moreover, early ART reduced phylogenetic diversity of intact genomes and limited the seeding and persistence of cytotoxic T lymphocyte immune escape variants in the reservoir. Conclusions Overall, our results show that whereas ART initiated in hyperacute HIV-1 subtype C infection did not impact reservoir seeding, it was nevertheless associated with more rapid decay of intact viral genomes, decreased genetic complexity and immune escape in reservoirs, which could accelerate reservoir clearance when combined with other interventional strategies.
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Armani-Tourret M, Bone B, Tan TS, Sun W, Bellefroid M, Struyve T, Louella M, Yu XG, Lichterfeld M. Immune targeting of HIV-1 reservoir cells: a path to elimination strategies and cure. Nat Rev Microbiol 2024; 22:328-344. [PMID: 38337034 PMCID: PMC11131351 DOI: 10.1038/s41579-024-01010-8] [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] [Accepted: 01/12/2024] [Indexed: 02/12/2024]
Abstract
Successful approaches for eradication or cure of HIV-1 infection are likely to include immunological mechanisms, but remarkably little is known about how human immune responses can recognize and interact with the few HIV-1-infected cells that harbour genome-intact viral DNA, persist long term despite antiretroviral therapy and represent the main barrier to a cure. For a long time regarded as being completely shielded from host immune responses due to viral latency, these cells do, on closer examination with single-cell analytic techniques, display discrete footprints of immune selection, implying that human immune responses may be able to effectively engage and target at least some of these cells. The failure to eliminate rebound-competent virally infected cells in the majority of persons likely reflects the evolution of a highly selected pool of reservoir cells that are effectively camouflaged from immune recognition or rely on sophisticated approaches for resisting immune-mediated killing. Understanding the fine-tuned interplay between host immune responses and viral reservoir cells will help to design improved interventions that exploit the immunological vulnerabilities of HIV-1 reservoir cells.
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Affiliation(s)
- Marie Armani-Tourret
- Infectious Disease Division, Brigham and Women's Hospital, Boston, MA, USA
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, USA
| | - Benjamin Bone
- Infectious Disease Division, Brigham and Women's Hospital, Boston, MA, USA
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, USA
| | - Toong Seng Tan
- Infectious Disease Division, Brigham and Women's Hospital, Boston, MA, USA
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, USA
| | - Weiwei Sun
- Infectious Disease Division, Brigham and Women's Hospital, Boston, MA, USA
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, USA
| | - Maxime Bellefroid
- Infectious Disease Division, Brigham and Women's Hospital, Boston, MA, USA
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, USA
| | - Tine Struyve
- HIV Cure Research Center, Ghent University, Ghent, Belgium
| | - Michael Louella
- Community Advisory Board, Delaney AIDS Research Enterprise (DARE), San Francisco, CA, USA
- Department of Laboratory Medicine, University of Washington, Seattle, WA, USA
| | - Xu G Yu
- Infectious Disease Division, Brigham and Women's Hospital, Boston, MA, USA
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, USA
| | - Mathias Lichterfeld
- Infectious Disease Division, Brigham and Women's Hospital, Boston, MA, USA.
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, USA.
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Wang M, Yoon J, Reisert H, Das B, Orlinick B, Chiarella J, Halvas EK, Mellors J, Pang AP, Barakat LA, Fikrig M, Cyktor J, Kluger Y, Spudich S, Corley MJ, Farhadian SF. HIV-1-infected T cell clones are shared across cerebrospinal fluid and blood during ART. JCI Insight 2024; 9:e176208. [PMID: 38587074 PMCID: PMC11128194 DOI: 10.1172/jci.insight.176208] [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: 10/17/2023] [Accepted: 02/27/2024] [Indexed: 04/09/2024] Open
Abstract
The central nervous system HIV reservoir is incompletely understood and is a major barrier to HIV cure. We profiled people with HIV (PWH) and uninfected controls through single-cell transcriptomic and T cell receptor (TCR) sequencing to understand the dynamics of HIV persistence in the CNS. In PWH on ART, we found that most participants had single cells containing HIV-1 RNA, which was found predominantly in CD4 central memory T cells, in both cerebrospinal fluid (CSF) and blood. HIV-1 RNA-containing cells were found more frequently in CSF than blood, indicating a higher burden of reservoir cells in the CNS than blood for some PWH. Most CD4 T cell clones containing infected cells were compartment specific, while some (22%) - including rare clones with members of the clone containing detectable HIV RNA in both blood and CSF - were found in both CSF and blood. These results suggest that infected T cells trafficked between tissue compartments and that maintenance and expansion of infected T cell clones contributed to the CNS reservoir in PWH on ART.
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Affiliation(s)
- Meng Wang
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, Connecticut, USA
| | | | | | | | | | - Jennifer Chiarella
- Department of Neurology, Yale School of Medicine, New Haven, Connecticut, USA
| | - Elias K. Halvas
- Department of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - John Mellors
- Department of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Alina P.S. Pang
- Department of Medicine, Division of Infectious Diseases, Weill Cornell Medicine, New York City, New York, USA
| | | | | | - Joshua Cyktor
- Department of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Yuval Kluger
- Department of Pathology, Yale School of Medicine, New Haven, Connecticut, USA
| | - Serena Spudich
- Department of Neurology, Yale School of Medicine, New Haven, Connecticut, USA
| | - Michael J. Corley
- Department of Medicine, Division of Infectious Diseases, Weill Cornell Medicine, New York City, New York, USA
| | - Shelli F. Farhadian
- Section of Infectious Diseases, and
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, Connecticut, USA
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Mbonye U, Karn J. The cell biology of HIV-1 latency and rebound. Retrovirology 2024; 21:6. [PMID: 38580979 PMCID: PMC10996279 DOI: 10.1186/s12977-024-00639-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/07/2024] Open
Abstract
Transcriptionally latent forms of replication-competent proviruses, present primarily in a small subset of memory CD4+ T cells, pose the primary barrier to a cure for HIV-1 infection because they are the source of the viral rebound that almost inevitably follows the interruption of antiretroviral therapy. Over the last 30 years, many of the factors essential for initiating HIV-1 transcription have been identified in studies performed using transformed cell lines, such as the Jurkat T-cell model. However, as highlighted in this review, several poorly understood mechanisms still need to be elucidated, including the molecular basis for promoter-proximal pausing of the transcribing complex and the detailed mechanism of the delivery of P-TEFb from 7SK snRNP. Furthermore, the central paradox of HIV-1 transcription remains unsolved: how are the initial rounds of transcription achieved in the absence of Tat? A critical limitation of the transformed cell models is that they do not recapitulate the transitions between active effector cells and quiescent memory T cells. Therefore, investigation of the molecular mechanisms of HIV-1 latency reversal and LRA efficacy in a proper physiological context requires the utilization of primary cell models. Recent mechanistic studies of HIV-1 transcription using latently infected cells recovered from donors and ex vivo cellular models of viral latency have demonstrated that the primary blocks to HIV-1 transcription in memory CD4+ T cells are restrictive epigenetic features at the proviral promoter, the cytoplasmic sequestration of key transcription initiation factors such as NFAT and NF-κB, and the vanishingly low expression of the cellular transcription elongation factor P-TEFb. One of the foremost schemes to eliminate the residual reservoir is to deliberately reactivate latent HIV-1 proviruses to enable clearance of persisting latently infected cells-the "Shock and Kill" strategy. For "Shock and Kill" to become efficient, effective, non-toxic latency-reversing agents (LRAs) must be discovered. Since multiple restrictions limit viral reactivation in primary cells, understanding the T-cell signaling mechanisms that are essential for stimulating P-TEFb biogenesis, initiation factor activation, and reversing the proviral epigenetic restrictions have become a prerequisite for the development of more effective LRAs.
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Affiliation(s)
- Uri Mbonye
- Department of Molecular Biology and Microbiology, Case Western Reserve University School of Medicine, Cleveland, OH, 44106, USA.
| | - Jonathan Karn
- Department of Molecular Biology and Microbiology, Case Western Reserve University School of Medicine, Cleveland, OH, 44106, USA.
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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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Harper J, Betts MR, Lichterfeld M, Müller-Trutwin M, Margolis D, Bar KJ, Li JZ, McCune JM, Lewin SR, Kulpa D, Ávila-Ríos S, Diallo DD, Lederman MM, Paiardini M. Erratum to: Progress Note 2024: Curing HIV; Not in My Lifetime or Just Around the Corner? Pathog Immun 2024; 8:179-222. [PMID: 38505662 PMCID: PMC10949969 DOI: 10.20411/pai.v8i2.696] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2024] [Accepted: 03/11/2024] [Indexed: 03/21/2024] Open
Abstract
[This corrects the article DOI: 10.20411/pai.v8i2.665.].
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Affiliation(s)
- Justin Harper
- Division of Microbiology and Immunology, Emory National Primate Research Center, Emory University, Atlanta, Georgia
| | - Michael R. Betts
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
- Center for AIDS Research, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Mathias Lichterfeld
- Ragon Institute of MGH, MIT and Harvard, Cambridge, Massachusetts
- Infectious Disease Division, Brigham and Women's Hospital, Boston, Massachusetts
| | - Michaela Müller-Trutwin
- HIV Inflammation and Persistence Unit, Institut Pasteur, Université Paris-Cité, Paris, France
| | - David Margolis
- Division of Infectious Diseases, Center for AIDS Research, University of North Carolina at Chapel Hill, School of Medicine, Chapel Hill, North Carolina
| | - Katharine J. Bar
- Center for AIDS Research, University of Pennsylvania, Philadelphia, Pennsylvania
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Jonathan Z. Li
- Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Joseph M. McCune
- HIV Frontiers, Global Health Accelerator, Bill & Melinda Gates Foundation
| | - Sharon R. Lewin
- Department of Infectious Diseases, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Australia
- Victorian Infectious Diseases Service, Royal Melbourne Hospital at the Peter Doherty Institute for Infection and Immunity, Melbourne, Australia
- Department of Infectious Diseases, Alfred Hospital and Monash University, Melbourne, Australia
| | - Deanna Kulpa
- Division of Microbiology and Immunology, Emory National Primate Research Center, Emory University, Atlanta, Georgia
- Department of Pathology and Laboratory Medicine, Emory University, Atlanta, Georgia
| | - Santiago Ávila-Ríos
- Centro de Investigación en Enfermedades Infecciosas, Instituto Nacional de Enfermedades Respiratorias, Mexico City, Mexico
| | | | - Michael M. Lederman
- Division of Infectious Diseases and HIV Medicine, Case Western Reserve University, Cleveland, Ohio
| | - Mirko Paiardini
- Division of Microbiology and Immunology, Emory National Primate Research Center, Emory University, Atlanta, Georgia
- Department of Pathology and Laboratory Medicine, Emory University, Atlanta, Georgia
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Pieren DKJ, Benítez-Martínez A, Genescà M. Targeting HIV persistence in the tissue. Curr Opin HIV AIDS 2024; 19:69-78. [PMID: 38169333 DOI: 10.1097/coh.0000000000000836] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2024]
Abstract
PURPOSE OF REVIEW The complex nature and distribution of the HIV reservoir in tissue of people with HIV remains one of the major obstacles to achieve the elimination of HIV persistence. Challenges include the tissue-specific states of latency and viral persistence, which translates into high levels of reservoir heterogeneity. Moreover, the best strategies to reach and eliminate these reservoirs may differ based on the intrinsic characteristics of the cellular and anatomical reservoir to reach. RECENT FINDINGS While major focus has been undertaken for lymphoid tissues and follicular T helper cells, evidence of viral persistence in HIV and non-HIV antigen-specific CD4 + T cells and macrophages resident in multiple tissues providing long-term protection presents new challenges in the quest for an HIV cure. Considering the microenvironments where these cellular reservoirs persist opens new venues for the delivery of drugs and immunotherapies to target these niches. New tools, such as single-cell RNA sequencing, CRISPR screenings, mRNA technology or tissue organoids are quickly developing and providing detailed information about the complex nature of the tissue reservoirs. SUMMARY Targeting persistence in tissue reservoirs represents a complex but essential step towards achieving HIV cure. Combinatorial strategies, particularly during the early phases of infection to impact initial reservoirs, capable of reaching and reactivating multiple long-lived reservoirs in the body may lead the path.
