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Hossain T, Lungu C, de Schrijver S, Kuali M, Crespo R, Reddy N, Ngubane A, Kan TW, Reddy K, Rao S, Palstra RJ, Madlala P, Ndung'u T, Mahmoudi T. Specific quantification of inducible HIV-1 reservoir by RT-LAMP. COMMUNICATIONS MEDICINE 2024; 4:123. [PMID: 38918506 PMCID: PMC11199587 DOI: 10.1038/s43856-024-00553-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2023] [Accepted: 06/18/2024] [Indexed: 06/27/2024] Open
Abstract
BACKGROUND Strategies toward HIV-1 cure aim to clear, inactivate, reduce, or immunologically control the virus from a pool of latently infected cells such that combination antiretroviral therapy (cART) can be safely interrupted. In order to assess the impact of any putative curative interventions on the size and inducibility of the latent HIV-1 reservoir, robust and scalable assays are needed to precisely quantify the frequency of infected cells containing inducible HIV-1. METHODS We developed Specific Quantification of Inducible HIV-1 by RT-LAMP (SQuHIVLa), leveraging the high sensitivity and specificity of RT-LAMP, performed in a single reaction, to detect and quantify cells expressing tat/rev HIV-1 multiply spliced RNA (msRNA) upon activation. The LAMP primer/probe used in SQuHIVLa was designed to exclusively detect HIV-1 tat/rev msRNA and adapted for different HIV-1 subtypes. RESULTS Using SQuHIVLa, we successfully quantify the inducible viral reservoir in CD4+ T cells from people living with HIV-1 subtypes B and C on cART. The assay demonstrates high sensitivity, specificity, and reproducibility. CONCLUSIONS SQuHIVLa offers a high throughput, scalable, and specific HIV-1 reservoir quantification tool that is amenable to resource-limited settings. This assay poses remarkable potential in facilitating the evaluation of potential interventional strategies toward achieving HIV-1 cure.
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Affiliation(s)
- Tanvir Hossain
- Department of Biochemistry, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Cynthia Lungu
- Department of Biochemistry, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Sten de Schrijver
- Department of Biochemistry, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Mamokoena Kuali
- HIV Pathogenesis Programme, The Doris Duke Medical Research Institute, University of KwaZulu-Natal, Durban, South Africa
| | - Raquel Crespo
- Department of Biochemistry, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Nicole Reddy
- Africa Health Research Institute, Durban, South Africa
| | - Ayanda Ngubane
- HIV Pathogenesis Programme, The Doris Duke Medical Research Institute, University of KwaZulu-Natal, Durban, South Africa
| | - Tsung Wai Kan
- Department of Urology, Erasmus University Medical Center, Rotterdam, The Netherlands
- Department of Pathology, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Kavidha Reddy
- Africa Health Research Institute, Durban, South Africa
| | - Shringar Rao
- Department of Biochemistry, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Robert-Jan Palstra
- Department of Urology, Erasmus University Medical Center, Rotterdam, The Netherlands
- Department of Pathology, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Paradise Madlala
- HIV Pathogenesis Programme, The Doris Duke Medical Research Institute, University of KwaZulu-Natal, Durban, South Africa
| | - Thumbi Ndung'u
- HIV Pathogenesis Programme, The Doris Duke Medical Research Institute, University of KwaZulu-Natal, Durban, South Africa
- Africa Health Research Institute, Durban, South Africa
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology and Harvard University, Boston, MA, USA
- Division of Infection and Immunity, University College London, London, UK
| | - Tokameh Mahmoudi
- Department of Biochemistry, Erasmus University Medical Center, Rotterdam, The Netherlands.
- Department of Urology, Erasmus University Medical Center, Rotterdam, The Netherlands.
- Department of Pathology, Erasmus University Medical Center, Rotterdam, The Netherlands.
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2
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Ramirez PW, Pantoja C, Beliakova-Bethell N. An Evaluation on the Role of Non-Coding RNA in HIV Transcription and Latency: A Review. HIV AIDS (Auckl) 2023; 15:115-134. [PMID: 36942082 PMCID: PMC10024501 DOI: 10.2147/hiv.s383347] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Accepted: 02/24/2023] [Indexed: 03/16/2023] Open
Abstract
The existence of latent cellular reservoirs is recognized as the major barrier to an HIV cure. Reactivating and eliminating "shock and kill" or permanently silencing "block and lock" the latent HIV reservoir, as well as gene editing, remain promising approaches, but so far have proven to be only partially successful. Moreover, using latency reversing agents or "block and lock" drugs pose additional considerations, including the ability to cause cellular toxicity, a potential lack of specificity for HIV, or low potency when each agent is used alone. RNA molecules, such as microRNAs (miRNAs) and long non-coding RNAs (lncRNAs) are becoming increasingly recognized as important regulators of gene expression. RNA-based approaches for combatting HIV latency represent a promising strategy since both miRNAs and lncRNAs are more cell-type and tissue specific than protein coding genes. Thus, a higher specificity of targeting the latent HIV reservoir with less overall cellular toxicity can likely be achieved. In this review, we summarize current knowledge about HIV gene expression regulation by miRNAs and lncRNAs encoded in the human genome, as well as regulatory molecules encoded in the HIV genome. We discuss both the transcriptional and post-transcriptional regulation of HIV gene expression to align with the current definition of latency, and describe RNA molecules that either promote HIV latency or have anti-latency properties. Finally, we provide perspectives on using each class of RNAs as potential targets for combatting HIV latency, and describe the complexity of the interactions between different RNA molecules, their protein targets, and HIV.
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Affiliation(s)
- Peter W Ramirez
- Department of Biological Sciences, California State University, Long Beach, CA, USA
| | - Christina Pantoja
- Department of Biological Sciences, California State University, Long Beach, CA, USA
| | - Nadejda Beliakova-Bethell
- VA San Diego Healthcare System and Veterans Medical Research Foundation, San Diego, CA, USA
- Department of Medicine, University of California, San Diego, CA, USA
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3
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New Assay Reveals Vast Excess of Defective over Intact HIV-1 Transcripts in Antiretroviral Therapy-Suppressed Individuals. J Virol 2022; 96:e0160522. [PMID: 36448806 PMCID: PMC9769383 DOI: 10.1128/jvi.01605-22] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/05/2022] Open
Abstract
Most of the HIV DNA in infected individuals is noninfectious because of deleterious mutations. However, it is unclear how much of the transcribed HIV RNA is potentially infectious or defective. To address this question, we developed and validated a novel intact viral RNA assay (IVRA) that uses droplet digital reverse transcriptase PCR (dd-RT-PCR) for the commonly mutated packaging signal (Psi) and Rev response element (RRE) regions (from the intact proviral DNA assay [IPDA]) to quantify likely intact (Psi+ RRE+), 3' defective (Psi+ RRE-), and 5' defective (Psi- RRE+) HIV RNA. We then applied the IPDA and IVRA to quantify intact and defective HIV DNA and RNA from peripheral CD4+ T cells from 9 antiretroviral therapy (ART)-suppressed individuals. Levels of 3' defective HIV DNA were not significantly different from those of 5' defective HIV DNA, and both were higher than intact HIV DNA. In contrast, 3' defective HIV RNA (median 86 copies/106 cells; 94% of HIV RNA) was much more abundant than 5' defective (2.1 copies/106 cells; 5.6%) or intact (0.6 copies/106 cells; <1%) HIV RNA. Likewise, the frequency of CD4+ T cells with 3' defective HIV RNA was greater than the frequency with 5' defective or intact HIV RNA. Intact HIV RNA was transcribed by a median of 0.018% of all proviruses and 2.2% of intact proviruses. The vast excess of 3' defective RNA over 5' defective or intact HIV RNA, which was not observed for HIV DNA, suggests that HIV transcription is completely blocked prior to the RRE in most cells with intact proviruses and/or that cells transcribing intact HIV RNA are cleared at very high rates. IMPORTANCE We developed a new assay that can distinguish and quantify intact (potentially infectious) as well as defective HIV RNA. In ART-treated individuals, we found that the vast majority of all HIV RNA is defective at the 3' end, possibly due to incomplete transcriptional processivity. Only a very small percentage of all HIV RNA is intact, and very few total or intact proviruses transcribe intact HIV RNA. Though rare, this intact HIV RNA is tremendously important because it is necessary to serve as the genome of infectious virions that allow transmission and spread, including rebound after stopping ART. Moreover, intact viral RNA may contribute disproportionately to the immune activation, inflammation, and organ damage observed with untreated and treated HIV infection. The intact viral RNA assay can be applied to many future studies aimed at better understanding HIV pathogenesis and barriers to HIV cure.
