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Keele BF, Okoye AA, Fennessey CM, Varco-Merth B, Immonen TT, Kose E, Conchas A, Pinkevych M, Lipkey L, Newman L, Macairan A, Bosche M, Bosche WJ, Berkemeier B, Fast R, Hull M, Oswald K, Shoemaker R, Silipino L, Gorelick RJ, Duell D, Marenco A, Brantley W, Smedley J, Axthelm M, Davenport MP, Lifson JD, Picker LJ. Early antiretroviral therapy in SIV-infected rhesus macaques reveals a multiphasic, saturable dynamic accumulation of the rebound competent viral reservoir. PLoS Pathog 2024; 20:e1012135. [PMID: 38593120 PMCID: PMC11003637 DOI: 10.1371/journal.ppat.1012135] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2023] [Accepted: 03/19/2024] [Indexed: 04/11/2024] Open
Abstract
The rebound competent viral reservoir (RCVR)-virus that persists during antiretroviral treatment (ART) and can reignite systemic infection when treatment is stopped-is the primary barrier to eradicating HIV. We used time to initiation of ART during primary infection of rhesus macaques (RMs) after intravenous challenge with barcoded SIVmac239 as a means to elucidate the dynamics of RCVR establishment in groups of RMs by creating a multi-log range of pre-ART viral loads and then assessed viral time-to-rebound and reactivation rates resulting from the discontinuation of ART after one year. RMs started on ART on days 3, 4, 5, 6, 7, 9 or 12 post-infection showed a nearly 10-fold difference in pre-ART viral measurements for successive ART-initiation timepoints. Only 1 of 8 RMs initiating ART on days 3 and 4 rebounded after ART interruption despite measurable pre-ART plasma viremia. Rebounding plasma from the 1 rebounding RM contained only a single barcode lineage detected at day 50 post-ART. All RMs starting ART on days 5 and 6 rebounded between 14- and 50-days post-ART with 1-2 rebounding variants each. RMs starting ART on days 7, 9, and 12 had similar time-to-measurable plasma rebound kinetics despite multiple log differences in pre-ART plasma viral load (pVL), with all RMs rebounding between 7- and 16-days post-ART with 3-28 rebounding lineages. Calculated reactivation rates per pre-ART pVL were highest for RMs starting ART on days 5, 6, and 7 after which the rate of accumulation of the RCVR markedly decreased for RMs treated on days 9 and 12, consistent with multiphasic establishment and near saturation of the RCVR within 2 weeks post infection. Taken together, these data highlight the heterogeneity of the RCVR between RMs, the stochastic establishment of the very early RCVR, and the saturability of the RCVR prior to peak viral infection.
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Affiliation(s)
- Brandon F. Keele
- AIDS and Cancer Virus Program, Frederick National Laboratory for Cancer Research, Frederick, Maryland, United States of America
| | - Afam A. Okoye
- Vaccine and Gene Therapy Institute and Oregon National Primate Research Center, Oregon Health & Science University, Beaverton, Oregon, United States of America
| | - Christine M. Fennessey
- AIDS and Cancer Virus Program, Frederick National Laboratory for Cancer Research, Frederick, Maryland, United States of America
| | - Benjamin Varco-Merth
- Vaccine and Gene Therapy Institute and Oregon National Primate Research Center, Oregon Health & Science University, Beaverton, Oregon, United States of America
| | - Taina T. Immonen
- AIDS and Cancer Virus Program, Frederick National Laboratory for Cancer Research, Frederick, Maryland, United States of America
| | - Emek Kose
- AIDS and Cancer Virus Program, Frederick National Laboratory for Cancer Research, Frederick, Maryland, United States of America
| | - Andrew Conchas
- AIDS and Cancer Virus Program, Frederick National Laboratory for Cancer Research, Frederick, Maryland, United States of America
| | - Mykola Pinkevych
- Infection Analytics Program, Kirby Institute for Infection and Immunity, University of New South Wales, Sydney, Australia
| | - Leslie Lipkey
- AIDS and Cancer Virus Program, Frederick National Laboratory for Cancer Research, Frederick, Maryland, United States of America
| | - Laura Newman
- AIDS and Cancer Virus Program, Frederick National Laboratory for Cancer Research, Frederick, Maryland, United States of America
| | - Agatha Macairan
- AIDS and Cancer Virus Program, Frederick National Laboratory for Cancer Research, Frederick, Maryland, United States of America
| | - Marjorie Bosche
- AIDS and Cancer Virus Program, Frederick National Laboratory for Cancer Research, Frederick, Maryland, United States of America
| | - William J. Bosche
- AIDS and Cancer Virus Program, Frederick National Laboratory for Cancer Research, Frederick, Maryland, United States of America
| | - Brian Berkemeier
- AIDS and Cancer Virus Program, Frederick National Laboratory for Cancer Research, Frederick, Maryland, United States of America
| | - Randy Fast
- AIDS and Cancer Virus Program, Frederick National Laboratory for Cancer Research, Frederick, Maryland, United States of America
| | - Mike Hull
- AIDS and Cancer Virus Program, Frederick National Laboratory for Cancer Research, Frederick, Maryland, United States of America
| | - Kelli Oswald
- AIDS and Cancer Virus Program, Frederick National Laboratory for Cancer Research, Frederick, Maryland, United States of America
| | - Rebecca Shoemaker
- AIDS and Cancer Virus Program, Frederick National Laboratory for Cancer Research, Frederick, Maryland, United States of America
| | - Lorna Silipino
- AIDS and Cancer Virus Program, Frederick National Laboratory for Cancer Research, Frederick, Maryland, United States of America
| | - Robert J. Gorelick
- AIDS and Cancer Virus Program, Frederick National Laboratory for Cancer Research, Frederick, Maryland, United States of America
| | - Derick Duell
- Vaccine and Gene Therapy Institute and Oregon National Primate Research Center, Oregon Health & Science University, Beaverton, Oregon, United States of America
| | - Alejandra Marenco
- Vaccine and Gene Therapy Institute and Oregon National Primate Research Center, Oregon Health & Science University, Beaverton, Oregon, United States of America
| | - William Brantley
- Vaccine and Gene Therapy Institute and Oregon National Primate Research Center, Oregon Health & Science University, Beaverton, Oregon, United States of America
| | - Jeremy Smedley
- Vaccine and Gene Therapy Institute and Oregon National Primate Research Center, Oregon Health & Science University, Beaverton, Oregon, United States of America
| | - Michael Axthelm
- Vaccine and Gene Therapy Institute and Oregon National Primate Research Center, Oregon Health & Science University, Beaverton, Oregon, United States of America
| | - Miles P. Davenport
- Infection Analytics Program, Kirby Institute for Infection and Immunity, University of New South Wales, Sydney, Australia
| | - Jeffrey D. Lifson
- AIDS and Cancer Virus Program, Frederick National Laboratory for Cancer Research, Frederick, Maryland, United States of America
| | - Louis J. Picker
- Vaccine and Gene Therapy Institute and Oregon National Primate Research Center, Oregon Health & Science University, Beaverton, Oregon, United States of America
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Mystakelis HA, Wilson E, Laidlaw E, Poole A, Krishnan S, Rupert A, Welker JL, Gorelick RJ, Lisco A, Manion M, Baker JV, Migueles SA, Sereti I. An open label randomized controlled trial of atorvastatin versus aspirin in elite controllers and antiretroviral-treated people with HIV. AIDS 2023; 37:1827-1835. [PMID: 37450602 PMCID: PMC10481929 DOI: 10.1097/qad.0000000000003656] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Revised: 06/17/2023] [Accepted: 07/06/2023] [Indexed: 07/18/2023]
Abstract
BACKGROUND Residual inflammation in people with HIV (PWH) despite suppression of HIV replication is associated with many comorbidities including cardiovascular disease. Targeting inflammation may decrease the risk of cardiovascular disease. METHODS An open label randomized study was conducted to evaluate the effect of nine months of 81 mg aspirin versus 40 mg atorvastatin in antiretroviral therapy (ART) treated PWH and elite controllers (EC), not on ART. Biomarkers associated with inflammation and virologic indices were measured and analyzed using nonparametric and linear mixed effect models. RESULTS Fifty-three participants were randomized and 44 were included in the final analysis. Median age was 54 years, 72% were male, 59% were Black. Median CD4 + count was 595 cells/μl in the aspirin and 717 cells/μl in the atorvastatin arm. After 9 months of treatment, plasma soluble (s) CD14 + was reduced in the aspirin group within both treated PWH and EC ( P = 0.0229), yet only within treated PWH in the atorvastatin group ( P = 0.0128). A 2.3% reduction from baseline in tissue factor levels was also observed in the aspirin arm, driven by the EC group. In the atorvastatin arm, there was a 4.3% reduction in interleukin-8 levels ( P = 0.02) and a small decrease of activated CD4 + T cells ( P < 0.001). No statistically significant differences were observed in the plasma HIV viral load and cell-associated (CA) HIV DNA and RNA. CONCLUSIONS Aspirin and atorvastatin could play a role in targeting HIV-associated inflammation. Elite controllers may warrant special consideration for anti-inflammatory strategies.
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Affiliation(s)
- Harry A. Mystakelis
- Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases, Bethesda
| | - Eleanor Wilson
- Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases, Bethesda
| | - Elizabeth Laidlaw
- Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases, Bethesda
| | - April Poole
- Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases, Bethesda
| | - Sonya Krishnan
- Johns Hopkins University, Department of Medicine, Division of Infectious Diseases, Baltimore
| | - Adam Rupert
- Leidos Biomedical Research Inc., Frederick National Laboratory for Cancer Research, Frederick
| | - Jorden L. Welker
- AIDS and Cancer Virus Program, Frederick National Laboratory for Cancer Research, Frederick, Maryland
| | - Robert J. Gorelick
- AIDS and Cancer Virus Program, Frederick National Laboratory for Cancer Research, Frederick, Maryland
| | - Andrea Lisco
- Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases, Bethesda
| | - Maura Manion
- Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases, Bethesda
| | - Jason V. Baker
- Hennepin Healthcare Research Institute
- University of Minnesota, Minneapolis, Minnesota, USA
| | - Stephen A. Migueles
- Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases, Bethesda
| | - Irini Sereti
- Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases, Bethesda
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Swanstrom AE, Gorelick RJ, Welker JL, Schmidt F, Lu B, Wang K, Rowe W, Breed MW, Killoran KE, Kramer JA, Donohue D, Roser JD, Bieniasz PD, Hatziioannou T, Pyle C, Thomas JA, Trubey CM, Zheng J, Blair W, Yant SR, Lifson JD, Del Prete GQ. Long-acting lenacapavir protects macaques against intravenous challenge with simian-tropic HIV. EBioMedicine 2023; 95:104764. [PMID: 37625266 PMCID: PMC10470178 DOI: 10.1016/j.ebiom.2023.104764] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Revised: 08/01/2023] [Accepted: 08/04/2023] [Indexed: 08/27/2023] Open
Abstract
BACKGROUND Long-acting subcutaneous lenacapavir (LEN), a first-in-class HIV capsid inhibitor approved by the US FDA for the treatment of multidrug-resistant HIV-1 with twice yearly dosing, is under investigation for HIV-1 pre-exposure prophylaxis (PrEP). We previously derived a simian-tropic HIV-1 clone (stHIV-A19) that encodes an HIV-1 capsid and replicates to high titres in pigtail macaques (PTM), resulting in a nonhuman primate model well-suited for evaluating LEN PrEP in vivo. METHODS Lenacapavir potency against stHIV-A19 in PTM peripheral blood mononuclear cells in vitro was determined and subcutaneous LEN pharmacokinetics were evaluated in naïve PTMs in vivo. To evaluate the protective efficacy of LEN PrEP, naïve PTMs received either a single subcutaneous injection of LEN (25 mg/kg, N = 3) or vehicle (N = 4) 30 days before a high-dose intravenous challenge with stHIV-A19, or 7 daily subcutaneous injections of a 3-drug control PrEP regimen starting 3 days before stHIV-A19 challenge (N = 3). FINDINGS In vitro, LEN showed potent antiviral activity against stHIV-A19, comparable to its potency against HIV-1. In vivo, subcutaneous LEN displayed sustained plasma drug exposures in PTMs. Following stHIV-A19 challenge, while all vehicle control animals became productively infected, all LEN and 3-drug control PrEP animals were protected from infection. INTERPRETATION These findings highlight the utility of the stHIV-A19/PTM model and support the clinical development of long-acting LEN for PrEP in humans. FUNDING Gilead Sciences as part of a Cooperative Research and Development Agreement between Gilead Sciences and Frederick National Lab; federal funds from the National Cancer Institute, National Institutes of Health, under Contract No. 75N91019D00024/HHSN261201500003I; NIH grant R01AI078788.
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Affiliation(s)
- Adrienne E Swanstrom
- AIDS and Cancer Virus Program, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Robert J Gorelick
- AIDS and Cancer Virus Program, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Jorden L Welker
- AIDS and Cancer Virus Program, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Fabian Schmidt
- Laboratory of Retrovirology, Rockefeller University, New York, NY, USA
| | - Bing Lu
- Gilead Sciences, Foster City, CA, USA
| | | | | | - Matthew W Breed
- Laboratory Animal Sciences Program, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Kristin E Killoran
- Laboratory Animal Sciences Program, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Joshua A Kramer
- Laboratory Animal Sciences Program, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Duncan Donohue
- DMS Applies Information Management Sciences, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - James D Roser
- AIDS and Cancer Virus Program, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Paul D Bieniasz
- Laboratory of Retrovirology, Rockefeller University, New York, NY, USA
| | | | - Cathi Pyle
- AIDS and Cancer Virus Program, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - James A Thomas
- AIDS and Cancer Virus Program, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Charles M Trubey
- AIDS and Cancer Virus Program, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Jim Zheng
- Gilead Sciences, Foster City, CA, USA
| | | | | | - Jeffrey D Lifson
- AIDS and Cancer Virus Program, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Gregory Q Del Prete
- AIDS and Cancer Virus Program, Frederick National Laboratory for Cancer Research, Frederick, MD, USA.
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4
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Lisco A, Lange C, Manion M, Kuriakose S, Dewar R, Gorelick RJ, Huik K, Yu Q, Hammoud DA, Smith BR, Muranski P, Rehm C, Sherman BT, Sykes C, Lindo N, Ye P, Bricker KM, Keele BF, Fennessey CM, Maldarelli F, Sereti I. Immune reconstitution inflammatory syndrome drives emergence of HIV drug resistance from multiple anatomic compartments in a person living with HIV. Nat Med 2023; 29:1364-1369. [PMID: 37322122 PMCID: PMC10494392 DOI: 10.1038/s41591-023-02387-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Accepted: 05/05/2023] [Indexed: 06/17/2023]
Abstract
Reservoirs of HIV maintained in anatomic compartments during antiretroviral therapy prevent HIV eradication. However, mechanisms driving their persistence and interventions to control them remain elusive. Here we report the presence of an inducible HIV reservoir within antigen-specific CD4+T cells in the central nervous system of a 59-year-old male with progressive multifocal leukoencephalopathy immune reconstitution inflammatory syndrome (PML-IRIS). HIV production during PML-IRIS was suppressed by modulating inflammation with corticosteroids; selection of HIV drug resistance caused subsequent breakthrough viremia. Therefore, inflammation can influence the composition, distribution and induction of HIV reservoirs, warranting it as a key consideration for developing effective HIV remission strategies.
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Affiliation(s)
- Andrea Lisco
- Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Camille Lange
- Clinical Retrovirology Section, HIV Dynamics and Replication Program National Cancer Institute, National Institutes of Health, Frederick, MD, USA.
- Military HIV Research Program, Walter Reed Army Institute of Research, Henry M. Jackson Foundation for the Advancement of Military Medicine, Silver Spring, MD, USA.
| | - Maura Manion
- Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Safia Kuriakose
- Clinical Research Directorate, Frederick National Laboratory for Cancer Research, Bethesda, MD, USA
| | - Robin Dewar
- Virus Isolation and Serology Laboratory, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Robert J Gorelick
- AIDS and Cancer Virus Program, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Kristi Huik
- Clinical Retrovirology Section, HIV Dynamics and Replication Program National Cancer Institute, National Institutes of Health, Frederick, MD, USA
| | - Quan Yu
- Hematology Branch, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - Dima A Hammoud
- Center for Infectious Disease Imaging, National Institutes of Health Clinical Center, National Institutes of Health, Bethesda, MD, USA
| | - Bryan R Smith
- Section of Infections of the Nervous System, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
| | - Pawel Muranski
- Hematology Branch, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - Catherine Rehm
- Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Brad T Sherman
- Laboratory of Human Retrovirology and Immunoinformatics, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Craig Sykes
- Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Natalie Lindo
- Clinical Retrovirology Section, HIV Dynamics and Replication Program National Cancer Institute, National Institutes of Health, Frederick, MD, USA
| | - Peiying Ye
- Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Katherine M Bricker
- 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
| | - Christine M Fennessey
- AIDS and Cancer Virus Program, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Frank Maldarelli
- Clinical Retrovirology Section, HIV Dynamics and Replication Program National Cancer Institute, National Institutes of Health, Frederick, MD, USA.
| | - Irini Sereti
- Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA.
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5
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Monette A, Niu M, Nijhoff Asser M, Gorelick RJ, Mouland AJ. Scaffolding viral protein NC nucleates phase separation of the HIV-1 biomolecular condensate. Cell Rep 2022; 40:111251. [PMID: 36001979 DOI: 10.1016/j.celrep.2022.111251] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2021] [Revised: 06/20/2022] [Accepted: 08/01/2022] [Indexed: 11/26/2022] Open
Abstract
Membraneless biomolecular condensates (BMCs) contribute to the replication of a growing number of viruses but remain to be functionally characterized. Previously, we demonstrated that pan-retroviral nucleocapsid (NC) proteins phase separated into condensates regulating virus assembly. Here we discover that intrinsically disordered human immunodeficiency virus-type 1 (HIV-1) core proteins condense with the viral genomic RNA (vRNA) to assemble as BMCs attaining a geometry characteristic of viral reverse transcription complexes. We explore the predisposition, mechanisms, and pharmacologic sensitivity of HIV-1 core BMCs in living cells. HIV-1 vRNA-interacting NC condensates were found to be scaffolds onto which client capsid, reverse transcriptase, and integrase condensates assemble. HIV-1 core BMCs exhibit fundamental characteristics of BMCs and are drug-sensitive. Lastly, protease-mediated maturation of Gag and Gag-Pol precursor proteins yield abundant and visible BMCs in cells. This study redefines HIV-1 core components as fluid BMCs and advances our understanding of the nature of viral cores during ingress.
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Affiliation(s)
- Anne Monette
- HIV-1 RNA Trafficking Lab, Lady Davis Institute at the Jewish General Hospital, Montreal, Quebec H3T 1E2, Canada.
| | - Meijuan Niu
- HIV-1 RNA Trafficking Lab, Lady Davis Institute at the Jewish General Hospital, Montreal, Quebec H3T 1E2, Canada
| | - Maya Nijhoff Asser
- HIV-1 RNA Trafficking Lab, Lady Davis Institute at the Jewish General Hospital, Montreal, Quebec H3T 1E2, Canada; Department of Microbiology and Immunology, McGill University, Montreal, Quebec H3A 2B4, Canada
| | - Robert J Gorelick
- AIDS and Cancer Virus Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD 21701, USA
| | - Andrew J Mouland
- HIV-1 RNA Trafficking Lab, Lady Davis Institute at the Jewish General Hospital, Montreal, Quebec H3T 1E2, Canada; Department of Microbiology and Immunology, McGill University, Montreal, Quebec H3A 2B4, Canada; Department of Medicine, McGill University, Montreal, Quebec H4A 3J1, Canada.
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6
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Gay CL, James KS, Tuyishime M, Falcinelli SD, Joseph SB, Moeser MJ, Allard B, Kirchherr JL, Clohosey M, Raines SLM, Montefiori DC, Shen X, Gorelick RJ, Gama L, McDermott AB, Koup RA, Mascola JR, Floris-Moore M, Kuruc JD, Ferrari G, Eron JJ, Archin NM, Margolis DM. Stable Latent HIV Infection and Low-level Viremia Despite Treatment With the Broadly Neutralizing Antibody VRC07-523LS and the Latency Reversal Agent Vorinostat. J Infect Dis 2022; 225:856-861. [PMID: 34562096 PMCID: PMC8889279 DOI: 10.1093/infdis/jiab487] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2021] [Accepted: 09/21/2021] [Indexed: 11/13/2022] Open
Abstract
We tested the combination of a broadly neutralizing HIV antibody with the latency reversal agent vorinostat (VOR). Eight participants received 2 month-long cycles of VRC07-523LS with VOR. Low-level viremia, resting CD4+ T-cell-associated HIV RNA (rca-RNA) was measured, and intact proviral DNA assay (IPDA) and quantitative viral outgrowth assay (QVOA) were performed at baseline and posttreatment. In 3 participants, IPDA and QVOA declines were accompanied by significant declines of rca-RNA. However, no IPDA or QVOA declines clearly exceeded assay variance or natural decay. Increased resistance to VRC07-523LS was not observed. This combination therapy did not reduce viremia or the HIV reservoir. Clinical Trials Registration. NCT03803605.
