1
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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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2
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Kim J, Bose D, Araínga M, Haque MR, Fennessey CM, Caddell RA, Thomas Y, Ferrell DE, Ali S, Grody E, Goyal Y, Cicala C, Arthos J, Keele BF, Vaccari M, Lorenzo-Redondo R, Hope TJ, Villinger F, Martinelli E. TGF-β blockade drives a transitional effector phenotype in T cells reversing SIV latency and decreasing SIV reservoirs in vivo. Nat Commun 2024; 15:1348. [PMID: 38355731 PMCID: PMC10867093 DOI: 10.1038/s41467-024-45555-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [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: 09/22/2023] [Accepted: 01/26/2024] [Indexed: 02/16/2024] Open
Abstract
HIV-1 persistence during ART is due to the establishment of long-lived viral reservoirs in resting immune cells. Using an NHP model of barcoded SIVmac239 intravenous infection and therapeutic dosing of anti-TGFBR1 inhibitor galunisertib (LY2157299), we confirm the latency reversal properties of in vivo TGF-β blockade, decrease viral reservoirs and stimulate immune responses. Treatment of eight female, SIV-infected macaques on ART with four 2-weeks cycles of galunisertib leads to viral reactivation as indicated by plasma viral load and immunoPET/CT with a 64Cu-DOTA-F(ab')2-p7D3-probe. Post-galunisertib, lymph nodes, gut and PBMC exhibit lower cell-associated (CA-)SIV DNA and lower intact pro-virus (PBMC). Galunisertib does not lead to systemic increase in inflammatory cytokines. High-dimensional cytometry, bulk, and single-cell (sc)RNAseq reveal a galunisertib-driven shift toward an effector phenotype in T and NK cells characterized by a progressive downregulation in TCF1. In summary, we demonstrate that galunisertib, a clinical stage TGF-β inhibitor, reverses SIV latency and decreases SIV reservoirs by driving T cells toward an effector phenotype, enhancing immune responses in vivo in absence of toxicity.
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Affiliation(s)
- Jinhee Kim
- Department of Medicine, Division of Infectious Diseases, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Deepanwita Bose
- New Iberia Research Center, University of Louisiana at Lafayette, New Iberia, LA, USA
| | - Mariluz Araínga
- New Iberia Research Center, University of Louisiana at Lafayette, New Iberia, LA, USA
| | - Muhammad R Haque
- Cell and Developmental Biology, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Christine M Fennessey
- AIDS and Cancer Virus Program, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Rachel A Caddell
- Division of Immunology, Tulane National Primate Research Center, Covington, LA, USA
| | - Yanique Thomas
- Cell and Developmental Biology, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Douglas E Ferrell
- New Iberia Research Center, University of Louisiana at Lafayette, New Iberia, LA, USA
| | - Syed Ali
- New Iberia Research Center, University of Louisiana at Lafayette, New Iberia, LA, USA
| | - Emanuelle Grody
- Cell and Developmental Biology, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
- Center for Synthetic Biology, Northwestern University, Chicago, IL, USA
| | - Yogesh Goyal
- Cell and Developmental Biology, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
- Center for Synthetic Biology, Northwestern University, Chicago, IL, USA
- Robert H. Lurie Comprehensive Cancer Center, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Claudia Cicala
- Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - James Arthos
- Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Brandon F Keele
- AIDS and Cancer Virus Program, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Monica Vaccari
- Division of Immunology, Tulane National Primate Research Center, Covington, LA, USA
- Department of Microbiology and Immunology, Tulane University School of Medicine, New Orleans, LA, USA
| | - Ramon Lorenzo-Redondo
- Department of Medicine, Division of Infectious Diseases, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
- Center for Pathogen Genomics and Microbial Evolution, Northwestern University Havey Institute for Global Health, Chicago, IL, USA
| | - Thomas J Hope
- Cell and Developmental Biology, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Francois Villinger
- New Iberia Research Center, University of Louisiana at Lafayette, New Iberia, LA, USA
| | - Elena Martinelli
- Department of Medicine, Division of Infectious Diseases, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA.
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3
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Grunst MW, Gil HM, Grandea AG, Snow BJ, Andrabi R, Nedellec R, Burton I, Clark NM, Janaka SK, Keles NK, Moriarty RV, Weiler AM, Capuano S, Fennessey CM, Friedrich TC, O’Connor SL, O’Connor DH, Broman AT, Keele BF, Lifson JD, Hangartner L, Burton DR, Evans DT. Potent antibody-dependent cellular cytotoxicity of a V2-specific antibody is not sufficient for protection of macaques against SIV challenge. PLoS Pathog 2024; 20:e1011819. [PMID: 38252675 PMCID: PMC10833561 DOI: 10.1371/journal.ppat.1011819] [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: 11/10/2023] [Revised: 02/01/2024] [Accepted: 01/14/2024] [Indexed: 01/24/2024] Open
Abstract
Fc-mediated antibody effector functions, such as antibody-dependent cellular cytotoxicity (ADCC), can contribute to the containment HIV-1 replication but whether such activities are sufficient for protection is unclear. We previously identified an antibody to the variable 2 (V2) apex of the HIV-1 Env trimer (PGT145) that potently directs the lysis of SIV-infected cells by NK cells but poorly neutralizes SIV infectivity. To determine if ADCC is sufficient for protection, separate groups of six rhesus macaques were treated with PGT145 or a control antibody (DEN3) by intravenous infusion followed five days later by intrarectal challenge with SIVmac239. Despite high concentrations of PGT145 and potent ADCC activity in plasma on the day of challenge, all animals became infected and viral loads did not differ between the PGT145- and DEN3-treated animals. To determine if PGT145 can protect against a neutralization-sensitive virus, two additional groups of six macaques were treated with PGT145 and DEN3 and challenged with an SIVmac239 variant with a single amino acid change in Env (K180S) that increases PGT145 binding and renders the virus susceptible to neutralization by this antibody. Although there was no difference in virus acquisition, peak and chronic phase viral loads were significantly lower and time to peak viremia was significantly delayed in the PGT145-treated animals compared to the DEN3-treated control animals. Env changes were also selected in the PGT145-treated animals that confer resistance to both neutralization and ADCC. These results show that ADCC is not sufficient for protection by this V2-specific antibody. However, protection may be achieved by increasing the affinity of antibody binding to Env above the threshold required for neutralization.