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Affiliation(s)
- Daan K J Pieren
- Infectious Diseases Department, Vall d'Hebron Institut de Recerca (VHIR), Vall d'Hebron Hospital Universitari, Vall d'Hebron Barcelona Hospital Campus, Barcelona, Spain
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Harper J, Betts MR, Lichterfeld M, Müller-Trutwin M, Margolis D, Bar KJ, Li JZ, McCune JM, Lewin SR, Kulpa D, Ávila-Ríos S, Diallo DD, Lederman MM, Paiardini M. Progress Note 2024: Curing HIV; Not in My Lifetime or Just Around the Corner? Pathog Immun 2024; 8:115-157. [PMID: 38455668 PMCID: PMC10919397 DOI: 10.20411/pai.v8i2.665] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2024] [Accepted: 02/14/2024] [Indexed: 03/09/2024] Open
Abstract
Once a death sentence, HIV is now considered a manageable chronic disease due to the development of antiretroviral therapy (ART) regimens with minimal toxicity and a high barrier for genetic resistance. While highly effective in arresting AIDS progression and rendering the virus untransmissible in people living with HIV (PLWH) with undetectable viremia (U=U) [1, 2]), ART alone is incapable of eradicating the "reservoir" of resting, latently infected CD4+ T cells from which virus recrudesces upon treatment cessation. As of 2022 estimates, there are 39 million PLWH, of whom 86% are aware of their status and 76% are receiving ART [3]. As of 2017, ART-treated PLWH exhibit near normalized life expectancies without adjustment for socioeconomic differences [4]. Furthermore, there is a global deceleration in the rate of new infections [3] driven by expanded access to pre-exposure prophylaxis (PrEP), HIV testing in vulnerable populations, and by ART treatment [5]. Therefore, despite outstanding issues pertaining to cost and access in developing countries, there is strong enthusiasm that aggressive testing, treatment, and effective viral suppression may be able to halt the ongoing HIV epidemic (ie, UNAIDS' 95-95-95 targets) [6-8]; especially as evidenced by recent encouraging observations in Sydney [9]. Despite these promising efforts to limit further viral transmission, for PLWH, a "cure" remains elusive; whether it be to completely eradicate the viral reservoir (ie, cure) or to induce long-term viral remission in the absence of ART (ie, control; Figure 1). In a previous salon hosted by Pathogens and Immunity in 2016 [10], some researchers were optimistic that a cure was a feasible, scalable goal, albeit with no clear consensus on the best route. So, how are these cure strategies panning out? In this commentary, 8 years later, we will provide a brief overview on recent advances and failures towards identifying determinants of viral persistence and developing a scalable cure for HIV. Based on these observations, and as in the earlier salon, we have asked several prominent HIV cure researchers for their perspectives.
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Affiliation(s)
- Justin Harper
- Division of Microbiology and Immunology, Emory National Primate Research Center, Emory University, Atlanta, Georgia
| | - Michael R. Betts
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
- Center for AIDS Research, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Mathias Lichterfeld
- Ragon Institute of MGH, MIT and Harvard, Cambridge, Massachusetts
- Infectious Disease Division, Brigham and Women's Hospital, Boston, Massachusetts
| | - Michaela Müller-Trutwin
- HIV Inflammation and Persistence Unit, Institut Pasteur, Université Paris-Cité, Paris, France
| | - David Margolis
- Division of Infectious Diseases, Center for AIDS Research, University of North Carolina at Chapel Hill, School of Medicine, Chapel Hill, North Carolina
| | - Katharine J. Bar
- Center for AIDS Research, University of Pennsylvania, Philadelphia, Pennsylvania
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Jonathan Z. Li
- Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Joseph M. McCune
- HIV Frontiers, Global Health Accelerator, Bill & Melinda Gates Foundation
| | - Sharon R. Lewin
- Department of Infectious Diseases, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Australia
- Victorian Infectious Diseases Service, Royal Melbourne Hospital at the Peter Doherty Institute for Infection and Immunity, Melbourne, Australia
- Department of Infectious Diseases, Alfred Hospital and Monash University, Melbourne, Australia
| | - Deanna Kulpa
- Division of Microbiology and Immunology, Emory National Primate Research Center, Emory University, Atlanta, Georgia
- Department of Pathology and Laboratory Medicine, Emory University, Atlanta, Georgia
| | - Santiago Ávila-Ríos
- Centro de Investigación en Enfermedades Infecciosas, Instituto Nacional de Enfermedades Respiratorias, Mexico City, Mexico
| | | | - Michael M. Lederman
- Division of Infectious Diseases and HIV Medicine, Case Western Reserve University, Cleveland, Ohio
| | - Mirko Paiardini
- Division of Microbiology and Immunology, Emory National Primate Research Center, Emory University, Atlanta, Georgia
- Department of Pathology and Laboratory Medicine, Emory University, Atlanta, Georgia
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10
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Faua C, Ursenbach A, Fuchs A, Caspar S, Jegou F, Ruch Y, Hoellinger B, Laugel E, Velay A, Rey D, Fafi-Kremer S, Gantner P. HIV Productively Infects Highly Differentiated and Exhausted CD4+ T Cells During AIDS. Pathog Immun 2024; 8:92-114. [PMID: 38420260 PMCID: PMC10901154 DOI: 10.20411/pai.v8i2.638] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2023] [Accepted: 01/24/2024] [Indexed: 03/02/2024] Open
Abstract
Background Throughout HIV infection, productively infected cells generate billions of viral particles and are thus responsible for body-wide HIV dissemination, but their phenotype during AIDS is unknown. As AIDS is associated with immunological changes, analyzing the phenotype of productively infected cells can help understand HIV production during this terminal stage. Methods Blood samples from 15 untreated viremic participants (recent infection, n=5; long-term infection, n=5; active opportunistic AIDS-defining disease, n=5) and 5 participants virologically controlled on antiretroviral therapy (ART) enrolled in the Analysis of the Persistence, Reservoir and HIV Latency (APRIL) study (NCT05752318) were analyzed. Cells expressing the capsid protein p24 (p24+ cells) after 18 hours of resting or 24 hours of stimulation (HIV-Flow) revealed productively infected cells from viremic participants or translation-competent reservoir cells from treated participants, respectively. Results The frequency of productively infected cells tended to be higher during AIDS in comparison with recent and long-term infections (median, 340, 72, and 32/million CD4+ T cells, respectively) and correlated with the plasma viral load at all stages of infection. Altogether, these cells were more frequently CD4low, HLA-ABClow, CD45RA-, Ki67+, PD-1+, with a non-negligible contribution from pTfh (CXCR5+PD-1+) cells, and were not significantly enriched in HIV coreceptors CCR5 nor CXCR4 expression. The comparison markers expression between stages showed that productively infected cells during AIDS were enriched in memory and exhausted cells. In contrast, the frequencies of infected pTfh were lower during AIDS compared to non-AIDS stages. A UMAP analysis revealed that total CD4+ T cells were grouped in 7 clusters and that productive p24+ cells were skewed to given clusters throughout the course of infection. Overall, the preferential targets of HIV during the latest stages seemed to be more frequently highly differentiated (memory, TTD-like) and exhausted cells and less frequently pTfh-like cells. In contrast, translation-competent reservoir cells were less frequent (5/million CD4+ T cells) and expressed more frequently HLA-ABC and less frequently PD-1. Conclusions In long-term infection and AIDS, productively infected cells were differentiated and exhausted. This could indicate that cells with these given features are responsible for HIV production and dissemination in an immune dysfunction environment occurring during the last stages of infection.
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Affiliation(s)
- Clayton Faua
- INSERM UMR_S1109, Strasbourg University, Strasbourg, France
| | - Axel Ursenbach
- Le Trait d'Union, HIV-Infection Care Center, Strasbourg University Hospital, Strasbourg, France
| | - Anne Fuchs
- Clinical Virology Laboratory, Strasbourg University Hospital, Strasbourg, France
| | - Stéphanie Caspar
- Clinical Virology Laboratory, Strasbourg University Hospital, Strasbourg, France
| | - Frédérick Jegou
- Clinical Virology Laboratory, Strasbourg University Hospital, Strasbourg, France
| | - Yvon Ruch
- Infectious Diseases Department, Strasbourg University Hospital, Strasbourg, France
| | - Baptiste Hoellinger
- Infectious Diseases Department, Strasbourg University Hospital, Strasbourg, France
| | - Elodie Laugel
- INSERM UMR_S1109, Strasbourg University, Strasbourg, France
- Clinical Virology Laboratory, Strasbourg University Hospital, Strasbourg, France
| | - Aurélie Velay
- INSERM UMR_S1109, Strasbourg University, Strasbourg, France
- Clinical Virology Laboratory, Strasbourg University Hospital, Strasbourg, France
| | - David Rey
- Le Trait d'Union, HIV-Infection Care Center, Strasbourg University Hospital, Strasbourg, France
| | - Samira Fafi-Kremer
- INSERM UMR_S1109, Strasbourg University, Strasbourg, France
- Clinical Virology Laboratory, Strasbourg University Hospital, Strasbourg, France
| | - Pierre Gantner
- INSERM UMR_S1109, Strasbourg University, Strasbourg, France
- Clinical Virology Laboratory, Strasbourg University Hospital, Strasbourg, France
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11
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Shahid A, MacLennan S, Jones BR, Sudderuddin H, Dang Z, Cobarrubias K, Duncan MC, Kinloch NN, Dapp MJ, Archin NM, Fischl MA, Ofotokun I, Adimora A, Gange S, Aouizerat B, Kuniholm MH, Kassaye S, Mullins JI, Goldstein H, Joy JB, Anastos K, Brumme ZL. The replication-competent HIV reservoir is a genetically restricted, younger subset of the overall pool of HIV proviruses persisting during therapy, which is highly genetically stable over time. J Virol 2024; 98:e0165523. [PMID: 38214547 PMCID: PMC10878278 DOI: 10.1128/jvi.01655-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2023] [Accepted: 12/07/2023] [Indexed: 01/13/2024] Open
Abstract
Within-host HIV populations continually diversify during untreated infection, and this diversity persists within infected cell reservoirs during antiretroviral therapy (ART). Achieving a better understanding of on-ART proviral evolutionary dynamics, and a better appreciation of how the overall persisting pool of (largely genetically defective) proviruses differs from the much smaller replication-competent HIV reservoir, is critical to HIV cure efforts. We reconstructed within-host HIV evolutionary histories in blood from seven participants of the Women's Interagency HIV Study who experienced HIV seroconversion, and used these data to characterize the diversity, lineage origins, and ages of proviral env-gp120 sequences sampled longitudinally up to 12 years on ART. We also studied HIV sequences emerging from the reservoir in two participants. We observed that proviral clonality generally increased over time on ART, with clones frequently persisting long term. While on-ART proviral integration dates generally spanned the duration of untreated infection, HIV emerging in plasma was exclusively younger (i.e., dated to the years immediately pre-ART). The genetic and age distributions of distinct proviral sequences remained stable during ART in all but one participant, in whom there was evidence that younger proviruses had been preferentially eliminated after 12 years on ART. Analysis of the gag region in three participants corroborated our env-gp120-based observations, indicating that our observations are not influenced by the HIV region studied. Our results underscore the remarkable genetic stability of the distinct proviral sequences that persist in blood during ART. Our results also suggest that the replication-competent HIV reservoir is a genetically restricted, younger subset of this overall proviral pool.IMPORTANCECharacterizing the genetically diverse HIV sequences that persist in the reservoir despite antiretroviral therapy (ART) is critical to cure efforts. Our observations confirm that proviruses persisting in blood on ART, which are largely genetically defective, broadly reflect the extent of within-host HIV evolution pre-ART. Moreover, on-ART clonal expansion is not appreciably accompanied by the loss of distinct proviral lineages. In fact, on-ART proviral genetic composition remained stable in all but one participant, in whom, after 12 years on ART, proviruses dating to around near ART initiation had been preferentially eliminated. We also identified recombinant proviruses between parental sequence fragments of different ages. Though rare, such sequences suggest that reservoir cells can be superinfected with HIV from another infection era. Overall, our finding that the replication-competent reservoir in blood is a genetically restricted, younger subset of all persisting proviruses suggests that HIV cure strategies will need to eliminate a reservoir that differs in key respects from the overall proviral pool.