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Affiliation(s)
- Cynthia L Gay
- University of North Carolina HIV Cure Center, University of North Carolina Chapel Hill School of Medicine, Chapel Hill, North Carolina, USA
- Department of Medicine, University of North Carolina Chapel Hill School of Medicine, Chapel Hill, North Carolina, USA
| | - Katherine S James
- University of North Carolina HIV Cure Center, University of North Carolina Chapel Hill School of Medicine, Chapel Hill, North Carolina, USA
| | - Marina Tuyishime
- Department of Surgery, Duke University Medical Center, Durham, North Carolina, USA
| | - Shane D Falcinelli
- University of North Carolina HIV Cure Center, University of North Carolina Chapel Hill School of Medicine, Chapel Hill, North Carolina, USA
- Department of Microbiology and Immunology, University of North Carolina Chapel Hill School of Medicine, Chapel Hill, North Carolina, USA
| | - Sarah B Joseph
- University of North Carolina HIV Cure Center, University of North Carolina Chapel Hill School of Medicine, Chapel Hill, North Carolina, USA
- Department of Microbiology and Immunology, University of North Carolina Chapel Hill School of Medicine, Chapel Hill, North Carolina, USA
| | - Matthew J Moeser
- University of North Carolina Center for AIDS Research, University of North Carolina Chapel Hill School of Medicine, Chapel Hill, North Carolina, USA
| | - Brigitte Allard
- University of North Carolina HIV Cure Center, University of North Carolina Chapel Hill School of Medicine, Chapel Hill, North Carolina, USA
| | - Jennifer L Kirchherr
- University of North Carolina HIV Cure Center, University of North Carolina Chapel Hill School of Medicine, Chapel Hill, North Carolina, USA
| | - Matthew Clohosey
- University of North Carolina HIV Cure Center, University of North Carolina Chapel Hill School of Medicine, Chapel Hill, North Carolina, USA
| | - Samuel L M Raines
- University of North Carolina HIV Cure Center, University of North Carolina Chapel Hill School of Medicine, Chapel Hill, North Carolina, USA
| | - David C Montefiori
- Department of Surgery, Duke University Medical Center, Durham, North Carolina, USA
| | - Xiaoying Shen
- Department of Surgery, Duke University Medical Center, Durham, North Carolina, USA
| | - Robert J Gorelick
- AIDS and Cancer Virus Program, Frederick National Laboratory for Cancer Research, Frederick, Maryland, USA
| | - Lucio Gama
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Adrian B McDermott
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Richard A Koup
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - John R Mascola
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Michelle Floris-Moore
- Department of Medicine, University of North Carolina Chapel Hill School of Medicine, Chapel Hill, North Carolina, USA
| | - JoAnn D Kuruc
- University of North Carolina HIV Cure Center, University of North Carolina Chapel Hill School of Medicine, Chapel Hill, North Carolina, USA
- Department of Medicine, University of North Carolina Chapel Hill School of Medicine, Chapel Hill, North Carolina, USA
| | - Guido Ferrari
- Department of Surgery, Duke University Medical Center, Durham, North Carolina, USA
| | - Joseph J Eron
- University of North Carolina HIV Cure Center, University of North Carolina Chapel Hill School of Medicine, Chapel Hill, North Carolina, USA
- Department of Medicine, University of North Carolina Chapel Hill School of Medicine, Chapel Hill, North Carolina, USA
| | - Nancie M Archin
- University of North Carolina HIV Cure Center, University of North Carolina Chapel Hill School of Medicine, Chapel Hill, North Carolina, USA
- Department of Medicine, University of North Carolina Chapel Hill School of Medicine, Chapel Hill, North Carolina, USA
| | - David M Margolis
- University of North Carolina HIV Cure Center, University of North Carolina Chapel Hill School of Medicine, Chapel Hill, North Carolina, USA
- Department of Medicine, University of North Carolina Chapel Hill School of Medicine, Chapel Hill, North Carolina, USA
- Department of Microbiology and Immunology, University of North Carolina Chapel Hill School of Medicine, Chapel Hill, North Carolina, USA
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7
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Uldrick TS, Adams SV, Fromentin R, Roche M, Fling SP, Gonçalves PH, Lurain K, Ramaswami R, Wang CCJ, Gorelick RJ, Welker JL, O'Donoghue L, Choudhary H, Lifson JD, Rasmussen TA, Rhodes A, Tumpach C, Yarchoan R, Maldarelli F, Cheever MA, Sékaly R, Chomont N, Deeks SG, Lewin SR. Pembrolizumab induces HIV latency reversal in people living with HIV and cancer on antiretroviral therapy. Sci Transl Med 2022; 14:eabl3836. [PMID: 35080914 DOI: 10.1126/scitranslmed.abl3836] [Citation(s) in RCA: 43] [Impact Index Per Article: 21.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
In people living with HIV (PLWH) on antiretroviral therapy (ART), virus persists in a latent form where there is minimal transcription or protein expression. Latently infected cells are a major barrier to curing HIV. Increasing HIV transcription and viral production in latently infected cells could facilitate immune recognition and reduce the pool of infected cells that persist on ART. Given that programmed cell death protein 1 (PD-1) expressing CD4+ T cells are preferentially infected with HIV in PLWH on ART, we aimed to determine whether administration of antibodies targeting PD-1 would reverse HIV latency in vivo. We therefore evaluated the impact of intravenous administration of pembrolizumab every 3 weeks on HIV latency in 32 PLWH and cancer on ART. After the first infusion of anti-PD-1, we observed a median 1.32-fold increase in unspliced HIV RNA and 1.61-fold increase in unspliced RNA:DNA ratio in sorted blood CD4+ T cells compared to baseline. We also observed a 1.65-fold increase in plasma HIV RNA. The frequency of CD4+ T cells with inducible virus evaluated using the tat/rev limiting dilution assay was higher after 6 cycles compared to baseline. Phylogenetic analyses of HIV env sequences in a participant who developed low concentrations of HIV viremia after 6 cycles of pembrolizumab did not demonstrate clonal expansion of HIV-infected cells. These data are consistent with anti-PD-1 being able to reverse HIV latency in vivo and support the rationale for combining anti-PD-1 with other interventions to reduce the HIV reservoir.
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Affiliation(s)
- Thomas S Uldrick
- Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA.,University of Washington, Seattle, WA 98109, USA.,HIV and AIDS Malignancy Branch, National Cancer Institute, Bethesda, MD 20892, USA
| | - Scott V Adams
- Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Remi Fromentin
- Department of Microbiology, Infectiology, and Immunology, Université de Montréal and Centre de Recherche du CHUM, Montréal H2X0A9, Canada
| | - Michael Roche
- RMIT University, Melbourne, VIC 3083, Australia.,Department of Infectious Diseases, University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC 3000, Australia
| | - Steven P Fling
- Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Priscila H Gonçalves
- HIV and AIDS Malignancy Branch, National Cancer Institute, Bethesda, MD 20892, USA
| | - Kathryn Lurain
- HIV and AIDS Malignancy Branch, National Cancer Institute, Bethesda, MD 20892, USA
| | - Ramya Ramaswami
- HIV and AIDS Malignancy Branch, National Cancer Institute, Bethesda, MD 20892, USA
| | | | - Robert J Gorelick
- AIDS and Cancer Virus Program, Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA
| | - Jorden L Welker
- AIDS and Cancer Virus Program, Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA
| | - Liz O'Donoghue
- Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | | | - Jeffrey D Lifson
- AIDS and Cancer Virus Program, Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA
| | - Thomas A Rasmussen
- Department of Infectious Diseases, University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC 3000, Australia.,Department of Infectious Diseases, Aarhus University Hospital, Aarhus 8200, Denmark
| | - Ajantha Rhodes
- Department of Infectious Diseases, University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC 3000, Australia
| | - Carolin Tumpach
- Department of Infectious Diseases, University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC 3000, Australia
| | - Robert Yarchoan
- HIV and AIDS Malignancy Branch, National Cancer Institute, Bethesda, MD 20892, USA
| | - Frank Maldarelli
- HIV and AIDS Malignancy Branch, National Cancer Institute, Bethesda, MD 20892, USA
| | | | | | - Nicolas Chomont
- Department of Microbiology, Infectiology, and Immunology, Université de Montréal and Centre de Recherche du CHUM, Montréal H2X0A9, Canada
| | - Steven G Deeks
- University of California, San Francisco, San Francisco, CA 94110, USA
| | - Sharon R Lewin
- Department of Infectious Diseases, University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC 3000, Australia.,Victorian Infectious Diseases Service, Royal Melbourne Hospital at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC 3000, Australia.,Department of Infectious Diseases, Alfred Hospital and Monash University, Melbourne, VIC 3004, Australia
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8
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Lyonnais S, Sadiq SK, Lorca-Oró C, Dufau L, Nieto-Marquez S, Escribà T, Gabrielli N, Tan X, Ouizougun-Oubari M, Okoronkwo J, Reboud-Ravaux M, Gatell JM, Marquet R, Paillart JC, Meyerhans A, Tisné C, Gorelick RJ, Mirambeau G. The HIV-1 Nucleocapsid Regulates Its Own Condensation by Phase-Separated Activity-Enhancing Sequestration of the Viral Protease during Maturation. Viruses 2021; 13:v13112312. [PMID: 34835118 PMCID: PMC8625067 DOI: 10.3390/v13112312] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2021] [Revised: 11/09/2021] [Accepted: 11/11/2021] [Indexed: 02/07/2023] Open
Abstract
A growing number of studies indicate that mRNAs and long ncRNAs can affect protein populations by assembling dynamic ribonucleoprotein (RNP) granules. These phase-separated molecular ‘sponges’, stabilized by quinary (transient and weak) interactions, control proteins involved in numerous biological functions. Retroviruses such as HIV-1 form by self-assembly when their genomic RNA (gRNA) traps Gag and GagPol polyprotein precursors. Infectivity requires extracellular budding of the particle followed by maturation, an ordered processing of ∼2400 Gag and ∼120 GagPol by the viral protease (PR). This leads to a condensed gRNA-NCp7 nucleocapsid and a CAp24-self-assembled capsid surrounding the RNP. The choreography by which all of these components dynamically interact during virus maturation is one of the missing milestones to fully depict the HIV life cycle. Here, we describe how HIV-1 has evolved a dynamic RNP granule with successive weak–strong–moderate quinary NC-gRNA networks during the sequential processing of the GagNC domain. We also reveal two palindromic RNA-binding triads on NC, KxxFxxQ and QxxFxxK, that provide quinary NC-gRNA interactions. Consequently, the nucleocapsid complex appears properly aggregated for capsid reassembly and reverse transcription, mandatory processes for viral infectivity. We show that PR is sequestered within this RNP and drives its maturation/condensation within minutes, this process being most effective at the end of budding. We anticipate such findings will stimulate further investigations of quinary interactions and emergent mechanisms in crowded environments throughout the wide and growing array of RNP granules.
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Affiliation(s)
- Sébastien Lyonnais
- Infectious Disease & AIDS Research Unit, Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Villaroel 170, 08036 Barcelona, Spain; (C.L.-O.); (S.N.-M.); (T.E.); (N.G.); (X.T.); (M.O.-O.); (J.O.); (J.M.G.)
- Centre d’Etudes des Maladies Infectieuses et Pharmacologie Anti-Infectieuse (CEMIPAI), CNRS UAR 3725, Université de Montpellier, 1919 Route de Mende, CEDEX 05, 34293 Montpellier, France
- Correspondence: (S.L.); (S.K.S.); (G.M.)
| | - S. Kashif Sadiq
- Infection Biology Laboratory, Department of Experimental and Health Sciences (DCEXS), Universitat Pompeu Fabra, Carrer Doctor Aiguader 88, 08003 Barcelona, Spain;
- Molecular and Cellular Modeling Group, Heidelberg Institute for Theoretical Studies (HITS), Schloss-Wolfsbrunnenweg 35, 69118 Heidelberg, Germany
- Genome Biology Unit, European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany
- Correspondence: (S.L.); (S.K.S.); (G.M.)
| | - Cristina Lorca-Oró
- Infectious Disease & AIDS Research Unit, Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Villaroel 170, 08036 Barcelona, Spain; (C.L.-O.); (S.N.-M.); (T.E.); (N.G.); (X.T.); (M.O.-O.); (J.O.); (J.M.G.)
| | - Laure Dufau
- Biological Adaptation and Ageing (B2A), CNRS UMR 8256 & INSERM ERL U1164, Institut de Biologie Paris-Seine (IBPS), Faculté des Sciences et d’Ingénierie (FSI), Sorbonne Université, 7 Quai St Bernard, CEDEX 05, 75252 Paris, France; (L.D.); (M.R.-R.)
| | - Sara Nieto-Marquez
- Infectious Disease & AIDS Research Unit, Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Villaroel 170, 08036 Barcelona, Spain; (C.L.-O.); (S.N.-M.); (T.E.); (N.G.); (X.T.); (M.O.-O.); (J.O.); (J.M.G.)
| | - Tuixent Escribà
- Infectious Disease & AIDS Research Unit, Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Villaroel 170, 08036 Barcelona, Spain; (C.L.-O.); (S.N.-M.); (T.E.); (N.G.); (X.T.); (M.O.-O.); (J.O.); (J.M.G.)
| | - Natalia Gabrielli
- Infectious Disease & AIDS Research Unit, Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Villaroel 170, 08036 Barcelona, Spain; (C.L.-O.); (S.N.-M.); (T.E.); (N.G.); (X.T.); (M.O.-O.); (J.O.); (J.M.G.)
| | - Xiao Tan
- Infectious Disease & AIDS Research Unit, Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Villaroel 170, 08036 Barcelona, Spain; (C.L.-O.); (S.N.-M.); (T.E.); (N.G.); (X.T.); (M.O.-O.); (J.O.); (J.M.G.)
- Biological Adaptation and Ageing (B2A), CNRS UMR 8256 & INSERM ERL U1164, Institut de Biologie Paris-Seine (IBPS), Faculté des Sciences et d’Ingénierie (FSI), Sorbonne Université, 7 Quai St Bernard, CEDEX 05, 75252 Paris, France; (L.D.); (M.R.-R.)
| | - Mohamed Ouizougun-Oubari
- Infectious Disease & AIDS Research Unit, Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Villaroel 170, 08036 Barcelona, Spain; (C.L.-O.); (S.N.-M.); (T.E.); (N.G.); (X.T.); (M.O.-O.); (J.O.); (J.M.G.)
| | - Josephine Okoronkwo
- Infectious Disease & AIDS Research Unit, Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Villaroel 170, 08036 Barcelona, Spain; (C.L.-O.); (S.N.-M.); (T.E.); (N.G.); (X.T.); (M.O.-O.); (J.O.); (J.M.G.)
| | - Michèle Reboud-Ravaux
- Biological Adaptation and Ageing (B2A), CNRS UMR 8256 & INSERM ERL U1164, Institut de Biologie Paris-Seine (IBPS), Faculté des Sciences et d’Ingénierie (FSI), Sorbonne Université, 7 Quai St Bernard, CEDEX 05, 75252 Paris, France; (L.D.); (M.R.-R.)
| | - José Maria Gatell
- Infectious Disease & AIDS Research Unit, Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Villaroel 170, 08036 Barcelona, Spain; (C.L.-O.); (S.N.-M.); (T.E.); (N.G.); (X.T.); (M.O.-O.); (J.O.); (J.M.G.)
- Facultat de Medicina y Ciencias de la Salud, Universitat de Barcelona, Carrer de Casanova 143, 08036 Barcelona, Spain
| | - Roland Marquet
- Architecture et Réactivité de l’ARN, CNRS UPR 9002, Université de Strasbourg, 2 Allée Conrad Roentgen, 67000 Strasbourg, France; (R.M.); (J.-C.P.)
| | - Jean-Christophe Paillart
- Architecture et Réactivité de l’ARN, CNRS UPR 9002, Université de Strasbourg, 2 Allée Conrad Roentgen, 67000 Strasbourg, France; (R.M.); (J.-C.P.)
| | - Andreas Meyerhans
- Infection Biology Laboratory, Department of Experimental and Health Sciences (DCEXS), Universitat Pompeu Fabra, Carrer Doctor Aiguader 88, 08003 Barcelona, Spain;
- Institució Catalana de Recerca i Estudis Avançats (ICREA), Passeig de Lluís Companys 23, 08010 Barcelona, Spain
| | - Carine Tisné
- Expression Génétique Microbienne, CNRS UMR 8261, Institut de Biologie Physico-Chimique (IBPC), Université de Paris, 13 Rue Pierre et Marie Curie, 75005 Paris, France;
| | - Robert J. Gorelick
- AIDS and Cancer Virus Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD 21701, USA;
| | - Gilles Mirambeau
- Infectious Disease & AIDS Research Unit, Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Villaroel 170, 08036 Barcelona, Spain; (C.L.-O.); (S.N.-M.); (T.E.); (N.G.); (X.T.); (M.O.-O.); (J.O.); (J.M.G.)
- Biologie Intégrative des Organismes Marins (BIOM), CNRS UMR 7232, Observatoire Océanologique de Banyuls (OOB), Faculté des Sciences et d’Ingénierie (FSI), Sorbonne Université, 1 Avenue Pierre Fabre, 66650 Banyuls-sur-Mer, France
- Correspondence: (S.L.); (S.K.S.); (G.M.)
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9
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Gatechompol S, Zheng L, Bao Y, Avihingsanon A, Kerr SJ, Kumarasamy N, Hakim JG, Maldarelli F, Gorelick RJ, Welker JL, Lifson JD, Hosseinipour MC, Eron JJ, Ruxrungtham K. Prevalence and risk of residual viremia after ART in low- and middle-income countries: A cross-sectional study. Medicine (Baltimore) 2021; 100:e26817. [PMID: 34477118 PMCID: PMC8415996 DOI: 10.1097/md.0000000000026817] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/09/2021] [Accepted: 07/14/2021] [Indexed: 01/05/2023] Open
Abstract
In order to design effective strategies to eradicate the HIV, an understanding of persistent viral reservoirs is needed. Many studies have demonstrated HIV residual viremia prevalence in high income countries, data from low- and middle-income countries (LMIC) are limited. We assessed the prevalence, and factors associated with residual viremia in people with HIV (PWH), who were virally-suppressed on antiretroviral therapy (ART) in LMIC. We also compared residual viremia prevalence between the LMIC and US.This is a cross-sectional, retrospective study that utilized stored specimen samples from the AIDS clinical trials group (ACTG) studies A5175 and A5208. The last available sample among participants with plasma HIV RNA < 400 copies/mL for ≥3 years were tested by the HIV molecular and monitoring core gag (HMMCgag) single copy assay (SCA). Residual viremia was defined as detectable if ≥1 copy/mL. Spearman's correlation and multivariable stepwise logistic regression were used to assess associations of various factors with SCA.A total of 320 participants, 246 (77%) from LMIC and 74 (23%) from US, were analyzed. Median (IQR) age was 33 (2840) years; baseline CD4 166 (88,230) cells/mm3; HIV RNA 5.0 (4.5, 5.3) log10 copies/mL; duration of viral suppression 3.4 (3.1, 4.0) years and 48% were male. In 85 participants with information available, 53% were subtype C, 42% subtype B and 5% other subtypes. Overall prevalence of residual viremia was 57% [95% CI, 52-63] with 51% [40-63] in US and 59% [53-65] in LMIC. Among participants with detectable SCA, the median (IQR) HIV RNA was 3.8 (2.2, 8.1) copies/mL. The multivariable model conducted in LMIC participants showed that higher baseline HIV RNA was associated with detectable residual RNA (OR 2.9, 95% CI 1.8, 4.6 for every log10 increase, P < .001). After including both US and LMIC in the final model, baseline HIV RNA remained significant. No difference in SCA detestability was found between US and LMIC sites (OR 1.1 [0.6, 2.0], P = .72) after adjusting for baseline RNA and parent study.The prevalence of residual viremia between both groups were not different and more than half of the participants had detectable viremia. Higher baseline HIV RNA was independently associated with residual viremia.