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Affiliation(s)
- Michael W. Grunst
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Hwi Min Gil
- Wisconsin National Primate Research Center, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Andres G. Grandea
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
- Wisconsin National Primate Research Center, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Brian J. Snow
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Raiees Andrabi
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, California, United States of America
- International AIDS Vaccine Initiative Neutralizing Antibody Center, the Collaboration for AIDS Vaccine Discovery (CAVD) and Consortium for HIV/AIDS Vaccine Development (CHAVD), The Scripps Research Institute, La Jolla, California, United States of America
| | - Rebecca Nedellec
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, California, United States of America
- International AIDS Vaccine Initiative Neutralizing Antibody Center, the Collaboration for AIDS Vaccine Discovery (CAVD) and Consortium for HIV/AIDS Vaccine Development (CHAVD), The Scripps Research Institute, La Jolla, California, United States of America
| | - Iszac Burton
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, California, United States of America
- International AIDS Vaccine Initiative Neutralizing Antibody Center, the Collaboration for AIDS Vaccine Discovery (CAVD) and Consortium for HIV/AIDS Vaccine Development (CHAVD), The Scripps Research Institute, La Jolla, California, United States of America
| | - Natasha M. Clark
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Sanath Kumar Janaka
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Nida K. Keles
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Ryan V. Moriarty
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
- Wisconsin National Primate Research Center, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Andrea M. Weiler
- Wisconsin National Primate Research Center, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Saverio Capuano
- Wisconsin National Primate Research Center, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Christine M. Fennessey
- AIDS and Cancer Virus Program, Frederick National Laboratory for Cancer Research, Frederick, Maryland, United States of America
| | - Thomas C. Friedrich
- Wisconsin National Primate Research Center, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
- Department of Pathobiological Sciences, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Shelby L. O’Connor
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
- Wisconsin National Primate Research Center, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - David H. O’Connor
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
- Wisconsin National Primate Research Center, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Aimee T. Broman
- Department of Biostatistics and Medical Informatics, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Brandon F. Keele
- AIDS and Cancer Virus Program, Frederick National Laboratory for Cancer Research, Frederick, Maryland, United States of America
| | - Jeffrey D. Lifson
- AIDS and Cancer Virus Program, Frederick National Laboratory for Cancer Research, Frederick, Maryland, United States of America
| | - Lars Hangartner
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, California, United States of America
- International AIDS Vaccine Initiative Neutralizing Antibody Center, the Collaboration for AIDS Vaccine Discovery (CAVD) and Consortium for HIV/AIDS Vaccine Development (CHAVD), The Scripps Research Institute, La Jolla, California, United States of America
| | - Dennis R. Burton
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, California, United States of America
- International AIDS Vaccine Initiative Neutralizing Antibody Center, the Collaboration for AIDS Vaccine Discovery (CAVD) and Consortium for HIV/AIDS Vaccine Development (CHAVD), The Scripps Research Institute, La Jolla, California, United States of America
- Ragon Institute of MGH, MIT and Harvard, Boston, Massachusetts, United States of America
| | - David T. Evans
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
- Wisconsin National Primate Research Center, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
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4
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Kime J, Bose D, Arainga M, Haque MR, Fennessey CM, Caddell RA, Thomas Y, Ferrell DE, Ali S, Grody E, Goyal Y, Cicala C, Arthos J, Keele BF, Vaccari M, Lorenzo-Redondo R, Hope TJ, Villinger FJ, Marinelli E. TGF-β blockade drives a transitional effector phenotype in T cells reversing SIV latency and decreasing SIV reservoirs in vivo. bioRxiv 2023:2023.09.05.556422. [PMID: 38014094 PMCID: PMC10680555 DOI: 10.1101/2023.09.05.556422] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/29/2023]
Abstract
HIV-1 persistence during ART is due to the establishment of long-lived viral reservoirs in resting immune cells. Using an NHP model of barcoded SIVmac239 intravenous infection and therapeutic dosing of the anti-TGFBR1 inhibitor galunisertib (LY2157299), we confirmed the latency reversal properties of in vivo TGF-β blockade, decreased viral reservoirs and stimulated immune responses. Eight SIV-infected macaques on suppressive ART were treated with 4 2-week cycles of galunisertib. ART was discontinued 3 weeks after the last dose, and macaques euthanized 6 weeks after ART-interruption(ATI). One macaque did not rebound, while the remaining rebounded between week 2 and 6 post-ATI. Galunisertib led to viral reactivation as indicated by plasma viral load and immunoPET/CT with the 64Cu-DOTA-F(ab')2-p7D3-probe. Half to 1 Log decrease in cell-associated (CA-)SIV DNA was detected in lymph nodes, gut and PBMC, while intact pro-virus in PBMC decreased by 3-fold. No systemic increase in inflammatory cytokines was observed. High-dimensions cytometry, bulk and single-cell RNAseq revealed a shift toward an effector phenotype in T and NK cells. In summary, we demonstrated that galunisertib, a clinical stage TGFβ inhibitor, reverses SIV latency and decreases SIV reservoirs by driving T cells toward an effector phenotype, enhancing immune responses in vivo in absence of toxicity.
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5
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Solis-Leal A, Boby N, Mallick S, Cheng Y, Wu F, De La Torre G, Dufour J, Alvarez X, Shivanna V, Liu Y, Fennessey CM, Lifson JD, Li Q, Keele BF, Ling B. Lymphoid tissues contribute to plasma viral clonotypes early after antiretroviral therapy interruption in SIV-infected rhesus macaques. Sci Transl Med 2023; 15:eadi9867. [PMID: 38091409 DOI: 10.1126/scitranslmed.adi9867] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2023] [Accepted: 11/17/2023] [Indexed: 12/18/2023]
Abstract
The rebound-competent viral reservoir, composed of a virus that is able to persist during antiretroviral therapy (ART) and mediate reactivation of systemic viral replication and rebound viremia after ART interruption (ATI), remains the biggest obstacle to treating HIV infection. A better understanding of the cellular and tissue origins and the dynamics of viral populations that initiate rebound upon ATI could help develop therapeutic strategies for reducing the rebound-competent viral reservoir. In this study, barcoded simian immunodeficiency virus (SIV), SIVmac239M, was used to infect rhesus macaques to enable monitoring of viral barcode clonotypes contributing to virus detectable in plasma after ATI. Blood and tissues from secondary lymphoid organs (spleen, mesenteric lymph nodes, and inguinal lymph nodes) and from the colon, ileum, lung, liver, and brain were analyzed using viral barcode sequencing, intact proviral DNA assay, single-cell RNA sequencing, and combined CODEX and RNAscope in situ hybridization. Four of seven animals had viral barcodes detectable by deep sequencing of plasma at necropsy, although plasma viral RNA remained below 22 copies per milliliter. Among the tissues studied, mesenteric lymph nodes, inguinal lymph nodes, and spleen contained viral barcodes detected in plasma. CD4+ T cells were the main cell type harboring viral RNA after ATI. Furthermore, T cell zones in lymphoid tissues showed higher viral RNA abundance than B cell zones for most animals. These findings are consistent with lymphoid tissues contributing to the virus present in plasma early after ATI.
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Affiliation(s)
- Antonio Solis-Leal
- Host-Pathogen Interactions Program, Texas Biomedical Research Institute, 8715 W Military Dr, San Antonio, TX 78227, USA
| | - Nongthombam Boby
- Host-Pathogen Interactions Program, Texas Biomedical Research Institute, 8715 W Military Dr, San Antonio, TX 78227, USA
| | - Suvadip Mallick
- Host-Pathogen Interactions Program, Texas Biomedical Research Institute, 8715 W Military Dr, San Antonio, TX 78227, USA
| | - Yilun Cheng
- Nebraska Center for Virology and School of Biological Sciences, University of Nebraska-Lincoln, 1400 R St, Lincoln, NE 68588, USA
| | - Fei Wu
- Host-Pathogen Interactions Program, Texas Biomedical Research Institute, 8715 W Military Dr, San Antonio, TX 78227, USA
| | - Grey De La Torre
- Host-Pathogen Interactions Program, Texas Biomedical Research Institute, 8715 W Military Dr, San Antonio, TX 78227, USA
| | - Jason Dufour
- Tulane National Primate Research Center, 18703 Three Rivers Rd, Covington, LA 70433, USA
| | - Xavier Alvarez
- Host-Pathogen Interactions Program, Texas Biomedical Research Institute, 8715 W Military Dr, San Antonio, TX 78227, USA
| | - Vinay Shivanna
- Host-Pathogen Interactions Program, Texas Biomedical Research Institute, 8715 W Military Dr, San Antonio, TX 78227, USA
| | - Yaozhong Liu
- Tulane University School of Public Health and Tropical Medicine, 1440 Canal St, New Orleans, LA 70112, USA
| | - Christine M Fennessey
- AIDS and Cancer Virus Program, Frederick National Laboratory, 8560 Progress Drive, Frederick, MD 21701, USA
| | - Jeffrey D Lifson
- AIDS and Cancer Virus Program, Frederick National Laboratory, 8560 Progress Drive, Frederick, MD 21701, USA
| | - Qingsheng Li
- Nebraska Center for Virology and School of Biological Sciences, University of Nebraska-Lincoln, 1400 R St, Lincoln, NE 68588, USA
| | - Brandon F Keele
- AIDS and Cancer Virus Program, Frederick National Laboratory, 8560 Progress Drive, Frederick, MD 21701, USA
| | - Binhua Ling
- Host-Pathogen Interactions Program, Texas Biomedical Research Institute, 8715 W Military Dr, San Antonio, TX 78227, USA
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6
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Docken SS, McCormick K, Pampena MB, Samer S, Lindemuth E, Pinkevych M, Viox EG, Wu Y, Schlub TE, Cromer D, Keele BF, Paiardini M, Betts MR, Bar KJ, Davenport MP. Preferential selection of viral escape mutants by CD8+ T cell 'sieving' of SIV reactivation from latency. PLoS Pathog 2023; 19:e1011755. [PMID: 38032851 PMCID: PMC10688670 DOI: 10.1371/journal.ppat.1011755] [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: 06/30/2023] [Accepted: 10/15/2023] [Indexed: 12/02/2023] Open
Abstract
HIV rapidly rebounds after interruption of antiretroviral therapy (ART). HIV-specific CD8+ T cells may act to prevent early events in viral reactivation. However, the presence of viral immune escape mutations may limit the effect of CD8+ T cells on viral rebound. Here, we studied the impact of CD8 immune pressure on post-treatment rebound of barcoded SIVmac293M in 14 Mamu-A*01 positive rhesus macaques that initiated ART on day 14, and subsequently underwent two analytic treatment interruptions (ATIs). Rebound following the first ATI (seven months after ART initiation) was dominated by virus that retained the wild-type sequence at the Mamu-A*01 restricted Tat-SL8 epitope. By the end of the two-month treatment interruption, the replicating virus was predominantly escaped at the Tat-SL8 epitope. Animals reinitiated ART for 3 months prior to a second treatment interruption. Time-to-rebound and viral reactivation rate were significantly slower during the second treatment interruption compared to the first. Tat-SL8 escape mutants dominated early rebound during the second treatment interruption, despite the dominance of wild-type virus in the proviral reservoir. Furthermore, the escape mutations detected early in the second treatment interruption were well predicted by those replicating at the end of the first, indicating that escape mutant virus in the second interruption originated from the latent reservoir as opposed to evolving de novo post rebound. SL8-specific CD8+ T cell levels in blood prior to the second interruption were marginally, but significantly, higher (median 0.73% vs 0.60%, p = 0.016). CD8+ T cell depletion approximately 95 days after the second treatment interruption led to the reappearance of wild-type virus. This work suggests that CD8+ T cells can actively suppress the rebound of wild-type virus, leading to the dominance of escape mutant virus after treatment interruption.