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4
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Dahal S, Clayton K, Been T, Fernet-Brochu R, Ocando AV, Balachandran A, Poirier M, Maldonado RK, Shkreta L, Boligan KF, Guvenc F, Rahman F, Branch D, Bell B, Chabot B, Gray-Owen SD, Parent LJ, Cochrane A. Opposing roles of CLK SR kinases in controlling HIV-1 gene expression and latency. Retrovirology 2022; 19:18. [PMID: 35986377 PMCID: PMC9389714 DOI: 10.1186/s12977-022-00605-4] [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: 03/17/2022] [Accepted: 07/29/2022] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND The generation of over 69 spliced HIV-1 mRNAs from one primary transcript by alternative RNA splicing emphasizes the central role that RNA processing plays in HIV-1 replication. Control is mediated in part through the action of host SR proteins whose activity is regulated by multiple SR kinases (CLK1-4, SRPKs). METHODS Both shRNA depletion and small molecule inhibitors of host SR kinases were used in T cell lines and primary cells to evaluate the role of these factors in the regulation of HIV-1 gene expression. Effects on virus expression were assessed using western blotting, RT-qPCR, and immunofluorescence. RESULTS The studies demonstrate that SR kinases play distinct roles; depletion of CLK1 enhanced HIV-1 gene expression, reduction of CLK2 or SRPK1 suppressed it, whereas CLK3 depletion had a modest impact. The opposing effects of CLK1 vs. CLK2 depletion were due to action at distinct steps; reduction of CLK1 increased HIV-1 promoter activity while depletion of CLK2 affected steps after transcript initiation. Reduced CLK1 expression also enhanced the response to several latency reversing agents, in part, by increasing the frequency of responding cells, consistent with a role in regulating provirus latency. To determine whether small molecule modulation of SR kinase function could be used to control HIV-1 replication, we screened a GSK library of protein kinase inhibitors (PKIS) and identified several pyrazolo[1,5-b] pyridazine derivatives that suppress HIV-1 gene expression/replication with an EC50 ~ 50 nM. The compounds suppressed HIV-1 protein and viral RNA accumulation with minimal impact on cell viability, inhibiting CLK1 and CLK2 but not CLK3 function, thereby selectively altering the abundance of individual CLK and SR proteins in cells. CONCLUSIONS These findings demonstrate the unique roles played by individual SR kinases in regulating HIV-1 gene expression, validating the targeting of these functions to either enhance latency reversal, essential for "Kick-and-Kill" strategies, or to silence HIV protein expression for "Block-and-Lock" strategies.
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Affiliation(s)
- Subha Dahal
- grid.17063.330000 0001 2157 2938Dept. of Molecular Genetics, University of Toronto, 1 King’s College Circle, Toronto, ON M5S1A8 Canada
| | - Kiera Clayton
- grid.168645.80000 0001 0742 0364Department of Pathology, University of Massachusetts Medical School, Worcester, MA 01605 USA
| | - Terek Been
- grid.17063.330000 0001 2157 2938Dept. of Molecular Genetics, University of Toronto, 1 King’s College Circle, Toronto, ON M5S1A8 Canada
| | - Raphaële Fernet-Brochu
- grid.17063.330000 0001 2157 2938Dept. of Molecular Genetics, University of Toronto, 1 King’s College Circle, Toronto, ON M5S1A8 Canada
| | - Alonso Villasmil Ocando
- grid.461656.60000 0004 0489 3491Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139 USA
| | - Ahalya Balachandran
- grid.17063.330000 0001 2157 2938Dept. of Molecular Genetics, University of Toronto, 1 King’s College Circle, Toronto, ON M5S1A8 Canada
| | - Mikaël Poirier
- grid.86715.3d0000 0000 9064 6198Dept. of Microbiology & Infectious Diseases, Université de Sherbrooke, Sherbrooke, QC Canada
| | - Rebecca Kaddis Maldonado
- grid.240473.60000 0004 0543 9901Department of Medicine, Penn State College of Medicine, Hershey, PA 17033 USA ,grid.240473.60000 0004 0543 9901Microbiology & Immunology, Penn State College of Medicine, Hershey, PA 17033 USA
| | - Lulzim Shkreta
- grid.86715.3d0000 0000 9064 6198Dept. of Microbiology & Infectious Diseases, Université de Sherbrooke, Sherbrooke, QC Canada
| | - Kayluz Frias Boligan
- grid.423370.10000 0001 0285 1288Center for Innovation, Canadian Blood Services, Toronto, ON Canada
| | - Furkan Guvenc
- grid.17063.330000 0001 2157 2938Dept. of Molecular Genetics, University of Toronto, 1 King’s College Circle, Toronto, ON M5S1A8 Canada
| | - Fariha Rahman
- grid.17063.330000 0001 2157 2938Dept. of Molecular Genetics, University of Toronto, 1 King’s College Circle, Toronto, ON M5S1A8 Canada
| | - Donald Branch
- grid.423370.10000 0001 0285 1288Center for Innovation, Canadian Blood Services, Toronto, ON Canada
| | - Brendan Bell
- grid.86715.3d0000 0000 9064 6198Dept. of Microbiology & Infectious Diseases, Université de Sherbrooke, Sherbrooke, QC Canada
| | - Benoit Chabot
- grid.86715.3d0000 0000 9064 6198Dept. of Microbiology & Infectious Diseases, Université de Sherbrooke, Sherbrooke, QC Canada
| | - Scott D. Gray-Owen
- grid.17063.330000 0001 2157 2938Dept. of Molecular Genetics, University of Toronto, 1 King’s College Circle, Toronto, ON M5S1A8 Canada
| | - Leslie J. Parent
- grid.240473.60000 0004 0543 9901Department of Medicine, Penn State College of Medicine, Hershey, PA 17033 USA ,grid.240473.60000 0004 0543 9901Microbiology & Immunology, Penn State College of Medicine, Hershey, PA 17033 USA
| | - Alan Cochrane
- grid.17063.330000 0001 2157 2938Dept. of Molecular Genetics, University of Toronto, 1 King’s College Circle, Toronto, ON M5S1A8 Canada
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5
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Lu MD, Telwatte S, Kumar N, Ferreira F, Martin HA, Kadiyala GN, Wedrychowski A, Moron-Lopez S, Chen TH, Goecker EA, Coombs RW, Lu CM, Wong JK, Tsibris A, Yukl SA. Novel assays to investigate the mechanisms of latent infection with HIV-2. PLoS One 2022; 17:e0267402. [PMID: 35476802 PMCID: PMC9045618 DOI: 10.1371/journal.pone.0267402] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2021] [Accepted: 03/14/2022] [Indexed: 11/18/2022] Open
Abstract
Although there have been great advancements in the field of HIV treatment and prevention, there is no cure. There are two types of HIV: HIV-1 and HIV-2. In addition to genetic differences between the two types of HIV, HIV-2 infection causes a slower disease progression, and the rate of new HIV-2 infections has dramatically decreased since 2003. Like HIV-1, HIV-2 is capable of establishing latent infection in CD4+ T cells, thereby allowing the virus to evade viral cytopathic effects and detection by the immune system. The mechanisms underlying HIV latency are not fully understood, rendering this a significant barrier to development of a cure. Using RT-ddPCR, we previously demonstrated that latent infection with HIV-1 may be due to blocks to HIV transcriptional elongation, distal transcription/polyadenylation, and multiple splicing. In this study, we describe the development of seven highly-specific RT-ddPCR assays for HIV-2 that can be applied to the study of HIV-2 infections and latency. We designed and validated seven assays targeting different HIV-2 RNA regions along the genome that can be used to measure the degree of progression through different blocks to HIV-2 transcription and splicing. Given that HIV-2 is vastly understudied relative to HIV-1 and that it can be considered a model of a less virulent infection, application of these assays to studies of HIV-2 latency may inform new therapies for HIV-2, HIV-1, and other retroviruses.
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Affiliation(s)
- Michael D. Lu
- Department of Medicine, University of California, San Francisco (UCSF), San Francisco, CA, United States of America
| | - Sushama Telwatte
- Department of Medicine, University of California, San Francisco (UCSF), San Francisco, CA, United States of America
- Department of Medicine, San Francisco VA Health Care System, San Francisco, CA, United States of America
| | - Nitasha Kumar
- Department of Medicine, University of California, San Francisco (UCSF), San Francisco, CA, United States of America
- Department of Medicine, San Francisco VA Health Care System, San Francisco, CA, United States of America
| | - Fernanda Ferreira
- Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, United States of America
| | - Holly Anne Martin
- Department of Medicine, University of California, San Francisco (UCSF), San Francisco, CA, United States of America
- Department of Medicine, San Francisco VA Health Care System, San Francisco, CA, United States of America
| | - Gayatri Nikhila Kadiyala
- Department of Medicine, University of California, San Francisco (UCSF), San Francisco, CA, United States of America
- Department of Medicine, San Francisco VA Health Care System, San Francisco, CA, United States of America
| | - Adam Wedrychowski
- Department of Medicine, University of California, San Francisco (UCSF), San Francisco, CA, United States of America
- Department of Medicine, San Francisco VA Health Care System, San Francisco, CA, United States of America
| | - Sara Moron-Lopez
- Department of Medicine, University of California, San Francisco (UCSF), San Francisco, CA, United States of America
- Department of Medicine, San Francisco VA Health Care System, San Francisco, CA, United States of America
| | - Tsui-Hua Chen
- Department of Medicine, San Francisco VA Health Care System, San Francisco, CA, United States of America
| | - Erin A. Goecker
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, United States of America
| | - Robert W. Coombs
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, United States of America
| | - Chuanyi M. Lu
- Department of Medicine, University of California, San Francisco (UCSF), San Francisco, CA, United States of America
- Department of Medicine, San Francisco VA Health Care System, San Francisco, CA, United States of America
| | - Joseph K. Wong
- Department of Medicine, University of California, San Francisco (UCSF), San Francisco, CA, United States of America
- Department of Medicine, San Francisco VA Health Care System, San Francisco, CA, United States of America
| | - Athe Tsibris
- Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, United States of America
| | - Steven A. Yukl
- Department of Medicine, University of California, San Francisco (UCSF), San Francisco, CA, United States of America
- Department of Medicine, San Francisco VA Health Care System, San Francisco, CA, United States of America
- * E-mail:
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6
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Bacchus-Souffan C, Fitch M, Symons J, Abdel-Mohsen M, Reeves DB, Hoh R, Stone M, Hiatt J, Kim P, Chopra A, Ahn H, York VA, Cameron DL, Hecht FM, Martin JN, Yukl SA, Mallal S, Cameron PU, Deeks SG, Schiffer JT, Lewin SR, Hellerstein MK, McCune JM, Hunt PW. Relationship between CD4 T cell turnover, cellular differentiation and HIV persistence during ART. PLoS Pathog 2021; 17:e1009214. [PMID: 33465157 PMCID: PMC7846027 DOI: 10.1371/journal.ppat.1009214] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Revised: 01/29/2021] [Accepted: 12/04/2020] [Indexed: 12/17/2022] Open
Abstract
The precise role of CD4 T cell turnover in maintaining HIV persistence during antiretroviral therapy (ART) has not yet been well characterized. In resting CD4 T cell subpopulations from 24 HIV-infected ART-suppressed and 6 HIV-uninfected individuals, we directly measured cellular turnover by heavy water labeling, HIV reservoir size by integrated HIV-DNA (intDNA) and cell-associated HIV-RNA (caRNA), and HIV reservoir clonality by proviral integration site sequencing. Compared to HIV-negatives, ART-suppressed individuals had similar fractional replacement rates in all subpopulations, but lower absolute proliferation rates of all subpopulations other than effector memory (TEM) cells, and lower plasma IL-7 levels (p = 0.0004). Median CD4 T cell half-lives decreased with cell differentiation from naïve to TEM cells (3 years to 3 months, p<0.001). TEM had the fastest replacement rates, were most highly enriched for intDNA and caRNA, and contained the most clonal proviral expansion. Clonal proviruses detected in less mature subpopulations were more expanded in TEM, suggesting that they were maintained through cell differentiation. Earlier ART initiation was associated with lower levels of intDNA, caRNA and fractional replacement rates. In conclusion, circulating integrated HIV proviruses appear to be maintained both by slow turnover of immature CD4 subpopulations, and by clonal expansion as well as cell differentiation into effector cells with faster replacement rates.