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Affiliation(s)
- Sivaporn Gatechompol
- HIV-NAT, Thai Red Cross AIDS Research Centre, Bangkok, Thailand
- Tuberculosis Research Unit, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Lu Zheng
- Harvard T.H. Chan School of Public Health, Boston, MA
| | - Yajing Bao
- Harvard T.H. Chan School of Public Health, Boston, MA
| | - Anchalee Avihingsanon
- HIV-NAT, Thai Red Cross AIDS Research Centre, Bangkok, Thailand
- Tuberculosis Research Unit, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Stephen J. Kerr
- HIV-NAT, Thai Red Cross AIDS Research Centre, Bangkok, Thailand
- Biostatistics Excellence Centre, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Nagalingeswaran Kumarasamy
- Chennai Antiviral Research and Treatment, Clinical Research Site, VHS Infectious Diseases Medical Centre, Chennai, India
| | | | | | | | - Jorden L. Welker
- Frederick National Laboratory for Cancer Research, Frederick, MD
| | | | | | - Joseph J. Eron
- University of North Carolina at Chapel Hill, Chapel Hill, NC
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10
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Kroon ED, Ananworanich J, Pagliuzza A, Rhodes A, Phanuphak N, Trautmann L, Mitchell JL, Chintanaphol M, Intasan J, Pinyakorn S, Benjapornpong K, Chang JJ, Colby DJ, Chomchey N, Fletcher JL, Eubanks K, Yang H, Kapson J, Dantanarayana A, Tennakoon S, Gorelick RJ, Maldarelli F, Robb ML, Kim JH, Spudich S, Chomont N, Phanuphak P, Lewin SR, de Souza MS. A randomized trial of vorinostat with treatment interruption after initiating antiretroviral therapy during acute HIV-1 infection. J Virus Erad 2020; 6:100004. [PMID: 33251022 PMCID: PMC7646672 DOI: 10.1016/j.jve.2020.100004] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2019] [Revised: 07/09/2020] [Accepted: 07/14/2020] [Indexed: 01/19/2023] Open
Abstract
OBJECTIVE AND DESIGN A randomized, open-label pilot study in individuals treated with antiretroviral therapy (ART) since acute HIV infection (AHI) with a regimen including a histone deacetylase inhibitor to induce HIV from latency and control HIV replication during subsequent treatment interruption (TI). METHODS Fifteen participants who initiated ART at AHI were randomized to vorinostat/hydroxychloroquine/maraviroc (VHM) plus ART (n = 10) or ART alone (n = 5). The VHM arm received three 14-day vorinostat cycles within 10 weeks before TI. ART was resumed for plasma viral load (VL) > 1,000 HIV RNA copies/mL. Primary outcome was proportion of participants on VHM + ART versus ART only with VL < 50 copies/mL for 24 weeks after TI. RESULTS Fifteen participants on ART (median: 178 weeks: range 79-295) enrolled. Two on VHM + ART experienced serious adverse events. Fourteen participants underwent TI; all experienced VL rebound with no difference in time between arms: VHM + ART (n = 9) median: 4 weeks and ART only (n = 5) median: 5 weeks. VHM induced a 2.2-fold increase in VL (p = 0.008) by single-copy HIV RNA assay after the first cycle. Neopterin levels increased significantly following the first two cycles. After VHM treatment, the frequencies of peripheral blood mononuclear cells harboring total HIV DNA and cell-associated RNA were unchanged. All participants achieved VL suppression following ART re-initiation. CONCLUSIONS Administration of VHM increased HIV VL in plasma, but this was not sustained. VHM did not impact time to viral rebound following TI and had no impact on the size of the HIV reservoir, suggesting that HIV reservoir elimination will require alternative treatment strategies.
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Affiliation(s)
| | - Jintanat Ananworanich
- SEARCH, Thai Red Cross AIDS Research Centre, Bangkok, Thailand
- The Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, USA
- United States Military HIV Research Program, Bethesda, MD, USA
- Bill and Melinda Gates Medical Research Institute, Cambridge, MA, USA
| | - Amélie Pagliuzza
- Centre de Recherche du CHUM and Department of Microbiology, Infectiology and Immunology, Université de Montréal, Montreal, Canada
| | - Ajantha Rhodes
- The Peter Doherty Institute for Infection and Immunity, University of Melbourne and Royal Melbourne Hospital, Melbourne, Australia
- Peter MacCallum Cancer Centre, Victorian Comprehensive Cancer Center, Melbourne, Australia
| | | | - Lydie Trautmann
- The Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, USA
- United States Military HIV Research Program, Bethesda, MD, USA
| | - Julie L. Mitchell
- The Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, USA
- United States Military HIV Research Program, Bethesda, MD, USA
| | - Michelle Chintanaphol
- SEARCH, Thai Red Cross AIDS Research Centre, Bangkok, Thailand
- Department of Neurology, Yale University School of Medicine, Yale University, New Haven, CT, USA
| | - Jintana Intasan
- SEARCH, Thai Red Cross AIDS Research Centre, Bangkok, Thailand
| | - Suteeraporn Pinyakorn
- SEARCH, Thai Red Cross AIDS Research Centre, Bangkok, Thailand
- The Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, USA
- United States Military HIV Research Program, Bethesda, MD, USA
| | | | - J. Judy Chang
- The Peter Doherty Institute for Infection and Immunity, University of Melbourne and Royal Melbourne Hospital, Melbourne, Australia
- Peter MacCallum Cancer Centre, Victorian Comprehensive Cancer Center, Melbourne, Australia
| | - Donn J. Colby
- SEARCH, Thai Red Cross AIDS Research Centre, Bangkok, Thailand
| | - Nitiya Chomchey
- SEARCH, Thai Red Cross AIDS Research Centre, Bangkok, Thailand
| | | | | | - Hua Yang
- Cooper Human Systems, Nashua, NH, USA
| | | | - Ashanti Dantanarayana
- The Peter Doherty Institute for Infection and Immunity, University of Melbourne and Royal Melbourne Hospital, Melbourne, Australia
- Peter MacCallum Cancer Centre, Victorian Comprehensive Cancer Center, Melbourne, Australia
| | - Surekha Tennakoon
- The Peter Doherty Institute for Infection and Immunity, University of Melbourne and Royal Melbourne Hospital, Melbourne, Australia
- Peter MacCallum Cancer Centre, Victorian Comprehensive Cancer Center, Melbourne, Australia
| | - Robert J. Gorelick
- AIDS and Cancer Virus Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Frank Maldarelli
- Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA
| | - Merlin L. Robb
- The Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, USA
- United States Military HIV Research Program, Bethesda, MD, USA
| | - Jerome H. Kim
- International Vaccine Initiative, Seoul, Republic of Korea
| | - Serena Spudich
- Department of Neurology, Yale University School of Medicine, Yale University, New Haven, CT, USA
| | - Nicolas Chomont
- Centre de Recherche du CHUM and Department of Microbiology, Infectiology and Immunology, Université de Montréal, Montreal, Canada
| | | | - Sharon R. Lewin
- The Peter Doherty Institute for Infection and Immunity, University of Melbourne and Royal Melbourne Hospital, Melbourne, Australia
- Peter MacCallum Cancer Centre, Victorian Comprehensive Cancer Center, Melbourne, Australia
- Department of Infectious Diseases, Alfred Health and Monash University, Melbourne, Australia
| | | | - for the SEARCH 019 and RV254 Study Teams
- SEARCH, Thai Red Cross AIDS Research Centre, Bangkok, Thailand
- The Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, USA
- United States Military HIV Research Program, Bethesda, MD, USA
- Bill and Melinda Gates Medical Research Institute, Cambridge, MA, USA
- Centre de Recherche du CHUM and Department of Microbiology, Infectiology and Immunology, Université de Montréal, Montreal, Canada
- The Peter Doherty Institute for Infection and Immunity, University of Melbourne and Royal Melbourne Hospital, Melbourne, Australia
- Peter MacCallum Cancer Centre, Victorian Comprehensive Cancer Center, Melbourne, Australia
- Department of Neurology, Yale University School of Medicine, Yale University, New Haven, CT, USA
- Cooper Human Systems, Nashua, NH, USA
- AIDS and Cancer Virus Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD, USA
- Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA
- International Vaccine Initiative, Seoul, Republic of Korea
- Department of Infectious Diseases, Alfred Health and Monash University, Melbourne, Australia
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11
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Anderson EM, Simonetti FR, Gorelick RJ, Hill S, Gouzoulis MA, Bell J, Rehm C, Pérez L, Boritz E, Wu X, Wells D, Hughes SH, Rao V, Coffin JM, Kearney MF, Maldarelli F. Dynamic Shifts in the HIV Proviral Landscape During Long Term Combination Antiretroviral Therapy: Implications for Persistence and Control of HIV Infections. Viruses 2020; 12:v12020136. [PMID: 31991737 PMCID: PMC7077288 DOI: 10.3390/v12020136] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2019] [Revised: 01/13/2020] [Accepted: 01/16/2020] [Indexed: 12/19/2022] Open
Abstract
Combination antiretroviral therapy (cART) controls but does not eradicate HIV infection; HIV persistence is the principal obstacle to curing infections. The proportion of defective proviruses increases during cART, but the dynamics of this process are not well understood, and a quantitative analysis of how the proviral landscape is reshaped after cART is initiated is critical to understanding how HIV persists. Here, we studied longitudinal samples from HIV infected individuals undergoing long term cART using multiplexed Droplet Digital PCR (ddPCR) approaches to quantify the proportion of deleted proviruses in lymphocytes. In most individuals undergoing cART, HIV proviruses that contain gag are lost more quickly than those that lack gag. Increases in the fraction of gag-deleted proviruses occurred only after 1–2 years of therapy, suggesting that the immune system, and/or toxicity of viral re-activation helps to gradually shape the proviral landscape. After 10–15 years on therapy, there were as many as 3.5–5 times more proviruses in which gag was deleted or highly defective than those containing intact gag. We developed a provirus-specific ddPCR approach to quantify individual clones. Investigation of a clone of cells containing a deleted HIV provirus integrated in the HORMAD2 gene revealed that the cells underwent a massive expansion shortly after cART was initiated until the clone, which was primarily in effector memory cells, dominated the population of proviruses for over 6 years. The expansion of this HIV-infected clone had substantial effects on the overall proviral population.
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Affiliation(s)
- Elizabeth M. Anderson
- HIV Dynamics and Replication Program, NCI, NIH, Frederick, MD 21702, USA; (E.M.A.); (F.R.S.); (S.H.); (M.A.G.); (S.H.H.); (M.F.K.)
- Department of Biology, The Catholic University of America, Washington, DC 20064, USA;
| | - Francesco R. Simonetti
- HIV Dynamics and Replication Program, NCI, NIH, Frederick, MD 21702, USA; (E.M.A.); (F.R.S.); (S.H.); (M.A.G.); (S.H.H.); (M.F.K.)
| | - Robert J. Gorelick
- Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA; (R.J.G.); (J.B.)
| | - Shawn Hill
- HIV Dynamics and Replication Program, NCI, NIH, Frederick, MD 21702, USA; (E.M.A.); (F.R.S.); (S.H.); (M.A.G.); (S.H.H.); (M.F.K.)
| | - Monica A. Gouzoulis
- HIV Dynamics and Replication Program, NCI, NIH, Frederick, MD 21702, USA; (E.M.A.); (F.R.S.); (S.H.); (M.A.G.); (S.H.H.); (M.F.K.)
| | - Jennifer Bell
- Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA; (R.J.G.); (J.B.)
| | - Catherine Rehm
- Laboratory of Immunoregulation, NIAID, NIH, Bethesda, MD 20814, USA;
| | - Liliana Pérez
- Virus Persistence and Dynamics Section, VRC, NIAID, NIH, Bethesda, MD 20814, USA; (L.P.); (E.B.)
| | - Eli Boritz
- Virus Persistence and Dynamics Section, VRC, NIAID, NIH, Bethesda, MD 20814, USA; (L.P.); (E.B.)
| | - Xiaolin Wu
- Cancer Research Technology Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA; (X.W.); (D.W.)
| | - Daria Wells
- Cancer Research Technology Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA; (X.W.); (D.W.)
| | - Stephen H. Hughes
- HIV Dynamics and Replication Program, NCI, NIH, Frederick, MD 21702, USA; (E.M.A.); (F.R.S.); (S.H.); (M.A.G.); (S.H.H.); (M.F.K.)
| | - Venigalla Rao
- Department of Biology, The Catholic University of America, Washington, DC 20064, USA;
| | - John M. Coffin
- Department of Biology, Tufts University, Boston, MA 02155, USA;
| | - Mary F. Kearney
- HIV Dynamics and Replication Program, NCI, NIH, Frederick, MD 21702, USA; (E.M.A.); (F.R.S.); (S.H.); (M.A.G.); (S.H.H.); (M.F.K.)
| | - Frank Maldarelli
- HIV Dynamics and Replication Program, NCI, NIH, Frederick, MD 21702, USA; (E.M.A.); (F.R.S.); (S.H.); (M.A.G.); (S.H.H.); (M.F.K.)
- Correspondence: ; Tel.: +01-301-846-5611
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12
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Solomon IH, Chettimada S, Misra V, Lorenz DR, Gorelick RJ, Gelman BB, Morgello S, Gabuzda D. White Matter Abnormalities Linked to Interferon, Stress Response, and Energy Metabolism Gene Expression Changes in Older HIV-Positive Patients on Antiretroviral Therapy. Mol Neurobiol 2019; 57:1115-1130. [PMID: 31691183 DOI: 10.1007/s12035-019-01795-3] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2019] [Accepted: 09/22/2019] [Indexed: 12/11/2022]
Abstract
Neurocognitive impairment (NCI) remains a significant cause of morbidity in human immunodeficiency virus (HIV)-positive individuals despite highly active antiretroviral therapy (HAART). White matter abnormalities have emerged as a key component of age-related neurodegeneration, and accumulating evidence suggests they play a role in HIV-associated neurocognitive disorders. Viral persistence in the brain induces chronic inflammation associated with lymphocytic infiltration, microglial proliferation, myelin loss, and cerebrovascular lesions. In this study, gene expression profiling was performed on frontal white matter from 34 older HIV+ individuals on HAART (18 with NCI) and 24 HIV-negative controls. We used the NanoString nCounter platform to evaluate 933 probes targeting inflammation, interferon and stress responses, energy metabolism, and central nervous system-related genes. Viral loads were measured using single-copy assays. Compared to HIV- controls, HIV+ individuals exhibited increased expression of genes related to interferon, MHC-1, and stress responses, myeloid cells, and T cells and decreased expression of genes associated with oligodendrocytes and energy metabolism in white matter. These findings correlated with increased white matter inflammation and myelin pallor, suggesting interferon (IRFs, IFITM1, ISG15, MX1, OAS3) and stress response (ATF4, XBP1, CHOP, CASP1, WARS) gene expression changes are associated with decreased energy metabolism (SREBF1, SREBF2, PARK2, TXNIP) and oligodendrocyte myelin production (MAG, MOG), leading to white matter dysfunction. Machine learning identified a 15-gene signature predictive of HIV status that was validated in an independent cohort. No specific gene expression patterns were associated with NCI. These findings suggest therapies that decrease chronic inflammation while protecting mitochondrial function may help to preserve white matter integrity in older HIV+ individuals.
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Affiliation(s)
- Isaac H Solomon
- Department of Pathology, Brigham and Women's Hospital, Boston, MA, USA.,Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, CLS 1010, 450 Brookline Ave, Boston, MA, 02215, USA
| | - Sukrutha Chettimada
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, CLS 1010, 450 Brookline Ave, Boston, MA, 02215, USA
| | - Vikas Misra
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, CLS 1010, 450 Brookline Ave, Boston, MA, 02215, USA
| | - David R Lorenz
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, CLS 1010, 450 Brookline Ave, Boston, MA, 02215, USA
| | - Robert J Gorelick
- AIDS and Cancer Virus Program, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Benjamin B Gelman
- Department of Pathology, University of Texas Medical Branch, Galveston, TX, USA
| | - Susan Morgello
- Department of Neurology, Icahn School of Medicine of Mount Sinai, New York, NY, USA
| | - Dana Gabuzda
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, CLS 1010, 450 Brookline Ave, Boston, MA, 02215, USA. .,Department of Neurology, Harvard Medical School, Boston, MA, USA.
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13
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Reid EG, Suazo A, Lensing SY, Dittmer DP, Ambinder RF, Maldarelli F, Gorelick RJ, Aboulafia D, Mitsuyasu R, Dickson MA, Wachsman W. Pilot Trial AMC-063: Safety and Efficacy of Bortezomib in AIDS-associated Kaposi Sarcoma. Clin Cancer Res 2019; 26:558-565. [PMID: 31624104 DOI: 10.1158/1078-0432.ccr-19-1044] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2019] [Revised: 06/10/2019] [Accepted: 10/14/2019] [Indexed: 11/16/2022]
Abstract
PURPOSE AIDS-related Kaposi sarcoma is often incompletely controlled, requiring serial therapies. Kaposi sarcoma herpesvirus (KSHV) induces transformation of endothelial cells, where it resides in a predominately latent state. We hypothesized proteasome inhibition would have direct antitumor activity, induce lytic activation of KSHV, and inhibit HIV infectivity, improving control of both Kaposi sarcoma and HIV. The primary objective was determining the MTD of bortezomib in AIDS-Kaposi sarcoma. Secondary objectives included estimating the impact of bortezomib on Kaposi sarcoma response, KSHV plasma DNA copy number (PDCN), and HIV viral loads (VL). PATIENTS AND METHODS A 3+3 dose escalation design was employed evaluating four dose levels of bortezomib (0.75, 1, 1.2, or 1.6 mg/m2) administered intravenously on days 1, 8, and 15 of 28-day cycles in patients with relapsed/refractory (r/r) AIDS-Kaposi sarcoma taking antiretroviral therapy. RESULTS Seventeen patients enrolled. No dose-limiting toxicities occurred and the MTD was not reached. The most common adverse events included diarrhea, fatigue and nausea. Among 15 evaluable patients, partial response (PR) occurred in nine (60%), with a PR rate of 83% in the 1.6 mg/m2 cohort; the remainder had stable disease (SD). Median time to response was 2.1 months. Median change in KSHV PDCN was significantly different between those with PR versus SD. During cycle 1, seven of 11 evaluable patients had decreases in HIV VL. CONCLUSIONS Bortezomib is well-tolerated and active in AIDS-Kaposi sarcoma. The 60% PR rate is notable given the dose-finding nature of the study in a r/r population. Changes in KSHV PDCN and HIV VL trended as hypothesized.
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Affiliation(s)
- Erin G Reid
- University of California, San Diego Moores Cancer Center, La Jolla, California.
| | - Adrienne Suazo
- University of California, San Diego Moores Cancer Center, La Jolla, California
| | - Shelly Y Lensing
- University of Arkansas for Medical Sciences, Little Rock, Arkansas
| | - Dirk P Dittmer
- Lineberger Comprehensive Cancer Center at the University of North Carolina at Chapel Hill, North Carolina
| | | | - Frank Maldarelli
- HIV Dynamics and Replication Program, National Cancer Institute, Frederick, Maryland
| | - Robert J Gorelick
- AIDS and Cancer Virus Program, Frederick National Laboratory for Cancer Research, Frederick, Maryland
| | - David Aboulafia
- Floyd and Delores Jones Cancer Institute at Virginia Mason Medical Center, Seattle, Washington
| | - Ronald Mitsuyasu
- Center for AIDS Research and Education, University of California, Los Angeles, Los Angeles, California
| | - Mark A Dickson
- Memorial Sloan Kettering Cancer Center and Weill Cornell Medical College, New York, New York
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14
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Mouhand A, Belfetmi A, Catala M, Larue V, Zargarian L, Brachet F, Gorelick RJ, Van Heijenoort C, Mirambeau G, Barraud P, Mauffret O, Tisné C. Modulation of the HIV nucleocapsid dynamics finely tunes its RNA-binding properties during virion genesis. Nucleic Acids Res 2019; 46:9699-9710. [PMID: 29986076 PMCID: PMC6182130 DOI: 10.1093/nar/gky612] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2018] [Accepted: 06/26/2018] [Indexed: 02/06/2023] Open
Abstract
During HIV-1 assembly and budding, Gag protein, in particular the C-terminal domain containing the nucleocapsid domain (NCd), p1 and p6, is the site of numerous interactions with viral and cellular factors. Most in vitro studies of Gag have used constructs lacking p1 and p6. Here, using NMR spectroscopy, we show that the p1-p6 region of Gag (NCp15) is largely disordered, but interacts transiently with the NCd. These interactions modify the dynamic properties of the NCd. Indeed, using isothermal titration calorimetry (ITC), we have measured a higher entropic penalty to RNA-binding for the NCd precursor, NCp15, than for the mature form, NCp7, which lacks p1 and p6. We propose that during assembly and budding of virions, concomitant with Gag oligomerization, transient interactions between NCd and p1-p6 become salient and responsible for (i) a higher level of structuration of p6, which favours recruitment of budding partners; and (ii) a higher entropic penalty to RNA-binding at specific sites that favours non-specific binding of NCd at multiple sites on the genomic RNA (gRNA). The contributions of p6 and p1 are sequentially removed via proteolysis during Gag maturation such that the RNA-binding specificity of the mature protein is governed by the properties of NCd.