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Affiliation(s)
- Steffen S. Docken
- Infection Analytics Program, Kirby Institute, UNSW Sydney, Sydney, New South Wales, Australia
| | - Kevin McCormick
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - M. Betina Pampena
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
- Center for AIDS Research and Institute for Immunology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Sadia Samer
- Division of Microbiology and Immunology, Emory National Primate Research Center, Emory University, Atlanta, Georgia, United States of America
| | - Emily Lindemuth
- Department of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Mykola Pinkevych
- Infection Analytics Program, Kirby Institute, UNSW Sydney, Sydney, New South Wales, Australia
| | - Elise G. Viox
- Division of Microbiology and Immunology, Emory National Primate Research Center, Emory University, Atlanta, Georgia, United States of America
| | - Yuhuang Wu
- Infection Analytics Program, Kirby Institute, UNSW Sydney, Sydney, New South Wales, Australia
| | - Timothy E. Schlub
- Sydney School of Public Health, Faculty of Medicine and Health, University of Sydney, Sydney, New South Wales, Australia
| | - Deborah Cromer
- Infection Analytics Program, Kirby Institute, UNSW Sydney, Sydney, New South Wales, Australia
| | - Brandon F. Keele
- AIDS and Cancer Virus Program, Frederick National Laboratory for Cancer Research, Frederick, Maryland, United States of America
| | - Mirko Paiardini
- Division of Microbiology and Immunology, Emory National Primate Research Center, Emory University, Atlanta, Georgia, United States of America
- Department of Pathology and Laboratory Medicine, School of Medicine, Emory University, Atlanta, Georgia, United States of America
| | - Michael R. Betts
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
- Center for AIDS Research and Institute for Immunology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Katharine J. Bar
- Department of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Miles P. Davenport
- Infection Analytics Program, Kirby Institute, UNSW Sydney, Sydney, New South Wales, Australia
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7
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Pinkevych M, Docken SS, Okoye AA, Fennessey CM, Del Prete GQ, Pino M, Harper JL, Betts MR, Paiardini M, Keele BF, Davenport MP. Timing of initiation of anti-retroviral therapy predicts post-treatment control of SIV replication. PLoS Pathog 2023; 19:e1011660. [PMID: 37801446 PMCID: PMC10558076 DOI: 10.1371/journal.ppat.1011660] [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: 01/17/2023] [Accepted: 09/04/2023] [Indexed: 10/08/2023] Open
Abstract
One approach to 'functional cure' of HIV infection is to induce durable control of HIV replication after the interruption of antiretroviral therapy (ART). However, the major factors that determine the viral 'setpoint' level after treatment interruption are not well understood. Here we combine data on ART interruption following SIV infection for 124 total animals from 10 independent studies across 3 institutional cohorts to understand the dynamics and predictors of post-treatment viral control. We find that the timing of treatment initiation is an important determinant of both the peak and early setpoint viral levels after treatment interruption. During the first 3 weeks of infection, every day of delay in treatment initiation is associated with a 0.22 log10 copies/ml decrease in post-rebound peak and setpoint viral levels. However, delay in initiation of ART beyond 3 weeks of infection is associated with higher post-rebound setpoint viral levels. For animals treated beyond 3 weeks post-infection, viral load at ART initiation was the primary predictor of post-rebound setpoint viral levels. Potential alternative predictors of post-rebound setpoint viral loads including cell-associated DNA or RNA, time from treatment interruption to rebound, and pre-interruption CD8+ T cell responses were also examined in the studies where these data were available. This analysis suggests that optimal timing of treatment initiation may be an important determinant of post-treatment control of HIV.
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Affiliation(s)
- Mykola Pinkevych
- Infection Analytics Program, Kirby Institute for Infection and Immunity, UNSW Australia, Sydney, New South Wales, Australia
| | - Steffen S. Docken
- Infection Analytics Program, Kirby Institute for Infection and Immunity, UNSW Australia, Sydney, New South Wales, Australia
| | - Afam A. Okoye
- Vaccine & Gene Therapy Institute, and Oregon National Primate Research Center, 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
| | - Gregory Q. Del Prete
- AIDS and Cancer Virus Program, Frederick National Laboratory for Cancer Research, Frederick, Maryland, United States of America
| | - Maria Pino
- Division of Microbiology and Immunology, Emory National Primate Research Center, Emory University, Atlanta, Georgia, United States of America
| | - Justin L. Harper
- Division of Microbiology and Immunology, Emory National Primate Research Center, Emory University, Atlanta, Georgia, United States of America
| | - Michael R. Betts
- Department of Microbiology and Center for AIDS Research, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Mirko Paiardini
- Division of Microbiology and Immunology, Emory National Primate Research Center, Emory University, Atlanta, Georgia, United States of America
- Department of Pathology and Laboratory Medicine, School of Medicine; Emory University, Atlanta, Georgia, United States of America
| | - Brandon F. Keele
- AIDS and Cancer Virus Program, Frederick National Laboratory for Cancer Research, Frederick, Maryland, United States of America
| | - Miles P. Davenport
- Infection Analytics Program, Kirby Institute for Infection and Immunity, UNSW Australia, Sydney, New South Wales, Australia
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8
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Harwood OE, Matschke LM, Moriarty RV, Balgeman AJ, Weaver AJ, Ellis-Connell AL, Weiler AM, Winchester LC, Fletcher CV, Friedrich TC, Keele BF, O’Connor DH, Lang JD, Reynolds MR, O’Connor SL. CD8+ cells and small viral reservoirs facilitate post-ART control of SIV replication in M3+ Mauritian cynomolgus macaques initiated on ART two weeks post-infection. PLoS Pathog 2023; 19:e1011676. [PMID: 37747933 PMCID: PMC10553806 DOI: 10.1371/journal.ppat.1011676] [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: 04/27/2023] [Revised: 10/05/2023] [Accepted: 09/12/2023] [Indexed: 09/27/2023] Open
Abstract
Sustainable HIV remission after antiretroviral therapy (ART) withdrawal, or post-treatment control (PTC), remains a top priority for HIV treatment. We observed surprising PTC in an MHC-haplomatched cohort of MHC-M3+ SIVmac239+ Mauritian cynomolgus macaques (MCMs) initiated on ART at two weeks post-infection (wpi). None of the MCMs possessed MHC haplotypes previously associated with SIV control. For six months after ART withdrawal, we observed undetectable or transient viremia in seven of the eight MCMs, despite detecting replication competent SIV using quantitative viral outgrowth assays. In vivo depletion of CD8α+ cells induced rebound in all animals, indicating the observed PTC was mediated, at least in part, by CD8α+ cells. With intact proviral DNA assays, we found that MCMs had significantly smaller viral reservoirs two wpi than a cohort of identically infected rhesus macaques, a population that rarely develops PTC. We found a similarly small viral reservoir among six additional SIV+ MCMs in which ART was initiated at eight wpi, some of whom exhibited viral rebound. These results suggest that an unusually small viral reservoir is a hallmark among SIV+ MCMs. By evaluating immunological differences between MCMs that did and did not rebound, we identified that PTC was associated with a reduced frequency of CD4+ and CD8+ lymphocyte subsets expressing exhaustion markers. Together, these results suggest a combination of small reservoirs and immune-mediated virus suppression contribute to PTC in MCMs. Further, defining the immunologic mechanisms that engender PTC in this model may identify therapeutic targets for inducing durable HIV remission in humans.