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Affiliation(s)
- Aniqa Shahid
- Faculty of Health Sciences, Simon Fraser University, Burnaby, British Columbia, Canada
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, British Columbia, Canada
| | - Signe MacLennan
- Faculty of Health Sciences, Simon Fraser University, Burnaby, British Columbia, Canada
| | - Bradley R. Jones
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, British Columbia, Canada
- Bioinformatics Program, University of British Columbia, Vancouver, British Columbia, Canada
| | - Hanwei Sudderuddin
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, British Columbia, Canada
| | - Zhong Dang
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, British Columbia, Canada
| | - Kyle Cobarrubias
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, British Columbia, Canada
| | - Maggie C. Duncan
- Faculty of Health Sciences, Simon Fraser University, Burnaby, British Columbia, Canada
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, British Columbia, Canada
| | - Natalie N. Kinloch
- Faculty of Health Sciences, Simon Fraser University, Burnaby, British Columbia, Canada
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, British Columbia, Canada
| | - Michael J. Dapp
- Department of Microbiology, University of Washington, School of Medicine, Seattle, Washington, USA
| | - Nancie M. Archin
- UNC HIV Cure Center, Institute of Global Health and Infectious Diseases, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Margaret A. Fischl
- Department of Medicine, University of Miami School of Medicine, Miami, Florida, USA
| | - Igho Ofotokun
- Division of Infectious Diseases, Department of Medicine, Emory University School of Medicine, Atlanta, Georgia, USA
| | - Adaora Adimora
- Department of Epidemiology, UNC Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Stephen Gange
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA
| | | | - Mark H. Kuniholm
- Department of Epidemiology and Biostatistics, University at Albany, State University of New York, Rensselaer, New York, New York, USA
| | - Seble Kassaye
- Division of Infectious Diseases and Tropical Medicine, Georgetown University, Washington, DC, USA
| | - James I. Mullins
- Department of Microbiology, University of Washington, School of Medicine, Seattle, Washington, USA
- Department of Global Health, University of Washington, School of Medicine, Seattle, Washington, USA
- Department of Medicine, University of Washington, School of Medicine, Seattle, Washington, USA
| | - Harris Goldstein
- Departments of Microbiology and Immunology and Pediatrics, Albert Einstein College of Medicine, Bronx, New York, New York, USA
| | - Jeffrey B. Joy
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, British Columbia, Canada
- Bioinformatics Program, University of British Columbia, Vancouver, British Columbia, Canada
- Department of Medicine, University of British Columbia, Vancouver, British Columbia, Canada
| | - Kathryn Anastos
- Department of Medicine, Albert Einstein College of Medicine, New York, New York, USA
| | - Zabrina L. Brumme
- Faculty of Health Sciences, Simon Fraser University, Burnaby, British Columbia, Canada
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, British Columbia, Canada
| | - the MACS/WIHS combined cohort study (MWCSS)OfotokunIghovwerha1ShethAnandi1WingoodGina1BrownTodd2MargolickJoseph2AnastosKathryn3HannaDavid3SharmaAnjali3GustafsonDeborah4WilsonTracey4D’SouzaGypsyamber5GangeStephen5TopperElizabeth5CohenMardge6FrenchAudrey6WolinskySteven7PalellaFrank7StosorValentina7AouizeratBradley8PriceJennifer8TienPhyllis8DetelsRoger9MimiagaMatthew9KassayeSeble10MerensteinDaniel10AlcaideMaria11FischlMargaret11JonesDeborah11MartinsonJeremy12RinaldoCharles12KempfMirjam-Colette13Dionne-OdomJodie13Konkle-ParkerDeborah13BrockJames B.13AdimoraAdaora14Floris-MooreMichelle14Emory University, Atlanta, Georgia, USAJohns Hopkins University, Baltimore, Maryland, USAAlbert Einstein College of Medicine, Bronx, New York, USASuny Downstate Medical Center, Brooklyn, New York, USAJohns Hopkins University, Baltimore, Maryland, USAHektoen Institute for Medical Research, Chicago, Illinois, USANorthwestern University at Chicago, Chicago, Illinois, USAUniversity of California San Francisco, San Francisco, California, USAUniversity of California Los Angeles, Los Angeles, California, USAGeorgetown University, Washington, DC, USAUniversity of Miami School of Medicine, Coral Gables, Florida, USAUniversity of Pittsburgh, Pittsburgh, Pennsylvania, USAUniversity of Alabama Birmingham, Birmingham, Alabama, USAUniversity of North Carolina Chapel Hill, Chapel Hill, North Carolina, USA
- Faculty of Health Sciences, Simon Fraser University, Burnaby, British Columbia, Canada
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, British Columbia, Canada
- Bioinformatics Program, University of British Columbia, Vancouver, British Columbia, Canada
- Department of Microbiology, University of Washington, School of Medicine, Seattle, Washington, USA
- UNC HIV Cure Center, Institute of Global Health and Infectious Diseases, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
- Department of Medicine, University of Miami School of Medicine, Miami, Florida, USA
- Division of Infectious Diseases, Department of Medicine, Emory University School of Medicine, Atlanta, Georgia, USA
- Department of Epidemiology, UNC Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA
- College of Dentistry, New York University, New York, New York, USA
- Department of Epidemiology and Biostatistics, University at Albany, State University of New York, Rensselaer, New York, New York, USA
- Division of Infectious Diseases and Tropical Medicine, Georgetown University, Washington, DC, USA
- Department of Global Health, University of Washington, School of Medicine, Seattle, Washington, USA
- Department of Medicine, University of Washington, School of Medicine, Seattle, Washington, USA
- Departments of Microbiology and Immunology and Pediatrics, Albert Einstein College of Medicine, Bronx, New York, New York, USA
- Department of Medicine, University of British Columbia, Vancouver, British Columbia, Canada
- Department of Medicine, Albert Einstein College of Medicine, New York, New York, USA
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12
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Kim J, Bose D, Araínga M, Haque MR, Fennessey CM, Caddell RA, Thomas Y, Ferrell DE, Ali S, Grody E, Goyal Y, Cicala C, Arthos J, Keele BF, Vaccari M, Lorenzo-Redondo R, Hope TJ, Villinger F, Martinelli E. TGF-β blockade drives a transitional effector phenotype in T cells reversing SIV latency and decreasing SIV reservoirs in vivo. Nat Commun 2024; 15:1348. [PMID: 38355731 PMCID: PMC10867093 DOI: 10.1038/s41467-024-45555-x] [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: 09/22/2023] [Accepted: 01/26/2024] [Indexed: 02/16/2024] Open
Abstract
HIV-1 persistence during ART is due to the establishment of long-lived viral reservoirs in resting immune cells. Using an NHP model of barcoded SIVmac239 intravenous infection and therapeutic dosing of anti-TGFBR1 inhibitor galunisertib (LY2157299), we confirm the latency reversal properties of in vivo TGF-β blockade, decrease viral reservoirs and stimulate immune responses. Treatment of eight female, SIV-infected macaques on ART with four 2-weeks cycles of galunisertib leads to viral reactivation as indicated by plasma viral load and immunoPET/CT with a 64Cu-DOTA-F(ab')2-p7D3-probe. Post-galunisertib, lymph nodes, gut and PBMC exhibit lower cell-associated (CA-)SIV DNA and lower intact pro-virus (PBMC). Galunisertib does not lead to systemic increase in inflammatory cytokines. High-dimensional cytometry, bulk, and single-cell (sc)RNAseq reveal a galunisertib-driven shift toward an effector phenotype in T and NK cells characterized by a progressive downregulation in TCF1. In summary, we demonstrate that galunisertib, a clinical stage TGF-β inhibitor, reverses SIV latency and decreases SIV reservoirs by driving T cells toward an effector phenotype, enhancing immune responses in vivo in absence of toxicity.
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Affiliation(s)
- Jinhee Kim
- Department of Medicine, Division of Infectious Diseases, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Deepanwita Bose
- New Iberia Research Center, University of Louisiana at Lafayette, New Iberia, LA, USA
| | - Mariluz Araínga
- New Iberia Research Center, University of Louisiana at Lafayette, New Iberia, LA, USA
| | - Muhammad R Haque
- Cell and Developmental Biology, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Christine M Fennessey
- AIDS and Cancer Virus Program, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Rachel A Caddell
- Division of Immunology, Tulane National Primate Research Center, Covington, LA, USA
| | - Yanique Thomas
- Cell and Developmental Biology, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Douglas E Ferrell
- New Iberia Research Center, University of Louisiana at Lafayette, New Iberia, LA, USA
| | - Syed Ali
- New Iberia Research Center, University of Louisiana at Lafayette, New Iberia, LA, USA
| | - Emanuelle Grody
- Cell and Developmental Biology, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
- Center for Synthetic Biology, Northwestern University, Chicago, IL, USA
| | - Yogesh Goyal
- Cell and Developmental Biology, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
- Center for Synthetic Biology, Northwestern University, Chicago, IL, USA
- Robert H. Lurie Comprehensive Cancer Center, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Claudia Cicala
- Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - James Arthos
- Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Brandon F Keele
- AIDS and Cancer Virus Program, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Monica Vaccari
- Division of Immunology, Tulane National Primate Research Center, Covington, LA, USA
- Department of Microbiology and Immunology, Tulane University School of Medicine, New Orleans, LA, USA
| | - Ramon Lorenzo-Redondo
- Department of Medicine, Division of Infectious Diseases, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
- Center for Pathogen Genomics and Microbial Evolution, Northwestern University Havey Institute for Global Health, Chicago, IL, USA
| | - Thomas J Hope
- Cell and Developmental Biology, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Francois Villinger
- New Iberia Research Center, University of Louisiana at Lafayette, New Iberia, LA, USA
| | - Elena Martinelli
- Department of Medicine, Division of Infectious Diseases, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA.