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Affiliation(s)
- Charline Bacchus-Souffan
- Division of Experimental Medicine, Department of Medicine, University of California, San Francisco, California, United States of America
| | - Mark Fitch
- Department of Nutritional Sciences and Toxicology, University of California, Berkeley, California, United States of America
| | - Jori Symons
- The Peter Doherty Institute for Infection and Immunity, University of Melbourne and Royal Melbourne Hospital, Melbourne, Australia
| | | | - Daniel B. Reeves
- Vaccine and Infectious Diseases Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
| | - Rebecca Hoh
- Division of HIV, Infectious Diseases and Global Medicine, Department of Medicine, Zuckerberg San Francisco General Hospital, University of California, San Francisco, California, United States of America
| | - Mars Stone
- Vitalant Research Institute and Department of Laboratory Medicine at the University of California, San Francisco, California, United States of America
| | - Joseph Hiatt
- Medical Scientist Training Program & Biomedical Sciences Graduate Program, University of California, San Francisco, California, United States of America
| | - Peggy Kim
- Infectious Diseases Section, Medical Service, San Francisco Veterans Affairs Medical Center, California, United States of America
| | - Abha Chopra
- Institute for Immunology and Infectious Diseases, Murdoch University, Perth, Australia
- Center for Translational Immunology and Infectious Diseases, Vanderbilt University Medical Center, Nashville, Tennessee, United States of America
| | - Haelee Ahn
- Division of Experimental Medicine, Department of Medicine, University of California, San Francisco, California, United States of America
| | - Vanessa A. York
- Division of Experimental Medicine, Department of Medicine, University of California, San Francisco, California, United States of America
| | - Daniel L. Cameron
- Division of Bioinformatics, Walter & Eliza Hall Institute of Medical Research, Parkville, Australia
| | - Frederick M. Hecht
- Division of HIV, Infectious Diseases and Global Medicine, Department of Medicine, Zuckerberg San Francisco General Hospital, University of California, San Francisco, California, United States of America
| | - Jeffrey N. Martin
- Division of HIV, Infectious Diseases and Global Medicine, Department of Medicine, Zuckerberg San Francisco General Hospital, University of California, San Francisco, California, United States of America
| | - Steven A. Yukl
- Division of HIV, Infectious Diseases and Global Medicine, Department of Medicine, Zuckerberg San Francisco General Hospital, University of California, San Francisco, California, United States of America
- Infectious Diseases Section, Medical Service, San Francisco Veterans Affairs Medical Center, California, United States of America
| | - Simon Mallal
- Institute for Immunology and Infectious Diseases, Murdoch University, Perth, Australia
- Center for Translational Immunology and Infectious Diseases, Vanderbilt University Medical Center, Nashville, Tennessee, United States of America
| | - Paul U. Cameron
- The Peter Doherty Institute for Infection and Immunity, University of Melbourne and Royal Melbourne Hospital, Melbourne, Australia
| | - Steven G. Deeks
- Division of HIV, Infectious Diseases and Global Medicine, Department of Medicine, Zuckerberg San Francisco General Hospital, University of California, San Francisco, California, United States of America
| | - Joshua T. Schiffer
- Vaccine and Infectious Diseases Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
| | - Sharon R. Lewin
- The Peter Doherty Institute for Infection and Immunity, University of Melbourne and Royal Melbourne Hospital, Melbourne, Australia
| | - Marc K. Hellerstein
- Department of Nutritional Sciences and Toxicology, University of California, Berkeley, California, United States of America
| | - Joseph M. McCune
- Global Health Innovative Technology Solutions/HIV Frontiers, Bill & Melinda Gates Foundation, Seattle, Washington, United States of America
| | - Peter W. Hunt
- Division of Experimental Medicine, Department of Medicine, University of California, San Francisco, California, United States of America
- * E-mail:
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7
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TELWATTE S, KIM P, CHEN TH, MILUSH JM, SOMSOUK M, DEEKS SG, HUNT PW, WONG JK, YUKL SA. Mechanistic differences underlying HIV latency in the gut and blood contribute to differential responses to latency-reversing agents. AIDS 2020; 34:2013-2024. [PMID: 32910065 PMCID: PMC7990078 DOI: 10.1097/qad.0000000000002684] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
OBJECTIVE While latently HIV-infected cells have been described in the blood, it is unclear whether a similar inducible reservoir exists in the gut, where most HIV-infected cells reside. Tissue-specific environments may contribute to differences in the mechanisms that govern latent HIV infection and amenability to reactivation. We sought to determine whether HIV-infected cells from the blood and gut differ in their responses to T-cell activation and mechanistically distinct latency reversing agents (LRAs). DESIGN Cross sectional study using samples from HIV-infected individuals (n = 11). METHODS Matched peripheral blood mononuclear cells (PBMC) and dissociated total cells from rectum ± ileum were treated ex vivo for 24 h with anti-CD3/CD28 or LRAs in the presence of antiretrovirals. HIV DNA and 'read-through', initiated, 5' elongated, completed, and multiply-spliced HIV transcripts were quantified using droplet digital PCR. RESULTS T-cell activation increased levels of all HIV transcripts in PBMC and gut cells, and was the only treatment that increased multiply-spliced HIV RNA. Disulfiram increased initiated HIV transcripts in PBMC but not gut cells, while ingenol mebutate increased HIV transcription more in gut cells. Romidepsin increased HIV transcription in PBMC and gut cells, but the increase in transcription initiation was greater in PBMC. CONCLUSION The gut harbors HIV-infected cells in a latent-like state that can be reversed by T-cell activation involving CD3/CD28 signaling. Histone deacetylation and protein kinase B may contribute less to HIV transcriptional initiation in the gut, whereas protein kinase C may contribute more. New LRAs or combinations are needed to induce multiply-spliced HIV and should be tested on both blood and gut.
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Affiliation(s)
- Sushama TELWATTE
- Department of Medicine, University of California San Francisco (UCSF), San Francisco, CA, 94110, USA
- Department of Medicine, San Francisco VA Medical Center, San Francisco, CA, 94121, USA
| | - Peggy KIM
- Department of Medicine, San Francisco VA Medical Center, San Francisco, CA, 94121, USA
| | - Tsui-Hua CHEN
- Department of Medicine, University of California San Francisco (UCSF), San Francisco, CA, 94110, USA
| | - Jeffrey M. MILUSH
- Department of Medicine, University of California San Francisco (UCSF), San Francisco, CA, 94110, USA
| | - Ma SOMSOUK
- Department of Medicine, University of California San Francisco (UCSF), San Francisco, CA, 94110, USA
| | - Steven G. DEEKS
- Department of Medicine, University of California San Francisco (UCSF), San Francisco, CA, 94110, USA
| | - Peter W. HUNT
- Department of Medicine, University of California San Francisco (UCSF), San Francisco, CA, 94110, USA
| | - Joseph K. WONG
- Department of Medicine, University of California San Francisco (UCSF), San Francisco, CA, 94110, USA
- Department of Medicine, San Francisco VA Medical Center, San Francisco, CA, 94121, USA
| | - Steven A. YUKL
- Department of Medicine, University of California San Francisco (UCSF), San Francisco, CA, 94110, USA
- Department of Medicine, San Francisco VA Medical Center, San Francisco, CA, 94121, USA
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8
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Neidleman J, Luo X, Frouard J, Xie G, Hsiao F, Ma T, Morcilla V, Lee A, Telwatte S, Thomas R, Tamaki W, Wheeler B, Hoh R, Somsouk M, Vohra P, Milush J, James KS, Archin NM, Hunt PW, Deeks SG, Yukl SA, Palmer S, Greene WC, Roan NR. Phenotypic analysis of the unstimulated in vivo HIV CD4 T cell reservoir. eLife 2020; 9:e60933. [PMID: 32990219 PMCID: PMC7524554 DOI: 10.7554/elife.60933] [Citation(s) in RCA: 54] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2020] [Accepted: 08/28/2020] [Indexed: 02/07/2023] Open
Abstract
The latent reservoir is a major barrier to HIV cure. As latently infected cells cannot be phenotyped directly, the features of the in vivo reservoir have remained elusive. Here, we describe a method that leverages high-dimensional phenotyping using CyTOF to trace latently infected cells reactivated ex vivo to their original pre-activation states. Our results suggest that, contrary to common assumptions, the reservoir is not randomly distributed among cell subsets, and is remarkably conserved between individuals. However, reservoir composition differs between tissues and blood, as do cells successfully reactivated by different latency reversing agents. By selecting 8-10 of our 39 original CyTOF markers, we were able to isolate highly purified populations of unstimulated in vivo latent cells. These purified populations were highly enriched for replication-competent and intact provirus, transcribed HIV, and displayed clonal expansion. The ability to isolate unstimulated latent cells from infected individuals enables previously impossible studies on HIV persistence.