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Affiliation(s)
- Olivia E. Harwood
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Lea M. Matschke
- Department of Pathobiological Sciences, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Ryan V. Moriarty
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Alexis J. Balgeman
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Abigail J. Weaver
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Amy L. Ellis-Connell
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Andrea M. Weiler
- Wisconsin National Primate Research Center, Madison, Wisconsin, United States of America
| | - Lee C. Winchester
- College of Pharmacy, University of Nebraska Medical Center, Omaha, Nebraska, United States of America
| | - Courtney V. Fletcher
- College of Pharmacy, University of Nebraska Medical Center, Omaha, Nebraska, United States of America
| | - Thomas C. Friedrich
- Department of Pathobiological Sciences, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
- Wisconsin National Primate Research Center, Madison, Wisconsin, United States of America
| | - Brandon F. Keele
- AIDS and Cancer Virus Program, Frederick National Laboratory for Cancer Research, Frederick, Maryland, United States of America
| | - David H. O’Connor
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
- Wisconsin National Primate Research Center, Madison, Wisconsin, United States of America
| | - Jessica D. Lang
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
- Center for Human Genomics and Precision Medicine, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Matthew R. Reynolds
- Department of Pathobiological Sciences, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
- Wisconsin National Primate Research Center, Madison, Wisconsin, United States of America
| | - Shelby L. O’Connor
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
- Wisconsin National Primate Research Center, Madison, Wisconsin, United States of America
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9
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Smedley J, Turkbey B, Bernardo ML, Del Prete GQ, Estes JD, Griffiths GL, Kobayashi H, Choyke PL, Lifson JD, Keele BF. Correction: Tracking the Luminal Exposure and Lymphatic Drainage Pathways of Intravaginal and Intrarectal Inocula Used in Nonhuman Primate Models of HIV Transmission. PLoS One 2023; 18:e0288566. [PMID: 37418480 DOI: 10.1371/journal.pone.0288566] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/09/2023] Open
Abstract
[This corrects the article DOI: 10.1371/journal.pone.0092830.].
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10
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Bauer A, Lindemuth E, Marino FE, Krause R, Joy J, Docken SS, Mallick S, McCormick K, Holt C, Georgiev I, Felber B, Keele BF, Veazey R, Davenport MP, Li H, Shaw GM, Bar KJ. Adaptation of a transmitted/founder simian-human immunodeficiency virus for enhanced replication in rhesus macaques. PLoS Pathog 2023; 19:e1011059. [PMID: 37399208 PMCID: PMC10348547 DOI: 10.1371/journal.ppat.1011059] [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: 12/10/2022] [Revised: 07/14/2023] [Accepted: 06/21/2023] [Indexed: 07/05/2023] Open
Abstract
Transmitted/founder (TF) simian-human immunodeficiency viruses (SHIVs) express HIV-1 envelopes modified at position 375 to efficiently infect rhesus macaques while preserving authentic HIV-1 Env biology. SHIV.C.CH505 is an extensively characterized virus encoding the TF HIV-1 Env CH505 mutated at position 375 shown to recapitulate key features of HIV-1 immunobiology, including CCR5-tropism, a tier 2 neutralization profile, reproducible early viral kinetics, and authentic immune responses. SHIV.C.CH505 is used frequently in nonhuman primate studies of HIV, but viral loads after months of infection are variable and typically lower than those in people living with HIV. We hypothesized that additional mutations besides Δ375 might further enhance virus fitness without compromising essential components of CH505 Env biology. From sequence analysis of SHIV.C.CH505-infected macaques across multiple experiments, we identified a signature of envelope mutations associated with higher viremia. We then used short-term in vivo mutational selection and competition to identify a minimally adapted SHIV.C.CH505 with just five amino acid changes that substantially improve virus replication fitness in macaques. Next, we validated the performance of the adapted SHIV in vitro and in vivo and identified the mechanistic contributions of selected mutations. In vitro, the adapted SHIV shows improved virus entry, enhanced replication on primary rhesus cells, and preserved neutralization profiles. In vivo, the minimally adapted virus rapidly outcompetes the parental SHIV with an estimated growth advantage of 0.14 days-1 and persists through suppressive antiretroviral therapy to rebound at treatment interruption. Here, we report the successful generation of a well-characterized, minimally adapted virus, termed SHIV.C.CH505.v2, with enhanced replication fitness and preserved native Env properties that can serve as a new reagent for NHP studies of HIV-1 transmission, pathogenesis, and cure.
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Affiliation(s)
- Anya Bauer
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Emily Lindemuth
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Francesco Elia Marino
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Ryan Krause
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Jaimy Joy
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | | | - Suvadip Mallick
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Kevin McCormick
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Clinton Holt
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University, Nashville, Tennessee, United States of America
| | - Ivelin Georgiev
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University, Nashville, Tennessee, United States of America
| | - Barbara Felber
- Human Retrovirus Pathogenesis Section, Vaccine Branch, Center for Cancer Research, National Cancer Institute, Maryland, United States of America
| | - Brandon F. Keele
- AIDS and Cancer Virus Program, Frederick National Laboratory for Cancer Research, Frederick, Maryland, United States of America
| | - Ronald Veazey
- Department of Pathology and Laboratory Medicine, Tulane School of Medicine, New Orleans, Louisiana, United States of America
| | | | - Hui Li
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
- Departments of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - George M. Shaw
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
- Departments of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Katharine J. Bar
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
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11
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Sanders-Beer BE, Archin NM, Brumme ZL, Busch MP, Deleage C, O'Doherty U, Hughes SH, Jerome KR, Jones RB, Karn J, Kearney MF, Keele BF, Kulpa DA, Laird GM, Li JZ, Lichterfeld MD, Nussenzweig MC, Persaud D, Yukl SA, Siliciano RF, Mellors JW. Current HIV/SIV Reservoir Assays for Preclinical and Clinical Applications: Recommendations from the Experts 2022 NIAID Workshop Summary. AIDS Res Hum Retroviruses 2023; 40:7-21. [PMID: 37126090 DOI: 10.1089/aid.2022.0188] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/02/2023] Open
Abstract
Since the first HIV-cured person was reported in 2009, a strong interest in developing highly sensitive HIV and SIV reservoir assays has emerged. In particular, the question arose about the comparative value of state-of-the-art assays to measure and characterize the HIV reservoir, and how these assays can be applied to accurately detect changes in the reservoir during efforts to develop a cure for HIV infection. Second, it is important to consider the impact on the outcome of clinical trials if these relatively new HIV reservoir assays are incorporated into clinical trial endpoints and/or used for clinical decision-making. To understand the advantages and limitations and the regulatory implications of HIV reservoir assays, the National Institute of Allergy and Infectious Diseases (NIAID) sponsored and convened a meeting on September 16, 2022, to discuss the state of knowledge concerning these questions and best practices for selecting HIV reservoir assays for a particular research question or clinical trial protocol.