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13
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McLaurin KA, Li H, Khalili K, Mactutus CF, Booze RM. HIV-1 mRNA knockdown with CRISPR/CAS9 enhances neurocognitive function. J Neurovirol 2024; 30:71-85. [PMID: 38355914 PMCID: PMC11035469 DOI: 10.1007/s13365-024-01193-z] [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: 08/15/2023] [Revised: 01/23/2024] [Accepted: 01/24/2024] [Indexed: 02/16/2024]
Abstract
Mixed glia are infiltrated with HIV-1 virus early in the course of infection leading to the development of a persistent viral reservoir in the central nervous system. Modification of the HIV-1 genome using gene editing techniques, including CRISPR/Cas9, has shown great promise towards eliminating HIV-1 viral reservoirs; whether these techniques are capable of removing HIV-1 viral proteins from mixed glia, however, has not been systematically evaluated. Herein, the efficacy of adeno-associated virus 9 (AAV9)-CRISPR/Cas9 gene editing for eliminating HIV-1 messenger RNA (mRNA) from cortical mixed glia was evaluated in vitro and in vivo. In vitro, a within-subjects experimental design was utilized to treat mixed glia isolated from neonatal HIV-1 transgenic (Tg) rats with varying doses (0, 0.9, 1.8, 2.7, 3.6, 4.5, or 5.4 µL corresponding to a physical titer of 0, 4.23 × 109, 8.46 × 109, 1.269 × 1010, 1.692 × 1010, 2.115 × 1010, and 2.538 × 1010 gc/µL) of CRISPR/Cas9 for 72 h. Dose-dependent decreases in the number of HIV-1 mRNA, quantified using an innovative in situ hybridization technique, were observed in a subset (i.e., n = 5 out of 8) of primary mixed glia. In vivo, HIV-1 Tg rats were retro-orbitally inoculated with CRISPR/Cas9 for two weeks, whereby treatment resulted in profound excision (i.e., approximately 53.2%) of HIV-1 mRNA from the medial prefrontal cortex. Given incomplete excision of the HIV-1 viral genome, the clinical relevance of HIV-1 mRNA knockdown for eliminating neurocognitive impairments was evaluated via examination of temporal processing, a putative neurobehavioral mechanism underlying HIV-1-associated neurocognitive disorders (HAND). Indeed, treatment with CRISPR/Cas9 protractedly, albeit not permanently, restored the developmental trajectory of temporal processing. Proof-of-concept studies, therefore, support the susceptibility of mixed glia to gene editing and the potential of CRISPR/Cas9 to serve as a novel therapeutic strategy for HAND, even in the absence of full viral eradication.
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Affiliation(s)
- Kristen A McLaurin
- Cognitive and Neural Science Program, Department of Psychology, Barnwell College, University of South Carolina, 1512 Pendleton Street, Columbia, SC, 29208, USA
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, 789 S Limestone Street, Lexington, KY, 40508, USA
| | - Hailong Li
- Cognitive and Neural Science Program, Department of Psychology, Barnwell College, University of South Carolina, 1512 Pendleton Street, Columbia, SC, 29208, USA
| | - Kamel Khalili
- Center for Neurovirology and Gene Editing, Department of Microbiology, Immunology, and Inflammation, Lewis Katz School of Medicine, Temple University, 3500 N. Broad Street, 7th Floor, Philadelphia, PA, 19140, USA
| | - Charles F Mactutus
- Cognitive and Neural Science Program, Department of Psychology, Barnwell College, University of South Carolina, 1512 Pendleton Street, Columbia, SC, 29208, USA
| | - Rosemarie M Booze
- Cognitive and Neural Science Program, Department of Psychology, Barnwell College, University of South Carolina, 1512 Pendleton Street, Columbia, SC, 29208, USA.
- Department of Psychology, Carolina Trustees Professor and Bicentennial Endowed Chair of Behavioral Neuroscience, University of South Carolina, 1512 Pendleton Street, Columbia, SC, 29208, USA.
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14
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Rausch JW, Parvez S, Pathak S, Capoferri AA, Kearney MF. HIV Expression in Infected T Cell Clones. Viruses 2024; 16:108. [PMID: 38257808 PMCID: PMC10820123 DOI: 10.3390/v16010108] [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: 12/13/2023] [Revised: 01/04/2024] [Accepted: 01/06/2024] [Indexed: 01/24/2024] Open
Abstract
The principal barrier to an HIV-1 cure is the persistence of infected cells harboring replication-competent proviruses despite antiretroviral therapy (ART). HIV-1 transcriptional suppression, referred to as viral latency, is foremost among persistence determinants, as it allows infected cells to evade the cytopathic effects of virion production and killing by cytotoxic T lymphocytes (CTL) and other immune factors. HIV-1 persistence is also governed by cellular proliferation, an innate and essential capacity of CD4+ T cells that both sustains cell populations over time and enables a robust directed response to immunological threats. However, when HIV-1 infects CD4+ T cells, this capacity for proliferation can enable surreptitious HIV-1 propagation without the deleterious effects of viral gene expression in latently infected cells. Over time on ART, the HIV-1 reservoir is shaped by both persistence determinants, with selective forces most often favoring clonally expanded infected cell populations harboring transcriptionally quiescent proviruses. Moreover, if HIV latency is incomplete or sporadically reversed in clonal infected cell populations that are replenished faster than they are depleted, such populations could both persist indefinitely and contribute to low-level persistent viremia during ART and viremic rebound if treatment is withdrawn. In this review, select genetic, epigenetic, cellular, and immunological determinants of viral transcriptional suppression and clonal expansion of HIV-1 reservoir T cells, interdependencies among these determinants, and implications for HIV-1 persistence will be presented and discussed.
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Affiliation(s)
- Jason W. Rausch
- HIV Dynamics and Replication Program, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702, USA; (S.P.); (S.P.); (A.A.C.); (M.F.K.)
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15
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Kime J, Bose D, Arainga M, Haque MR, Fennessey CM, Caddell RA, Thomas Y, Ferrell DE, Ali S, Grody E, Goyal Y, Cicala C, Arthos J, Keele BF, Vaccari M, Lorenzo-Redondo R, Hope TJ, Villinger FJ, Marinelli E. TGF-β blockade drives a transitional effector phenotype in T cells reversing SIV latency and decreasing SIV reservoirs in vivo. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.09.05.556422. [PMID: 38014094 PMCID: PMC10680555 DOI: 10.1101/2023.09.05.556422] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/29/2023]
Abstract
HIV-1 persistence during ART is due to the establishment of long-lived viral reservoirs in resting immune cells. Using an NHP model of barcoded SIVmac239 intravenous infection and therapeutic dosing of the anti-TGFBR1 inhibitor galunisertib (LY2157299), we confirmed the latency reversal properties of in vivo TGF-β blockade, decreased viral reservoirs and stimulated immune responses. Eight SIV-infected macaques on suppressive ART were treated with 4 2-week cycles of galunisertib. ART was discontinued 3 weeks after the last dose, and macaques euthanized 6 weeks after ART-interruption(ATI). One macaque did not rebound, while the remaining rebounded between week 2 and 6 post-ATI. Galunisertib led to viral reactivation as indicated by plasma viral load and immunoPET/CT with the 64Cu-DOTA-F(ab')2-p7D3-probe. Half to 1 Log decrease in cell-associated (CA-)SIV DNA was detected in lymph nodes, gut and PBMC, while intact pro-virus in PBMC decreased by 3-fold. No systemic increase in inflammatory cytokines was observed. High-dimensions cytometry, bulk and single-cell RNAseq revealed a shift toward an effector phenotype in T and NK cells. In summary, we demonstrated that galunisertib, a clinical stage TGFβ inhibitor, reverses SIV latency and decreases SIV reservoirs by driving T cells toward an effector phenotype, enhancing immune responses in vivo in absence of toxicity.
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16
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Solis-Leal A, Boby N, Mallick S, Cheng Y, Wu F, De La Torre G, Dufour J, Alvarez X, Shivanna V, Liu Y, Fennessey CM, Lifson JD, Li Q, Keele BF, Ling B. Lymphoid tissues contribute to plasma viral clonotypes early after antiretroviral therapy interruption in SIV-infected rhesus macaques. Sci Transl Med 2023; 15:eadi9867. [PMID: 38091409 DOI: 10.1126/scitranslmed.adi9867] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2023] [Accepted: 11/17/2023] [Indexed: 12/18/2023]
Abstract
The rebound-competent viral reservoir, composed of a virus that is able to persist during antiretroviral therapy (ART) and mediate reactivation of systemic viral replication and rebound viremia after ART interruption (ATI), remains the biggest obstacle to treating HIV infection. A better understanding of the cellular and tissue origins and the dynamics of viral populations that initiate rebound upon ATI could help develop therapeutic strategies for reducing the rebound-competent viral reservoir. In this study, barcoded simian immunodeficiency virus (SIV), SIVmac239M, was used to infect rhesus macaques to enable monitoring of viral barcode clonotypes contributing to virus detectable in plasma after ATI. Blood and tissues from secondary lymphoid organs (spleen, mesenteric lymph nodes, and inguinal lymph nodes) and from the colon, ileum, lung, liver, and brain were analyzed using viral barcode sequencing, intact proviral DNA assay, single-cell RNA sequencing, and combined CODEX and RNAscope in situ hybridization. Four of seven animals had viral barcodes detectable by deep sequencing of plasma at necropsy, although plasma viral RNA remained below 22 copies per milliliter. Among the tissues studied, mesenteric lymph nodes, inguinal lymph nodes, and spleen contained viral barcodes detected in plasma. CD4+ T cells were the main cell type harboring viral RNA after ATI. Furthermore, T cell zones in lymphoid tissues showed higher viral RNA abundance than B cell zones for most animals. These findings are consistent with lymphoid tissues contributing to the virus present in plasma early after ATI.
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Affiliation(s)
- Antonio Solis-Leal
- Host-Pathogen Interactions Program, Texas Biomedical Research Institute, 8715 W Military Dr, San Antonio, TX 78227, USA
| | - Nongthombam Boby
- Host-Pathogen Interactions Program, Texas Biomedical Research Institute, 8715 W Military Dr, San Antonio, TX 78227, USA
| | - Suvadip Mallick
- Host-Pathogen Interactions Program, Texas Biomedical Research Institute, 8715 W Military Dr, San Antonio, TX 78227, USA
| | - Yilun Cheng
- Nebraska Center for Virology and School of Biological Sciences, University of Nebraska-Lincoln, 1400 R St, Lincoln, NE 68588, USA
| | - Fei Wu
- Host-Pathogen Interactions Program, Texas Biomedical Research Institute, 8715 W Military Dr, San Antonio, TX 78227, USA
| | - Grey De La Torre
- Host-Pathogen Interactions Program, Texas Biomedical Research Institute, 8715 W Military Dr, San Antonio, TX 78227, USA
| | - Jason Dufour
- Tulane National Primate Research Center, 18703 Three Rivers Rd, Covington, LA 70433, USA
| | - Xavier Alvarez
- Host-Pathogen Interactions Program, Texas Biomedical Research Institute, 8715 W Military Dr, San Antonio, TX 78227, USA
| | - Vinay Shivanna
- Host-Pathogen Interactions Program, Texas Biomedical Research Institute, 8715 W Military Dr, San Antonio, TX 78227, USA
| | - Yaozhong Liu
- Tulane University School of Public Health and Tropical Medicine, 1440 Canal St, New Orleans, LA 70112, USA
| | - Christine M Fennessey
- AIDS and Cancer Virus Program, Frederick National Laboratory, 8560 Progress Drive, Frederick, MD 21701, USA
| | - Jeffrey D Lifson
- AIDS and Cancer Virus Program, Frederick National Laboratory, 8560 Progress Drive, Frederick, MD 21701, USA
| | - Qingsheng Li
- Nebraska Center for Virology and School of Biological Sciences, University of Nebraska-Lincoln, 1400 R St, Lincoln, NE 68588, USA
| | - Brandon F Keele
- AIDS and Cancer Virus Program, Frederick National Laboratory, 8560 Progress Drive, Frederick, MD 21701, USA
| | - Binhua Ling
- Host-Pathogen Interactions Program, Texas Biomedical Research Institute, 8715 W Military Dr, San Antonio, TX 78227, USA
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17
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Brandt L, Angelino P, Martinez R, Cristinelli S, Ciuffi A. Sex and Age Impact CD4+ T Cell Susceptibility to HIV In Vitro through Cell Activation Dynamics. Cells 2023; 12:2689. [PMID: 38067117 PMCID: PMC10706042 DOI: 10.3390/cells12232689] [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: 10/13/2023] [Revised: 11/19/2023] [Accepted: 11/20/2023] [Indexed: 12/18/2023] Open
Abstract
Cellular composition and the responsiveness of the immune system evolve upon aging and are influenced by biological sex. CD4+ T cells from women living with HIV exhibit a decreased viral replication ex vivo compared to men's. We, thus, hypothesized that these findings could be recapitulated in vitro and infected primary CD4+ T cells with HIV-based vectors pseudotyped with VSV-G or HIV envelopes. We used cells isolated from twenty donors to interrogate the effect of sex and age on permissiveness over a six-day activation kinetics. Our data identified an increased permissiveness to HIV between 24 and 72 h post-stimulation. Sex- and age-based analyses at these time points showed an increased susceptibility to HIV of the cells isolated from males and from donors over 50 years of age, respectively. A parallel assessment of surface markers' expression revealed higher frequencies of activation marker CD69 and of immune checkpoint inhibitors (PD-1 and CTLA-4) in the cells from highly permissive donors. Furthermore, positive correlations were identified between the expression kinetics of CD69, PD-1 and CTLA-4 and HIV expression kinetics. The cell population heterogeneity was assessed using a single-cell RNA-Seq analysis and no cell subtype enrichment was identified according to sex. Finally, transcriptomic analyses further highlighted the role of activation in those differences with enriched activation and cell cycle gene sets in male and older female cells. Altogether, this study brought further evidence about the individual features affecting HIV replication at the cellular level and should be considered in latency reactivation studies for an HIV cure.