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Affiliation(s)
- Jason Neidleman
- Gladstone Institutes, San Francisco, United States
- Department of Urology, University of California, San Francisco, San Francisco, United States
| | - Xiaoyu Luo
- Gladstone Institutes, San Francisco, United States
| | - Julie Frouard
- Gladstone Institutes, San Francisco, United States
- Department of Urology, University of California, San Francisco, San Francisco, United States
| | - Guorui Xie
- Gladstone Institutes, San Francisco, United States
- Department of Urology, University of California, San Francisco, San Francisco, United States
| | - Feng Hsiao
- Gladstone Institutes, San Francisco, United States
- Department of Urology, University of California, San Francisco, San Francisco, United States
| | - Tongcui Ma
- Gladstone Institutes, San Francisco, United States
- Department of Urology, University of California, San Francisco, San Francisco, United States
| | - Vincent Morcilla
- Centre for Virus Research, the Westmead Institute for Medical Research, The University of Sydney, Sydney, Australia
| | - Ashley Lee
- Centre for Virus Research, the Westmead Institute for Medical Research, The University of Sydney, Sydney, Australia
| | - Sushama Telwatte
- San Francisco Veterans Affairs (VA) Medical Center and University of California, San Francisco, San Francisco, United States
| | | | - Whitney Tamaki
- Department of Medicine, University of California, San Francisco, San Francisco, United States
| | - Benjamin Wheeler
- Department of Medicine, University of California, San Francisco, San Francisco, United States
| | - Rebecca Hoh
- Division of HIV, Infectious Diseases and Global Medicine, University of California, San Francisco, San Francisco, United States
| | - Ma Somsouk
- Department of Medicine, Division of Gastroenterology, San Francisco General Hospital and University of California, San Francisco, San Francisco, United States
| | - Poonam Vohra
- Department of Pathology, University of California, San Francisco, San Francisco, United States
| | - Jeffrey Milush
- Department of Medicine, University of California, San Francisco, San Francisco, United States
| | - Katherine Sholtis James
- Division of Infectious Diseases, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, United States
| | - Nancie M Archin
- Division of Infectious Diseases, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, United States
| | - Peter W Hunt
- Division of Experimental Medicine, University of California, San Francisco, San Francisco, United States
| | - Steven G Deeks
- Division of HIV, Infectious Diseases and Global Medicine, University of California, San Francisco, San Francisco, United States
| | - Steven A Yukl
- San Francisco Veterans Affairs (VA) Medical Center and University of California, San Francisco, San Francisco, United States
| | - Sarah Palmer
- Centre for Virus Research, the Westmead Institute for Medical Research, The University of Sydney, Sydney, Australia
| | - Warner C Greene
- Gladstone Institutes, San Francisco, United States
- Department of Medicine, University of California, San Francisco, San Francisco, United States
| | - Nadia R Roan
- Gladstone Institutes, San Francisco, United States
- Department of Urology, University of California, San Francisco, San Francisco, United States
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9
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Ward AR, Mota TM, Jones RB. Immunological approaches to HIV cure. Semin Immunol 2020; 51:101412. [PMID: 32981836 DOI: 10.1016/j.smim.2020.101412] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/23/2020] [Accepted: 09/10/2020] [Indexed: 02/07/2023]
Abstract
Combination antiretroviral therapy (ART) to treat human immunodeficiency virus (HIV) infection has proven remarkably successful - for those who can access and afford it - yet HIV infection persists indefinitely in a reservoir of cells, despite effective ART and despite host antiviral immune responses. An HIV cure is therefore the next aspirational goal and challenge, though approaches differ in their objectives - with 'functional cures' aiming for durable viral control in the absence of ART, and 'sterilizing cures' aiming for the more difficult to realize objective of complete viral eradication. Mechanisms of HIV persistence, including viral latency, anatomical sequestration, suboptimal immune functioning, reservoir replenishment, target cell-intrinsic immune resistance, and, potentially, target cell distraction of immune effectors, likely need to be overcome in order to achieve a cure. A small fraction of people living with HIV (PLWH) naturally control infection via immune-mediated mechanisms, however, providing both sound rationale and optimism that an immunological approach to cure is possible. Herein we review up to date knowledge and emerging evidence on: the mechanisms contributing to HIV persistence, as well as potential strategies to overcome these barriers; promising immunological approaches to achieve viral control and elimination of reservoir-harboring cells, including harnessing adaptive immune responses to HIV and engineered therapies, as well as enhancers of their functions and of complementary innate immune functioning; and combination strategies that are most likely to succeed. Ultimately, a cure must be safe, effective, durable, and, eventually, scalable in order to be widely acceptable and available.
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Affiliation(s)
- Adam R Ward
- Division of Infectious Diseases, Weill Cornell Medicine, New York, NY, USA; Department of Microbiology, Immunology, and Tropical Medicine, The George Washington University, Washington, DC, USA; PhD Program in Epidemiology, The George Washington University, Washington, DC, USA
| | - Talia M Mota
- Division of Infectious Diseases, Weill Cornell Medicine, New York, NY, USA
| | - R Brad Jones
- Division of Infectious Diseases, Weill Cornell Medicine, New York, NY, USA; Department of Microbiology, Immunology, and Tropical Medicine, The George Washington University, Washington, DC, USA.
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10
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Chromatin maturation of the HIV-1 provirus in primary resting CD4+ T cells. PLoS Pathog 2020; 16:e1008264. [PMID: 31999790 PMCID: PMC6991963 DOI: 10.1371/journal.ppat.1008264] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2019] [Accepted: 12/09/2019] [Indexed: 12/14/2022] Open
Abstract
Human immunodeficiency virus type 1 (HIV-1) infection is a chronic condition, where viral DNA integrates into the genome. Latently infected cells form a persistent, heterogeneous reservoir that at any time can reactivate the integrated HIV-1. Here we confirmed that latently infected cells from HIV-1 positive study participants exhibited active HIV-1 transcription but without production of mature spliced mRNAs. To elucidate the mechanisms behind this we employed primary HIV-1 latency models to study latency establishment and maintenance. We characterized proviral transcription and chromatin development in cultures of resting primary CD4+ T-cells for four months after ex vivo HIV-1 infection. As heterochromatin (marked with H3K9me3 or H3K27me3) gradually stabilized, the provirus became less accessible with reduced activation potential. In a subset of infected cells, active marks (e.g. H3K27ac) and elongating RNAPII remained detectable at the latent provirus, despite prolonged proviral silencing. In many aspects, latent HIV-1 resembled an active enhancer in a subset of resting cells. The enhancer chromatin actively promoted latency and the enhancer-specific CBP/P300-inhibitor GNE049 was identified as a new latency reversal agent. The division of the latent reservoir according to distinct chromatin compositions with different reactivation potential enforces the notion that even though a relatively large set of cells contains the HIV-1 provirus, only a discrete subset is readily able to reactivate the provirus and spread the infection. HIV infection is a devastating disease affecting 35 million people worldwide. Current anti-retroviral treatment is highly effective and has made the HIV infection chronic. However, despite more effective treatments, the prospects of a cure are distant. The problem for an HIV cure is that, even though the virus particles are eradicated, the infected cells maintain the information of remake the virus. This information is integrated in the host cell as a provirus. The provirus switches between active and inactive states. Thereby, the infected cells evade both the immune system and death associated with massive viral production. We have characterized the composition of proviral chromatin and how it connects with transcription and viral production. In resting primary CD4+ T-cells, we follow the fate of the provirus starting at infection until latency is firmly established. Only in a fraction of intact proviruses were we able to reverse latency and that this was highly regulated by the chromatin composition. Whereas the proviruses encompassed in heterochromatin were refractory to activation, latent proviruses with “enhancer” characteristics were readily activated. Our study provides key insights as to detect the remaining HIV-1 infected cells capable of reseeding the infection, and the mechanisms whereby they are maintained.
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11
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Ait-Ammar A, Kula A, Darcis G, Verdikt R, De Wit S, Gautier V, Mallon PWG, Marcello A, Rohr O, Van Lint C. Current Status of Latency Reversing Agents Facing the Heterogeneity of HIV-1 Cellular and Tissue Reservoirs. Front Microbiol 2020; 10:3060. [PMID: 32038533 PMCID: PMC6993040 DOI: 10.3389/fmicb.2019.03060] [Citation(s) in RCA: 96] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2019] [Accepted: 12/18/2019] [Indexed: 12/15/2022] Open
Abstract
One of the most explored therapeutic approaches aimed at eradicating HIV-1 reservoirs is the "shock and kill" strategy which is based on HIV-1 reactivation in latently-infected cells ("shock" phase) while maintaining antiretroviral therapy (ART) in order to prevent spreading of the infection by the neosynthesized virus. This kind of strategy allows for the "kill" phase, during which latently-infected cells die from viral cytopathic effects or from host cytolytic effector mechanisms following viral reactivation. Several latency reversing agents (LRAs) with distinct mechanistic classes have been characterized to reactivate HIV-1 viral gene expression. Some LRAs have been tested in terms of their potential to purge latent HIV-1 in vivo in clinical trials, showing that reversing HIV-1 latency is possible. However, LRAs alone have failed to reduce the size of the viral reservoirs. Together with the inability of the immune system to clear the LRA-activated reservoirs and the lack of specificity of these LRAs, the heterogeneity of the reservoirs largely contributes to the limited success of clinical trials using LRAs. Indeed, HIV-1 latency is established in numerous cell types that are characterized by distinct phenotypes and metabolic properties, and these are influenced by patient history. Hence, the silencing mechanisms of HIV-1 gene expression in these cellular and tissue reservoirs need to be better understood to rationally improve this cure strategy and hopefully reach clinical success.