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Affiliation(s)
- Brigitte E Sanders-Beer
- National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Nancie M Archin
- Division of Infectious Diseases, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Zabrina L Brumme
- Faculty of Health Sciences, Simon Fraser University, Burnaby, British Columbia, Canada
| | - Michael P Busch
- Vitalant Research Institute, University of California, San Francisco, California, USA
| | - Claire Deleage
- AIDS and Cancer Virus Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research (FNLCR), Frederick, Maryland, USA
| | - Una O'Doherty
- Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Stephen H Hughes
- HIV Dynamics and Replication Program, CCR, National Cancer Institute, Frederick, Maryland, USA
| | - Keith R Jerome
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, and Department of Laboratory Medicine and Pathology, University of Washington, Seattle, Washington, USA
| | - R Brad Jones
- Division of Infectious Diseases, Department of Medicine, Weill Cornell Medicine, New York, New York, USA
| | - Jonathan Karn
- Department of Molecular Biology and Microbiology, Case Western Reserve University, Cleveland, Ohio, USA
| | - Mary F Kearney
- HIV Dynamics and Replication Program, CCR, National Cancer Institute, Frederick, Maryland, USA
| | - Brandon F Keele
- AIDS and Cancer Virus Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research (FNLCR), Frederick, Maryland, USA
| | - Deanna A Kulpa
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, Georgia, USA
| | | | - Jonathan Z Li
- Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Mathias D Lichterfeld
- Brigham and Women's Hospital and Ragon Institute of MGH, MIT and Harvard, Boston, Massachusetts, USA
| | - Michel C Nussenzweig
- Laboratory of Molecular Immunology, The Rockefeller University, New York, New York, USA
| | - Deborah Persaud
- Department of Pediatric Infectious Disease, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Steven A Yukl
- Department of Medicine, University of California San Francisco (UCSF) and San Francisco VA Medical Center, San Francisco, California, USA
| | - Robert F Siliciano
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - John W Mellors
- Division of Infectious Diseases, Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
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12
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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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13
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Solis-Leal A, Boby N, Mallick S, Cheng Y, Wu F, De La Torre G, Dufour J, Alvarez X, Shivanna V, Liu Y, Fennessey CM, Lifson JD, Li Q, Keele BF, Ling B. Lymphoid tissues contribute to viral clonotypes present in plasma at early post-ATI in SIV-infected rhesus macaques. bioRxiv 2023:2023.05.30.542512. [PMID: 37398418 PMCID: PMC10312542 DOI: 10.1101/2023.05.30.542512] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/04/2023]
Abstract
The rebound-competent viral reservoir (RCVR), comprised of virus that is able to persist during antiretroviral therapy (ART) and mediate reactivation of systemic viral replication and rebound viremia after antiretroviral therapy interruption (ATI), remains the biggest obstacle to the eradication of HIV infection. A better understanding of the cellular and tissue origins and the dynamics of viral populations that initiate rebound upon ATI could help develop targeted therapeutic strategies for reducing the RCVR. In this study, barcoded SIVmac239M was used to infect rhesus macaques to enable monitoring of viral barcode clonotypes contributing to virus detectable in plasma after ATI. Blood, lymphoid tissues (LTs, spleen, mesenteric and inguinal lymph nodes), and non-lymphoid tissues (NLTs, colon, ileum, lung, liver, and brain) were analyzed using viral barcode sequencing, intact proviral DNA assay, single-cell RNA sequencing, and combined CODEX/RNAscope/ in situ hybridization. Four of seven animals had viral barcodes detectable by deep sequencing of plasma at necropsy although plasma viral RNA remained < 22 copies/mL. Among the tissues studied, mesenteric and inguinal lymph nodes, and spleen contained viral barcodes detected in plasma, and trended to have higher cell-associated viral loads, higher intact provirus levels, and greater diversity of viral barcodes. CD4+ T cells were the main cell type harboring viral RNA (vRNA) after ATI. Further, T cell zones in LTs showed higher vRNA levels than B cell zones for most animals. These findings are consistent with LTs contributing to virus present in plasma early after ATI. One Sentence Summary The reemerging of SIV clonotypes at early post-ATI are likely from the secondary lymphoid tissues.
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14
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Bochart RM, Busman-Sahay K, Bondoc S, Morrow DW, Ortiz AM, Fennessey CM, Fischer MB, Shiel O, Swanson T, Shriver-Munsch CM, Crank HB, Armantrout KM, Barber-Axthelm AM, Langner C, Moats CR, Labriola CS, MacAllister R, Axthelm MK, Brenchley JM, Keele BF, Estes JD, Hansen SG, Smedley JV. Correction: Mitigation of endemic GI-tract pathogen-mediated inflammation through development of multimodal treatment regimen and its impact on SIV acquisition in rhesus macaques. PLoS Pathog 2023; 19:e1011343. [PMID: 37075022 PMCID: PMC10115249 DOI: 10.1371/journal.ppat.1011343] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/20/2023] Open
Abstract
[This corrects the article DOI: 10.1371/journal.ppat.1009565.].
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15
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Harwood OE, Matschke LM, Moriarty RV, Balgeman AJ, Weaver AJ, Ellis-Connell AL, Weiler AM, Winchester LC, Fletcher CV, Friedrich TC, Keele BF, O'Connor DH, Lang JD, Reynolds MR, O'Connor SL. CD8+ cells and small viral reservoirs facilitate post-ART control of SIV in Mauritian cynomolgus macaques. bioRxiv 2023:2023.03.01.530655. [PMID: 36909458 PMCID: PMC10002716 DOI: 10.1101/2023.03.01.530655] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/07/2023]
Abstract
Sustainable HIV remission after antiretroviral therapy (ART) withdrawal, or post-treatment control (PTC), remains a top priority for HIV treatment. We observed surprising PTC in an MHC-haplomatched cohort of MHC-M3+ SIVmac239+ Mauritian cynomolgus macaques (MCMs) initiated on ART at two weeks post-infection (wpi). For six months after ART withdrawal, we observed undetectable or transient viremia in seven of eight MCMs. In vivo depletion of CD8α+ cells induced rebound in all animals, indicating the PTC was mediated, at least in part, by CD8α+ cells. We found that MCMs had smaller acute viral reservoirs than a cohort of identically infected rhesus macaques, a population that rarely develops PTC. The mechanisms by which unusually small viral reservoirs and CD8α+ cell-mediated virus suppression enable PTC can be investigated using this MHC-haplomatched MCM model. Further, defining the immunologic mechanisms that engender PTC in this model may identify therapeutic targets for inducing durable HIV remission in humans.