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Affiliation(s)
- Ludivine Brandt
- Institute of Microbiology, Lausanne University Hospital and University of Lausanne, 1010 Lausanne, Switzerland; (L.B.)
| | - Paolo Angelino
- Institute of Microbiology, Lausanne University Hospital and University of Lausanne, 1010 Lausanne, Switzerland; (L.B.)
- Translational Data Science (TDS)-Facility, AGORA Cancer Research Center, Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland
| | - Raquel Martinez
- Institute of Microbiology, Lausanne University Hospital and University of Lausanne, 1010 Lausanne, Switzerland; (L.B.)
| | - Sara Cristinelli
- Institute of Microbiology, Lausanne University Hospital and University of Lausanne, 1010 Lausanne, Switzerland; (L.B.)
| | - Angela Ciuffi
- Institute of Microbiology, Lausanne University Hospital and University of Lausanne, 1010 Lausanne, Switzerland; (L.B.)
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18
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Więcek K, Chen HC. Understanding latent HIV-1 reservoirs through host genomics approaches. iScience 2023; 26:108342. [PMID: 38026212 PMCID: PMC10665824 DOI: 10.1016/j.isci.2023.108342] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2023] Open
Abstract
Genetically intact HIV-1 proviruses are a major concern with regard to curing infection because they cause viral rebound after the cessation of antiretroviral therapy. However, intact proviruses are not prevalent in HIV-1 reservoirs. As such, it is essential to precisely determine the position of these proviruses before putting forward a better antiretroviral cure. Recently, a revised HIV-1 deeply latent reservoir concept has been proposed, stating that the progress of the establishment of HIV-1 reservoirs is influenced by immune-mediated selection during the course of infection. This selection force leads to the persistence of genetically intact proviruses as those with the best fit to avoid clearance. This hypothesis refreshes our understanding of HIV-1 latent reservoirs. For this reason, we reviewed current studies relevant to this theme and provide our perspectives to reinforce the overall understanding of HIV-1 latency in the context of the host genome.
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Affiliation(s)
- Kamil Więcek
- Epigenetics of Infectious Diseases Research Group, Population Diagnostics Center, Lukasiewicz Research Network – PORT Polish Center for Technology Development, Stablowicka 147, 54-066 Wroclaw, Poland
| | - Heng-Chang Chen
- Epigenetics of Infectious Diseases Research Group, Population Diagnostics Center, Lukasiewicz Research Network – PORT Polish Center for Technology Development, Stablowicka 147, 54-066 Wroclaw, Poland
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19
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Kinloch NN, Shahid A, Dong W, Kirkby D, Jones BR, Beelen CJ, MacMillan D, Lee GQ, Mota TM, Sudderuddin H, Barad E, Harris M, Brumme CJ, Jones RB, Brockman MA, Joy JB, Brumme ZL. HIV reservoirs are dominated by genetically younger and clonally enriched proviruses. mBio 2023; 14:e0241723. [PMID: 37971267 PMCID: PMC10746175 DOI: 10.1128/mbio.02417-23] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2023] [Accepted: 10/09/2023] [Indexed: 11/19/2023] Open
Abstract
IMPORTANCE Characterizing the human immunodeficiency virus (HIV) reservoir that endures despite antiretroviral therapy (ART) is critical to cure efforts. We observed that the oldest proviruses persisting during ART were exclusively defective, while intact proviruses (and rebound HIV) dated to nearer ART initiation. This helps explain why studies that sampled sub-genomic proviruses on-ART (which are largely defective) routinely found sequences dating to early infection, whereas those that sampled replication-competent HIV found almost none. Together with our findings that intact proviruses were more likely to be clonal, and that on-ART low-level/isolated viremia originated from proviruses of varying ages (including possibly defective ones), our observations indicate that (i) on-ART and rebound viremia can have distinct within-host origins, (ii) intact proviruses have shorter lifespans than grossly defective ones and thus depend more heavily on clonal expansion for persistence, and (iii) an HIV reservoir predominantly "dating" to near ART initiation will be substantially adapted to within-host pressures, complicating immune-based cure strategies.
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Affiliation(s)
- Natalie N. Kinloch
- Faculty of Health Sciences, Simon Fraser University, Burnaby, British Columbia, Canada
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, British Columbia, Canada
| | - Aniqa Shahid
- Faculty of Health Sciences, Simon Fraser University, Burnaby, British Columbia, Canada
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, British Columbia, Canada
| | - Winnie Dong
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, British Columbia, Canada
| | - Don Kirkby
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, British Columbia, Canada
| | - Bradley R. Jones
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, British Columbia, Canada
- Bioinformatics Program, University of British Columbia, Vancouver, British Columbia, Canada
| | - Charlotte J. Beelen
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, British Columbia, Canada
| | - Daniel MacMillan
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, British Columbia, Canada
| | - Guinevere Q. Lee
- Infectious Diseases Division, Department of Medicine, Weill Cornell Medical College, New York, New York, USA
| | - Talia M. Mota
- Infectious Diseases Division, Department of Medicine, Weill Cornell Medical College, New York, New York, USA
| | - Hanwei Sudderuddin
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, British Columbia, Canada
- Experimental Medicine Program, University of British Columbia, Vancouver, British Columbia, Canada
| | - Evan Barad
- Faculty of Health Sciences, Simon Fraser University, Burnaby, British Columbia, Canada
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, British Columbia, Canada
| | - Marianne Harris
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, British Columbia, Canada
- Department of Family Practice, Faculty of Medicine, University of British Columbia, Vancouver, British Columbia, Canada
| | - Chanson J. Brumme
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, British Columbia, Canada
- Department of Medicine, University of British Columbia, Vancouver, British Columbia, Canada
| | - R. Brad Jones
- Infectious Diseases Division, Department of Medicine, Weill Cornell Medical College, New York, New York, USA
| | - Mark A. Brockman
- Faculty of Health Sciences, Simon Fraser University, Burnaby, British Columbia, Canada
- Department of Molecular Biology and Biochemistry, Faculty of Science, Simon Fraser University, Burnaby, British Columbia, Canada
| | - Jeffrey B. Joy
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, British Columbia, Canada
- Bioinformatics Program, University of British Columbia, Vancouver, British Columbia, Canada
- Department of Medicine, University of British Columbia, Vancouver, British Columbia, Canada
| | - Zabrina L. Brumme
- Faculty of Health Sciences, Simon Fraser University, Burnaby, British Columbia, Canada
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, British Columbia, Canada
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20
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Wei Y, Davenport TC, Collora JA, Ma HK, Pinto-Santini D, Lama J, Alfaro R, Duerr A, Ho YC. Single-cell epigenetic, transcriptional, and protein profiling of latent and active HIV-1 reservoir revealed that IKZF3 promotes HIV-1 persistence. Immunity 2023; 56:2584-2601.e7. [PMID: 37922905 PMCID: PMC10843106 DOI: 10.1016/j.immuni.2023.10.002] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2023] [Revised: 06/26/2023] [Accepted: 10/04/2023] [Indexed: 11/07/2023]
Abstract
Understanding how HIV-1-infected cells proliferate and persist is key to HIV-1 eradication, but the heterogeneity and rarity of HIV-1-infected cells hamper mechanistic interrogations. Here, we used single-cell DOGMA-seq to simultaneously capture transcription factor accessibility, transcriptome, surface proteins, HIV-1 DNA, and HIV-1 RNA in memory CD4+ T cells from six people living with HIV-1 during viremia and after suppressive antiretroviral therapy. We identified increased transcription factor accessibility in latent HIV-1-infected cells (RORC) and transcriptionally active HIV-1-infected cells (interferon regulatory transcription factor [IRF] and activator protein 1 [AP-1]). A proliferation program (IKZF3, IL21, BIRC5, and MKI67 co-expression) promoted the survival of transcriptionally active HIV-1-infected cells. Both latent and transcriptionally active HIV-1-infected cells had increased IKZF3 (Aiolos) expression. Distinct epigenetic programs drove the heterogeneous cellular states of HIV-1-infected cells: IRF:activation, Eomes:cytotoxic effector differentiation, AP-1:migration, and cell death. Our study revealed the single-cell epigenetic, transcriptional, and protein states of latent and transcriptionally active HIV-1-infected cells and cellular programs promoting HIV-1 persistence.
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Affiliation(s)
- Yulong Wei
- Department of Microbial Pathogenesis, Yale University School of Medicine, New Haven, CT 06519, USA
| | - Timothy C Davenport
- Department of Microbial Pathogenesis, Yale University School of Medicine, New Haven, CT 06519, USA
| | - Jack A Collora
- Department of Microbial Pathogenesis, Yale University School of Medicine, New Haven, CT 06519, USA
| | - Haocong Katherine Ma
- Department of Microbial Pathogenesis, Yale University School of Medicine, New Haven, CT 06519, USA
| | - Delia Pinto-Santini
- Vaccine and Infectious Disease, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Javier Lama
- Asociación Civil Impacta Salud y Educación, Lima 15063, Perú
| | - Ricardo Alfaro
- Centro de Investigaciones Tecnológicas Biomédicas y Medioambientales (CITBM), Lima 07006, Perú
| | - Ann Duerr
- Vaccine and Infectious Disease, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Ya-Chi Ho
- Department of Microbial Pathogenesis, Yale University School of Medicine, New Haven, CT 06519, USA.