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Affiliation(s)
- Amina Ait-Ammar
- Service of Molecular Virology, Department of Molecular Virology (DBM), Université Libre de Bruxelles (ULB), Gosselies, Belgium
| | - Anna Kula
- Malopolska Centre of Biotechnology, Laboratory of Virology, Jagiellonian University, Krakow, Poland
| | - Gilles Darcis
- Infectious Diseases Department, Liège University Hospital, Liège, Belgium
| | - Roxane Verdikt
- Service of Molecular Virology, Department of Molecular Virology (DBM), Université Libre de Bruxelles (ULB), Gosselies, Belgium
| | - Stephane De Wit
- Service des Maladies Infectieuses, CHU Saint-Pierre, Université Libre de Bruxelles, Bruxelles, Belgium
| | - Virginie Gautier
- UCD Centre for Experimental Pathogen Host Research (CEPHR), School of Medicine, University College Dublin, Dublin, Ireland
| | - Patrick W G Mallon
- UCD Centre for Experimental Pathogen Host Research (CEPHR), School of Medicine, University College Dublin, Dublin, Ireland
| | - Alessandro Marcello
- Laboratory of Molecular Virology, International Centre for Genetic Engineering and Biotechnology (ICGEB), Trieste, Italy
| | - Olivier Rohr
- Université de Strasbourg, EA7292, FMTS, IUT Louis Pasteur, Schiltigheim, France
| | - Carine Van Lint
- Service of Molecular Virology, Department of Molecular Virology (DBM), Université Libre de Bruxelles (ULB), Gosselies, Belgium
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12
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Stunnenberg M, Sprokholt JK, van Hamme JL, Kaptein TM, Zijlstra-Willems EM, Gringhuis SI, Geijtenbeek TBH. Synthetic Abortive HIV-1 RNAs Induce Potent Antiviral Immunity. Front Immunol 2020; 11:8. [PMID: 32038656 PMCID: PMC6990453 DOI: 10.3389/fimmu.2020.00008] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2019] [Accepted: 01/06/2020] [Indexed: 12/12/2022] Open
Abstract
Strong innate and adaptive immune responses are paramount in combating viral infections. Dendritic cells (DCs) detect viral infections via cytosolic RIG-I like receptors (RLRs) RIG-I and MDA5 leading to MAVS-induced immunity. The DEAD-box RNA helicase DDX3 senses abortive human immunodeficiency virus 1 (HIV-1) transcripts and induces MAVS-dependent type I interferon (IFN) responses, suggesting that abortive HIV-1 RNA transcripts induce antiviral immunity. Little is known about the induction of antiviral immunity by DDX3-ligand abortive HIV-1 RNA. Here we synthesized a 58 nucleotide-long capped RNA (HIV-1 Cap-RNA58) that mimics abortive HIV-1 RNA transcripts. HIV-1 Cap-RNA58 induced potent type I IFN responses in monocyte-derived DCs, monocytes, macrophages and primary CD1c+ DCs. Compared with RLR agonist poly-I:C, HIV-1 Cap-RNA58 induced comparable levels of type I IFN responses, identifying HIV-1 Cap-RNA58 as a potent trigger of antiviral immunity. In monocyte-derived DCs, HIV-1 Cap-RNA58 activated the transcription factors IRF3 and NF-κB. Moreover, HIV-1 Cap-RNA58 induced DC maturation and the expression of pro-inflammatory cytokines. HIV-1 Cap-RNA58-stimulated DCs induced proliferation of CD4+ and CD8+ T cells and differentiated naïve T helper (TH) cells toward a TH2 phenotype. Importantly, treatment of DCs with HIV-1 Cap-RNA58 resulted in an efficient antiviral innate immune response that reduced ongoing HIV-1 replication in DCs. Our data strongly suggest that HIV-1 Cap-RNA58 induces potent innate and adaptive immune responses, making it an interesting addition in vaccine design strategies.
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Affiliation(s)
- Melissa Stunnenberg
- Department of Experimental Immunology, Amsterdam Infection and Immunity Institute, Amsterdam UMC, University of Amsterdam, Amsterdam, Netherlands
| | - Joris K Sprokholt
- Department of Experimental Immunology, Amsterdam Infection and Immunity Institute, Amsterdam UMC, University of Amsterdam, Amsterdam, Netherlands
| | - John L van Hamme
- Department of Experimental Immunology, Amsterdam Infection and Immunity Institute, Amsterdam UMC, University of Amsterdam, Amsterdam, Netherlands
| | - Tanja M Kaptein
- Department of Experimental Immunology, Amsterdam Infection and Immunity Institute, Amsterdam UMC, University of Amsterdam, Amsterdam, Netherlands
| | - Esther M Zijlstra-Willems
- Department of Experimental Immunology, Amsterdam Infection and Immunity Institute, Amsterdam UMC, University of Amsterdam, Amsterdam, Netherlands
| | - Sonja I Gringhuis
- Department of Experimental Immunology, Amsterdam Infection and Immunity Institute, Amsterdam UMC, University of Amsterdam, Amsterdam, Netherlands
| | - Teunis B H Geijtenbeek
- Department of Experimental Immunology, Amsterdam Infection and Immunity Institute, Amsterdam UMC, University of Amsterdam, Amsterdam, Netherlands
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13
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Telwatte S, Morón-López S, Aran D, Kim P, Hsieh C, Joshi S, Montano M, Greene WC, Butte AJ, Wong JK, Yukl SA. Heterogeneity in HIV and cellular transcription profiles in cell line models of latent and productive infection: implications for HIV latency. Retrovirology 2019; 16:32. [PMID: 31711503 PMCID: PMC6849327 DOI: 10.1186/s12977-019-0494-x] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2019] [Accepted: 11/04/2019] [Indexed: 12/14/2022] Open
Abstract
Background HIV-infected cell lines are widely used to study latent HIV infection, which is considered the main barrier to HIV cure. We hypothesized that these cell lines differ from each other and from cells from HIV-infected individuals in the mechanisms underlying latency. Results To quantify the degree to which HIV expression is inhibited by blocks at different stages of HIV transcription, we employed a recently-described panel of RT-ddPCR assays to measure levels of 7 HIV transcripts (“read-through,” initiated, 5′ elongated, mid-transcribed/unspliced [Pol], distal-transcribed [Nef], polyadenylated, and multiply-sliced [Tat-Rev]) in bulk populations of latently-infected (U1, ACH-2, J-Lat) and productively-infected (8E5, activated J-Lat) cell lines. To assess single-cell variation and investigate cellular genes associated with HIV transcriptional blocks, we developed a novel multiplex qPCR panel and quantified single cell levels of 7 HIV targets and 89 cellular transcripts in latently- and productively-infected cell lines. The bulk cell HIV transcription profile differed dramatically between cell lines and cells from ART-suppressed individuals. Compared to cells from ART-suppressed individuals, latent cell lines showed lower levels of HIV transcriptional initiation and higher levels of polyadenylation and splicing. ACH-2 and J-Lat cells showed different forms of transcriptional interference, while U1 cells showed a block to elongation. Single-cell studies revealed marked variation between/within cell lines in expression of HIV transcripts, T cell phenotypic markers, antiviral factors, and genes implicated in latency. Expression of multiply-spliced HIV Tat-Rev was associated with expression of cellular genes involved in activation, tissue retention, T cell transcription, and apoptosis/survival. Conclusions HIV-infected cell lines differ from each other and from cells from ART-treated individuals in the mechanisms governing latent HIV infection. These differences in viral and cellular gene expression must be considered when gauging the suitability of a given cell line for future research on HIV. At the same time, some features were shared across cell lines, such as low expression of antiviral defense genes and a relationship between productive infection and genes involved in survival. These features may contribute to HIV latency or persistence in vivo, and deserve further study using novel single cell assays such as those described in this manuscript.
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Affiliation(s)
- Sushama Telwatte
- San Francisco VA Medical Center, San Francisco, CA, USA.,University of California San Francisco, San Francisco, CA, USA
| | - Sara Morón-López
- San Francisco VA Medical Center, San Francisco, CA, USA.,University of California San Francisco, San Francisco, CA, USA
| | - Dvir Aran
- Bakar Computational Health Sciences Institute, University of California, San Francisco, San Francisco, CA, USA
| | - Peggy Kim
- San Francisco VA Medical Center, San Francisco, CA, USA
| | - Christine Hsieh
- San Francisco VA Medical Center, San Francisco, CA, USA.,University of California San Francisco, San Francisco, CA, USA
| | - Sunil Joshi
- San Francisco VA Medical Center, San Francisco, CA, USA.,University of California San Francisco, San Francisco, CA, USA
| | - Mauricio Montano
- University of California San Francisco, San Francisco, CA, USA.,Gladstone Institute of Virology and Immunology, San Francisco, CA, USA
| | - Warner C Greene
- University of California San Francisco, San Francisco, CA, USA.,Gladstone Institute of Virology and Immunology, San Francisco, CA, USA
| | - Atul J Butte
- Bakar Computational Health Sciences Institute, University of California, San Francisco, San Francisco, CA, USA
| | - Joseph K Wong
- San Francisco VA Medical Center, San Francisco, CA, USA.,University of California San Francisco, San Francisco, CA, USA
| | - Steven A Yukl
- San Francisco VA Medical Center, San Francisco, CA, USA. .,University of California San Francisco, San Francisco, CA, USA.