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Affiliation(s)
- Olivia E Harwood
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, Madison, WI 53711
| | - Lea M Matschke
- Department of Pathobiological Sciences, University of Wisconsin-Madison, Madison, WI 53711
| | - Ryan V Moriarty
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, Madison, WI 53711
| | - Alexis J Balgeman
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, Madison, WI 53711
| | - Abigail J Weaver
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, Madison, WI 53711
| | - Amy L Ellis-Connell
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, Madison, WI 53711
| | - Andrea M Weiler
- Wisconsin National Primate Research Center, Madison, WI, 53711
| | - Lee C Winchester
- College of Pharmacy, University of Nebraska Medical Center, Omaha, NE 68198
| | | | - Thomas C Friedrich
- Department of Pathobiological Sciences, University of Wisconsin-Madison, Madison, WI 53711
- Wisconsin National Primate Research Center, Madison, WI, 53711
| | - Brandon F Keele
- AIDS and Cancer Virus Program, Frederick National Laboratory for Cancer Research, Frederick, MD 21701
| | - David H O'Connor
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, Madison, WI 53711
- Wisconsin National Primate Research Center, Madison, WI, 53711
| | - Jessica D Lang
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, Madison, WI 53711
- Center for Human Genomics and Precision Medicine, University of Wisconsin-Madison, Madison, WI 53711
| | - Matthew R Reynolds
- Department of Pathobiological Sciences, University of Wisconsin-Madison, Madison, WI 53711
- Wisconsin National Primate Research Center, Madison, WI, 53711
| | - Shelby L O'Connor
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, Madison, WI 53711
- Wisconsin National Primate Research Center, Madison, WI, 53711
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16
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Statzu M, Jin W, Fray EJ, Wong AKH, Kumar MR, Ferrer E, Docken SS, Pinkevych M, McBrien JB, Fennessey CM, Keele BF, Liang S, Harper JL, Mutascio S, Franchitti L, Wang H, Cicetti D, Bosinger SE, Carnathan DG, Vanderford TH, Margolis DM, Garcia-Martinez JV, Chahroudi A, Paiardini M, Siliciano J, Davenport MP, Kulpa DA, Siliciano RS, Silvestri G. CD8 + lymphocytes do not impact SIV reservoir establishment under ART. Nat Microbiol 2023; 8:299-308. [PMID: 36690860 PMCID: PMC9894752 DOI: 10.1038/s41564-022-01311-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Accepted: 12/15/2022] [Indexed: 01/24/2023]
Abstract
Persistence of the human immunodeficiency virus type-1 (HIV-1) latent reservoir in infected individuals remains a problem despite fully suppressive antiretroviral therapy (ART). While reservoir formation begins during acute infection, the mechanisms responsible for its establishment remain unclear. CD8+ T cells are important during the initial control of viral replication. Here we examined the effect of CD8+ T cells on formation of the latent reservoir in simian immunodeficiency virus (SIV)-infected macaques by performing experimental CD8+ depletion either before infection or before early (that is, day 14 post-infection) ART initiation. We found that CD8+ depletion resulted in slower decline of viremia, indicating that CD8+ lymphocytes reduce the average lifespan of productively infected cells during acute infection and early ART, presumably through SIV-specific cytotoxic T lymphocyte (CTL) activity. However, CD8+ depletion did not change the frequency of infected CD4+ T cells in the blood or lymph node as measured by the total cell-associated viral DNA or intact provirus DNA assay. In addition, the size of the persistent reservoir remained the same when measuring the kinetics of virus rebound after ART interruption. These data indicate that during early SIV infection, the viral reservoir that persists under ART is established largely independent of CTL control.
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Grants
- P30 AI050409 NIAID NIH HHS
- P51 OD011132 NIH HHS
- R01 AI143414 NIAID NIH HHS
- 75N91019D00024 NCI NIH HHS
- HHSN261201500003I NCI NIH HHS
- UM1 AI164562 NIAID NIH HHS
- UM1 AI164567 NIAID NIH HHS
- R01 AI125064 NIAID NIH HHS
- CU | National Cancer Institute, Cairo University (NCI)
- National Cancer Institute, National Institutes of Health, under Contract No. 75N91019D00024/HHSN261201500003I.
- This work was supported by UM1AI164562, co-funded by National Heart, Lung and Blood Institute, National Institute of Diabetes and Digestive and Kidney Diseases, National Institute of Neurological Disorders and Stroke, National Institute on Drug Abuse and the National Institute of Allergy and Infectious Diseases (to G.S., D.A.K., M.P.1), and NIH NIAID R01-AI143414 (to G.S. and D.A.K), and R01-AI125064 (to G.S., A.C., D.A.K.).
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Affiliation(s)
- Maura Statzu
- Emory National Primate Research Center, Department of Pathology and Laboratory Medicine, and Emory Vaccine Center, Emory University, Atlanta, GA, USA
| | - Wang Jin
- Kirby Institute, University of New South Wales, Sydney, Australia
| | - Emily J Fray
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Andrew Kam Ho Wong
- Emory National Primate Research Center, Department of Pathology and Laboratory Medicine, and Emory Vaccine Center, Emory University, Atlanta, GA, USA
| | - Mithra R Kumar
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Elizabeth Ferrer
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Steffen S Docken
- Kirby Institute, University of New South Wales, Sydney, Australia
| | - Mykola Pinkevych
- Kirby Institute, University of New South Wales, Sydney, Australia
| | - Julia B McBrien
- Emory National Primate Research Center, Department of Pathology and Laboratory Medicine, and Emory Vaccine Center, Emory University, Atlanta, GA, USA
| | - Christine M Fennessey
- AIDS and Cancer Virus Program, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Brandon F Keele
- AIDS and Cancer Virus Program, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Shan Liang
- Emory National Primate Research Center, Department of Pathology and Laboratory Medicine, and Emory Vaccine Center, Emory University, Atlanta, GA, USA
| | - Justin L Harper
- Emory National Primate Research Center, Department of Pathology and Laboratory Medicine, and Emory Vaccine Center, Emory University, Atlanta, GA, USA
| | - Simona Mutascio
- Emory National Primate Research Center, Department of Pathology and Laboratory Medicine, and Emory Vaccine Center, Emory University, Atlanta, GA, USA
| | - Lavinia Franchitti
- Emory National Primate Research Center, Department of Pathology and Laboratory Medicine, and Emory Vaccine Center, Emory University, Atlanta, GA, USA
| | - Hong Wang
- Emory National Primate Research Center, Department of Pathology and Laboratory Medicine, and Emory Vaccine Center, Emory University, Atlanta, GA, USA
| | - Davide Cicetti
- Emory National Primate Research Center, Department of Pathology and Laboratory Medicine, and Emory Vaccine Center, Emory University, Atlanta, GA, USA
| | - Steven E Bosinger
- Emory National Primate Research Center, Department of Pathology and Laboratory Medicine, and Emory Vaccine Center, Emory University, Atlanta, GA, USA
| | - Diane G Carnathan
- Emory National Primate Research Center, Department of Pathology and Laboratory Medicine, and Emory Vaccine Center, Emory University, Atlanta, GA, USA
| | - Thomas H Vanderford
- Emory National Primate Research Center, Department of Pathology and Laboratory Medicine, and Emory Vaccine Center, Emory University, Atlanta, GA, USA
| | - David M Margolis
- Division of Infectious Diseases, Center for AIDS Research, University of North Carolina at Chapel Hill, School of Medicine, Chapel Hill, NC, USA
| | - J Victor Garcia-Martinez
- Division of Infectious Diseases, Center for AIDS Research, University of North Carolina at Chapel Hill, School of Medicine, Chapel Hill, NC, USA
| | - Ann Chahroudi
- Emory National Primate Research Center, Department of Pathology and Laboratory Medicine, and Emory Vaccine Center, Emory University, Atlanta, GA, USA
- Department of Pediatrics, Emory University, Atlanta, GA, USA
| | - Mirko Paiardini
- Emory National Primate Research Center, Department of Pathology and Laboratory Medicine, and Emory Vaccine Center, Emory University, Atlanta, GA, USA
| | - Janet Siliciano
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | | | - Deanna A Kulpa
- Emory National Primate Research Center, Department of Pathology and Laboratory Medicine, and Emory Vaccine Center, Emory University, Atlanta, GA, USA
| | - Robert S Siliciano
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Guido Silvestri
- Emory National Primate Research Center, Department of Pathology and Laboratory Medicine, and Emory Vaccine Center, Emory University, Atlanta, GA, USA.
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17
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Ortiz AM, Baker PJ, Langner CA, Simpson J, Stacy A, Flynn JK, Starke CE, Vinton CL, Fennessey CM, Belkaid Y, Keele BF, Brenchley JM. Experimental bacterial dysbiosis with consequent immune alterations increase intrarectal SIV acquisition susceptibility. Cell Rep 2023; 42:112020. [PMID: 36848230 PMCID: PMC9989505 DOI: 10.1016/j.celrep.2023.112020] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2022] [Revised: 12/16/2022] [Accepted: 01/06/2023] [Indexed: 01/24/2023] Open
Abstract
Variations in the composition of the intestinal bacterial microbiome correlate with acquisition of some sexually transmitted pathogens. To experimentally assess the contribution of intestinal dysbiosis to rectal lentiviral acquisition, we induce dysbiosis in rhesus macaques (RMs) with the antibiotic vancomycin prior to repeated low-dose intrarectal challenge with simian immunodeficiency virus (SIV) SIVmac239X. Vancomycin administration reduces T helper 17 (TH17) and TH22 frequencies, increases expression of host bacterial sensors and antibacterial peptides, and increases numbers of transmitted-founder (T/F) variants detected upon SIV acquisition. We observe that SIV acquisition does not correlate with measures of dysbiosis but rather associates with perturbations in the host antimicrobial program. These findings establish a functional association between the intestinal microbiome and susceptibility to lentiviral acquisition across the rectal epithelial barrier.