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21
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Lambrechts L, Bonine N, Verstraeten R, Pardons M, Noppe Y, Rutsaert S, Van Nieuwerburgh F, Van Criekinge W, Cole B, Vandekerckhove L. HIV-PULSE: a long-read sequencing assay for high-throughput near full-length HIV-1 proviral genome characterization. Nucleic Acids Res 2023; 51:e102. [PMID: 37819007 PMCID: PMC10639044 DOI: 10.1093/nar/gkad790] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2023] [Revised: 07/25/2023] [Accepted: 09/19/2023] [Indexed: 10/13/2023] Open
Abstract
A deep understanding of the composition of the HIV-1 reservoir is necessary for the development of targeted therapies and the evaluation of curative efforts. However, current near full-length (NFL) HIV-1 proviral genome sequencing assays are based on labor-intensive and costly principles of repeated PCRs at limiting dilution, restricting their scalability. To address this, we developed a high-throughput, long-read sequencing assay called HIV-PULSE (HIV Proviral UMI-mediated Long-read Sequencing). This assay uses unique molecular identifiers (UMIs) to tag individual HIV-1 genomes, allowing for the omission of the limiting dilution step and enabling long-range PCR amplification of many NFL genomes in a single PCR reaction, while simultaneously overcoming poor single-read accuracy. We optimized the assay using HIV-infected cell lines and then applied it to blood samples from 18 individuals living with HIV on antiretroviral therapy, yielding a total of 1308 distinct HIV-1 genomes. Benchmarking against the widely applied Full-Length Individual Proviral Sequencing assay revealed similar sensitivity (11 vs 18%) and overall good concordance, although at a significantly higher throughput. In conclusion, HIV-PULSE is a cost-efficient and scalable assay that allows for the characterization of the HIV-1 proviral landscape, making it an attractive method to study the HIV-1 reservoir composition and dynamics.
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Affiliation(s)
- Laurens Lambrechts
- HIV Cure Research Center, Department of Internal Medicine and Pediatrics, Ghent University Hospital, Ghent University, 9000 Ghent, Belgium
- BioBix, Department of Data Analysis and Mathematical Modelling, Faculty of Bioscience Engineering, Ghent University, 9000 Ghent, Belgium
| | - Noah Bonine
- HIV Cure Research Center, Department of Internal Medicine and Pediatrics, Ghent University Hospital, Ghent University, 9000 Ghent, Belgium
- BioBix, Department of Data Analysis and Mathematical Modelling, Faculty of Bioscience Engineering, Ghent University, 9000 Ghent, Belgium
| | - Rita Verstraeten
- HIV Cure Research Center, Department of Internal Medicine and Pediatrics, Ghent University Hospital, Ghent University, 9000 Ghent, Belgium
- BioBix, Department of Data Analysis and Mathematical Modelling, Faculty of Bioscience Engineering, Ghent University, 9000 Ghent, Belgium
| | - Marion Pardons
- HIV Cure Research Center, Department of Internal Medicine and Pediatrics, Ghent University Hospital, Ghent University, 9000 Ghent, Belgium
| | - Ytse Noppe
- HIV Cure Research Center, Department of Internal Medicine and Pediatrics, Ghent University Hospital, Ghent University, 9000 Ghent, Belgium
| | - Sofie Rutsaert
- HIV Cure Research Center, Department of Internal Medicine and Pediatrics, Ghent University Hospital, Ghent University, 9000 Ghent, Belgium
| | - Filip Van Nieuwerburgh
- Laboratory of Pharmaceutical Biotechnology, Faculty of Pharmaceutical Sciences, Ghent University, 9000 Ghent, Belgium
| | - Wim Van Criekinge
- BioBix, Department of Data Analysis and Mathematical Modelling, Faculty of Bioscience Engineering, Ghent University, 9000 Ghent, Belgium
| | - Basiel Cole
- HIV Cure Research Center, Department of Internal Medicine and Pediatrics, Ghent University Hospital, Ghent University, 9000 Ghent, Belgium
| | - Linos Vandekerckhove
- HIV Cure Research Center, Department of Internal Medicine and Pediatrics, Ghent University Hospital, Ghent University, 9000 Ghent, Belgium
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22
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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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23
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Cobos Jiménez V, Geretz A, Tokarev A, Ehrenberg PK, Deletsu S, Machmach K, Mudvari P, Howard JN, Zelkoski A, Paquin-Proulx D, Del Prete GQ, Subra C, Boritz EA, Bosque A, Thomas R, Bolton DL. AP-1/c-Fos supports SIV and HIV-1 latency in CD4 T cells infected in vivo. iScience 2023; 26:108015. [PMID: 37860759 PMCID: PMC10582365 DOI: 10.1016/j.isci.2023.108015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2023] [Revised: 08/24/2023] [Accepted: 09/18/2023] [Indexed: 10/21/2023] Open
Abstract
Persistent HIV-1 reservoirs of infected CD4 T cells are a major barrier to HIV-1 cure, although the mechanisms by which they are established and maintained in vivo remain poorly characterized. To elucidate host cell gene expression patterns that govern virus gene expression, we analyzed viral RNA+ (vRNA) CD4 T cells of untreated simian immunodeficiency virus (SIV)-infected macaques by single-cell RNA sequencing. A subset of vRNA+ cells distinguished by spliced and high total vRNA (7-10% of reads) expressed diminished FOS, a component of the Activator protein 1 (AP-1) transcription factor, relative to vRNA-low and -negative cells. Conversely, FOS and JUN, another AP-1 component, were upregulated in HIV DNA+ infected cells compared to uninfected cells from people with HIV-1 on suppressive therapy. Inhibiting c-Fos in latently infected primary cells augmented reactivatable HIV-1 infection. These findings implicate AP-1 in latency establishment and maintenance and as a potential therapeutic target to limit HIV-1 reservoirs.
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Affiliation(s)
- Viviana Cobos Jiménez
- US Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD, USA
- The Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, USA
| | - Aviva Geretz
- US Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD, USA
- The Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, USA
| | - Andrey Tokarev
- US Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD, USA
- The Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, USA
| | - Philip K. Ehrenberg
- US Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD, USA
| | | | - Kawthar Machmach
- US Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD, USA
- The Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, USA
| | - Prakriti Mudvari
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | | | - Amanda Zelkoski
- US Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD, USA
- The Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, USA
| | - Dominic Paquin-Proulx
- US Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD, USA
- The Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, USA
| | - Gregory Q. Del Prete
- AIDS and Cancer Virus Program, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Caroline Subra
- US Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD, USA
- The Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, USA
| | - Eli A. Boritz
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | | | - Rasmi Thomas
- US Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD, USA
| | - Diane L. Bolton
- US Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD, USA
- The Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, USA
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24
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McLaurin KA, Li H, Khalili K, Mactutus CF, Booze RM. HIV-1 mRNA Knockdown with CRISPR/Cas9 Enhances Neurocognitive Function. RESEARCH SQUARE 2023:rs.3.rs-3266933. [PMID: 37886577 PMCID: PMC10602171 DOI: 10.21203/rs.3.rs-3266933/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/28/2023]
Abstract
Mixed glia are infiltrated with HIV-1 virus early in the course of infection leading to the development of a persistent viral reservoir in the central nervous system. Modification of the HIV-1 genome using gene editing techniques, including CRISPR/Cas9, has shown great promise towards eliminating HIV-1 viral reservoirs; whether these techniques are capable of removing HIV-1 viral proteins from mixed glia, however, has not been systematically evaluated. Herein, the efficacy of adeno-associated virus 9 (AAV9)-CRISPR/Cas9 gene editing for eliminating HIV-1 mRNA from cortical mixed glia was evaluated in vitro and in vivo. In vitro, a within-subjects experimental design was utilized to treat mixed glia isolated from neonatal HIV-1 transgenic (Tg) rats with varying doses (0, 0.9, 1.8, 2.7, 3.6, 4.5, or 5.4 μL) of CRISPR/Cas9 for 72 hours. Dose-dependent decreases in the number of HIV-1 mRNA, quantified using an innovative in situ hybridization technique, were observed in a subset (i.e., n=5 out of 8) of primary mixed glia. In vivo, HIV-1 Tg rats were retro-orbitally inoculated with CRISPR/Cas9 for two weeks, whereby treatment resulted in profound excision (i.e., approximately 53.2%) of HIV-1 mRNA from the mPFC. Given incomplete excision of the HIV-1 viral genome, the clinical relevance of HIV-1 mRNA knockdown for eliminating neurocognitive impairments was evaluated via examination of temporal processing, a putative neurobehavioral mechanism underlying HIV-1 associated neurocognitive disorders (HAND). Indeed, treatment with CRISPR/Cas9 partially restored the developmental trajectory of temporal processing. Proof-of-concept studies, therefore, support the susceptibility of mixed glia to gene editing and the potential of CRISPR/Cas9 to serve as a novel therapeutic strategy for HAND, even in the absence of full viral eradication.
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Takata H, Mitchell JL, Pacheco J, Pagliuzza A, Pinyakorn S, Buranapraditkun S, Sacdalan C, Leyre L, Nathanson S, Kakazu JC, Intasan J, Prueksakaew P, Chomchey N, Phanuphak N, de Souza M, Haddad EK, Rolland M, Tovanabutra S, Vasan S, Hsu DC, Chomont N, Trautmann L. An active HIV reservoir during ART is associated with maintenance of HIV-specific CD8 + T cell magnitude and short-lived differentiation status. Cell Host Microbe 2023; 31:1494-1506.e4. [PMID: 37708852 PMCID: PMC10564289 DOI: 10.1016/j.chom.2023.08.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Revised: 06/02/2023] [Accepted: 08/14/2023] [Indexed: 09/16/2023]
Abstract
Before initiation of antiretroviral therapy (ART), HIV-specific CD8+ T cells are dysfunctional and short lived. To better understand the relationship between the HIV reservoir in CD4+ T cells and the magnitude and differentiation status of HIV-specific CD8+ T cells, we investigated these cells from acute and chronic HIV-infected individuals after 2 years of ART. Although both the HIV reservoir and the CD8+ T cell responses declined significantly after 2 years of ART, sustained HIV-specific CD8+ T cell responses correlated with a greater reduction of integrated HIV provirus. However, the magnitude of CD8+ T cells specific for HIV Gag, Pol, Nef, and Vif proteins positively associated with the active reservoir size during ART, measured as cell-associated RNA. Importantly, high HIV DNA levels strongly associate with maintenance of short-lived HIV-specific CD8+ T cells, regardless of ART initiation time. Our data suggest that the active reservoir maintains HIV-specific CD8+ T cell magnitude but prevents their differentiation into functional cells.
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Affiliation(s)
- Hiroshi Takata
- Vaccine and Gene Therapy Institute, Oregon Health & Science University, Beaverton, OR 97006, USA; U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD 20910, USA; Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., Bethesda, MD 20817, USA
| | - Julie L Mitchell
- Vaccine and Gene Therapy Institute, Oregon Health & Science University, Beaverton, OR 97006, USA; U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD 20910, USA; Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., Bethesda, MD 20817, USA
| | - Julian Pacheco
- Vaccine and Gene Therapy Institute, Oregon Health & Science University, Beaverton, OR 97006, USA
| | - Amélie Pagliuzza
- Centre de Recherche du CHUM and Department of Microbiology, Infectiology and Immunology, Université de Montréal, Montréal, QC, Canada
| | - Suteeraporn Pinyakorn
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD 20910, USA; Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., Bethesda, MD 20817, USA
| | | | - Carlo Sacdalan
- SEARCH Research Foundation, Bangkok, Thailand; Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Louise Leyre
- Centre de Recherche du CHUM and Department of Microbiology, Infectiology and Immunology, Université de Montréal, Montréal, QC, Canada
| | - Sam Nathanson
- Vaccine and Gene Therapy Institute, Oregon Health & Science University, Beaverton, OR 97006, USA
| | - Juyeon C Kakazu
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD 20910, USA; Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., Bethesda, MD 20817, USA
| | | | | | | | | | | | - Elias K Haddad
- Department of Medicine, Division of Infectious Diseases and HIV Medicine, Drexel University, Philadelphia, PA 19102, USA
| | - Morgane Rolland
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD 20910, USA; Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., Bethesda, MD 20817, USA
| | - Sodsai Tovanabutra
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD 20910, USA; Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., Bethesda, MD 20817, USA
| | - Sandhya Vasan
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD 20910, USA; Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., Bethesda, MD 20817, USA
| | - Denise C Hsu
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD 20910, USA; Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., Bethesda, MD 20817, USA
| | - Nicolas Chomont
- Centre de Recherche du CHUM and Department of Microbiology, Infectiology and Immunology, Université de Montréal, Montréal, QC, Canada
| | - Lydie Trautmann
- Vaccine and Gene Therapy Institute, Oregon Health & Science University, Beaverton, OR 97006, USA; U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD 20910, USA; Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., Bethesda, MD 20817, USA.