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14
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Yukl SA, Kaiser P, Kim P, Telwatte S, Joshi SK, Vu M, Lampiris H, Wong JK. HIV latency in isolated patient CD4 + T cells may be due to blocks in HIV transcriptional elongation, completion, and splicing. Sci Transl Med 2019; 10:10/430/eaap9927. [PMID: 29491188 DOI: 10.1126/scitranslmed.aap9927] [Citation(s) in RCA: 212] [Impact Index Per Article: 42.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2017] [Accepted: 11/10/2017] [Indexed: 12/16/2022]
Abstract
Latently infected CD4+ T cells are the main barrier to complete clearance of HIV infection, but it is unclear what mechanisms govern latent HIV infection in vivo. To address this question, we developed a new panel of reverse transcription droplet digital polymerase chain reaction (RT-ddPCR) assays specific for different HIV transcripts that define distinct blocks to transcription. We applied this panel of assays to CD4+ T cells freshly isolated from HIV-infected patients on suppressive antiretroviral therapy (ART) to quantify the degree to which different mechanisms inhibit HIV transcription. In addition, we measured the degree to which these transcriptional blocks could be reversed ex vivo by T cell activation (using anti-CD3/CD28 antibodies) or latency-reversing agents. We found that the main reversible block to HIV RNA transcription was not inhibition of transcriptional initiation but rather a series of blocks to proximal elongation, distal transcription/polyadenylation (completion), and multiple splicing. Cell dilution experiments suggested that these mechanisms operated in most of the HIV-infected CD4+ T cells examined. Latency-reversing agents exerted differential effects on the three blocks to HIV transcription, suggesting that these blocks may be governed by different mechanisms.
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Affiliation(s)
- Steven A Yukl
- San Francisco Veterans Affairs Medical Center and University of California, San Francisco, 4150 Clement Street, 111W, San Francisco, CA 94121, USA.
| | - Philipp Kaiser
- San Francisco Veterans Affairs Medical Center and University of California, San Francisco, 4150 Clement Street, 111W, San Francisco, CA 94121, USA
| | - Peggy Kim
- San Francisco Veterans Affairs Medical Center and University of California, San Francisco, 4150 Clement Street, 111W, San Francisco, CA 94121, USA
| | - Sushama Telwatte
- San Francisco Veterans Affairs Medical Center and University of California, San Francisco, 4150 Clement Street, 111W, San Francisco, CA 94121, USA
| | - Sunil K Joshi
- San Francisco Veterans Affairs Medical Center and University of California, San Francisco, 4150 Clement Street, 111W, San Francisco, CA 94121, USA
| | - Mai Vu
- San Francisco Veterans Affairs Medical Center and University of California, San Francisco, 4150 Clement Street, 111W, San Francisco, CA 94121, USA
| | - Harry Lampiris
- San Francisco Veterans Affairs Medical Center and University of California, San Francisco, 4150 Clement Street, 111W, San Francisco, CA 94121, USA
| | - Joseph K Wong
- San Francisco Veterans Affairs Medical Center and University of California, San Francisco, 4150 Clement Street, 111W, San Francisco, CA 94121, USA
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15
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Das AT, Pasternak AO, Berkhout B. On the generation of the MSD-Ѱ class of defective HIV proviruses. Retrovirology 2019; 16:19. [PMID: 31296234 PMCID: PMC6625037 DOI: 10.1186/s12977-019-0481-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2019] [Accepted: 07/05/2019] [Indexed: 11/10/2022] Open
Abstract
Antiretroviral therapy (ART) can effectively suppress ongoing HIV replication and block disease progression, but the infection is never cured due to the persistence of a small pool of latently infected cells hosting integrated replication-competent HIV proviruses. However, the vast majority of HIV proviruses in ART-treated patients are replication-incompetent due to a variety of genetic defects. Most defective proviruses (around 90%) contain large internal deletions or are G-to-A hypermutated, resulting in destruction of most if not all viral open reading frames, which is consistent with the idea that cytotoxic T cells (CTLs) effectively remove cells that produce viral antigens. An intriguing subclass of defective proviruses (around 10%) that are consistently detected in such patients carry a small deletion or a point mutation in a relatively precise and well conserved region near the 5ʹ end of the HIV genome, in the area that encodes the major splice donor (MSD) site and the packaging signal Ѱ in the viral RNA genome. Why this subclass of proviruses is defective has never been properly understood. We now propose a mechanistic scenario for how these MSD-Ѱ mutations can prevent viral protein expression. Based on ample results in literature, we argue that MSD inactivation triggers the activity of the 5ʹ-polyadenylation site, resulting in the production of ultra-short non-protein-coding HIV transcripts.
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Affiliation(s)
- Atze T Das
- Laboratory of Experimental Virology, Department of Medical Microbiology, Amsterdam University Medical Centers, University of Amsterdam, Amsterdam, The Netherlands
| | - Alexander O Pasternak
- Laboratory of Experimental Virology, Department of Medical Microbiology, Amsterdam University Medical Centers, University of Amsterdam, Amsterdam, The Netherlands
| | - Ben Berkhout
- Laboratory of Experimental Virology, Department of Medical Microbiology, Amsterdam University Medical Centers, University of Amsterdam, Amsterdam, The Netherlands. .,Laboratory of Molecular Virology, Department of Life and Environmental Sciences, University of Cagliari, Cagliari, Italy.
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16
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Jiang G, Maverakis E, Cheng MY, Elsheikh MM, Deleage C, Méndez-Lagares G, Shimoda M, Yukl SA, Hartigan-O’Connor DJ, Thompson GR, Estes JD, Wong JK, Dandekar S. Disruption of latent HIV in vivo during the clearance of actinic keratosis by ingenol mebutate. JCI Insight 2019; 4:126027. [PMID: 30944245 PMCID: PMC6483647 DOI: 10.1172/jci.insight.126027] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2018] [Accepted: 02/14/2019] [Indexed: 01/20/2023] Open
Abstract
Actinic keratosis (AK) is a precancerous skin lesion that is common in HIV-positive patients. Without effective treatment, AKs can progress to squamous cell carcinoma. Ingenol mebutate, a PKC agonist, is a US Food and Drug Administration-approved (FDA-approved) topical treatment for AKs. It can induce reactivation of latent HIV transcription in CD4+ T cells both in vitro and ex vivo. Although PKC agonists are known to be potent inducers of HIV expression from latency, their effects in vivo are not known because of the concerns of toxicity. Therefore, we sought to determine the effects of topical ingenol mebutate gel on the HIV transcription profile in HIV-infected individuals with AKs, specifically in the setting of suppressive antiretroviral therapy (ART). We found that AKs cleared following topical application of ingenol mebutate and detected marginal changes in immune activation in the peripheral blood and in skin biopsies. An overall increase in the level of HIV transcription initiation, elongation, and complete transcription was detected only in skin biopsies after the treatment. Our data demonstrate that application of ingenol mebutate to AKs in ART-suppressed HIV-positive patients can effectively cure AKs as well as disrupt HIV latency in the skin tissue microenvironment in vivo without causing massive immune activation.
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Affiliation(s)
- Guochun Jiang
- Department of Medical Microbiology and Immunology and
| | | | | | | | - Claire Deleage
- AIDS and Cancer Virus Program, Leidos Biomedical Research Inc., Frederick National Laboratory for Cancer Research, Frederick, Maryland, USA
| | | | | | - Steven A. Yukl
- San Francisco Veterans Affairs (VA) Medical Center and UCSF, San Francisco, California, USA
| | | | | | - Jacob D. Estes
- AIDS and Cancer Virus Program, Leidos Biomedical Research Inc., Frederick National Laboratory for Cancer Research, Frederick, Maryland, USA
| | - Joseph K. Wong
- San Francisco Veterans Affairs (VA) Medical Center and UCSF, San Francisco, California, USA
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17
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BCL6 Inhibitor-Mediated Downregulation of Phosphorylated SAMHD1 and T Cell Activation Are Associated with Decreased HIV Infection and Reactivation. J Virol 2019; 93:JVI.01073-18. [PMID: 30355686 DOI: 10.1128/jvi.01073-18] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2018] [Accepted: 10/10/2018] [Indexed: 12/14/2022] Open
Abstract
Clearance of HIV-infected germinal center (GC) CD4+ follicular helper T cells (Tfh) after combination antiretroviral therapy (ART) is essential to an HIV cure. Blocking B cell lymphoma 6 (BCL6; the master transcription factor for Tfh cells) represses HIV infection of tonsillar CD4+ Tfh ex vivo, reduces GC formation, and limits immune activation in vivo We assessed the anti-HIV activity of a novel BCL6 inhibitor, FX1, in Tfh/non-Tfh CD4+ T cells and its impact on T cell activation and SAMHD1 phosphorylation (Thr592). FX1 repressed HIV-1 infection of peripheral CD4+ T cells and tonsillar Tfh/non-Tfh CD4+ T cells (P < 0.05) and total elongated and multispliced HIV-1 RNA production during the first round of viral life cycle (P < 0.01). Using purified circulating CD4+ T cells from uninfected donors, we demonstrate that FX1 treatment resulted in downregulation pSAMHD1 expression (P < 0.05) and T cell activation (HLA-DR, CD25, and Ki67; P < 0.01) ex vivo corresponding with inhibition of HIV-1 and HIV-2 replication. Ex vivo HIV-1 reactivation using purified peripheral CD4+ T cells from HIV-infected ART-suppressed donors was also blocked by FX1 treatment (P < 0.01). Our results indicate that BCL6 function contributes to Tfh/non-Tfh CD4+ T cell activation and cellular susceptibility to HIV infection. BCL6 inhibition represents a novel therapeutic strategy to potentiate HIV suppression in Tfh/non-Tfh CD4+ T cells without reactivation of latent virus.IMPORTANCE The expansion and accumulation of HIV-infected BCL6+ Tfh CD4+ T cells are thought to contribute to the persistence of viral reservoirs in infected subjects undergoing ART. Two mechanisms have been raised for the preferential retention of HIV within Tfh CD4+ T cells: (i) antiretroviral drugs have limited tissue distribution, resulting in insufficient tissue concentration and lower efficacy in controlling HIV replication in lymphoid tissues, and (ii) cytotoxic CD8+ T cells within lymphoid tissues express low levels of chemokine receptor (CXCR5), thus limiting their ability to enter the GCs to control/eliminate HIV-infected Tfh cells. Our results indicate that the BCL6 inhibitor FX1 can not only repress HIV infection of tonsillar Tfh ex vivo but also suppress HIV infection and reactivation in primary, non-Tfh CD4+ T cells. Our study provides a rationale for targeting BCL6 protein to extend ART-mediated reduction of persistent HIV and/or support strategies toward HIV remission beyond ART cessation.