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Affiliation(s)
- Assia Mouhand
- Laboratoire de Cristallographie et RMN biologiques, CNRS, Université Paris Descartes, USPC, 4 avenue de l'Observatoire, 75006 Paris, France.,Laboratoire d'Expression génétique microbienne, IBPC, CNRS, Université Paris Diderot, USPC, 13 rue Pierre et Marie Curie, 75005 Paris, France
| | - Anissa Belfetmi
- LBPA, CNRS UMR 8113, ENS Paris-Saclay, Université Paris-Saclay, 61 Avenue du Pdt Wilson, F-94235 Cachan, France
| | - Marjorie Catala
- Laboratoire de Cristallographie et RMN biologiques, CNRS, Université Paris Descartes, USPC, 4 avenue de l'Observatoire, 75006 Paris, France.,Laboratoire d'Expression génétique microbienne, IBPC, CNRS, Université Paris Diderot, USPC, 13 rue Pierre et Marie Curie, 75005 Paris, France
| | - Valéry Larue
- Laboratoire de Cristallographie et RMN biologiques, CNRS, Université Paris Descartes, USPC, 4 avenue de l'Observatoire, 75006 Paris, France
| | - Loussiné Zargarian
- LBPA, CNRS UMR 8113, ENS Paris-Saclay, Université Paris-Saclay, 61 Avenue du Pdt Wilson, F-94235 Cachan, France
| | - Franck Brachet
- Laboratoire de Cristallographie et RMN biologiques, CNRS, Université Paris Descartes, USPC, 4 avenue de l'Observatoire, 75006 Paris, France
| | - Robert J Gorelick
- AIDS and Cancer Virus Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, MD 21702-1201, USA
| | - Carine Van Heijenoort
- Institut de Chimie des Substances Naturelles, CNRS UPR2301, Univ. Paris Sud, Université Paris-Saclay, Avenue de la Terrasse, 91190 Gif-sur-Yvette, France
| | - Gilles Mirambeau
- Infectious disease & AIDS Research unit, IDIBAPS, Barcelona, Barcelona, Spain.,Sorbonne Université, Faculté des Sciences et Ingénierie, UFR 927 des Sciences de la Vie, Paris, France
| | - Pierre Barraud
- Laboratoire de Cristallographie et RMN biologiques, CNRS, Université Paris Descartes, USPC, 4 avenue de l'Observatoire, 75006 Paris, France.,Laboratoire d'Expression génétique microbienne, IBPC, CNRS, Université Paris Diderot, USPC, 13 rue Pierre et Marie Curie, 75005 Paris, France
| | - Olivier Mauffret
- LBPA, CNRS UMR 8113, ENS Paris-Saclay, Université Paris-Saclay, 61 Avenue du Pdt Wilson, F-94235 Cachan, France
| | - Carine Tisné
- Laboratoire de Cristallographie et RMN biologiques, CNRS, Université Paris Descartes, USPC, 4 avenue de l'Observatoire, 75006 Paris, France.,Laboratoire d'Expression génétique microbienne, IBPC, CNRS, Université Paris Diderot, USPC, 13 rue Pierre et Marie Curie, 75005 Paris, France
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15
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Boulougoura A, Gabriel E, Laidlaw E, Khetani V, Arakawa K, Higgins J, Rupert A, Gorelick RJ, Lumbard K, Pau A, Poole A, Kibiy A, Kumar P, Sereti I. A Phase I, Randomized, Controlled Clinical Study of CC-11050 in People Living With HIV With Suppressed Plasma Viremia on Antiretroviral Therapy (APHRODITE). Open Forum Infect Dis 2019; 6:ofz246. [PMID: 31211164 DOI: 10.1093/ofid/ofz246] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2019] [Accepted: 06/02/2019] [Indexed: 12/16/2022] Open
Abstract
Objective Phosphodiesterase 4 inhibitors (PDE4i) are novel anti-inflammatory medications that have been approved for rheumatologic diseases and have been tested as host-directed therapy in tuberculosis. We examined the safety of CC-11050, a potent PDE4i in people living with HIV (PLWH) with suppressed HIV plasma viremia. We hypothesized that CC-11050 could be used to modulate HIV-related inflammation. Method Thirty PLWH on antiretroviral therapy (ART) ≥ 1 year with suppressed HIV viremia were enrolled and randomized 2:1 to 12 weeks of CC-11050 200mg twice daily or placebo with follow-up at weeks 2, 4, 8, 12, and 16. Primary endpoint was safety. Secondary endpoints were the effect of CC-11050 on cytokines, monocyte, and T-cell activation and potential pharmacokinetic interaction between CC-11050 and Efavirenz (EFV). Results At baseline, median age was 49.5 years and CD4 count 459 cells/µL. Most frequent adverse events (grade 1 and 2 only) in CC-11050 group were headache, diarrhea, nausea, cough, nasal congestion, and restlessness. Over a 12-week period, the CC-11050 group had lower level of IL-8, adjusted for baseline level, group, and week (0.72-fold, P = .02), lower percentage of NK cells (0.87-fold, P = .02) and higher IL-6 level (1.48-fold, P = .03) compared to placebo (0.87-fold, P = .02). CC-11050 and EFV co-administration did not reveal any pharmacokinetic interaction. Conclusions CC-11050 was well tolerated in PLWH, without affecting CD4 counts or plasma viremia, and led to a decrease in NK cells and plasma IL-8 level after 12-weeks of administration. Further study will be needed to elucidate the efficacy of CC-11050 as potential anti-inflammatory adjuvant strategy in HIV.
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Affiliation(s)
- Afroditi Boulougoura
- National Institute of Allergy and Infectious Diseases, Bethesda, Maryland.,Department of Internal Medicine, MedStar Georgetown University Hospital, Washington, District of Columbia
| | - Erin Gabriel
- Department of Medical Epidemiology and Biostatistics, Karolinska Institute, Stockholm, Sweden
| | - Elizabeth Laidlaw
- National Institute of Allergy and Infectious Diseases, Bethesda, Maryland
| | | | | | | | | | | | - Keith Lumbard
- Clinical Monitoring Research Program Directorate, Frederick National Laboratory for Cancer Research, Frederick, Maryland
| | - Alice Pau
- National Institute of Allergy and Infectious Diseases, Bethesda, Maryland
| | - April Poole
- National Institute of Allergy and Infectious Diseases, Bethesda, Maryland
| | - Angela Kibiy
- National Institute of Allergy and Infectious Diseases, Bethesda, Maryland
| | - Princy Kumar
- Department of Infectious Disease, MedStar Georgetown University Hospital, Washington, District of Columbia
| | - Irini Sereti
- National Institute of Allergy and Infectious Diseases, Bethesda, Maryland
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16
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Miller Jenkins LM, Paine EL, Deshmukh L, Nikolayevskiy H, Lyons GC, Scerba MT, Rosenker KG, Luecke HF, Louis JM, Chertova E, Gorelick RJ, Ott DE, Clore GM, Appella DH. Inhibition of HIV Maturation via Selective Unfolding and Cross-Linking of Gag Polyprotein by a Mercaptobenzamide Acetylator. J Am Chem Soc 2019; 141:8327-8338. [PMID: 31042030 PMCID: PMC8496520 DOI: 10.1021/jacs.9b02743] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
For HIV to become infectious, any new virion produced from an infected cell must undergo a maturation process that involves the assembly of viral polyproteins Gag and Gag-Pol at the membrane surface. The self-assembly of these viral proteins drives formation of a new viral particle as well as the activation of HIV protease, which is needed to cleave the polyproteins so that the final core structure of the virus will properly form. Molecules that interfere with HIV maturation will prevent any new virions from infecting additional cells. In this manuscript, we characterize the unique mechanism by which a mercaptobenzamide thioester small molecule (SAMT-247) interferes with HIV maturation via a series of selective acetylations at highly conserved cysteine and lysine residues in Gag and Gag-Pol polyproteins. The results provide the first insights into how acetylation can be utilized to perturb the process of HIV maturation and reveal a new strategy to limit the infectivity of HIV.
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Affiliation(s)
- Lisa M. Miller Jenkins
- Laboratory of Cell Biology, National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892, United States
| | - Elliott L. Paine
- Laboratory of Cell Biology, National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892, United States
| | - Lalit Deshmukh
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, Bethesda, Maryland 20892, United States
| | - Herman Nikolayevskiy
- Laboratory of Bioorganic Chemistry, National Institute of Diabetes and Digestive and Kidney Diseases, Bethesda, Maryland 20892, United States
| | - Gaelyn C. Lyons
- Laboratory of Cell Biology, National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892, United States
| | - Michael T. Scerba
- Laboratory of Bioorganic Chemistry, National Institute of Diabetes and Digestive and Kidney Diseases, Bethesda, Maryland 20892, United States
| | - Kara George Rosenker
- Laboratory of Bioorganic Chemistry, National Institute of Diabetes and Digestive and Kidney Diseases, Bethesda, Maryland 20892, United States
| | - Hans F. Luecke
- Advanced Mass Spectrometry Core, National Institute of Diabetes and Digestive and Kidney Diseases, Bethesda, Maryland 20892, United States
| | - John M. Louis
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, Bethesda, Maryland 20892, United States
| | - Elena Chertova
- AIDS and Cancer Virus Program, Leidos Biomedical Research Inc., Frederick National Laboratory for Cancer Research, Frederick, Maryland 21701, United States
| | - Robert J. Gorelick
- AIDS and Cancer Virus Program, Leidos Biomedical Research Inc., Frederick National Laboratory for Cancer Research, Frederick, Maryland 21701, United States
| | - David E. Ott
- AIDS and Cancer Virus Program, Leidos Biomedical Research Inc., Frederick National Laboratory for Cancer Research, Frederick, Maryland 21701, United States
| | - G. Marius Clore
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, Bethesda, Maryland 20892, United States
| | - Daniel H. Appella
- Laboratory of Bioorganic Chemistry, National Institute of Diabetes and Digestive and Kidney Diseases, Bethesda, Maryland 20892, United States
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17
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Boulougoura A, Gabriel E, Laidlaw E, Khetani V, Arakawa K, Higgins J, Rupert A, Gorelick RJ, Lumbard K, Pau A, Poole A, Kibiy A, Kumar P, Sereti I. A phase 1, randomized, controlled clinical study of CC-11050 in people living with HIV with suppressed plasma viremia on antiretroviral therapy (APHRODITE). The Journal of Immunology 2019. [DOI: 10.4049/jimmunol.202.supp.182.88] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Abstract
Background
Phosphodiesterase 4 inhibitors (PDE4i) block the degradation of cyclic adenosine monophosphate and modulate both innate and adaptive immune responses. PDE4i have been approved for rheumatologic diseases and tested as host-directed therapy in TB. We examined the safety of CC-11050, a new potent PDE4i, in HIV+ people with suppressed viral load (VL). We hypothesized that CC-11050 could be used to modulate HIV-related inflammatory responses.
Methods
Thirty HIV+ participants, on antiretroviral therapy (ART) ≥ 1 year with HIV VL <50 copies/mL were randomized 2:1 to 12 weeks of CC-11050 200mg BID or placebo with follow-up at weeks 2, 4, 8, 12 and 16. Primary endpoint was safety. We also assessed the effect of CC-11050 on CD4+, CD8+, NK, VL, plasma cytokines, monocyte and T-cell activation.
Results
At baseline, median age was 49.5 years and CD4+ 459 cells/μL. Most frequent adverse events (only grades 1–2) in CC-11050 group were headache, diarrhea, nausea, cough and nasal congestion. The CC-11050 group had lower IL-8 level after adjustment for baseline level, group and week (0.72 fold, p=0.02) and lower %NK cells compared to placebo (0.87 fold, p=0.02). At week 12, the CC-11050 group had higher %CD14++CD16+ monocytes than placebo (median 58.5% vs 50.7%, p=0.03). There was no significant effect on plasma HIV viremia, assessed by single copy assay and on cell-associated DNA and RNA in PBMC.
Conclusions
CC-11050 was well tolerated in HIV+ participants without affecting controlled viremia. CC-11050 had an effect on innate immune mechanisms, by decreasing NK cells and IL-8 level and increasing intermediate monocytes. Further study is needed to elucidate the efficacy of CC-11050 as potential anti-inflammatory adjuvant strategy in HIV.
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Affiliation(s)
- Afroditi Boulougoura
- 1National Institute of Allergy and Infectious Diseases, National Institutes of Health
- 2Department of Internal Medicine, MedStar Georgetown University Hospital, Washington, DC, USA
| | - Erin Gabriel
- 3Department of Medical Epidemiology and Biostatistics, Karolinska Institute, Stockholm, Sweden
| | - Elizabeth Laidlaw
- 1National Institute of Allergy and Infectious Diseases, National Institutes of Health
| | | | | | - Jeanette Higgins
- 5Leidos Biomedical Research Inc, Frederick National Laboratory for Cancer Research
| | - Adam Rupert
- 5Leidos Biomedical Research Inc, Frederick National Laboratory for Cancer Research
| | - Robert J. Gorelick
- 5Leidos Biomedical Research Inc, Frederick National Laboratory for Cancer Research
| | - Keith Lumbard
- 6Clinical Monitoring Research Program Directorate, Frederick National Laboratory for Cancer Research
| | - Alice Pau
- 1National Institute of Allergy and Infectious Diseases, National Institutes of Health
| | - April Poole
- 1National Institute of Allergy and Infectious Diseases, National Institutes of Health
| | - Angela Kibiy
- 1National Institute of Allergy and Infectious Diseases, National Institutes of Health
| | - Princy Kumar
- 7Department of Infectious Disease, MedStar Georgetown University Hospital, Washington, DC, USA
| | - Irini Sereti
- 1National Institute of Allergy and Infectious Diseases, National Institutes of Health
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18
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Crowell TA, Colby DJ, Pinyakorn S, Sacdalan C, Pagliuzza A, Intasan J, Benjapornpong K, Tangnaree K, Chomchey N, Kroon E, de Souza MS, Tovanabutra S, Rolland M, Eller MA, Paquin-Proulx D, Bolton DL, Tokarev A, Thomas R, Takata H, Trautmann L, Krebs SJ, Modjarrad K, McDermott AB, Bailer RT, Doria-Rose N, Patel B, Gorelick RJ, Fullmer BA, Schuetz A, Grandin PV, O'Connell RJ, Ledgerwood JE, Graham BS, Tressler R, Mascola JR, Chomont N, Michael NL, Robb ML, Phanuphak N, Ananworanich J. Safety and efficacy of VRC01 broadly neutralising antibodies in adults with acutely treated HIV (RV397): a phase 2, randomised, double-blind, placebo-controlled trial. Lancet HIV 2019; 6:e297-e306. [PMID: 31000477 DOI: 10.1016/s2352-3018(19)30053-0] [Citation(s) in RCA: 50] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2018] [Revised: 02/06/2019] [Accepted: 02/12/2019] [Indexed: 12/12/2022]
Abstract
BACKGROUND HIV-1-specific broadly neutralising antibodies such as VRC01 could promote HIV remission by halting viral replication and clearing infected cells. We investigated whether VRC01 could promote sustained viral control off antiretroviral therapy (ART) in adults who initiated ART during acute HIV infection. METHODS We did a randomised, double-blind, placebo-controlled trial at the Thai Red Cross AIDS Research Centre in Bangkok, Thailand. Eligible participants were aged 20-50 years, had initiated ART during acute infection (ie, Fiebig stages I-III), had been taking ART for more than 24 months, had fewer than 50 HIV-1 RNA copies per mL on three consecutive measurements, had more than 400 CD4 cells per μL, had fewer than ten copies of integrated HIV-1 DNA per 106 peripheral blood mononuclear cells, and were in generally good health. Eligible participants were randomly assigned (3:1) based on computer-generated lists with a blocking factor of 4 to receive VRC01 (40 mg/kg) or placebo (saline) intravenously every 3 weeks for up to 24 weeks during analytic interruption of ART, followed by continued observation off all therapies. Randomisation was stratified by Fiebig stage (I vs II vs III) at HIV diagnosis. Participants were monitored closely and resumed ART if 1000 or more HIV-1 RNA copies were detected per mL of plasma. The primary outcomes were the frequency of serious adverse events and the proportion of participants with fewer than 50 HIV-1 RNA copies per mL 24 weeks after treatment interruption. Efficacy analyses included all participants who received at least one full dose of study product, and safety analyses included all participants exposed to any study product. The trial was registered with ClinicalTrials.gov, number NCT02664415. This trial is completed. FINDINGS Between Aug 8, 2016, and Jan 9, 2017, 19 men were randomly assigned, 14 to the VRC01 group and five to the placebo group. One participant in the VRC01 group received a partial infusion without undergoing treatment interruption. The other 18 participants all received at least one full study infusion and underwent ART interruption. No serious adverse events were reported in either group. Only one participant in the VRC01 group achieved the primary efficacy endpoint of viral suppression 24 weeks after ART interruption. The other 17 restarted ART because of a confirmed recording of 1000 or more HIV-1 RNA copies per mL before 24 weeks. INTERPRETATION VRC01 monotherapy in individuals who initiated ART during acute HIV infection was well tolerated but did not significantly increase the number of participants with viral suppression 24 weeks after ART interruption. Further development of VRC01 and other immunotherapies for HIV will probably occur as part of combination regimens that include several treatments directed against unique therapeutic targets. FUNDING US Department of the Army, US National Institutes of Health, and the Thai Red Cross AIDS Research Centre.
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Affiliation(s)
- Trevor A Crowell
- US Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD, USA; Henry M Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, USA.
| | - Donn J Colby
- SEARCH, the Thai Red Cross AIDS Research Center, Bangkok, Thailand
| | - Suteeraporn Pinyakorn
- US Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD, USA; Henry M Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, USA
| | - Carlo Sacdalan
- SEARCH, the Thai Red Cross AIDS Research Center, Bangkok, Thailand
| | - Amélie Pagliuzza
- Centre de Recherche du CHUM and Department of Microbiology, Infectiology and Immunology, Université de Montréal, Montreal, QC, Canada
| | - Jintana Intasan
- SEARCH, the Thai Red Cross AIDS Research Center, Bangkok, Thailand
| | | | | | - Nitiya Chomchey
- SEARCH, the Thai Red Cross AIDS Research Center, Bangkok, Thailand
| | - Eugène Kroon
- SEARCH, the Thai Red Cross AIDS Research Center, Bangkok, Thailand
| | - Mark S de Souza
- Henry M Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, USA; SEARCH, the Thai Red Cross AIDS Research Center, Bangkok, Thailand
| | - Sodsai Tovanabutra
- US Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD, USA; Henry M Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, USA
| | - Morgane Rolland
- US Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD, USA; Henry M Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, USA
| | - Michael A Eller
- US Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD, USA; 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; Henry M Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, USA
| | - Diane L Bolton
- US Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD, USA; 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; Henry M Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, USA
| | - Rasmi Thomas
- US Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD, USA; Henry M Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, USA
| | - Hiroshi Takata
- US Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD, USA; Henry M Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, USA
| | - Lydie Trautmann
- US Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD, USA; Henry M Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, USA
| | - Shelly J Krebs
- US Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD, USA; Henry M Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, USA
| | - Kayvon Modjarrad
- US Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD, USA
| | - Adrian B McDermott
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Robert T Bailer
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Nicole Doria-Rose
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Bijal Patel
- Division of AIDS, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Robert J Gorelick
- AIDS and Cancer Virus Program, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Brandie A Fullmer
- AIDS and Cancer Virus Program, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Alexandra Schuetz
- US Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD, USA; Henry M Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, USA; Armed Forces Research Institute of Medical Sciences, Bangkok, Thailand
| | - Pornsuk V Grandin
- Armed Forces Research Institute of Medical Sciences, Bangkok, Thailand
| | - Robert J O'Connell
- US Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD, USA; Armed Forces Research Institute of Medical Sciences, Bangkok, Thailand
| | - Julie E Ledgerwood
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Barney S Graham
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Randall Tressler
- Division of AIDS, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - John R Mascola
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Nicolas Chomont
- Centre de Recherche du CHUM and Department of Microbiology, Infectiology and Immunology, Université de Montréal, Montreal, QC, Canada
| | - Nelson L Michael
- US Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD, USA
| | - Merlin L Robb
- US Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD, USA; Henry M Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, USA
| | | | - Jintanat Ananworanich
- US Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD, USA; Henry M Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, USA; SEARCH, the Thai Red Cross AIDS Research Center, Bangkok, Thailand; Department of Global Health, University of Amsterdam, Amsterdam, Netherlands
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Swanstrom AE, Gorelick RJ, Wu G, Howell B, Vijayagopalan A, Shoemaker R, Oswald K, Datta SA, Keele BF, Del Prete GQ, Chertova E, Bess JW, Lifson JD. Ultrasensitive Immunoassay for Simian Immunodeficiency Virus p27 CA. AIDS Res Hum Retroviruses 2018; 34:993-1001. [PMID: 29869527 DOI: 10.1089/aid.2018.0075] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
Abstract
Although effective for suppressing viral replication, combination antiretroviral treatment (cART) does not represent definitive therapy for HIV infection due to persistence of replication-competent viral reservoirs. The advent of effective cART regimens for simian immunodeficiency virus (SIV)-infected nonhuman primates (NHP) has enabled the development of relevant models for studying viral reservoirs and intervention strategies targeting them. Viral reservoir measurements are crucial for such studies but are problematic. Quantitative polymerase chain reaction (PCR) assays overestimate the size of the replication competent viral reservoir, as not all detected viral genomes are intact. Quantitative viral outgrowth assays measure replication competence, but they suffer from limited precision and dynamic range, and require large numbers of cells. Ex vivo virus induction assays to detect cells harboring inducible virus represent an experimental middle ground, but detection of inducible viral RNA in such assays does not necessarily indicate production of virions, while detection of more immunologically relevant viral proteins, including p27CA, by conventional enzyme-linked immunosorbent assays (ELISA) lacks sensitivity. An ultrasensitive digital SIV Gag p27 assay was developed, which is 100-fold more sensitive than a conventional ELISA. In ex vivo virus induction assays, the quantification of SIV Gag p27 produced by stimulated CD4+ T cells from rhesus macaques receiving cART enabled earlier and more sensitive detection than conventional ELISA-based approaches and was highly correlated with SIV RNA, as measured by quantitative reverse transcription PCR. This ultrasensitive p27 assay provides a new tool to assess ongoing replication and reactivation of infectious virus from reservoirs in SIV-infected NHP.