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26
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Wong M, Wei Y, Ho YC. Single-cell multiomic understanding of HIV-1 reservoir at epigenetic, transcriptional, and protein levels. Curr Opin HIV AIDS 2023; 18:246-256. [PMID: 37535039 PMCID: PMC10442869 DOI: 10.1097/coh.0000000000000809] [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: 08/04/2023]
Abstract
PURPOSE OF REVIEW The success of HIV-1 eradication strategies relies on in-depth understanding of HIV-1-infected cells. However, HIV-1-infected cells are extremely heterogeneous and rare. Single-cell multiomic approaches resolve the heterogeneity and rarity of HIV-1-infected cells. RECENT FINDINGS Advancement in single-cell multiomic approaches enabled HIV-1 reservoir profiling across the epigenetic (ATAC-seq), transcriptional (RNA-seq), and protein levels (CITE-seq). Using HIV-1 RNA as a surrogate, ECCITE-seq identified enrichment of HIV-1-infected cells in clonally expanded cytotoxic CD4+ T cells. Using HIV-1 DNA PCR-activated microfluidic sorting, FIND-seq captured the bulk transcriptome of HIV-1 DNA+ cells. Using targeted HIV-1 DNA amplification, PheP-seq identified surface protein expression of intact versus defective HIV-1-infected cells. Using ATAC-seq to identify HIV-1 DNA, ASAP-seq captured transcription factor activity and surface protein expression of HIV-1 DNA+ cells. Combining HIV-1 mapping by ATAC-seq and HIV-1 RNA mapping by RNA-seq, DOGMA-seq captured the epigenetic, transcriptional, and surface protein expression of latent and transcriptionally active HIV-1-infected cells. To identify reproducible biological insights and authentic HIV-1-infected cells and avoid false-positive discovery of artifacts, we reviewed current practices of single-cell multiomic experimental design and bioinformatic analysis. SUMMARY Single-cell multiomic approaches may identify innovative mechanisms of HIV-1 persistence, nominate therapeutic strategies, and accelerate discoveries.
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Affiliation(s)
- Michelle Wong
- Department of Microbial Pathogenesis, Yale University School of Medicine, New Haven, Connecticut, USA
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27
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Shahid A, MacLennan S, Jones BR, Sudderuddin H, Dang Z, Cobamibias K, Duncan MC, Kinloch NN, Dapp MJ, Archin NM, Fischl MA, Ofotokun I, Adimora A, Gange S, Aouizerat B, Kuniholm MH, Kassaye S, Mullins JI, Goldstein H, Joy JB, Anastos K, Brumme ZL. The replication-competent HIV reservoir is a genetically restricted, younger subset of the overall pool of HIV proviruses persisting during therapy, which is highly genetically stable over time. RESEARCH SQUARE 2023:rs.3.rs-3259040. [PMID: 37645749 PMCID: PMC10462229 DOI: 10.21203/rs.3.rs-3259040/v1] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/31/2023]
Abstract
Within-host HIV populations continually diversify during untreated infection, and members of these diverse forms persist within infected cell reservoirs, even during antiretroviral therapy (ART). Characterizing the diverse viral sequences that persist during ART is critical to HIV cure efforts, but our knowledge of on-ART proviral evolutionary dynamics remains incomplete, as does our understanding of the differences between the overall pool of persisting proviral DNA (which is largely genetically defective) and the subset of intact HIV sequences capable of reactivating. Here, we reconstructed within-host HIV evolutionary histories in blood from seven participants of the Women's Interagency HIV Study (WIHS) who experienced HIV seroconversion. We measured diversity, lineage origins and ages of proviral sequences (env-gp120) sampled up to four times, up to 12 years on ART. We used the same techniques to study HIV sequences emerging from the reservoir in two participants. Proviral clonality generally increased over time on ART, with clones frequently persisting across multiple time points. The integration dates of proviruses persisting on ART generally spanned the duration of untreated infection (though were often skewed towards years immediately pre-ART), while in contrast, reservoir-origin viremia emerging in plasma was exclusively "younger" (i.e., dated to the years immediately pre-ART). The genetic and age distributions of distinct proviral sequences remained highly stable during ART in all but one participant in whom, after 12 years, there was evidence that "younger" proviruses had been preferentially eliminated. Analysis of within-host recombinant proviral sequences also suggested that HIV reservoirs can be superinfected with virus reactivated from an older era, yielding infectious viral progeny with mosaic genomes of sequences with different ages. Overall, results underscore the remarkable genetic stability of distinct proviral sequences that persist on ART, yet suggest that replication-competent HIV reservoir represents a genetically-restricted and overall "younger" subset of the overall persisting proviral pool in blood.
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Affiliation(s)
- Aniqa Shahid
- Faculty of Health Sciences, Simon Fraser University, Burnaby, BC, Canada
| | - Signe MacLennan
- Faculty of Health Sciences, Simon Fraser University, Burnaby, BC, Canada
| | - Bradley R Jones
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, BC, Canada
| | - Hanwei Sudderuddin
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, BC, Canada
| | - Zhong Dang
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, BC, Canada
| | - Kyle Cobamibias
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, BC, Canada
| | - Maggie C Duncan
- Faculty of Health Sciences, Simon Fraser University, Burnaby, BC, Canada
| | - Natalie N Kinloch
- Faculty of Health Sciences, Simon Fraser University, Burnaby, BC, Canada
| | - Michael J Dapp
- Department of Microbiology, University of Washington, School of Medicine, Seattle, WA, USA
| | - Nande M Archin
- UNC HIV Cure Center, Institute of Global Health and Infectious Diseases, University of North Carolina at Chapel Hill, NC, USA
| | - Margaret A Fischl
- Department of Medicine, University of Miami School of Medicine, Miami, FL, USA
| | - Igho Ofotokun
- Division of Infectious Diseases, Department of Medicine, Emory University School of Medicine, Atlanta, GA, USA
| | - Adaora Adimora
- Departments of Medicine and Epidemiology, University of North Carolina School of Medicine, UNC Gillings School of Global Public Health, Chapel Hill, NC, USA
| | - Stephen Gange
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | | | - Mark H Kuniholm
- Department of Epidemiology and Biostatistics, University at Albany, State University of New York, Rensselaer, New York, NY, USA
| | - Seble Kassaye
- Division of Infectious Diseases and Tropical Medicine, Georgetown University, Washington, DC, USA
| | - James I Mullins
- Department of Microbiology, University of Washington, School of Medicine, Seattle, WA, USA
| | - Harris Goldstein
- Departments of Microbiology and Immunology and Pediatrics, Albert Einstein College of Medicine, Bronx, New York, NY, USA
| | - Jeffrey B Joy
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, BC, Canada
| | - Kathryn Anastos
- Department of Medicine, Albert Einstein College of Medicine, New York, NY, USA
| | - Zabrina L Brumme
- Faculty of Health Sciences, Simon Fraser University, Burnaby, BC, Canada
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28
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Geretz A, Ehrenberg PK, Clifford RJ, Laliberté A, Prelli Bozzo C, Eiser D, Kundu G, Yum LK, Apps R, Creegan M, Gunady M, Shangguan S, Sanders-Buell E, Sacdalan C, Phanuphak N, Tovanabutra S, Russell RM, Bibollet-Ruche F, Robb ML, Michael NL, Ake JA, Vasan S, Hsu DC, Hahn BH, Kirchhoff F, Thomas R. Single-cell transcriptomics identifies prothymosin α restriction of HIV-1 in vivo. Sci Transl Med 2023; 15:eadg0873. [PMID: 37531416 DOI: 10.1126/scitranslmed.adg0873] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Accepted: 06/21/2023] [Indexed: 08/04/2023]
Abstract
Host restriction factors play key roles in innate antiviral defense, but it remains poorly understood which of them restricts HIV-1 in vivo. Here, we used single-cell transcriptomic analysis to identify host factors associated with HIV-1 control during acute infection by correlating host gene expression with viral RNA abundance within individual cells. Wide sequencing of cells from one participant with the highest plasma viral load revealed that intracellular viral RNA transcription correlates inversely with expression of the gene PTMA, which encodes prothymosin α. This association was genome-wide significant (Padjusted < 0.05) and was validated in 28 additional participants from Thailand and the Americas with HIV-1 CRF01_AE and subtype B infections, respectively. Overexpression of prothymosin α in vitro confirmed that this cellular factor inhibits HIV-1 transcription and infectious virus production. Our results identify prothymosin α as a host factor that restricts HIV-1 infection in vivo, which has implications for viral transmission and cure strategies.