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Affiliation(s)
- Alexandra M Ortiz
- Barrier Immunity Section, Laboratory of Viral Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Phillip J Baker
- Barrier Immunity Section, Laboratory of Viral Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Charlotte A Langner
- Barrier Immunity Section, Laboratory of Viral Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Jennifer Simpson
- Barrier Immunity Section, Laboratory of Viral Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Apollo Stacy
- Metaorganism Immunity Section, Laboratory of Immune System Biology and Laboratory of Host Immunity and Microbiome, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA; Department of Cardiovascular and Metabolic Sciences, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44195, USA
| | - Jacob K Flynn
- Barrier Immunity Section, Laboratory of Viral Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Carly E Starke
- Barrier Immunity Section, Laboratory of Viral Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Carol L Vinton
- Barrier Immunity Section, Laboratory of Viral Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Christine M Fennessey
- AIDS and Cancer Virus Program, Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA
| | - Yasmine Belkaid
- Metaorganism Immunity Section, Laboratory of Immune System Biology and Laboratory of Host Immunity and Microbiome, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA; NIAID Microbiome Program, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Brandon F Keele
- AIDS and Cancer Virus Program, Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA
| | - Jason M Brenchley
- Barrier Immunity Section, Laboratory of Viral Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA.
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18
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Gorman J, Wang C, Mason RD, Nazzari AF, Welles HC, Zhou T, Bess JW, Bylund T, Lee M, Tsybovsky Y, Verardi R, Wang S, Yang Y, Zhang B, Rawi R, Keele BF, Lifson JD, Liu J, Roederer M, Kwong PD. Cryo-EM structures of prefusion SIV envelope trimer. Nat Struct Mol Biol 2022; 29:1080-1091. [PMID: 36344847 PMCID: PMC10606957 DOI: 10.1038/s41594-022-00852-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [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: 11/03/2021] [Accepted: 09/25/2022] [Indexed: 11/09/2022]
Abstract
Simian immunodeficiency viruses (SIVs) are lentiviruses that naturally infect non-human primates of African origin and seeded cross-species transmissions of HIV-1 and HIV-2. Here we report prefusion stabilization and cryo-EM structures of soluble envelope (Env) trimers from rhesus macaque SIV (SIVmac) in complex with neutralizing antibodies. These structures provide residue-level definition for SIV-specific disulfide-bonded variable loops (V1 and V2), which we used to delineate variable-loop coverage of the Env trimer. The defined variable loops enabled us to investigate assembled Env-glycan shields throughout SIV, which we found to comprise both N- and O-linked glycans, the latter emanating from V1 inserts, which bound the O-link-specific lectin jacalin. We also investigated in situ SIVmac-Env trimers on virions, determining cryo-electron tomography structures at subnanometer resolutions for an antibody-bound complex and a ligand-free state. Collectively, these structures define the prefusion-closed structure of the SIV-Env trimer and delineate variable-loop and glycan-shielding mechanisms of immune evasion conserved throughout SIV evolution.
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Affiliation(s)
- Jason Gorman
- Vaccine Research Center, National Institutes of Health, Bethesda, MD, USA
| | - Chunyan Wang
- Department of Microbial Pathogenesis, Yale School of Medicine, New Haven, CT, USA
- Microbial Sciences Institute, Yale University, West Haven, CT, USA
| | - Rosemarie D Mason
- Vaccine Research Center, National Institutes of Health, Bethesda, MD, USA
| | | | - Hugh C Welles
- Vaccine Research Center, National Institutes of Health, Bethesda, MD, USA
| | - Tongqing Zhou
- Vaccine Research Center, National Institutes of Health, Bethesda, MD, USA
| | - Julian W Bess
- AIDS and Cancer Virus Program, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Tatsiana Bylund
- Vaccine Research Center, National Institutes of Health, Bethesda, MD, USA
| | - Myungjin Lee
- Vaccine Research Center, National Institutes of Health, Bethesda, MD, USA
| | - Yaroslav Tsybovsky
- Electron Microscopy Laboratory, Cancer Research Technology Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Raffaello Verardi
- Vaccine Research Center, National Institutes of Health, Bethesda, MD, USA
| | - Shuishu Wang
- Vaccine Research Center, National Institutes of Health, Bethesda, MD, USA
| | - Yongping Yang
- Vaccine Research Center, National Institutes of Health, Bethesda, MD, USA
| | - Baoshan Zhang
- Vaccine Research Center, National Institutes of Health, Bethesda, MD, USA
| | - Reda Rawi
- Vaccine Research Center, National Institutes of Health, Bethesda, MD, USA
| | - Brandon F Keele
- AIDS and Cancer Virus Program, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Jeffrey D Lifson
- AIDS and Cancer Virus Program, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Jun Liu
- Department of Microbial Pathogenesis, Yale School of Medicine, New Haven, CT, USA.
- Microbial Sciences Institute, Yale University, West Haven, CT, USA.
| | - Mario Roederer
- Vaccine Research Center, National Institutes of Health, Bethesda, MD, USA.
| | - Peter D Kwong
- Vaccine Research Center, National Institutes of Health, Bethesda, MD, USA.
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19
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Marshall VA, Fisher NC, Goodman CA, Castro EMC, Liu I, Khanal S, Holdridge BM, Thorpe AL, Labo N, Stolka KB, Hemingway-Foday JJ, Abassora M, N’Dom P, Smith JS, Sallah N, Palser AL, Kellam P, Keele BF, Whitby D. Systematic analysis of Kaposi's sarcoma (KS)-associated herpesvirus genomes from a KS case-control study in Cameroon: Evidence of dual infections but no association between viral sequence variation and KS risk. Int J Cancer 2022; 151:1127-1141. [PMID: 35608873 PMCID: PMC10043945 DOI: 10.1002/ijc.34136] [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: 12/14/2021] [Revised: 04/12/2022] [Accepted: 04/23/2022] [Indexed: 11/06/2022]
Abstract
In sub-Saharan Africa, Kaposi's sarcoma-associated herpesvirus (KSHV) is endemic, and Kaposi's sarcoma (KS) is a significant public health problem. Until recently, KSHV genotype analysis was performed using variable gene regions, representing a small fraction of the genome, and thus the contribution of sequence variation to viral transmission or pathogenesis are understudied. We performed near full-length KSHV genome sequence analysis on samples from 43 individuals selected from a large Cameroonian KS case-control study. KSHV genomes were obtained from 21 KS patients and 22 control participants. Phylogenetic analysis of the K1 region indicated the majority of sequences were A5 or B1 subtypes and all three K15 alleles were represented. Unique polymorphisms in the KSHV genome were observed including large gene deletions. We found evidence of multiple distinct KSHV genotypes in three individuals. Additionally, our analyses indicate that recombination is prevalent suggesting that multiple KSHV infections may not be uncommon overall. Most importantly, a detailed analysis of KSHV genomes from KS patients and control participants did not find a correlation between viral sequence variations and disease. Our study is the first to systematically compare near full-length KSHV genome sequences between KS cases and controls in the same endemic region to identify possible sequence variations associated with disease risk.