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Affiliation(s)
- Adrienne E. Swanstrom
- AIDS and Cancer Virus Program, Frederick National Laboratory for Cancer Research sponsored by the National Cancer Institute, Leidos Biomedical Research, Inc., Frederick, Maryland
| | - Robert J. Gorelick
- AIDS and Cancer Virus Program, Frederick National Laboratory for Cancer Research sponsored by the National Cancer Institute, Leidos Biomedical Research, Inc., Frederick, Maryland
| | - Guoxin Wu
- Department of Infectious Disease, Merck & Co., Inc., Kenilworth, New Jersey
| | - Bonnie Howell
- Department of Infectious Disease, Merck & Co., Inc., Kenilworth, New Jersey
| | - Anitha Vijayagopalan
- AIDS and Cancer Virus Program, Frederick National Laboratory for Cancer Research sponsored by the National Cancer Institute, Leidos Biomedical Research, Inc., Frederick, Maryland
| | - Rebecca Shoemaker
- AIDS and Cancer Virus Program, Frederick National Laboratory for Cancer Research sponsored by the National Cancer Institute, Leidos Biomedical Research, Inc., Frederick, Maryland
| | - Kelli Oswald
- AIDS and Cancer Virus Program, Frederick National Laboratory for Cancer Research sponsored by the National Cancer Institute, Leidos Biomedical Research, Inc., Frederick, Maryland
| | - Siddhartha A. Datta
- HIV Dynamics and Replication Program, Center for Cancer Research, National Cancer Institute, Frederick, Maryland
| | - Brandon F. Keele
- AIDS and Cancer Virus Program, Frederick National Laboratory for Cancer Research sponsored by the National Cancer Institute, Leidos Biomedical Research, Inc., Frederick, Maryland
| | - Gregory Q. Del Prete
- AIDS and Cancer Virus Program, Frederick National Laboratory for Cancer Research sponsored by the National Cancer Institute, Leidos Biomedical Research, Inc., Frederick, Maryland
| | - Elena Chertova
- AIDS and Cancer Virus Program, Frederick National Laboratory for Cancer Research sponsored by the National Cancer Institute, Leidos Biomedical Research, Inc., Frederick, Maryland
| | - Julian W. Bess
- AIDS and Cancer Virus Program, Frederick National Laboratory for Cancer Research sponsored by the National Cancer Institute, Leidos Biomedical Research, Inc., Frederick, Maryland
| | - Jeffrey D. Lifson
- AIDS and Cancer Virus Program, Frederick National Laboratory for Cancer Research sponsored by the National Cancer Institute, Leidos Biomedical Research, Inc., Frederick, Maryland
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20
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Lee SA, Elliott JH, McMahon J, Hartogenesis W, Bumpus NN, Lifson JD, Gorelick RJ, Bacchetti P, Deeks SG, Lewin SR, Savic RM. Population Pharmacokinetics and Pharmacodynamics of Disulfiram on Inducing Latent HIV-1 Transcription in a Phase IIb Trial. Clin Pharmacol Ther 2018; 105:692-702. [PMID: 30137649 DOI: 10.1002/cpt.1220] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2018] [Revised: 07/23/2018] [Accepted: 07/30/2018] [Indexed: 11/09/2022]
Abstract
Disulfiram (DSF) was well tolerated and activated viral transcription (cell-associated unspliced (CA-US) and plasma human immunodeficiency virus (HIV) RNA) in a phase II dose-escalation trial in HIV+ antiretroviral therapy (ART)-suppressed participants. Here, we investigated whether exposure to DSF and its metabolites predicted these changes in HIV transcription. Participants were administered 500 (N = 10), 1,000 (N = 10), or 2,000 (N = 10) mg of DSF for 3 consecutive days. DSF and four metabolites were measured by ultraperformance liquid chromatography-tandem mass spectrometry. Changes in CA-US and plasma HIV RNA were quantified by polymerase chain reaction (PCR) and analyzed in NONMEM. A seven-compartment pharmacokinetic (PK) model demonstrated nonlinear elimination kinetics. The fitted median area under the curve values for 72 hours (AUC0-72 ) were 3,816, 8,386, and 22,331 mg*hour/L, respectively. Higher exposure predicted greater increases in CA-US (maximum effect (Emax ) = 78%, AUC50 = 1,600 μg*hour/L, P = 0.013) but not plasma HIV RNA. These results provide support for further development of DSF as an important drug for future HIV cure strategies.
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Affiliation(s)
- Sulggi A Lee
- Department of Medicine, Division of HIV/AIDS, University of California, San Francisco, San Francisco, California, USA
| | - Julian H Elliott
- Department of Infectious Diseases, Alfred Hospital and Monash University, Melbourne, Victoria, Australia
| | - James McMahon
- Department of Infectious Diseases, Alfred Hospital and Monash University, Melbourne, Victoria, Australia
| | - Wendy Hartogenesis
- Department of Medicine, Division of HIV/AIDS, University of California, San Francisco, San Francisco, California, USA
| | - Namandje N Bumpus
- Department of Pharmacology and Molecular Sciences, Johns Hopkins University, Baltimore, Maryland, USA
| | - Jeffrey D Lifson
- Frederick National Laboratory for Cancer Research, AIDS and Cancer Virus Program, Frederick, Maryland, USA
| | - Robert J Gorelick
- Frederick National Laboratory for Cancer Research, AIDS and Cancer Virus Program, Frederick, Maryland, USA
| | - Peter Bacchetti
- Department of Epidemiology and Biostatistics, University of California, San Francisco, San Francisco, California, USA
| | - Steven G Deeks
- Department of Medicine, Division of HIV/AIDS, University of California, San Francisco, San Francisco, California, USA
| | - Sharon R Lewin
- Department of Infectious Diseases, Alfred Hospital and Monash University, Melbourne, Victoria, Australia.,The Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Melbourne, Victoria, Australia
| | - Radojka M Savic
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, California, USA
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21
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Colby DJ, Trautmann L, Pinyakorn S, Leyre L, Pagliuzza A, Kroon E, Rolland M, Takata H, Buranapraditkun S, Intasan J, Chomchey N, Muir R, Haddad EK, Tovanabutra S, Ubolyam S, Bolton DL, Fullmer BA, Gorelick RJ, Fox L, Crowell TA, Trichavaroj R, O'Connell R, Chomont N, Kim JH, Michael NL, Robb ML, Phanuphak N, Ananworanich J. Rapid HIV RNA rebound after antiretroviral treatment interruption in persons durably suppressed in Fiebig I acute HIV infection. Nat Med 2018; 24:923-926. [PMID: 29892063 PMCID: PMC6092240 DOI: 10.1038/s41591-018-0026-6] [Citation(s) in RCA: 215] [Impact Index Per Article: 35.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2017] [Accepted: 03/23/2018] [Indexed: 01/24/2023]
Abstract
Antiretroviral therapy during the earliest stage of acute HIV infection (Fiebig I) might minimize establishment of a latent HIV reservoir and thereby facilitate viremic control after analytical treatment interruption. We show that 8 participants, who initiated treatment during Fiebig I and were treated for a median of 2.8 years, all experienced rapid viral load rebound following analytical treatment interruption, indicating that additional strategies are required to control or eradicate HIV.
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Affiliation(s)
- Donn J Colby
- SEARCH, Thai Red Cross AIDS Research Centre, Bangkok, Thailand
| | - Lydie Trautmann
- US Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD, USA
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, USA
| | - Suteeraporn Pinyakorn
- US Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD, USA
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, USA
| | - Louise Leyre
- Centre de Recherche du CHUM and Department of Microbiology, Infectiology and Immunology, Université de Montréal, Montreal, QC, Canada
| | - Amélie Pagliuzza
- Centre de Recherche du CHUM and Department of Microbiology, Infectiology and Immunology, Université de Montréal, Montreal, QC, Canada
| | - Eugène Kroon
- SEARCH, Thai Red Cross AIDS Research Centre, Bangkok, Thailand
| | - Morgane Rolland
- US Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD, USA
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, USA
| | - Hiroshi Takata
- US Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD, USA
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, USA
| | - Supranee Buranapraditkun
- US Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD, USA
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, USA
- Division of Allergy and Clinical Immunology, Department of Medicine, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
- Chulalongkorn Vaccine Research Center, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Jintana Intasan
- SEARCH, Thai Red Cross AIDS Research Centre, Bangkok, Thailand
| | - Nitiya Chomchey
- SEARCH, Thai Red Cross AIDS Research Centre, Bangkok, Thailand
| | - Roshell Muir
- Department of Medicine, Division of Infectious Diseases & HIV Medicine at Drexel University College of Medicine, Philadelphia, PA, USA
| | - Elias K Haddad
- Department of Medicine, Division of Infectious Diseases & HIV Medicine at Drexel University College of Medicine, Philadelphia, PA, USA
| | - Sodsai Tovanabutra
- US Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD, USA
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, USA
| | | | - Diane L Bolton
- US Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD, USA
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, USA
| | - Brandie A Fullmer
- AIDS and Cancer Virus Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Robert J Gorelick
- AIDS and Cancer Virus Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Lawrence Fox
- Division of AIDS, National Institute of Allergy and Infectious Diseases, Rockville, MD, USA
| | - Trevor A Crowell
- US Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD, USA
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, USA
| | - Rapee Trichavaroj
- Department of Retrovirology, Armed Forces Research Institute of Medical Sciences United States Component, Bangkok, Thailand
| | - Robert O'Connell
- Department of Retrovirology, Armed Forces Research Institute of Medical Sciences United States Component, Bangkok, Thailand
| | - Nicolas Chomont
- Centre de Recherche du CHUM and Department of Microbiology, Infectiology and Immunology, Université de Montréal, Montreal, QC, Canada
| | - Jerome H Kim
- US Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD, USA
- International Vaccine Institute, Seoul, Korea
| | - Nelson L Michael
- US Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD, USA
| | - Merlin L Robb
- US Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD, USA
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, USA
| | | | - Jintanat Ananworanich
- SEARCH, Thai Red Cross AIDS Research Centre, Bangkok, Thailand.
- US Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD, USA.
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, USA.
- Department of Global Health, University of Amsterdam, Amsterdam, the Netherlands.
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22
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Post K, Olson ED, Naufer MN, Gorelick RJ, Rouzina I, Williams MC, Musier-Forsyth K, Levin JG. Mechanistic differences between HIV-1 and SIV nucleocapsid proteins and cross-species HIV-1 genomic RNA recognition. Retrovirology 2016; 13:89. [PMID: 28034301 PMCID: PMC5198506 DOI: 10.1186/s12977-016-0322-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2016] [Accepted: 11/29/2016] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The nucleocapsid (NC) domain of HIV-1 Gag is responsible for specific recognition and packaging of genomic RNA (gRNA) into new viral particles. This occurs through specific interactions between the Gag NC domain and the Psi packaging signal in gRNA. In addition to this critical function, NC proteins are also nucleic acid (NA) chaperone proteins that facilitate NA rearrangements during reverse transcription. Although the interaction with Psi and chaperone activity of HIV-1 NC have been well characterized in vitro, little is known about simian immunodeficiency virus (SIV) NC. Non-human primates are frequently used as a platform to study retroviral infection in vivo; thus, it is important to understand underlying mechanistic differences between HIV-1 and SIV NC. RESULTS Here, we characterize SIV NC chaperone activity for the first time. Only modest differences are observed in the ability of SIV NC to facilitate reactions that mimic the minus-strand annealing and transfer steps of reverse transcription relative to HIV-1 NC, with the latter displaying slightly higher strand transfer and annealing rates. Quantitative single molecule DNA stretching studies and dynamic light scattering experiments reveal that these differences are due to significantly increased DNA compaction energy and higher aggregation capability of HIV-1 NC relative to the SIV protein. Using salt-titration binding assays, we find that both proteins are strikingly similar in their ability to specifically interact with HIV-1 Psi RNA. In contrast, they do not demonstrate specific binding to an RNA derived from the putative SIV packaging signal. CONCLUSIONS Based on these studies, we conclude that (1) HIV-1 NC is a slightly more efficient NA chaperone protein than SIV NC, (2) mechanistic differences between the NA interactions of highly similar retroviral NC proteins are revealed by quantitative single molecule DNA stretching, and (3) SIV NC demonstrates cross-species recognition of the HIV-1 Psi RNA packaging signal.
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Affiliation(s)
- Klara Post
- Section on Viral Gene Regulation, Program in Genomics of Differentiation, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892-2780 USA
| | - Erik D. Olson
- Department of Chemistry and Biochemistry, Center for Retrovirus Research, and Center for RNA Biology, The Ohio State University, Columbus, OH 43210 USA
| | - M. Nabuan Naufer
- Department of Physics, Northeastern University, Boston, MA 02115 USA
| | - Robert J. Gorelick
- AIDS and Cancer Virus Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD 21702-1201 USA
| | - Ioulia Rouzina
- Department of Chemistry and Biochemistry, Center for Retrovirus Research, and Center for RNA Biology, The Ohio State University, Columbus, OH 43210 USA
| | - Mark C. Williams
- Department of Physics, Northeastern University, Boston, MA 02115 USA
| | - Karin Musier-Forsyth
- Department of Chemistry and Biochemistry, Center for Retrovirus Research, and Center for RNA Biology, The Ohio State University, Columbus, OH 43210 USA
| | - Judith G. Levin
- Section on Viral Gene Regulation, Program in Genomics of Differentiation, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892-2780 USA
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23
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Delviks-Frankenberry KA, Nikolaitchik OA, Burdick RC, Gorelick RJ, Keele BF, Hu WS, Pathak VK. Minimal Contribution of APOBEC3-Induced G-to-A Hypermutation to HIV-1 Recombination and Genetic Variation. PLoS Pathog 2016; 12:e1005646. [PMID: 27186986 PMCID: PMC4871359 DOI: 10.1371/journal.ppat.1005646] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2016] [Accepted: 04/28/2016] [Indexed: 11/19/2022] Open
Abstract
Although the predominant effect of host restriction APOBEC3 proteins on HIV-1 infection is to block viral replication, they might inadvertently increase retroviral genetic variation by inducing G-to-A hypermutation. Numerous studies have disagreed on the contribution of hypermutation to viral genetic diversity and evolution. Confounding factors contributing to the debate include the extent of lethal (stop codon) and sublethal hypermutation induced by different APOBEC3 proteins, the inability to distinguish between G-to-A mutations induced by APOBEC3 proteins and error-prone viral replication, the potential impact of hypermutation on the frequency of retroviral recombination, and the extent to which viral recombination occurs in vivo, which can reassort mutations in hypermutated genomes. Here, we determined the effects of hypermutation on the HIV-1 recombination rate and its contribution to genetic variation through recombination to generate progeny genomes containing portions of hypermutated genomes without lethal mutations. We found that hypermutation did not significantly affect the rate of recombination, and recombination between hypermutated and wild-type genomes only increased the viral mutation rate by 3.9 × 10-5 mutations/bp/replication cycle in heterozygous virions, which is similar to the HIV-1 mutation rate. Since copackaging of hypermutated and wild-type genomes occurs very rarely in vivo, recombination between hypermutated and wild-type genomes does not significantly contribute to the genetic variation of replicating HIV-1. We also analyzed previously reported hypermutated sequences from infected patients and determined that the frequency of sublethal mutagenesis for A3G and A3F is negligible (4 × 10-21 and1 × 10-11, respectively) and its contribution to viral mutations is far below mutations generated during error-prone reverse transcription. Taken together, we conclude that the contribution of APOBEC3-induced hypermutation to HIV-1 genetic variation is substantially lower than that from mutations during error-prone replication.
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Affiliation(s)
- Krista A. Delviks-Frankenberry
- Viral Mutation Section, HIV Dynamics and Replication Program, National Cancer Institute at Frederick, Frederick, Maryland, United States of America
| | - Olga A. Nikolaitchik
- Viral Recombination Section, HIV Dynamics and Replication Program, National Cancer Institute at Frederick, Frederick, Maryland, United States of America
| | - Ryan C. Burdick
- Viral Mutation Section, HIV Dynamics and Replication Program, National Cancer Institute at Frederick, Frederick, Maryland, United States of America
| | - Robert J. Gorelick
- AIDS and Cancer Virus Program, Leidos Biomedical Research, Inc., Frederick National Lab, Frederick, Maryland, United States of America
| | - Brandon F. Keele
- AIDS and Cancer Virus Program, Leidos Biomedical Research, Inc., Frederick National Lab, Frederick, Maryland, United States of America
| | - Wei-Shau Hu
- Viral Recombination Section, HIV Dynamics and Replication Program, National Cancer Institute at Frederick, Frederick, Maryland, United States of America
| | - Vinay K. Pathak
- Viral Mutation Section, HIV Dynamics and Replication Program, National Cancer Institute at Frederick, Frederick, Maryland, United States of America
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Lynch RM, Boritz E, Coates EE, DeZure A, Madden P, Costner P, Enama ME, Plummer S, Holman L, Hendel CS, Gordon I, Casazza J, Conan-Cibotti M, Migueles SA, Tressler R, Bailer RT, McDermott A, Narpala S, O’Dell S, Wolf G, Lifson JD, Freemire BA, Gorelick RJ, Pandey JP, Mohan S, Chomont N, Fromentin R, Chun TW, Fauci AS, Schwartz RM, Koup RA, Douek DC, Hu Z, Capparelli E, Graham BS, Mascola JR, Ledgerwood JE. Virologic effects of broadly neutralizing antibody VRC01 administration during chronic HIV-1 infection. Sci Transl Med 2015; 7:319ra206. [DOI: 10.1126/scitranslmed.aad5752] [Citation(s) in RCA: 344] [Impact Index Per Article: 38.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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25
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Elliott JH, McMahon JH, Chang CC, Lee SA, Hartogensis W, Bumpus N, Savic R, Roney J, Hoh R, Solomon A, Piatak M, Gorelick RJ, Lifson J, Bacchetti P, Deeks SG, Lewin SR. Short-term administration of disulfiram for reversal of latent HIV infection: a phase 2 dose-escalation study. Lancet HIV 2015; 2:e520-9. [PMID: 26614966 DOI: 10.1016/s2352-3018(15)00226-x] [Citation(s) in RCA: 190] [Impact Index Per Article: 21.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2015] [Revised: 10/27/2015] [Accepted: 10/27/2015] [Indexed: 02/07/2023]
Abstract
BACKGROUND In vitro, disulfiram activated HIV transcription in a primary T-cell model of HIV latency and in a pilot clinical study increased plasma HIV RNA in individuals with adequate drug exposure. We assessed the effect of disulfiram on HIV transcription in a dose-escalation study. METHODS In this prospective dose-escalation study, to optimise disulfiram exposure we included adults with HIV on suppressive antiretroviral therapy, with plasma HIV RNA of less than 50 copies per mL and a CD4 cell count greater than 350 cells per μL. Participants were allocated sequentially to one of three dosing groups (500 mg, 1000 mg, and 2000 mg) and received disulfiram daily for 3 days. Only the staff who did laboratory assays were masked to group assignment. The primary endpoint was change in cell-associated unspliced HIV RNA in CD4 cells. The primary analysis method was a negative binomial regression, with the number of copies as the outcome variable and the input total RNA or plasma volume as an exposure variable, which is equivalent to modelling copies or input. We used these models to estimate changes from before disulfiram to timepoints during and after disulfiram administration. This study is registered with ClinicalTrials.gov, number NCT01944371. FINDINGS Of 34 participants screened for eligibility at The Alfred Hospital (Melbourne, VIC, Australia), and San Francisco General Hospital (San Francisco, CA, USA), 30 people were enrolled between Sept 24, 2013, and March 31, 2014. The estimated fold increases in cell-associated unspliced HIV RNA from baseline were 1·7 (95% CI 1·3-2·2; p<0·0001) to the timepoint during disulfiram treatment and 2·1 (1·5-2·9; p<0·0001) to the timepoint after disulfiram in the 500 mg group; 1·9 (1·6-2·4; p<0·0001) and 2·5 (1·9-3·3; p<0·0001) in the 1000 mg group; and 1·6 (1·2-2·1; p=0·0026) and 2·1 (1·5-3·1; p=0·0001) in the 2000 mg group. No deaths occurred, and no serious adverse events were noted. Disulfiram was well tolerated at all doses. INTERPRETATION Short-term administration of disulfiram resulted in increases in cell-associated unspliced HIV RNA at all doses, consistent with activating HIV latency. Disulfiram may be suited for future studies of combination and prolonged therapy to activate latent HIV. FUNDING The Foundation for AIDS Research (amfAR); National Institute of Allergy and Infectious Diseases, National Institutes of Health; Australian National Health and Medical Research Council.