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Affiliation(s)
- Aviva Geretz
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD 20910, USA
- Henry M. Jackson Foundation for the Advancement of Military Medicine Inc., Bethesda, MD 20817, USA
| | - Philip K Ehrenberg
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD 20910, USA
| | - Robert J Clifford
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD 20910, USA
- Henry M. Jackson Foundation for the Advancement of Military Medicine Inc., Bethesda, MD 20817, USA
| | - Alexandre Laliberté
- Institute of Molecular Virology, Ulm University Medical Center, Ulm 89081, Germany
| | | | - Daina Eiser
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD 20910, USA
- Henry M. Jackson Foundation for the Advancement of Military Medicine Inc., Bethesda, MD 20817, USA
| | - Gautam Kundu
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD 20910, USA
- Henry M. Jackson Foundation for the Advancement of Military Medicine Inc., Bethesda, MD 20817, USA
| | - Lauren K Yum
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD 20910, USA
- Henry M. Jackson Foundation for the Advancement of Military Medicine Inc., Bethesda, MD 20817, USA
| | - Richard Apps
- NIH Center for Human Immunology, National Institutes of Health, Bethesda, MD 20892, USA
| | - Matthew Creegan
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD 20910, USA
- Henry M. Jackson Foundation for the Advancement of Military Medicine Inc., Bethesda, MD 20817, USA
| | - Mohamed Gunady
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD 20910, USA
- Henry M. Jackson Foundation for the Advancement of Military Medicine Inc., Bethesda, MD 20817, USA
| | - Shida Shangguan
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD 20910, USA
- Henry M. Jackson Foundation for the Advancement of Military Medicine Inc., Bethesda, MD 20817, USA
| | - Eric Sanders-Buell
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD 20910, USA
- Henry M. Jackson Foundation for the Advancement of Military Medicine Inc., Bethesda, MD 20817, USA
| | - Carlo Sacdalan
- SEARCH, Thai Red Cross AIDS Research Centre, Bangkok 10330, Thailand
| | - Nittaya Phanuphak
- SEARCH, Thai Red Cross AIDS Research Centre, Bangkok 10330, Thailand
| | - Sodsai Tovanabutra
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD 20910, USA
- Henry M. Jackson Foundation for the Advancement of Military Medicine Inc., Bethesda, MD 20817, USA
| | - Ronnie M Russell
- Departments of Medicine and Microbiology, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Frederic Bibollet-Ruche
- Departments of Medicine and Microbiology, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Merlin L Robb
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD 20910, USA
- Henry M. Jackson Foundation for the Advancement of Military Medicine Inc., Bethesda, MD 20817, USA
| | - Nelson L Michael
- Walter Reed Army Institute of Research, Silver Spring, MD 20910, USA
| | - Julie A Ake
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD 20910, USA
| | - Sandhya Vasan
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD 20910, USA
- Henry M. Jackson Foundation for the Advancement of Military Medicine Inc., Bethesda, MD 20817, USA
| | - Denise C Hsu
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD 20910, USA
- Henry M. Jackson Foundation for the Advancement of Military Medicine Inc., Bethesda, MD 20817, USA
| | - Beatrice H Hahn
- Departments of Medicine and Microbiology, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Frank Kirchhoff
- Institute of Molecular Virology, Ulm University Medical Center, Ulm 89081, Germany
| | - Rasmi Thomas
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD 20910, USA
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29
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Moretti S, Schietroma I, Sberna G, Maggiorella MT, Sernicola L, Farcomeni S, Giovanetti M, Ciccozzi M, Borsetti A. HIV-1-Host Interaction in Gut-Associated Lymphoid Tissue (GALT): Effects on Local Environment and Comorbidities. Int J Mol Sci 2023; 24:12193. [PMID: 37569570 PMCID: PMC10418605 DOI: 10.3390/ijms241512193] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Revised: 07/20/2023] [Accepted: 07/28/2023] [Indexed: 08/13/2023] Open
Abstract
HIV-1 replication in the gastrointestinal (GI) tract causes severe CD4+ T-cell depletion and disruption of the protective epithelial barrier in the intestinal mucosa, causing microbial translocation, the main driver of inflammation and immune activation, even in people living with HIV (PLWH) taking antiretroviral drug therapy. The higher levels of HIV DNA in the gut compared to the blood highlight the importance of the gut as a viral reservoir. CD4+ T-cell subsets in the gut differ in phenotypic characteristics and differentiation status from the ones in other tissues or in peripheral blood, and little is still known about the mechanisms by which the persistence of HIV is maintained at this anatomical site. This review aims to describe the interaction with key subsets of CD4+ T cells in the intestinal mucosa targeted by HIV-1 and the role of gut microbiome and its metabolites in HIV-associated systemic inflammation and immune activation that are crucial in the pathogenesis of HIV infection and related comorbidities.
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Affiliation(s)
- Sonia Moretti
- National HIV/AIDS Research Center, Istituto Superiore di Sanità, 00162 Rome, Italy; (S.M.); (I.S.); (G.S.); (M.T.M.); (L.S.); (S.F.)
| | - Ivan Schietroma
- National HIV/AIDS Research Center, Istituto Superiore di Sanità, 00162 Rome, Italy; (S.M.); (I.S.); (G.S.); (M.T.M.); (L.S.); (S.F.)
| | - Giuseppe Sberna
- National HIV/AIDS Research Center, Istituto Superiore di Sanità, 00162 Rome, Italy; (S.M.); (I.S.); (G.S.); (M.T.M.); (L.S.); (S.F.)
| | - Maria Teresa Maggiorella
- National HIV/AIDS Research Center, Istituto Superiore di Sanità, 00162 Rome, Italy; (S.M.); (I.S.); (G.S.); (M.T.M.); (L.S.); (S.F.)
| | - Leonardo Sernicola
- National HIV/AIDS Research Center, Istituto Superiore di Sanità, 00162 Rome, Italy; (S.M.); (I.S.); (G.S.); (M.T.M.); (L.S.); (S.F.)
| | - Stefania Farcomeni
- National HIV/AIDS Research Center, Istituto Superiore di Sanità, 00162 Rome, Italy; (S.M.); (I.S.); (G.S.); (M.T.M.); (L.S.); (S.F.)
| | - Marta Giovanetti
- Instituto Rene Rachou, Fundação Oswaldo Cruz, Belo Horizonte 30190-009, Minas Gerais, Brazil;
- Sciences and Technologies for Sustainable Development and One Health, University Campus Bio-Medico of Rome, 00128 Rome, Italy
| | - Massimo Ciccozzi
- Unit of Medical Statistics and Molecular Epidemiology, University Campus Bio-Medico of Rome, 00128 Rome, Italy;
| | - Alessandra Borsetti
- National HIV/AIDS Research Center, Istituto Superiore di Sanità, 00162 Rome, Italy; (S.M.); (I.S.); (G.S.); (M.T.M.); (L.S.); (S.F.)
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30
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Faua C, Fafi-Kremer S, Gantner P. Antigen specificities of HIV-infected cells: A role in infection and persistence? J Virus Erad 2023; 9:100329. [PMID: 37440870 PMCID: PMC10334354 DOI: 10.1016/j.jve.2023.100329] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2022] [Revised: 05/12/2023] [Accepted: 05/31/2023] [Indexed: 07/15/2023] Open
Abstract
Antigen-experienced memory CD4+ T cells are the major target of HIV infection and support both productive and latent infections, thus playing a key role in HIV dissemination and persistence, respectively. Here, we reviewed studies that have shown direct association between HIV infection and antigen specificity. During untreated infection, some HIV-specific cells host productive infection, while other pathogen-specific cells such as cytomegalovirus (CMV) and Mycobacterium tuberculosis also contribute to viral persistence on antiretroviral therapy (ART). These patterns could be explained by phenotypic features differing between these pathogen-specific cells. Mechanisms involved in these preferential infection and selection processes include HIV entry and restriction, cell exhaustion, survival, self-renewal and immune escape. For instance, MIP-1β expressing cells such as CMV-specific memory cells were shown to resist infection by HIV CCR5 coreceptor downregulation/inhibition. Conversely, HIV-infected CMV-specific cells undergo clonal expansion during ART. We have identified several research areas that need further focus such as the role of other pathogens, viral genome intactness, inducibility and phenotypic features. However, given the sheer diversity of both the CD4+ T cell repertoire and antigenic history of each individual, studying HIV-infected, antigen-experienced cells still imposes numerous challenges.
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Affiliation(s)
- Clayton Faua
- INSERM UMR_S1109, University of Strasbourg, Strasbourg, France
| | - Samira Fafi-Kremer
- INSERM UMR_S1109, University of Strasbourg, Strasbourg, France
- Medical Virology Laboratory, University Hospital of Strasbourg, Strasbourg, France
| | - Pierre Gantner
- INSERM UMR_S1109, University of Strasbourg, Strasbourg, France
- Medical Virology Laboratory, University Hospital of Strasbourg, Strasbourg, France
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31
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Kinloch NN, Shahid A, Dong W, Kirkby D, Jones BR, Beelen CJ, MacMillan D, Lee GQ, Mota TM, Sudderuddin H, Barad E, Harris M, Brumme CJ, Jones RB, Brockman MA, Joy JB, Brumme ZL. HIV reservoirs are dominated by genetically younger and clonally enriched proviruses. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.04.12.536611. [PMID: 37090500 PMCID: PMC10120704 DOI: 10.1101/2023.04.12.536611] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/25/2023]
Abstract
In order to cure HIV, we need to better understand the within-host evolutionary origins of the small reservoir of genome-intact proviruses that persists within infected cells during antiretroviral therapy (ART). Most prior studies on reservoir evolutionary dynamics however did not discriminate genome-intact proviruses from the vast background of defective ones. We reconstructed within-host pre-ART HIV evolutionary histories in six individuals and leveraged this information to infer the ages of intact and defective proviruses sampled after an average >9 years on ART, along with the ages of rebound and low-level/isolated viremia occurring during this time. We observed that the longest-lived proviruses persisting on ART were exclusively defective, usually due to large deletions. In contrast, intact proviruses and rebound HIV exclusively dated to the years immediately preceding ART. These observations are consistent with genome-intact proviruses having shorter lifespans, likely due to the cumulative risk of elimination following viral reactivation and protein production. Consistent with this, intact proviruses (and those with packaging signal defects) were three times more likely to be genetically identical compared to other proviral types, highlighting clonal expansion as particularly important in ensuring their survival. By contrast, low-level/isolated viremia sequences were genetically heterogeneous and sometimes ancestral, where viremia may have originated from defective proviruses. Results reveal that the HIV reservoir is dominated by clonally-enriched and genetically younger sequences that date to the untreated infection period when viral populations had been under within-host selection pressures for the longest duration. Knowledge of these qualities may help focus strategies for reservoir elimination.
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Affiliation(s)
- Natalie N. Kinloch
- Faculty of Health Sciences, Simon Fraser University, Burnaby, BC
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, BC
| | - Aniqa Shahid
- Faculty of Health Sciences, Simon Fraser University, Burnaby, BC
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, BC
| | - Winnie Dong
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, BC
| | - Don Kirkby
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, BC
| | - Bradley R. Jones
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, BC
- Bioinformatics Program, University of British Columbia, Vancouver, BC
| | | | - Daniel MacMillan
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, BC
| | - Guinevere Q. Lee
- Infectious Diseases Division, Department of Medicine, Weill Cornell Medical College, New York, NY, USA
| | - Talia M. Mota
- Infectious Diseases Division, Department of Medicine, Weill Cornell Medical College, New York, NY, USA
| | - Hanwei Sudderuddin
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, BC
- Experimental Medicine Program, University of British Columbia, Vancouver, BC
| | - Evan Barad
- Faculty of Health Sciences, Simon Fraser University, Burnaby, BC
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, BC
| | - Marianne Harris
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, BC
- Department of Family Practice, Faculty of Medicine, University of British Columbia, Vancouver, BC
| | - Chanson J. Brumme
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, BC
- Department of Medicine, University of British Columbia, Vancouver, BC
| | - R. Brad Jones
- Infectious Diseases Division, Department of Medicine, Weill Cornell Medical College, New York, NY, USA
| | - Mark A. Brockman
- Faculty of Health Sciences, Simon Fraser University, Burnaby, BC
- Department of Molecular Biology and Biochemistry, Faculty of Science, Simon Fraser University, Burnaby BC
| | - Jeffrey B. Joy
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, BC
- Bioinformatics Program, University of British Columbia, Vancouver, BC
- Department of Medicine, University of British Columbia, Vancouver, BC
| | - Zabrina L. Brumme
- Faculty of Health Sciences, Simon Fraser University, Burnaby, BC
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, BC
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32
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Moran JA, Marsden MD. HIV establishes an early foothold. Cell Host Microbe 2023; 31:571-573. [PMID: 37054675 DOI: 10.1016/j.chom.2023.03.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/15/2023]
Abstract
The weeks following HIV acquisition are a critical time when the virus causes significant immunological damage and establishes long-term latent reservoirs. A recent study in Immunity by Gantner et al. uses single-cell analysis to explore these key early infection events, providing insights into early HIV pathogenesis and reservoir formation.
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Affiliation(s)
- Jose A Moran
- Department of Microbiology & Molecular Genetics, School of Medicine, University of California Irvine, Irvine, CA, USA
| | - Matthew D Marsden
- Department of Microbiology & Molecular Genetics, School of Medicine, University of California Irvine, Irvine, CA, USA; Department of Medicine (Division of Infectious Diseases), School of Medicine, University of California Irvine, Irvine, CA, USA.
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