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Telwatte S, Lee S, Somsouk M, Hatano H, Baker C, Kaiser P, Kim P, Chen TH, Milush J, Hunt PW, Deeks SG, Wong JK, Yukl SA. Gut and blood differ in constitutive blocks to HIV transcription, suggesting tissue-specific differences in the mechanisms that govern HIV latency. PLoS Pathog 2018; 14:e1007357. [PMID: 30440043 PMCID: PMC6237391 DOI: 10.1371/journal.ppat.1007357] [Citation(s) in RCA: 70] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2018] [Accepted: 09/27/2018] [Indexed: 02/07/2023] Open
Abstract
Latently-infected CD4+ T cells are widely considered to be the major barrier to a cure for HIV. Much of our understanding of HIV latency comes from latency models and blood cells, but most HIV-infected cells reside in lymphoid tissues such as the gut. We hypothesized that tissue-specific environments may impact the mechanisms that govern HIV expression. To assess the degree to which different mechanisms inhibit HIV transcription in the gut and blood, we quantified HIV transcripts suggestive of transcriptional interference (U3-U5; "Read-through"), initiation (TAR), 5' elongation (R-U5-pre-Gag; "Long LTR"), distal transcription (Nef), completion (U3-polyA; "PolyA"), and multiple splicing (Tat-Rev) in matched peripheral blood mononuclear cells (PBMCs) and rectal biopsies, and matched FACS-sorted CD4+ T cells from blood and rectum, from two cohorts of ART-suppressed individuals. Like the PBMCs, rectal biopsies showed low levels of read-through transcripts (median = 23 copies/106 cells) and a gradient of total (679)>elongated(75)>Nef(16)>polyadenylated (11)>multiply-spliced HIV RNAs(<1) [p<0.05 for all], demonstrating blocks to HIV transcriptional elongation, completion, and splicing. Rectal CD4+ T cells showed a similar gradient of total>polyadenylated>multiply-spliced transcripts, but the ratio of total to elongated transcripts was 6-fold lower than in blood CD4+ T cells (P = 0.016), suggesting less of a block to HIV transcriptional elongation in rectal CD4+ T cells. Levels of total transcripts per provirus were significantly lower in rectal biopsies compared to PBMCs (median 3.5 vs. 15.4; P = 0.008) and in sorted CD4+ T cells from rectum compared to blood (median 2.7 vs. 31.8; P = 0.016). The lower levels of HIV transcriptional initiation and of most HIV transcripts per provirus in the rectum suggest that this site may be enriched for latently-infected cells, cells in which latency is maintained by different mechanisms, or cells in a "deeper" state of latency. These are important considerations for designing therapies that aim to disrupt HIV latency in all tissue compartments.
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Affiliation(s)
- Sushama Telwatte
- San Francisco Veterans Affairs (VA) Medical Center and University of California, San Francisco (UCSF), San Francisco, CA, United States of America
| | - Sulggi Lee
- Zuckerberg San Francisco General Hospital and the University of California, San Francisco (UCSF), San Francisco, CA, United States of America
| | - Ma Somsouk
- Zuckerberg San Francisco General Hospital and the University of California, San Francisco (UCSF), San Francisco, CA, United States of America
| | - Hiroyu Hatano
- Zuckerberg San Francisco General Hospital and the University of California, San Francisco (UCSF), San Francisco, CA, United States of America
| | - Christopher Baker
- Zuckerberg San Francisco General Hospital and the University of California, San Francisco (UCSF), San Francisco, CA, United States of America
| | - Philipp Kaiser
- San Francisco Veterans Affairs (VA) Medical Center and University of California, San Francisco (UCSF), San Francisco, CA, United States of America
| | - Peggy Kim
- San Francisco Veterans Affairs (VA) Medical Center and University of California, San Francisco (UCSF), San Francisco, CA, United States of America
| | - Tsui-Hua Chen
- San Francisco Veterans Affairs (VA) Medical Center and University of California, San Francisco (UCSF), San Francisco, CA, United States of America
| | - Jeffrey Milush
- Zuckerberg San Francisco General Hospital and the University of California, San Francisco (UCSF), San Francisco, CA, United States of America
| | - Peter W. Hunt
- Zuckerberg San Francisco General Hospital and the University of California, San Francisco (UCSF), San Francisco, CA, United States of America
| | - Steven G. Deeks
- Zuckerberg San Francisco General Hospital and the University of California, San Francisco (UCSF), San Francisco, CA, United States of America
| | - Joseph K. Wong
- San Francisco Veterans Affairs (VA) Medical Center and University of California, San Francisco (UCSF), San Francisco, CA, United States of America
| | - Steven A. Yukl
- San Francisco Veterans Affairs (VA) Medical Center and University of California, San Francisco (UCSF), San Francisco, CA, United States of America
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Jiang G, Nguyen D, Archin NM, Yukl SA, Méndez-Lagares G, Tang Y, Elsheikh MM, Thompson GR, Hartigan-O'Connor DJ, Margolis DM, Wong JK, Dandekar S. HIV latency is reversed by ACSS2-driven histone crotonylation. J Clin Invest 2018; 128:1190-1198. [PMID: 29457784 DOI: 10.1172/jci98071] [Citation(s) in RCA: 97] [Impact Index Per Article: 16.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2017] [Accepted: 01/09/2018] [Indexed: 12/21/2022] Open
Abstract
Eradication of HIV-1 (HIV) is hindered by stable viral reservoirs. Viral latency is epigenetically regulated. While the effects of histone acetylation and methylation at the HIV long-terminal repeat (LTR) have been described, our knowledge of the proviral epigenetic landscape is incomplete. We report that a previously unrecognized epigenetic modification of the HIV LTR, histone crotonylation, is a regulator of HIV latency. Reactivation of latent HIV was achieved following the induction of histone crotonylation through increased expression of the crotonyl-CoA-producing enzyme acyl-CoA synthetase short-chain family member 2 (ACSS2). This reprogrammed the local chromatin at the HIV LTR through increased histone acetylation and reduced histone methylation. Pharmacologic inhibition or siRNA knockdown of ACSS2 diminished histone crotonylation-induced HIV replication and reactivation. ACSS2 induction was highly synergistic in combination with either a protein kinase C agonist (PEP005) or a histone deacetylase inhibitor (vorinostat) in reactivating latent HIV. In the SIV-infected nonhuman primate model of AIDS, the expression of ACSS2 was significantly induced in intestinal mucosa in vivo, which correlated with altered fatty acid metabolism. Our study links the HIV/SIV infection-induced fatty acid enzyme ACSS2 to HIV latency and identifies histone lysine crotonylation as a novel epigenetic regulator for HIV transcription that can be targeted for HIV eradication.
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Affiliation(s)
- Guochun Jiang
- Department of Medical Microbiology and Immunology, UCD, Davis, California, USA
| | - Don Nguyen
- Department of Medical Microbiology and Immunology, UCD, Davis, California, USA
| | - Nancie M Archin
- Department of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Steven A Yukl
- Department of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Gema Méndez-Lagares
- Department of Medical Microbiology and Immunology, UCD, Davis, California, USA
| | - Yuyang Tang
- Department of Medical Microbiology and Immunology, UCD, Davis, California, USA
| | - Maher M Elsheikh
- Department of Medical Microbiology and Immunology, UCD, Davis, California, USA
| | - George R Thompson
- Department of Medical Microbiology and Immunology, UCD, Davis, California, USA
| | | | - David M Margolis
- Department of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Joseph K Wong
- Department of Medicine, UCSF, and San Francisco Veterans Affairs Medical Center, San Francisco, California, USA
| | - Satya Dandekar
- Department of Medical Microbiology and Immunology, UCD, Davis, California, USA
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20
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Wang Z, Simonetti FR, Siliciano RF, Laird GM. Measuring replication competent HIV-1: advances and challenges in defining the latent reservoir. Retrovirology 2018; 15:21. [PMID: 29433524 PMCID: PMC5810003 DOI: 10.1186/s12977-018-0404-7] [Citation(s) in RCA: 48] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2017] [Accepted: 02/06/2018] [Indexed: 12/24/2022] Open
Abstract
Antiretroviral therapy cannot cure HIV-1 infection due to the persistence of a small number of latently infected cells harboring replication-competent proviruses. Measuring persistent HIV-1 is challenging, as it consists of a mosaic population of defective and intact proviruses that can shift from a state of latency to active HIV-1 transcription. Due to this complexity, most of the current assays detect multiple categories of persistent HIV-1, leading to an overestimate of the true size of the latent reservoir. Here, we review the development of the viral outgrowth assay, the gold-standard quantification of replication-competent proviruses, and discuss the insights provided by full-length HIV-1 genome sequencing methods, which allowed us to unravel the composition of the proviral landscape. In this review, we provide a dissection of what defines HIV-1 persistence and we examine the unmet needs to measure the efficacy of interventions aimed at eliminating the HIV-1 reservoir.