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Affiliation(s)
- Julian H Elliott
- Department of Infectious Diseases, Monash University and Alfred Hospital, Melbourne, VIC, Australia
| | - James H McMahon
- Department of Infectious Diseases, Monash University and Alfred Hospital, Melbourne, VIC, Australia
| | - Christina C Chang
- Department of Infectious Diseases, Monash University and Alfred Hospital, Melbourne, VIC, Australia; The Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, VIC, Australia
| | - Sulggi A Lee
- University of California San Francisco, San Francisco, CA, USA
| | | | | | - Rada Savic
- University of California San Francisco, San Francisco, CA, USA
| | - Janine Roney
- Department of Infectious Diseases, Monash University and Alfred Hospital, Melbourne, VIC, Australia
| | - Rebecca Hoh
- University of California San Francisco, San Francisco, CA, USA
| | - Ajantha Solomon
- The Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, VIC, Australia
| | - Michael Piatak
- AIDS and Cancer Virus Program, Leidos Biomedical Research Inc, Frederick National Laboratory, Frederick, MD, USA
| | - Robert J Gorelick
- AIDS and Cancer Virus Program, Leidos Biomedical Research Inc, Frederick National Laboratory, Frederick, MD, USA
| | - Jeff Lifson
- AIDS and Cancer Virus Program, Leidos Biomedical Research Inc, Frederick National Laboratory, Frederick, MD, USA
| | - Peter Bacchetti
- University of California San Francisco, San Francisco, CA, USA
| | - Steven G Deeks
- University of California San Francisco, San Francisco, CA, USA
| | - Sharon R Lewin
- Department of Infectious Diseases, Monash University and Alfred Hospital, Melbourne, VIC, Australia; The Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, VIC, Australia.
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Lavender CA, Gorelick RJ, Weeks KM. Structure-Based Alignment and Consensus Secondary Structures for Three HIV-Related RNA Genomes. PLoS Comput Biol 2015; 11:e1004230. [PMID: 25992893 PMCID: PMC4439019 DOI: 10.1371/journal.pcbi.1004230] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2014] [Accepted: 03/08/2015] [Indexed: 11/30/2022] Open
Abstract
HIV and related primate lentiviruses possess single-stranded RNA genomes. Multiple regions of these genomes participate in critical steps in the viral replication cycle, and the functions of many RNA elements are dependent on the formation of defined structures. The structures of these elements are still not fully understood, and additional functional elements likely exist that have not been identified. In this work, we compared three full-length HIV-related viral genomes: HIV-1NL4-3, SIVcpz, and SIVmac (the latter two strains are progenitors for all HIV-1 and HIV-2 strains, respectively). Model-free RNA structure comparisons were performed using whole-genome structure information experimentally derived from nucleotide-resolution SHAPE reactivities. Consensus secondary structures were constructed for strongly correlated regions by taking into account both SHAPE probing structural data and nucleotide covariation information from structure-based alignments. In these consensus models, all known functional RNA elements were recapitulated with high accuracy. In addition, we identified multiple previously unannotated structural elements in the HIV-1 genome likely to function in translation, splicing and other replication cycle processes; these are compelling targets for future functional analyses. The structure-informed alignment strategy developed here will be broadly useful for efficient RNA motif discovery. Human immunodeficiency virus (HIV) is a persistent and critical threat to human health. Replication and pathogenesis of HIV is governed by information encoded in its single-stranded RNA genome. In addition to coding for viral proteins, the HIV genomic RNA forms base paired and higher-order structures that are critical for viral replication. It is likely that only a subset of functional RNA motifs has been identified. Here, we interrogate the structures of three diverse HIV-related viral genomes by nucleotide-resolution chemical probing. The three genomes include HIV-1, the virus that infects humans, and SIVcpz and SIVmac, which are progenitors for the main branches of the two HIV evolutionary groups. We used a structure-informed alignment approach to generate consensus models for base-paired secondary structures that are shared by these three HIV-related genomes. With this approach, we were able to recapitulate all known RNA structures and, additionally, discovered multiple previously undescribed structural elements that are clearly conserved among major HIV groups. We anticipate that the methods described here will be broadly useful for RNA structure motif discovery and, more immediately, for identification of RNA targets in HIV that are promising sites for therapeutic intervention.
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Affiliation(s)
- Christopher A. Lavender
- Department of Chemistry, University of North Carolina, Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Robert J. Gorelick
- AIDS and Cancer Virus Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, Maryland, United States of America
| | - Kevin M. Weeks
- Department of Chemistry, University of North Carolina, Chapel Hill, Chapel Hill, North Carolina, United States of America
- * E-mail:
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Caskey M, Klein F, Lorenzi JCC, Seaman MS, West AP, Buckley N, Kremer G, Nogueira L, Braunschweig M, Scheid JF, Horwitz JA, Shimeliovich I, Ben-Avraham S, Witmer-Pack M, Platten M, Lehmann C, Burke LA, Hawthorne T, Gorelick RJ, Walker BD, Keler T, Gulick RM, Fätkenheuer G, Schlesinger SJ, Nussenzweig MC. Viraemia suppressed in HIV-1-infected humans by broadly neutralizing antibody 3BNC117. Nature 2015; 522:487-91. [PMID: 25855300 DOI: 10.1038/nature14411] [Citation(s) in RCA: 581] [Impact Index Per Article: 64.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2015] [Accepted: 03/19/2015] [Indexed: 02/07/2023]
Abstract
HIV-1 immunotherapy with a combination of first generation monoclonal antibodies was largely ineffective in pre-clinical and clinical settings and was therefore abandoned. However, recently developed single-cell-based antibody cloning methods have uncovered a new generation of far more potent broadly neutralizing antibodies to HIV-1 (refs 4, 5). These antibodies can prevent infection and suppress viraemia in humanized mice and nonhuman primates, but their potential for human HIV-1 immunotherapy has not been evaluated. Here we report the results of a first-in-man dose escalation phase 1 clinical trial of 3BNC117, a potent human CD4 binding site antibody, in uninfected and HIV-1-infected individuals. 3BNC117 infusion was well tolerated and demonstrated favourable pharmacokinetics. A single 30 mg kg(-1) infusion of 3BNC117 reduced the viral load in HIV-1-infected individuals by 0.8-2.5 log10 and viraemia remained significantly reduced for 28 days. Emergence of resistant viral strains was variable, with some individuals remaining sensitive to 3BNC117 for a period of 28 days. We conclude that, as a single agent, 3BNC117 is safe and effective in reducing HIV-1 viraemia, and that immunotherapy should be explored as a new modality for HIV-1 prevention, therapy and cure.
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Affiliation(s)
- Marina Caskey
- Laboratory of Molecular Immunology, The Rockefeller University, New York, New York 10065, USA
| | - Florian Klein
- Laboratory of Molecular Immunology, The Rockefeller University, New York, New York 10065, USA
| | - Julio C C Lorenzi
- Laboratory of Molecular Immunology, The Rockefeller University, New York, New York 10065, USA
| | - Michael S Seaman
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts 02215, USA
| | - Anthony P West
- Division of Biology, California Institute of Technology, Pasadena, California 91125, USA
| | - Noreen Buckley
- Laboratory of Molecular Immunology, The Rockefeller University, New York, New York 10065, USA
| | - Gisela Kremer
- 1] First Department of Internal Medicine, University Hospital of Cologne, D-50924 Cologne, Germany [2] Clinical Trials Center Cologne, ZKS Köln, BMBF 01KN1106, University of Cologne, Cologne, Germany
| | - Lilian Nogueira
- Laboratory of Molecular Immunology, The Rockefeller University, New York, New York 10065, USA
| | - Malte Braunschweig
- 1] Laboratory of Molecular Immunology, The Rockefeller University, New York, New York 10065, USA [2] Albert Ludwigs University of Freiburg, 79085 Freiburg, Germany
| | - Johannes F Scheid
- Laboratory of Molecular Immunology, The Rockefeller University, New York, New York 10065, USA
| | - Joshua A Horwitz
- Laboratory of Molecular Immunology, The Rockefeller University, New York, New York 10065, USA
| | - Irina Shimeliovich
- Laboratory of Molecular Immunology, The Rockefeller University, New York, New York 10065, USA
| | - Sivan Ben-Avraham
- Laboratory of Molecular Immunology, The Rockefeller University, New York, New York 10065, USA
| | - Maggi Witmer-Pack
- Laboratory of Molecular Immunology, The Rockefeller University, New York, New York 10065, USA
| | - Martin Platten
- 1] First Department of Internal Medicine, University Hospital of Cologne, D-50924 Cologne, Germany [2] German Center for Infection Research (DZIF), partner site Bonn-Cologne, Cologne, Germany
| | - Clara Lehmann
- 1] First Department of Internal Medicine, University Hospital of Cologne, D-50924 Cologne, Germany [2] German Center for Infection Research (DZIF), partner site Bonn-Cologne, Cologne, Germany
| | - Leah A Burke
- 1] Laboratory of Molecular Immunology, The Rockefeller University, New York, New York 10065, USA [2] Division of Infectious Diseases, Weill Medical College of Cornell University, New York, New York 10065, USA
| | | | - Robert J Gorelick
- AIDS and Cancer Virus Program, Leidos Biomedical Research, Frederick, Frederick National Laboratory for Cancer Research, Frederick, Maryland 21702, USA
| | - Bruce D Walker
- Ragon Institute of MGH, MIT and Harvard, Howard Hughes Medical Institute, Massachusetts General Hospital and Harvard Medical School, Cambridge, Massachusetts 02139, USA
| | - Tibor Keler
- Celldex Therapeutics, Inc., Hampton, New Jersey 08827, USA
| | - Roy M Gulick
- Division of Infectious Diseases, Weill Medical College of Cornell University, New York, New York 10065, USA
| | - Gerd Fätkenheuer
- 1] First Department of Internal Medicine, University Hospital of Cologne, D-50924 Cologne, Germany [2] German Center for Infection Research (DZIF), partner site Bonn-Cologne, Cologne, Germany
| | - Sarah J Schlesinger
- Laboratory of Molecular Immunology, The Rockefeller University, New York, New York 10065, USA
| | - Michel C Nussenzweig
- 1] Laboratory of Molecular Immunology, The Rockefeller University, New York, New York 10065, USA [2] Howard Hughes Medical Institute, The Rockefeller University, New York, New York 10065, USA
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Mitra M, Singer D, Mano Y, Hritz J, Nam G, Gorelick RJ, Byeon IJL, Gronenborn AM, Iwatani Y, Levin JG. Sequence and structural determinants of human APOBEC3H deaminase and anti-HIV-1 activities. Retrovirology 2015; 12:3. [PMID: 25614027 PMCID: PMC4323217 DOI: 10.1186/s12977-014-0130-8] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2014] [Accepted: 12/17/2014] [Indexed: 12/17/2022] Open
Abstract
Background Human APOBEC3H (A3H) belongs to the A3 family of host restriction factors, which are cytidine deaminases that catalyze conversion of deoxycytidine to deoxyuridine in single-stranded DNA. A3 proteins contain either one (A3A, A3C, A3H) or two (A3B, A3D, A3F, A3G) Zn-binding domains. A3H has seven haplotypes (I-VII) that exhibit diverse biological phenotypes and geographical distribution in the human population. Its single Zn-coordinating deaminase domain belongs to a phylogenetic cluster (Z3) that is different from the Z1- and Z2-type domains in other human A3 proteins. A3H HapII, unlike A3A or A3C, has potent activity against HIV-1. Here, we sought to identify the determinants of A3H HapII deaminase and antiviral activities, using site-directed sequence- and structure-guided mutagenesis together with cell-based, biochemical, and HIV-1 infectivity assays. Results We have constructed a homology model of A3H HapII, which is similar to the known structures of other A3 proteins. The model revealed a large cluster of basic residues (not present in A3A or A3C) that are likely to be involved in nucleic acid binding. Indeed, RNase A pretreatment of 293T cell lysates expressing A3H was shown to be required for detection of deaminase activity, indicating that interaction with cellular RNAs inhibits A3H catalytic function. Similar observations have been made with A3G. Analysis of A3H deaminase substrate specificity demonstrated that a 5′ T adjacent to the catalytic C is preferred. Changing the putative nucleic acid binding residues identified by the model resulted in reduction or abrogation of enzymatic activity, while substituting Z3-specific residues in A3H to the corresponding residues in other A3 proteins did not affect enzyme function. As shown for A3G and A3F, some A3H mutants were defective in catalysis, but retained antiviral activity against HIV-1vif (−) virions. Furthermore, endogenous reverse transcription assays demonstrated that the E56A catalytic mutant inhibits HIV-1 DNA synthesis, although not as efficiently as wild type. Conclusions The molecular and biological activities of A3H are more similar to those of the double-domain A3 proteins than to those of A3A or A3C. Importantly, A3H appears to use both deaminase-dependent and -independent mechanisms to target reverse transcription and restrict HIV-1 replication. Electronic supplementary material The online version of this article (doi:10.1186/s12977-014-0130-8) contains supplementary material, which is available to authorized users.
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McCauley MJ, Rouzina I, Hoadley K, Gorelick RJ, Musier-Forsyth K, Williams MC. Specific Binding of the Nucleocapsid Protein Transforms the Folding Landscape of the HIV-1 TAR RNA Hairpin. Biophys J 2015. [DOI: 10.1016/j.bpj.2014.11.2183] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022] Open
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Abstract
![]()
The
HIV-1 ribosomal frameshift element is highly structured, regulates
translation of all virally encoded enzymes, and is a promising therapeutic
target. The prior model for this motif contains two helices separated
by a three-nucleotide bulge. Modifications to this model were suggested
by SHAPE chemical probing of an entire HIV-1 RNA genome. Novel features
of the SHAPE-directed model include alternate helical conformations
and a larger, more complex structure. These structural elements also
support the presence of a secondary frameshift site within the frameshift
domain. Here, we use oligonucleotide-directed structure perturbation,
probing in the presence of formamide, and in-virion experiments to
examine these models. Our data support a model in which the frameshift
domain is anchored by a stable helix outside the conventional domain.
Less stable helices within the domain can switch from the SHAPE-predicted
to the two-helix conformation. Translational frameshifting assays
with frameshift domain mutants support a functional role for the interactions
predicted by and specific to the SHAPE-directed model. These results
reveal that the HIV-1 frameshift domain is a complex, dynamic structure
and underscore the importance of analyzing folding in the context
of full-length RNAs.
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Affiliation(s)
- Justin T Low
- Department of Chemistry, University of North Carolina , Chapel Hill, North Carolina 27599-3290, United States
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Wu H, Wang W, Naiyer N, Fichtenbaum E, Qualley DF, McCauley MJ, Gorelick RJ, Rouzina I, Musier-Forsyth K, Williams MC. Single aromatic residue location alters nucleic acid binding and chaperone function of FIV nucleocapsid protein. Virus Res 2014; 193:39-51. [PMID: 24915282 DOI: 10.1016/j.virusres.2014.06.002] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2014] [Revised: 05/28/2014] [Accepted: 06/02/2014] [Indexed: 10/25/2022]
Abstract
Feline immunodeficiency virus (FIV) is a retrovirus that infects domestic cats, and is an excellent animal model for human immunodeficiency virus type 1 (HIV-1) pathogenesis. The nucleocapsid (NC) protein is critical for replication in both retroviruses. FIV NC has several structural features that differ from HIV-1 NC. While both NC proteins have a single conserved aromatic residue in each of the two zinc fingers, the aromatic residue on the second finger of FIV NC is located on the opposite C-terminal side relative to its location in HIV-1 NC. In addition, whereas HIV-1 NC has a highly charged cationic N-terminal tail and a relatively short C-terminal extension, the opposite is true for FIV NC. To probe the impact of these differences on the nucleic acid (NA) binding and chaperone properties of FIV NC, we carried out ensemble and single-molecule assays with wild-type (WT) and mutant proteins. The ensemble studies show that FIV NC binding to DNA is strongly electrostatic, with a higher effective charge than that observed for HIV-1 NC. The C-terminal basic domain contributes significantly to the NA binding capability of FIV NC. In addition, the non-electrostatic component of DNA binding is much weaker for FIV NC than for HIV-1 NC. Mutation of both aromatic residues in the zinc fingers to Ala (F12A/W44A) further increases the effective charge of FIV NC and reduces its non-electrostatic binding affinity. Interestingly, switching the location of the C-terminal aromatic residue to mimic the HIV-1 NC sequence (N31W/W44A) reduces the effective charge of FIV NC and increases its non-electrostatic binding affinity to values similar to HIV-1 NC. Consistent with the results of these ensemble studies, single-molecule DNA stretching studies show that while WT FIV NC has reduced stacking capability relative to HIV-1 NC, the aromatic switch mutant recovers the ability to intercalate between the DNA bases. Our results demonstrate that altering the position of a single aromatic residue switches the binding mode of FIV NC from primarily electrostatic binding to more non-electrostatic binding, conferring upon it NA interaction properties comparable to that of HIV-1 NC.
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Affiliation(s)
- Hao Wu
- Northeastern University, Department of Physics, Boston, MA 02115, USA
| | - Wei Wang
- The Ohio State University, Department of Chemistry and Biochemistry, Center for Retrovirus Research, and Center for RNA Biology, Columbus, OH 43210, USA
| | - Nada Naiyer
- The Ohio State University, Department of Chemistry and Biochemistry, Center for Retrovirus Research, and Center for RNA Biology, Columbus, OH 43210, USA
| | - Eric Fichtenbaum
- The Ohio State University, Department of Chemistry and Biochemistry, Center for Retrovirus Research, and Center for RNA Biology, Columbus, OH 43210, USA
| | - Dominic F Qualley
- The Ohio State University, Department of Chemistry and Biochemistry, Center for Retrovirus Research, and Center for RNA Biology, Columbus, OH 43210, USA
| | - Micah J McCauley
- Northeastern University, Department of Physics, Boston, MA 02115, USA
| | - Robert J Gorelick
- AIDS and Cancer Virus Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA
| | - Ioulia Rouzina
- University of Minnesota, Department of Biochemistry, Molecular Biology, and Biophysics, Minneapolis, MN 55455, USA
| | - Karin Musier-Forsyth
- The Ohio State University, Department of Chemistry and Biochemistry, Center for Retrovirus Research, and Center for RNA Biology, Columbus, OH 43210, USA.
| | - Mark C Williams
- Northeastern University, Department of Physics, Boston, MA 02115, USA.
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Grohman JK, Gorelick RJ, Kottegoda S, Allbritton NL, Rein A, Weeks KM. An immature retroviral RNA genome resembles a kinetically trapped intermediate state. J Virol 2014; 88:6061-8. [PMID: 24623442 PMCID: PMC4093898 DOI: 10.1128/jvi.03277-13] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2013] [Accepted: 03/09/2014] [Indexed: 11/20/2022] Open
Abstract
UNLABELLED Retroviral virions initially assemble in an immature form that differs from that of the mature infectious particle. The RNA genomes in both immature and infectious particles are dimers, and interactions between the RNA dimer and the viral Gag protein ensure selective packaging into nascent immature virions. We used high-sensitivity selective 2'-hydroxyl acylation analyzed by primer extension (SHAPE) to obtain nucleotide-resolution structural information from scarce, femtomole quantities of Moloney murine leukemia virus (MuLV) RNA inside authentic virions and from viral RNA extracted from immature (protease-minus) virions. Our secondary structure model of the dimerization and packaging domain indicated that a stable intermolecular duplex known as PAL2, previously shown to be present in mature infectious MuLV particles, was sequestered in an alternate stem-loop structure inside immature virions. The intermediate state corresponded closely to a late-folding intermediate that we detected in time-resolved studies of the free MuLV RNA, suggesting that the immature RNA structure reflects trapping of the intermediate folding state by interactions in the immature virion. We propose models for the RNA-protein interactions that trap the RNA in the immature state and for the conformational rearrangement that occurs during maturation of virion particles. IMPORTANCE The structure of the RNA genome in mature retroviruses has been studied extensively, whereas very little was known about the RNA structure in immature virions. The immature RNA structure is important because it is the form initially selected for packaging in new virions and may have other roles. This lack of information was due to the difficulty of isolating sufficient viral RNA for study. In this work, we apply a high-sensitivity and nucleotide-resolution approach to examine the structure of the dimerization and packaging domain of Moloney murine leukemia virus. We find that the genomic RNA is packaged in a high-energy state, suggesting that interactions within the virion hold or capture the RNA before it reaches its most stable state. This new structural information makes it possible to propose models for the conformational changes in the RNA genome that accompany retroviral maturation.