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Affiliation(s)
- Zheng Wang
- Department of Pharmacology and Molecular Sciences, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
| | - Francesco R Simonetti
- Department of Medicine, Johns Hopkins University School of Medicine, Room 879, Edward D. Miller Research Building, 733 N. Broadway, Baltimore, MD, 21205, USA
| | - Robert F Siliciano
- Department of Medicine, Johns Hopkins University School of Medicine, Room 879, Edward D. Miller Research Building, 733 N. Broadway, Baltimore, MD, 21205, USA. .,Howard Hughes Medical Institute, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA.
| | - Gregory M Laird
- Department of Medicine, Johns Hopkins University School of Medicine, Room 879, Edward D. Miller Research Building, 733 N. Broadway, Baltimore, MD, 21205, USA
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21
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Pasternak AO, Berkhout B. What do we measure when we measure cell-associated HIV RNA. Retrovirology 2018; 15:13. [PMID: 29378657 PMCID: PMC5789533 DOI: 10.1186/s12977-018-0397-2] [Citation(s) in RCA: 62] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2017] [Accepted: 01/16/2018] [Indexed: 12/21/2022] Open
Abstract
Cell-associated (CA) HIV RNA has received much attention in recent years as a surrogate measure of the efficiency of HIV latency reversion and because it may provide an estimate of the viral reservoir size. This review provides an update on some recent insights in the biology and clinical utility of this biomarker. We discuss a number of important considerations to be taken into account when interpreting CA HIV RNA measurements, as well as different methods to measure this biomarker.
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Affiliation(s)
- Alexander O Pasternak
- Laboratory of Experimental Virology, Department of Medical Microbiology, Academic Medical Center of the University of Amsterdam, Meibergdreef 15, 1105 AZ, Amsterdam, The Netherlands.
| | - Ben Berkhout
- Laboratory of Experimental Virology, Department of Medical Microbiology, Academic Medical Center of the University of Amsterdam, Meibergdreef 15, 1105 AZ, Amsterdam, The Netherlands
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Plantin J, Massanella M, Chomont N. Inducible HIV RNA transcription assays to measure HIV persistence: pros and cons of a compromise. Retrovirology 2018; 15:9. [PMID: 29343255 PMCID: PMC5773137 DOI: 10.1186/s12977-017-0385-y] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2017] [Accepted: 12/23/2017] [Indexed: 12/25/2022] Open
Abstract
With the increasing number of therapeutic strategies tested in humans to reduce the size of the latent reservoir, the development of a robust, precise and clinical trial scalable assay that measures the frequency of infected cells carrying inducible replication-competent HIV is urgently needed. The size of the pool of cells carrying replication-competent HIV is largely overestimated by DNA assays, as a result of a large proportion of defective viruses, and underestimated by co-culture outgrowth assays. New culture methods that measure the inducible HIV reservoir have been developed during the past few years. In these induction assays, CD4+ T cells from virally suppressed individuals are activated and HIV RNA is measured in cell extracts or cell supernatants. In this review, we summarize the principle and outcomes of these assays and discuss the potential of these methods in the evaluation of HIV eradication strategies.
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Affiliation(s)
- Johann Plantin
- Department of Microbiology, Infectiology and Immunology, Faculté de Médecine, Université de Montréal, Montréal, QC, Canada.,Centre de Recherche du CHUM, Université de Montréal, 900 rue St-Denis, H2X0A9, Montréal, QC, Canada
| | - Marta Massanella
- Department of Microbiology, Infectiology and Immunology, Faculté de Médecine, Université de Montréal, Montréal, QC, Canada.,Centre de Recherche du CHUM, Université de Montréal, 900 rue St-Denis, H2X0A9, Montréal, QC, Canada
| | - Nicolas Chomont
- Department of Microbiology, Infectiology and Immunology, Faculté de Médecine, Université de Montréal, Montréal, QC, Canada. .,Centre de Recherche du CHUM, Université de Montréal, 900 rue St-Denis, H2X0A9, Montréal, QC, Canada.
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Khan S, Telwatte S, Trapecar M, Yukl S, Sanjabi S. Differentiating Immune Cell Targets in Gut-Associated Lymphoid Tissue for HIV Cure. AIDS Res Hum Retroviruses 2017; 33:S40-S58. [PMID: 28882067 PMCID: PMC5685216 DOI: 10.1089/aid.2017.0153] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
The single greatest challenge to an HIV cure is the persistence of latently infected cells containing inducible, replication-competent proviral genomes, which constitute only a small fraction of total or infected cells in the body. Although resting CD4+ T cells in the blood are a well-known source of viral rebound, more than 90% of the body's lymphocytes reside elsewhere. Many are in gut tissue, where HIV DNA levels per million CD4+ T cells are considerably higher than in the blood. Despite the significant contribution of gut tissue to viral replication and persistence, little is known about the cell types that support persistence of HIV in the gut; importantly, T cells in the gut have phenotypic, functional, and survival properties that are distinct from T cells in other tissues. The mechanisms by which latency is established and maintained will likely depend on the location and cytokine milieu surrounding the latently infected cells in each compartment. Therefore, successful HIV cure strategies require identification and characterization of the exact cell types that support viral persistence, particularly in the gut. In this review, we describe the seeding of the latent HIV reservoir in the gut mucosa; highlight the evidence for compartmentalization and depletion of T cells; summarize the immunologic consequences of HIV infection within the gut milieu; propose how the damaged gut environment may promote the latent HIV reservoir; and explore several immune cell targets in the gut and their place on the path toward HIV cure.
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Affiliation(s)
- Shahzada Khan
- Gladstone Institute of Virology and Immunology, Gladstone Institutes, San Francisco, California
| | - Sushama Telwatte
- San Francisco VA Health Care System and University of California, San Francisco (UCSF), San Francisco, California
| | - Martin Trapecar
- Gladstone Institute of Virology and Immunology, Gladstone Institutes, San Francisco, California
| | - Steven Yukl
- San Francisco VA Health Care System and University of California, San Francisco (UCSF), San Francisco, California
| | - Shomyseh Sanjabi
- Gladstone Institute of Virology and Immunology, Gladstone Institutes, San Francisco, California
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, California
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Single-cell analysis of HIV-1 transcriptional activity reveals expression of proviruses in expanded clones during ART. Proc Natl Acad Sci U S A 2017; 114:E3659-E3668. [PMID: 28416661 DOI: 10.1073/pnas.1617961114] [Citation(s) in RCA: 118] [Impact Index Per Article: 16.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Little is known about the fraction of human immunodeficiency virus type 1 (HIV-1) proviruses that express unspliced viral RNA in vivo or about the levels of HIV RNA expression within single infected cells. We developed a sensitive cell-associated HIV RNA and DNA single-genome sequencing (CARD-SGS) method to investigate fractional proviral expression of HIV RNA (1.3-kb fragment of p6, protease, and reverse transcriptase) and the levels of HIV RNA in single HIV-infected cells from blood samples obtained from individuals with viremia or individuals on long-term suppressive antiretroviral therapy (ART). Spiking experiments show that the CARD-SGS method can detect a single cell expressing HIV RNA. Applying CARD-SGS to blood mononuclear cells in six samples from four HIV-infected donors (one with viremia and not on ART and three with viremia suppressed on ART) revealed that an average of 7% of proviruses (range: 2-18%) expressed HIV RNA. Levels of expression varied from one to 62 HIV RNA molecules per cell (median of 1). CARD-SGS also revealed the frequent expression of identical HIV RNA sequences across multiple single cells and across multiple time points in donors on suppressive ART consistent with constitutive expression of HIV RNA in infected cell clones. Defective proviruses were found to express HIV RNA at levels similar to those proviruses that had no obvious defects. CARD-SGS is a useful tool to characterize fractional proviral expression in single infected cells that persist despite ART and to assess the impact of experimental interventions on proviral populations and their expression.
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Telwatte S, Yukl SA. Exploring HIV latency using transcription profiling. MICROBIOLOGY AUSTRALIA 2017. [DOI: 10.1071/ma17050] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
The major barrier to a cure for HIV is the existence of reservoirs consisting predominantly of latently infected CD4+ T cells, which do not produce virus constitutively but can be induced to produce infectious virus on activation. HIV latency research has largely focused on peripheral blood, yet most HIV-infected cells reside in tissues, especially the gut, where differences in drug penetration, cell types, and immune responses may impact mechanisms of persistence. Exploring the differences between the gut and the blood in transcriptional blocks may reveal fundamental insights into mechanisms that contribute to HIV latency. Our novel transcriptional profiling assays enable us to determine where blocks to HIV transcription occur in various tissues and the magnitude of their contribution. These assays could also be adapted to investigate latency established by other retroviridae or even DNA viruses such as herpesviridae with a view to pinpointing mechanisms underlying latency in vivo and ultimately contribute to designing a cure.
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