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Affiliation(s)
- Jacob K. Grohman
- Department of Chemistry, University of North Carolina, Chapel Hill, North Carolina, USA
| | - Robert J. Gorelick
- AIDS and Cancer Virus Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, Maryland, USA
| | - Sumith Kottegoda
- Department of Chemistry, University of North Carolina, Chapel Hill, North Carolina, USA
| | - Nancy L. Allbritton
- Department of Chemistry, University of North Carolina, Chapel Hill, North Carolina, USA
- Department of Biomedical Engineering, University of North Carolina, Chapel Hill, and North Carolina State University, Raleigh, North Carolina, USA
| | - Alan Rein
- HIV Drug Resistance Program, National Cancer Institute at Frederick, Frederick, Maryland, USA
| | - Kevin M. Weeks
- Department of Chemistry, University of North Carolina, Chapel Hill, North Carolina, USA
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Wang W, Naiyer N, Mitra M, Li J, Williams MC, Rouzina I, Gorelick RJ, Wu Z, Musier-Forsyth K. Distinct nucleic acid interaction properties of HIV-1 nucleocapsid protein precursor NCp15 explain reduced viral infectivity. Nucleic Acids Res 2014; 42:7145-59. [PMID: 24813443 PMCID: PMC4066767 DOI: 10.1093/nar/gku335] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
During human immunodeficiency virus type 1 (HIV-1) maturation, three different forms of nucleocapsid (NC) protein—NCp15 (p9 + p6), NCp9 (p7 + SP2) and NCp7—appear successively. A mutant virus expressing NCp15 shows greatly reduced infectivity. Mature NCp7 is a chaperone protein that facilitates remodeling of nucleic acids (NAs) during reverse transcription. To understand the strict requirement for NCp15 processing, we compared the chaperone function of the three forms of NC. NCp15 anneals tRNA to the primer-binding site at a similar rate as NCp7, whereas NCp9 is the most efficient annealing protein. Assays to measure NA destabilization show a similar trend. Dynamic light scattering studies reveal that NCp15 forms much smaller aggregates relative to those formed by NCp7 and NCp9. Nuclear magnetic resonance studies suggest that the acidic p6 domain of HIV-1 NCp15 folds back and interacts with the basic zinc fingers. Neutralizing the acidic residues in p6 improves the annealing and aggregation activity of NCp15 to the level of NCp9 and increases the protein–NA aggregate size. Slower NCp15 dissociation kinetics is observed by single-molecule DNA stretching, consistent with the formation of electrostatic inter-protein contacts, which likely contribute to the distinct aggregate morphology, irregular HIV-1 core formation and non-infectious virus.
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Affiliation(s)
- Wei Wang
- Department of Chemistry and Biochemistry, Center for Retrovirus Research and Center for RNA Biology, The Ohio State University, Columbus, OH 43210, USA
| | - Nada Naiyer
- Department of Chemistry and Biochemistry, Center for Retrovirus Research and Center for RNA Biology, The Ohio State University, Columbus, OH 43210, USA
| | - Mithun Mitra
- Department of Chemistry and Biochemistry, Center for Retrovirus Research and Center for RNA Biology, The Ohio State University, Columbus, OH 43210, USA
| | - Jialin Li
- Department of Physics, Northeastern University, Boston, MA 02115, USA
| | - Mark C Williams
- Department of Physics, Northeastern University, Boston, MA 02115, USA
| | - Ioulia Rouzina
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN 55455, USA
| | - Robert J Gorelick
- AIDS and Cancer Virus Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA
| | - Zhengrong Wu
- Department of Chemistry and Biochemistry, Center for Retrovirus Research and Center for RNA Biology, The Ohio State University, Columbus, OH 43210, USA
| | - Karin Musier-Forsyth
- Department of Chemistry and Biochemistry, Center for Retrovirus Research and Center for RNA Biology, The Ohio State University, Columbus, OH 43210, USA
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Pant K, Gorelick RJ, Rouzina I, Williams MC. Single Molecule Study of HIV-1 Reverse Transcriptase Polymerization Activity in the Presence of NC. Biophys J 2014. [DOI: 10.1016/j.bpj.2013.11.1594] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022] Open
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Rajendran A, Endo M, Hidaka K, Tran PLT, Mergny JL, Gorelick RJ, Sugiyama H. HIV-1 nucleocapsid proteins as molecular chaperones for tetramolecular antiparallel G-quadruplex formation. J Am Chem Soc 2013; 135:18575-85. [PMID: 24224650 PMCID: PMC3898174 DOI: 10.1021/ja409085j] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
HIV-1 nucleocapsid proteins (NCps) facilitate remodeling of nucleic acids to fold thermodynamically stable conformations, and thus called nucleic acid chaperones. To date only little is known on the stoichiometry, NCp-NCp interactions, chaperone activity on G-quadruplex formation, and so on. We report here the direct and real-time analysis on such properties of proteolytic intermediate NCp15 and mature NCp7 using DNA origami. The protein particles were found to predominantly exist in monomeric form, while dimeric and multimeric forms were also observed both in free solution and bound to the quadruplex structure. The formation and the dissociation events of the G-quadruplexes were well documented in real-time and the intermediate-like states were also visualized. We anticipate that this pioneering study will strengthen our understanding on the chaperone activity of HIV-1 proteins which in turn will be helpful for the drug design based on G-quadruplex and also for the development of drugs against AIDS.
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Affiliation(s)
- Arivazhagan Rajendran
- Department of Chemistry, Graduate School of Science, Kyoto University, Kitashirakawa-oiwakecho, Sakyo-ku, Kyoto 606-8502, Japan
| | - Masayuki Endo
- Institute for Integrated Cell-Material Sciences (WPI-iCeMS), Kyoto University, Yoshida-ushinomiyacho, Sakyo-ku, Kyoto 606-8501, Japan
- CREST, Japan Science and Technology Corporation (JST), Sanbancho, Chiyoda-ku, Tokyo 102-0075, Japan
| | - Kumi Hidaka
- Department of Chemistry, Graduate School of Science, Kyoto University, Kitashirakawa-oiwakecho, Sakyo-ku, Kyoto 606-8502, Japan
| | - Phong Lan Thao Tran
- Univ. Bordeaux, INSERM, U869, ARNA Laboratory, 2 rue Robert Escarpit, Pessac, F-33607, France
| | - Jean-Louis Mergny
- Univ. Bordeaux, INSERM, U869, ARNA Laboratory, 2 rue Robert Escarpit, Pessac, F-33607, France
| | - Robert J. Gorelick
- SAIC-Frederick, Inc, Frederick National Laboratory for Cancer Research, P. O. Box B, Frederick, Maryland 21702-1201, USA
| | - Hiroshi Sugiyama
- Department of Chemistry, Graduate School of Science, Kyoto University, Kitashirakawa-oiwakecho, Sakyo-ku, Kyoto 606-8502, Japan
- Institute for Integrated Cell-Material Sciences (WPI-iCeMS), Kyoto University, Yoshida-ushinomiyacho, Sakyo-ku, Kyoto 606-8501, Japan
- CREST, Japan Science and Technology Corporation (JST), Sanbancho, Chiyoda-ku, Tokyo 102-0075, Japan
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Wu H, Mitra M, Naufer MN, McCauley MJ, Gorelick RJ, Rouzina I, Musier-Forsyth K, Williams MC. Differential contribution of basic residues to HIV-1 nucleocapsid protein's nucleic acid chaperone function and retroviral replication. Nucleic Acids Res 2013; 42:2525-37. [PMID: 24293648 PMCID: PMC3936775 DOI: 10.1093/nar/gkt1227] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
The human immunodeficiency virus type 1 (HIV-1) nucleocapsid (NC) protein contains 15 basic residues located throughout its 55-amino acid sequence, as well as one aromatic residue in each of its two CCHC-type zinc finger motifs. NC facilitates nucleic acid (NA) rearrangements via its chaperone activity, but the structural basis for this activity and its consequences in vivo are not completely understood. Here, we investigate the role played by basic residues in the N-terminal domain, the N-terminal zinc finger and the linker region between the two zinc fingers. We use in vitro ensemble and single-molecule DNA stretching experiments to measure the characteristics of wild-type and mutant HIV-1 NC proteins, and correlate these results with cell-based HIV-1 replication assays. All of the cationic residue mutations lead to NA interaction defects, as well as reduced HIV-1 infectivity, and these effects are most pronounced on neutralizing all five N-terminal cationic residues. HIV-1 infectivity in cells is correlated most strongly with NC’s NA annealing capabilities as well as its ability to intercalate the DNA duplex. Although NC’s aromatic residues participate directly in DNA intercalation, our findings suggest that specific basic residues enhance these interactions, resulting in optimal NA chaperone activity.
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Affiliation(s)
- Hao Wu
- Department of Physics, Northeastern University, Boston, MA 02115, USA, Department of Chemistry and Biochemistry, Center for RNA Biology, and Center for Retrovirus Research, The Ohio State University, Columbus, OH 43210, USA, AIDS and Cancer Virus Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA and Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, MN 55455, USA
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37
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Eidahl JO, Crowe BL, North JA, McKee CJ, Shkriabai N, Feng L, Plumb M, Graham RL, Gorelick RJ, Hess S, Poirier MG, Foster MP, Kvaratskhelia M. Structural basis for high-affinity binding of LEDGF PWWP to mononucleosomes. Nucleic Acids Res 2013; 41:3924-36. [PMID: 23396443 PMCID: PMC3616739 DOI: 10.1093/nar/gkt074] [Citation(s) in RCA: 148] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2012] [Revised: 12/27/2012] [Accepted: 01/18/2013] [Indexed: 01/19/2023] Open
Abstract
Lens epithelium-derived growth factor (LEDGF/p75) tethers lentiviral preintegration complexes (PICs) to chromatin and is essential for effective HIV-1 replication. LEDGF/p75 interactions with lentiviral integrases are well characterized, but the structural basis for how LEDGF/p75 engages chromatin is unknown. We demonstrate that cellular LEDGF/p75 is tightly bound to mononucleosomes (MNs). Our proteomic experiments indicate that this interaction is direct and not mediated by other cellular factors. We determined the solution structure of LEDGF PWWP and monitored binding to the histone H3 tail containing trimethylated Lys36 (H3K36me3) and DNA by NMR. Results reveal two distinct functional interfaces of LEDGF PWWP: a well-defined hydrophobic cavity, which selectively interacts with the H3K36me3 peptide and adjacent basic surface, which non-specifically binds DNA. LEDGF PWWP exhibits nanomolar binding affinity to purified native MNs, but displays markedly lower affinities for the isolated H3K36me3 peptide and DNA. Furthermore, we show that LEDGF PWWP preferentially and tightly binds to in vitro reconstituted MNs containing a tri-methyl-lysine analogue at position 36 of H3 and not to their unmodified counterparts. We conclude that cooperative binding of the hydrophobic cavity and basic surface to the cognate histone peptide and DNA wrapped in MNs is essential for high-affinity binding to chromatin.
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Affiliation(s)
- Jocelyn O. Eidahl
- College of Pharmacy, The Ohio State University, Columbus, OH 43210, USA, Center for Retrovirus Research, The Ohio State University, Columbus, OH 43210, USA, Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210, USA, Department of Physics, The Ohio State University, Columbus, OH 43210, USA, Proteome Exploration Laboratory, Beckman Institute, California Institute of Technology, Pasadena, CA 91125, USA and AIDS and Cancer Virus Program, SAIC-Frederick, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA
| | - Brandon L. Crowe
- College of Pharmacy, The Ohio State University, Columbus, OH 43210, USA, Center for Retrovirus Research, The Ohio State University, Columbus, OH 43210, USA, Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210, USA, Department of Physics, The Ohio State University, Columbus, OH 43210, USA, Proteome Exploration Laboratory, Beckman Institute, California Institute of Technology, Pasadena, CA 91125, USA and AIDS and Cancer Virus Program, SAIC-Frederick, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA
| | - Justin A. North
- College of Pharmacy, The Ohio State University, Columbus, OH 43210, USA, Center for Retrovirus Research, The Ohio State University, Columbus, OH 43210, USA, Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210, USA, Department of Physics, The Ohio State University, Columbus, OH 43210, USA, Proteome Exploration Laboratory, Beckman Institute, California Institute of Technology, Pasadena, CA 91125, USA and AIDS and Cancer Virus Program, SAIC-Frederick, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA
| | - Christopher J. McKee
- College of Pharmacy, The Ohio State University, Columbus, OH 43210, USA, Center for Retrovirus Research, The Ohio State University, Columbus, OH 43210, USA, Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210, USA, Department of Physics, The Ohio State University, Columbus, OH 43210, USA, Proteome Exploration Laboratory, Beckman Institute, California Institute of Technology, Pasadena, CA 91125, USA and AIDS and Cancer Virus Program, SAIC-Frederick, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA
| | - Nikoloz Shkriabai
- College of Pharmacy, The Ohio State University, Columbus, OH 43210, USA, Center for Retrovirus Research, The Ohio State University, Columbus, OH 43210, USA, Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210, USA, Department of Physics, The Ohio State University, Columbus, OH 43210, USA, Proteome Exploration Laboratory, Beckman Institute, California Institute of Technology, Pasadena, CA 91125, USA and AIDS and Cancer Virus Program, SAIC-Frederick, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA
| | - Lei Feng
- College of Pharmacy, The Ohio State University, Columbus, OH 43210, USA, Center for Retrovirus Research, The Ohio State University, Columbus, OH 43210, USA, Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210, USA, Department of Physics, The Ohio State University, Columbus, OH 43210, USA, Proteome Exploration Laboratory, Beckman Institute, California Institute of Technology, Pasadena, CA 91125, USA and AIDS and Cancer Virus Program, SAIC-Frederick, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA
| | - Matthew Plumb
- College of Pharmacy, The Ohio State University, Columbus, OH 43210, USA, Center for Retrovirus Research, The Ohio State University, Columbus, OH 43210, USA, Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210, USA, Department of Physics, The Ohio State University, Columbus, OH 43210, USA, Proteome Exploration Laboratory, Beckman Institute, California Institute of Technology, Pasadena, CA 91125, USA and AIDS and Cancer Virus Program, SAIC-Frederick, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA
| | - Robert L. Graham
- College of Pharmacy, The Ohio State University, Columbus, OH 43210, USA, Center for Retrovirus Research, The Ohio State University, Columbus, OH 43210, USA, Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210, USA, Department of Physics, The Ohio State University, Columbus, OH 43210, USA, Proteome Exploration Laboratory, Beckman Institute, California Institute of Technology, Pasadena, CA 91125, USA and AIDS and Cancer Virus Program, SAIC-Frederick, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA
| | - Robert J. Gorelick
- College of Pharmacy, The Ohio State University, Columbus, OH 43210, USA, Center for Retrovirus Research, The Ohio State University, Columbus, OH 43210, USA, Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210, USA, Department of Physics, The Ohio State University, Columbus, OH 43210, USA, Proteome Exploration Laboratory, Beckman Institute, California Institute of Technology, Pasadena, CA 91125, USA and AIDS and Cancer Virus Program, SAIC-Frederick, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA
| | - Sonja Hess
- College of Pharmacy, The Ohio State University, Columbus, OH 43210, USA, Center for Retrovirus Research, The Ohio State University, Columbus, OH 43210, USA, Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210, USA, Department of Physics, The Ohio State University, Columbus, OH 43210, USA, Proteome Exploration Laboratory, Beckman Institute, California Institute of Technology, Pasadena, CA 91125, USA and AIDS and Cancer Virus Program, SAIC-Frederick, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA
| | - Michael G. Poirier
- College of Pharmacy, The Ohio State University, Columbus, OH 43210, USA, Center for Retrovirus Research, The Ohio State University, Columbus, OH 43210, USA, Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210, USA, Department of Physics, The Ohio State University, Columbus, OH 43210, USA, Proteome Exploration Laboratory, Beckman Institute, California Institute of Technology, Pasadena, CA 91125, USA and AIDS and Cancer Virus Program, SAIC-Frederick, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA
| | - Mark P. Foster
- College of Pharmacy, The Ohio State University, Columbus, OH 43210, USA, Center for Retrovirus Research, The Ohio State University, Columbus, OH 43210, USA, Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210, USA, Department of Physics, The Ohio State University, Columbus, OH 43210, USA, Proteome Exploration Laboratory, Beckman Institute, California Institute of Technology, Pasadena, CA 91125, USA and AIDS and Cancer Virus Program, SAIC-Frederick, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA
| | - Mamuka Kvaratskhelia
- College of Pharmacy, The Ohio State University, Columbus, OH 43210, USA, Center for Retrovirus Research, The Ohio State University, Columbus, OH 43210, USA, Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210, USA, Department of Physics, The Ohio State University, Columbus, OH 43210, USA, Proteome Exploration Laboratory, Beckman Institute, California Institute of Technology, Pasadena, CA 91125, USA and AIDS and Cancer Virus Program, SAIC-Frederick, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA
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Nikolaitchik OA, Dilley KA, Fu W, Gorelick RJ, Tai SHS, Soheilian F, Ptak RG, Nagashima K, Pathak VK, Hu WS. Dimeric RNA recognition regulates HIV-1 genome packaging. PLoS Pathog 2013; 9:e1003249. [PMID: 23555259 PMCID: PMC3605237 DOI: 10.1371/journal.ppat.1003249] [Citation(s) in RCA: 66] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2012] [Accepted: 01/30/2013] [Indexed: 11/18/2022] Open
Abstract
How retroviruses regulate the amount of RNA genome packaged into each virion has remained a long-standing question. Our previous study showed that most HIV-1 particles contain two copies of viral RNA, indicating that the number of genomes packaged is tightly regulated. In this report, we examine the mechanism that controls the number of RNA genomes encapsidated into HIV-1 particles. We hypothesize that HIV-1 regulates genome packaging by either the mass or copy number of the viral RNA. These two distinct mechanisms predict different outcomes when the genome size deviates significantly from that of wild type. Regulation by RNA mass would result in multiple copies of a small genome or one copy of a large genome being packaged, whereas regulation by copy number would result in two copies of a genome being packaged independent of size. To distinguish between these two hypotheses, we examined the packaging of viral RNA that was larger (≈17 kb) or smaller (≈3 kb) than that of wild-type HIV-1 (≈9 kb) and found that most particles packaged two copies of the viral genome regardless of whether they were 17 kb or 3 kb. Therefore, HIV-1 regulates RNA genome encapsidation not by the mass of RNA but by packaging two copies of RNA. To further explore the mechanism that governs this regulation, we examined the packaging of viral RNAs containing two packaging signals that can form intermolecular dimers or intramolecular dimers (self-dimers) and found that one self-dimer is packaged. Therefore, HIV-1 recognizes one dimeric RNA instead of two copies of RNA. Our findings reveal that dimeric RNA recognition is the key mechanism that regulates HIV-1 genome encapsidation and provide insights into a critical step in the generation of infectious viruses.
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Affiliation(s)
- Olga A. Nikolaitchik
- HIV Drug Resistance Program, National Cancer Institute, Frederick, Maryland, United States of America
| | - Kari A. Dilley
- HIV Drug Resistance Program, National Cancer Institute, Frederick, Maryland, United States of America
| | - William Fu
- Southern Research Institute, Frederick, Maryland, United States of America
| | - Robert J. Gorelick
- AIDS and Cancer Virology Program, SAIC-Frederick Inc., Frederick National Laboratory for Cancer Research, Frederick, Maryland, United States of America
| | - S.-H. Sheldon Tai
- HIV Drug Resistance Program, National Cancer Institute, Frederick, Maryland, United States of America
| | - Ferri Soheilian
- Electron Microscopy Laboratory, SAIC-Frederick Inc., Frederick National Laboratory for Cancer Research, Frederick, Maryland, United States of America
| | - Roger G. Ptak
- Southern Research Institute, Frederick, Maryland, United States of America
| | - Kunio Nagashima
- Electron Microscopy Laboratory, SAIC-Frederick Inc., Frederick National Laboratory for Cancer Research, Frederick, Maryland, United States of America
| | - Vinay K. Pathak
- HIV Drug Resistance Program, National Cancer Institute, Frederick, Maryland, United States of America
| | - Wei-Shau Hu
- HIV Drug Resistance Program, National Cancer Institute, Frederick, Maryland, United States of America
- * E-mail:
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Abstract
RNA chaperones are ubiquitous, heterogeneous proteins essential for RNA structural biogenesis and function. We investigated the mechanism of chaperone-mediated RNA folding by following the time-resolved dimerization of the packaging domain of a retroviral RNA at nucleotide resolution. In the absence of the nucleocapsid (NC) chaperone, dimerization proceeded through multiple, slow-folding intermediates. In the presence of NC, dimerization occurred rapidly through a single structural intermediate. The RNA binding domain of heterogeneous nuclear ribonucleoprotein A1 protein, a structurally unrelated chaperone, also accelerated dimerization. Both chaperones interacted primarily with guanosine residues. Replacing guanosine with more weakly pairing inosine yielded an RNA that folded rapidly without a facilitating chaperone. These results show that RNA chaperones can simplify RNA folding landscapes by weakening intramolecular interactions involving guanosine and explain many RNA chaperone activities.
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Affiliation(s)
- Jacob K Grohman
- Department of Chemistry, University of North Carolina, Chapel Hill, NC 27599-3290, USA
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McCauley MJ, Rouzina I, Hoadley K, Gorelick RJ, Musier-Forsyth K, Williams MC. Nucleic Acid Chaperone Activity Transforms the Energy Landscape of HIV-1 TAR RNA. Biophys J 2013. [DOI: 10.1016/j.bpj.2012.11.1118] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022] Open
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41
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Li J, Gorelick RJ, Rouzina I, Williams MC. Nucleic Acid Binding Kinetics of HIV-1 Nucleocapsid Proteins from Single Molecule DNA Stretching. Biophys J 2013. [DOI: 10.1016/j.bpj.2012.11.1428] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022] Open
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42
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Aduri R, Briggs KT, Gorelick RJ, Marino JP. Molecular determinants of HIV-1 NCp7 chaperone activity in maturation of the HIV-1 dimerization initiation site. Nucleic Acids Res 2012; 41:2565-80. [PMID: 23275531 PMCID: PMC3575791 DOI: 10.1093/nar/gks1350] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
Human immunodeficiency virus genome dimerization is initiated through an RNA-RNA kissing interaction formed via the dimerization initiation site (DIS) loop sequence, which has been proposed to be converted to a more thermodynamically stable linkage by the viral p7 form of the nucleocapsid protein (NC). Here, we systematically probed the role of specific amino acids of NCp7 in its chaperone activity in the DIS conversion using 2-aminopurine (2-AP) fluorescence and nuclear magnetic resonance spectroscopy. Through comparative analysis of NCp7 mutants, the presence of positively charged residues in the N-terminus was found to be essential for both helix destabilization and strand transfer functions. It was also observed that the presence and type of the Zn finger is important for NCp7 chaperone activity, but not the order of the Zn fingers. Swapping single aromatic residues between Zn fingers had a significant effect on NCp7 activity; however, these mutants did not exhibit the same activity as mutants in which the order of the Zn fingers was changed, indicating a functional role for other flanking residues. RNA chaperone activity is further correlated with NCp7 structure and interaction with RNA through comparative analysis of nuclear magnetic resonance spectra of NCp7 variants, and complexes of these proteins with the DIS dimer.
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Affiliation(s)
- Raviprasad Aduri
- Institute for Bioscience and Biotechnology Research of the University of Maryland and the National Institute of Standards and Technology, Rockville, MD 20850, USA
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Hergott CB, Mitra M, Guo J, Wu T, Miller JT, Iwatani Y, Gorelick RJ, Levin JG. Zinc finger function of HIV-1 nucleocapsid protein is required for removal of 5'-terminal genomic RNA fragments: a paradigm for RNA removal reactions in HIV-1 reverse transcription. Virus Res 2012; 171:346-55. [PMID: 23149014 DOI: 10.1016/j.virusres.2012.08.013] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2012] [Revised: 07/27/2012] [Accepted: 08/20/2012] [Indexed: 11/28/2022]
Abstract
During (-) strong-stop DNA [(-) SSDNA] synthesis, RNase H cleavage of genomic viral RNA generates small 5'-terminal RNA fragments (14-18 nt) that remain annealed to the DNA. Unless these fragments are removed, the minus-strand transfer reaction, required for (-) SSDNA elongation, cannot occur. Here, we describe the mechanism of 5'-terminal RNA removal and the roles of HIV-1 nucleocapsid protein (NC) and RNase H cleavage in this process. Using an NC-dependent system that models minus-strand transfer, we show that the presence of short terminal fragments pre-annealed to (-) SSDNA has no impact on strand transfer, implying efficient fragment removal. Moreover, in reactions with an RNase H(-) reverse transcriptase mutant, NC alone is able to facilitate fragment removal, albeit less efficiently than in the presence of both RNase H activity and NC. Results obtained from novel electrophoretic gel mobility shift and Förster Resonance Energy Transfer assays, which each directly measure RNA fragment release from a duplex in the absence of DNA synthesis, demonstrate for the first time that the architectural integrity of NC's zinc finger (ZF) domains is absolutely required for this reaction. This suggests that NC's helix destabilizing activity (associated with the ZFs) facilitates strand exchange through the displacement of these short terminal RNAs by the longer 3' acceptor RNA, which forms a more stable duplex with (-) SSDNA. Taken together with previously published results, we conclude that NC-mediated fragment removal is linked mechanistically with selection of the correct primer for plus-strand DNA synthesis and tRNA removal step prior to plus-strand transfer. Thus, HIV-1 has evolved a single mechanism for these RNA removal reactions that are critical for successful reverse transcription.
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Affiliation(s)
- Christopher B Hergott
- Section on Viral Gene Regulation, Program on Genomics of Differentiation, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892-2780, USA
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Lyonnais S, Gorelick RJ, Heniche-Boukhalfa F, Bouaziz S, Parissi V, Mouscadet JF, Restle T, Gatell JM, Le Cam E, Mirambeau G. A protein ballet around the viral genome orchestrated by HIV-1 reverse transcriptase leads to an architectural switch: from nucleocapsid-condensed RNA to Vpr-bridged DNA. Virus Res 2012; 171:287-303. [PMID: 23017337 DOI: 10.1016/j.virusres.2012.09.008] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2012] [Revised: 09/13/2012] [Accepted: 09/14/2012] [Indexed: 12/15/2022]
Abstract
HIV-1 reverse transcription is achieved in the newly infected cell before viral DNA (vDNA) nuclear import. Reverse transcriptase (RT) has previously been shown to function as a molecular motor, dismantling the nucleocapsid complex that binds the viral genome as soon as plus-strand DNA synthesis initiates. We first propose a detailed model of this dismantling in close relationship with the sequential conversion from RNA to double-stranded (ds) DNA, focusing on the nucleocapsid protein (NCp7). The HIV-1 DNA-containing pre-integration complex (PIC) resulting from completion of reverse transcription is translocated through the nuclear pore. The PIC nucleoprotein architecture is poorly understood but contains at least two HIV-1 proteins initially from the virion core, namely integrase (IN) and the viral protein r (Vpr). We next present a set of electron micrographs supporting that Vpr behaves as a DNA architectural protein, initiating multiple DNA bridges over more than 500 base pairs (bp). These complexes are shown to interact with NCp7 bound to single-stranded nucleic acid regions that are thought to maintain IN binding during dsDNA synthesis, concurrently with nucleocapsid complex dismantling. This unexpected binding of Vpr conveniently leads to a compacted but filamentous folding of the vDNA that should favor its nuclear import. Finally, nucleocapsid-like aggregates engaged in dsDNA synthesis appear to efficiently bind to F-actin filaments, a property that may be involved in targeting complexes to the nuclear envelope. More generally, this article highlights unique possibilities offered by in vitro reconstitution approaches combined with macromolecular imaging to gain insights into the mechanisms that alter the nucleoprotein architecture of the HIV-1 genome, ultimately enabling its insertion into the nuclear chromatin.
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Wu H, Mitra M, McCauley MJ, Thomas JA, Rouzina I, Musier-Forsyth K, Williams MC, Gorelick RJ. Aromatic residue mutations reveal direct correlation between HIV-1 nucleocapsid protein's nucleic acid chaperone activity and retroviral replication. Virus Res 2012; 171:263-77. [PMID: 22814429 DOI: 10.1016/j.virusres.2012.07.008] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2012] [Revised: 07/02/2012] [Accepted: 07/07/2012] [Indexed: 10/28/2022]
Abstract
The human immunodeficiency virus type 1 (HIV-1) nucleocapsid (NC) protein plays an essential role in several stages of HIV-1 replication. One important function of HIV-1 NC is to act as a nucleic acid chaperone, in which the protein facilitates nucleic acid rearrangements important for reverse transcription and recombination. NC contains only 55 amino acids, with 15 basic residues and two zinc fingers, each having a single aromatic residue (Phe16 and Trp37). Despite its simple structure, HIV-1 NC appears to have optimal chaperone activity, including the ability to strongly aggregate nucleic acids, destabilize nucleic acid secondary structure, and facilitate rapid nucleic acid annealing. Here we combine single molecule DNA stretching experiments with ensemble solution studies of protein-nucleic acid binding affinity, oligonucleotide annealing, and nucleic acid aggregation to measure the characteristics of wild-type (WT) and aromatic residue mutants of HIV-1 NC that are important for nucleic acid chaperone activity. These in vitro results are compared to in vivo HIV-1 replication for viruses containing the same mutations. This work allows us to directly relate HIV-1 NC structure with its function as a nucleic acid chaperone in vitro and in vivo. We show that replacement of either aromatic residue with another aromatic residue results in a protein that strongly resembles WT NC. In contrast, single amino acid substitutions of either Phe16Ala or Trp37Ala significantly slow down NC's DNA interaction kinetics, while retaining some helix-destabilization capability. A double Phe16Ala/Trp37Ala substitution further reduces the latter activity. Surprisingly, the ensemble nucleic acid binding, annealing, and aggregation properties are not significantly altered for any mutant except the double aromatic substitution with Ala. Thus, elimination of a single aromatic residue from either zinc finger strongly reduces NC's chaperone activity as determined by single molecule DNA stretching experiments without significantly altering its ensemble-averaged biochemical properties. Importantly, the substitution of aromatic residues with Ala progressively decreases NC's nucleic acid chaperone activity while also progressively inhibiting viral replication. Taken together, these data support the critical role of HIV-1 NC's aromatic residues, and establish a direct and statistically significant correlation between nucleic acid chaperone activity and viral replication.
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Affiliation(s)
- Hao Wu
- Northeastern University, Department of Physics, Boston, MA 02115, USA
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Berg RK, Melchjorsen J, Rintahaka J, Diget E, Søby S, Horan KA, Gorelick RJ, Matikainen S, Larsen CS, Ostergaard L, Paludan SR, Mogensen TH. Genomic HIV RNA induces innate immune responses through RIG-I-dependent sensing of secondary-structured RNA. PLoS One 2012; 7:e29291. [PMID: 22235281 PMCID: PMC3250430 DOI: 10.1371/journal.pone.0029291] [Citation(s) in RCA: 113] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2011] [Accepted: 11/24/2011] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND Innate immune responses have recently been appreciated to play an important role in the pathogenesis of HIV infection. Whereas inadequate innate immune sensing of HIV during acute infection may contribute to failure to control and eradicate infection, persistent inflammatory responses later during infection contribute in driving chronic immune activation and development of immunodeficiency. However, knowledge on specific HIV PAMPs and cellular PRRs responsible for inducing innate immune responses remains sparse. METHODS/PRINCIPAL FINDINGS Here we demonstrate a major role for RIG-I and the adaptor protein MAVS in induction of innate immune responses to HIV genomic RNA. We found that secondary structured HIV-derived RNAs induced a response similar to genomic RNA. In primary human peripheral blood mononuclear cells and primary human macrophages, HIV RNA induced expression of IFN-stimulated genes, whereas only low levels of type I IFN and tumor necrosis factor α were produced. Furthermore, secondary structured HIV-derived RNA activated pathways to NF-κB, MAP kinases, and IRF3 and co-localized with peroxisomes, suggesting a role for this organelle in RIG-I-mediated innate immune sensing of HIV RNA. CONCLUSIONS/SIGNIFICANCE These results establish RIG-I as an innate immune sensor of cytosolic HIV genomic RNA with secondary structure, thereby expanding current knowledge on HIV molecules capable of stimulating the innate immune system.
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MESH Headings
- Adaptor Proteins, Signal Transducing/metabolism
- Animals
- Cell Line, Tumor
- DEAD Box Protein 58
- DEAD-box RNA Helicases/metabolism
- Genome, Viral/immunology
- HIV-1/genetics
- HIV-1/immunology
- HIV-1/metabolism
- Humans
- Immunity, Innate
- Interferon Regulatory Factors/metabolism
- Leukocytes, Mononuclear/cytology
- Leukocytes, Mononuclear/immunology
- Leukocytes, Mononuclear/metabolism
- Leukocytes, Mononuclear/virology
- Mice
- Mice, Inbred C57BL
- NF-kappa B/metabolism
- Nucleic Acid Conformation
- Oligoribonucleotides/chemistry
- Oligoribonucleotides/metabolism
- Peroxisomes/metabolism
- Peroxisomes/virology
- Protein Transport
- RNA, Viral/chemistry
- RNA, Viral/metabolism
- Receptors, Immunologic
- Signal Transduction/immunology
- Viral Proteins/metabolism
- p38 Mitogen-Activated Protein Kinases/metabolism
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Affiliation(s)
- Randi K. Berg
- Department of Infectious Diseases, Aarhus University Hospital - Skejby, Aarhus, Denmark
| | - Jesper Melchjorsen
- Department of Infectious Diseases, Aarhus University Hospital - Skejby, Aarhus, Denmark
| | - Johanna Rintahaka
- Unit of Excellence for Immunotoxicology, Finnish Institute of Occupational Health, Helsinki, Finland
| | - Elisabeth Diget
- Department of Infectious Diseases, Aarhus University Hospital - Skejby, Aarhus, Denmark
| | - Stine Søby
- Department of Infectious Diseases, Aarhus University Hospital - Skejby, Aarhus, Denmark
| | - Kristy A. Horan
- Department of Biomedicine, University of Aarhus, Aarhus, Denmark
| | - Robert J. Gorelick
- AIDS and Cancer Virus Program, SAIC-Frederick, Inc., National Cancer Institute-Frederick, Frederick, Maryland, United States of America
| | - Sampsa Matikainen
- Unit of Excellence for Immunotoxicology, Finnish Institute of Occupational Health, Helsinki, Finland
| | - Carsten S. Larsen
- Department of Infectious Diseases, Aarhus University Hospital - Skejby, Aarhus, Denmark
| | - Lars Ostergaard
- Department of Infectious Diseases, Aarhus University Hospital - Skejby, Aarhus, Denmark
| | - Søren R. Paludan
- Department of Biomedicine, University of Aarhus, Aarhus, Denmark
| | - Trine H. Mogensen
- Department of Infectious Diseases, Aarhus University Hospital - Skejby, Aarhus, Denmark
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Wu H, McCauley MJ, Gorelick RJ, Rouzina I, Musier-Forsyth K, Williams MC. Nucleic Acid Chaperone Activity of Wild Type and Mutant FIV Nucleocapsid Proteins. Biophys J 2012. [DOI: 10.1016/j.bpj.2011.11.358] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2022] Open
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Jiang J, Ablan S, Derebail S, Hercík K, Soheilian F, Thomas JA, Tang S, Hewlett I, Nagashima K, Gorelick RJ, Freed EO, Levin JG. The interdomain linker region of HIV-1 capsid protein is a critical determinant of proper core assembly and stability. Virology 2011; 421:253-65. [PMID: 22036671 PMCID: PMC3573886 DOI: 10.1016/j.virol.2011.09.012] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2011] [Revised: 08/17/2011] [Accepted: 09/14/2011] [Indexed: 11/20/2022]
Abstract
The HIV-1 capsid protein consists of two independently folded domains connected by a flexible peptide linker (residues 146-150), the function of which remains to be defined. To investigate the role of this region in virus replication, we made alanine or leucine substitutions in each linker residue and two flanking residues. Three classes of mutants were identified: (i) S146A and T148A behave like wild type (WT); (ii) Y145A, I150A, and L151A are noninfectious, assemble unstable cores with aberrant morphology, and synthesize almost no viral DNA; and (iii) P147L and S149A display a poorly infectious, attenuated phenotype. Infectivity of P147L and S149A is rescued specifically by pseudotyping with vesicular stomatitis virus envelope glycoprotein. Moreover, despite having unstable cores, these mutants assemble WT-like structures and synthesize viral DNA, although less efficiently than WT. Collectively, these findings demonstrate that the linker region is essential for proper assembly and stability of cores and efficient replication.
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Affiliation(s)
- Jiyang Jiang
- Section on Viral Gene Regulation, Program in Genomics of Differentiation, Eunice Kennedy Shriver National Institute of Child Health, National Institutes of Health, Building 6B, Room 216, 6 Center Drive, Bethesda, MD 20892-2780, USA
| | - Sherimay Ablan
- Virus-Cell Interaction Section, Drug Resistance Program, National Cancer Institute Frederick, Frederick, MD 21702-1201, USA
| | - Suchitra Derebail
- Section on Viral Gene Regulation, Program in Genomics of Differentiation, Eunice Kennedy Shriver National Institute of Child Health, National Institutes of Health, Building 6B, Room 216, 6 Center Drive, Bethesda, MD 20892-2780, USA
| | - Kamil Hercík
- Section on Viral Gene Regulation, Program in Genomics of Differentiation, Eunice Kennedy Shriver National Institute of Child Health, National Institutes of Health, Building 6B, Room 216, 6 Center Drive, Bethesda, MD 20892-2780, USA
| | - Ferri Soheilian
- Image Analysis Laboratory, SAIC-Frederick, Inc., National Cancer Institute-Frederick, Frederick, MD 21702-1201, USA
| | - James A. Thomas
- AIDS and Cancer Virus Program, SAIC-Frederick, Inc., National Cancer Institute-Frederick, Frederick, MD 21702-1201, USA
| | - Shixing Tang
- Laboratory of Molecular Virology, Center for Biologics Evaluation and Research, Food and Drug Administration, Bethesda, MD 20892, USA
| | - Indira Hewlett
- Laboratory of Molecular Virology, Center for Biologics Evaluation and Research, Food and Drug Administration, Bethesda, MD 20892, USA
| | - Kunio Nagashima
- Image Analysis Laboratory, SAIC-Frederick, Inc., National Cancer Institute-Frederick, Frederick, MD 21702-1201, USA
| | - Robert J. Gorelick
- AIDS and Cancer Virus Program, SAIC-Frederick, Inc., National Cancer Institute-Frederick, Frederick, MD 21702-1201, USA
| | - Eric O. Freed
- Virus-Cell Interaction Section, Drug Resistance Program, National Cancer Institute Frederick, Frederick, MD 21702-1201, USA
| | - Judith G. Levin
- Section on Viral Gene Regulation, Program in Genomics of Differentiation, Eunice Kennedy Shriver National Institute of Child Health, National Institutes of Health, Building 6B, Room 216, 6 Center Drive, Bethesda, MD 20892-2780, USA
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Grohman JK, Kottegoda S, Gorelick RJ, Allbritton NL, Weeks KM. Femtomole SHAPE reveals regulatory structures in the authentic XMRV RNA genome. J Am Chem Soc 2011; 133:20326-34. [PMID: 22126209 DOI: 10.1021/ja2070945] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Higher-order structure influences critical functions in nearly all noncoding and coding RNAs. Most single-nucleotide resolution RNA structure determination technologies cannot be used to analyze RNA from scarce biological samples, like viral genomes. To make quantitative RNA structure analysis applicable to a much wider array of RNA structure-function problems, we developed and applied high-sensitivity selective 2'-hydroxyl acylation analyzed by primer extension (SHAPE) to structural analysis of authentic genomic RNA of the xenotropic murine leukemia virus-related virus (XMRV). For analysis of fluorescently labeled cDNAs generated in high-sensitivity SHAPE experiments, we developed a two-color capillary electrophoresis approach with zeptomole molecular detection limits and subfemtomole sensitivity for complete SHAPE experiments involving hundreds of individual RNA structure measurements. High-sensitivity SHAPE data correlated closely (R = 0.89) with data obtained by conventional capillary electrophoresis. Using high-sensitivity SHAPE, we determined the dimeric structure of the XMRV packaging domain, examined dynamic interactions between the packaging domain RNA and viral nucleocapsid protein inside virion particles, and identified the packaging signal for this virus. Despite extensive sequence differences between XMRV and the intensively studied Moloney murine leukemia virus, architectures of the regulatory domains are similar and reveal common principles of gammaretrovirus RNA genome packaging.
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Affiliation(s)
- Jacob K Grohman
- Department of Chemistry, University of North Carolina, Chapel Hill, North Carolina 27599-3290, USA
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Shen W, Gorelick RJ, Bambara RA. HIV-1 nucleocapsid protein increases strand transfer recombination by promoting dimeric G-quartet formation. J Biol Chem 2011; 286:29838-47. [PMID: 21737842 PMCID: PMC3191025 DOI: 10.1074/jbc.m111.262352] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2011] [Revised: 07/07/2011] [Indexed: 11/06/2022] Open
Abstract
A preferred site for HIV-1 recombination was identified in vivo and in vitro surrounding the beginning of the HIV-1 gag gene. This G-rich gag hotspot for recombination contains three evenly spaced G-runs that stalled reverse transcriptase. Disruption of the G-runs suppressed both the associated pausing and strand transfer in vitro. Significantly, this same gag sequence was able to fold into a G-quartet monomer, dimer, and tetramer, depending on the cations employed. The pause band at the G-run (nucleotide (nt) 405-409), which was predicted to be involved in forming a G-quartet monomer, diminished with increased HIV-1 nucleocapsid (NC) protein. More NC induced stronger pauses at other G-runs (nt 363-367 and nt 382-384), a region that forms a G-quartet dimer, adhering the two RNA templates. We hypothesized that NC induces the unfolding of the monomeric G-quartet but stabilizes the dimeric interaction. We tested this by inserting a known G-quartet formation sequence, 5'-(UGGGGU)(4)-3', into a relatively structure-free template from the HIV-1 pol gene. Strand transfer assays were performed with cations that either encourage (K(+)) or discourage (Li(+)) G-quartet formation with or without NC. Strikingly, a G-quartet monomer was observed without NC, whereas a G-quartet dimer was observed with NC, both only in the presence of K(+). Moreover, the transfer efficiency of the dimerized template (with K(+) and NC) reached about 90%, approximately 2.5-fold of that of the non-dimerized template. Evidently, template dimerization induced by NC creates a proximity effect, leading to the unique high peak of transfer at the gag recombination hotspot.
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Affiliation(s)
- Wen Shen
- From the Department of Biochemistry and Biophysics and the Center for RNA Biology, University of Rochester Medical Center, Rochester, New York 14642 and
| | - Robert J. Gorelick
- the AIDS and Cancer Virus Program, SAIC-Frederick, Inc. NCI-Frederick, Frederick, Maryland 21702-1201
| | - Robert A. Bambara
- From the Department of Biochemistry and Biophysics and the Center for RNA Biology, University of Rochester Medical Center, Rochester, New York 14642 and
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