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Affiliation(s)
- Vickie A. Marshall
- Viral Oncology Section, AIDS and Cancer Virus Program, Frederick National Laboratory for Cancer Research, Frederick, Maryland, USA
| | - Nicholas C. Fisher
- Viral Oncology Section, AIDS and Cancer Virus Program, Frederick National Laboratory for Cancer Research, Frederick, Maryland, USA
| | - Charles A. Goodman
- Retroviral Evolution Section, AIDS and Cancer Virus Program, Frederick National Laboratory for Cancer Research, Frederick, Maryland, USA
| | - Elena M. Cornejo Castro
- Viral Oncology Section, AIDS and Cancer Virus Program, Frederick National Laboratory for Cancer Research, Frederick, Maryland, USA
| | - Isabella Liu
- Viral Oncology Section, AIDS and Cancer Virus Program, Frederick National Laboratory for Cancer Research, Frederick, Maryland, USA
| | - Sirish Khanal
- Retroviral Evolution Section, AIDS and Cancer Virus Program, Frederick National Laboratory for Cancer Research, Frederick, Maryland, USA
| | - Benjamin M. Holdridge
- Viral Oncology Section, AIDS and Cancer Virus Program, Frederick National Laboratory for Cancer Research, Frederick, Maryland, USA
| | - Abigail L. Thorpe
- Retroviral Evolution Section, AIDS and Cancer Virus Program, Frederick National Laboratory for Cancer Research, Frederick, Maryland, USA
| | - Nazzarena Labo
- Viral Oncology Section, AIDS and Cancer Virus Program, Frederick National Laboratory for Cancer Research, Frederick, Maryland, USA
| | | | | | | | | | | | - Neneh Sallah
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK
| | | | - Paul Kellam
- Kymab Ltd., Babraham Research Campus, Cambridge, UK
- Department of Medicine, Division of Infectious Diseases, Imperial College London, London, UK
| | - Brandon F. Keele
- Retroviral Evolution Section, AIDS and Cancer Virus Program, Frederick National Laboratory for Cancer Research, Frederick, Maryland, USA
| | - Denise Whitby
- Viral Oncology Section, AIDS and Cancer Virus Program, Frederick National Laboratory for Cancer Research, Frederick, Maryland, USA
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20
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Rawson JMO, Nikolaitchik OA, Shakya S, Keele BF, Pathak VK, Hu WS. Transcription Start Site Heterogeneity and Preferential Packaging of Specific Full-Length RNA Species Are Conserved Features of Primate Lentiviruses. Microbiol Spectr 2022; 10:e0105322. [PMID: 35736240 PMCID: PMC9430795 DOI: 10.1128/spectrum.01053-22] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [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] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Accepted: 06/05/2022] [Indexed: 11/22/2022] Open
Abstract
HIV-1 must package its RNA genome to generate infectious viruses. Recent studies have revealed that during genome packaging, HIV-1 not only excludes cellular mRNAs, but also distinguishes among full-length viral RNAs. Using NL4-3 and MAL molecular clones, multiple transcription start sites (TSS) were identified, which generate full-length RNAs that differ by only a few nucleotides at the 5' end. However, HIV-1 selectively packages RNAs containing one guanosine (1G RNA) over RNAs with three guanosines (3G RNA) at the 5' end. Thus, the 5' context of HIV-1 full-length RNA can affect its function. To determine whether the regulation of genome packaging by TSS usage is unique to NL4-3 and MAL, we examined 15 primate lentiviruses including transmitted founder viruses of HIV-1, HIV-2, and several simian immunodeficiency viruses (SIVs). We found that all 15 viruses used multiple TSS to some extent. However, the level of TSS heterogeneity in infected cells varied greatly, even among closely related viruses belonging to the same subtype. Most viruses also exhibited selective packaging of specific full-length viral RNA species into particles. These findings demonstrate that TSS heterogeneity and selective packaging of certain full-length viral RNA species are conserved features of primate lentiviruses. In addition, an SIV strain closely related to the progenitor virus that gave rise to HIV-1 group M, the pandemic pathogen, exhibited TSS usage similar to some HIV-1 strains and preferentially packaged 1G RNA. These findings indicate that multiple TSS usage and selective packaging of a particular unspliced RNA species predate the emergence of HIV-1. IMPORTANCE Unspliced HIV-1 RNA serves two important roles during viral replication: as the virion genome and as the template for translation of Gag/Gag-Pol. Previous studies of two HIV-1 molecular clones have concluded that the TSS usage affects unspliced HIV-1 RNA structures and functions. To investigate the evolutionary origin of this replication strategy, we determined TSS of HIV-1 RNA in infected cells and virions for 15 primate lentiviruses. All HIV-1 isolates examined, including several transmitted founder viruses, utilized multiple TSS and selected a particular RNA species for packaging. Furthermore, these features were observed in SIVs related to the progenitors of HIV-1, suggesting that these characteristics originated from the ancestral viruses. HIV-2, SIVs related to HIV-2, and other SIVs also exhibited multiple TSS and preferential packaging of specific unspliced RNA species, demonstrating that this replication strategy is broadly conserved across primate lentiviruses.
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Affiliation(s)
- Jonathan M. O. Rawson
- Viral Recombination Section, HIV Dynamics and Replication Program, National Cancer Institute at Frederick, Frederick, Maryland, USA
| | - Olga A. Nikolaitchik
- Viral Recombination Section, HIV Dynamics and Replication Program, National Cancer Institute at Frederick, Frederick, Maryland, USA
| | - Saurabh Shakya
- Viral Recombination Section, HIV Dynamics and Replication Program, National Cancer Institute at Frederick, Frederick, Maryland, USA
| | - Brandon F. Keele
- AIDS and Cancer Virus Program, Frederick National Laboratory, Frederick, Maryland, USA
| | - Vinay K. Pathak
- Viral Mutation Section, HIV Dynamics and Replication Program, National Cancer Institute at Frederick, Frederick, Maryland, USA
| | - Wei-Shau Hu
- Viral Recombination Section, HIV Dynamics and Replication Program, National Cancer Institute at Frederick, Frederick, Maryland, USA
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21
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Lawrence SP, Elser SE, Torben W, Blair RV, Pahar B, Aye PP, Schiro F, Szeltner D, Doyle-Meyers LA, Haggarty BS, Jordan APO, Romano J, Leslie GJ, Alvarez X, O’Connor DH, Wiseman RW, Fennessey CM, Li Y, Piatak M, Lifson JD, LaBranche CC, Lackner AA, Keele BF, Maness NJ, Marsh M, Hoxie JA. A cellular trafficking signal in the SIV envelope protein cytoplasmic domain is strongly selected for in pathogenic infection. PLoS Pathog 2022; 18:e1010507. [PMID: 35714165 PMCID: PMC9275724 DOI: 10.1371/journal.ppat.1010507] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [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: 12/21/2021] [Revised: 07/12/2022] [Accepted: 04/07/2022] [Indexed: 01/01/2023] Open
Abstract
The HIV/SIV envelope glycoprotein (Env) cytoplasmic domain contains a highly conserved Tyr-based trafficking signal that mediates both clathrin-dependent endocytosis and polarized sorting. Despite extensive analysis, the role of these functions in viral infection and pathogenesis is unclear. An SIV molecular clone (SIVmac239) in which this signal is inactivated by deletion of Gly-720 and Tyr-721 (SIVmac239ΔGY), replicates acutely to high levels in pigtail macaques (PTM) but is rapidly controlled. However, we previously reported that rhesus macaques and PTM can progress to AIDS following SIVmac239ΔGY infection in association with novel amino acid changes in the Env cytoplasmic domain. These included an R722G flanking the ΔGY deletion and a nine nucleotide deletion encoding amino acids 734-736 (ΔQTH) that overlaps the rev and tat open reading frames. We show that molecular clones containing these mutations reconstitute signals for both endocytosis and polarized sorting. In one PTM, a novel genotype was selected that generated a new signal for polarized sorting but not endocytosis. This genotype, together with the ΔGY mutation, was conserved in association with high viral loads for several months when introduced into naïve PTMs. For the first time, our findings reveal strong selection pressure for Env endocytosis and particularly for polarized sorting during pathogenic SIV infection in vivo.
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Affiliation(s)
- Scott P. Lawrence
- MRC Laboratory for Molecular Cell Biology, University College London, London, United Kingdom
| | - Samra E. Elser
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Workineh Torben
- Tulane National Primate Research Center, Covington, Louisiana, United States of America
| | - Robert V. Blair
- Tulane National Primate Research Center, Covington, Louisiana, United States of America
| | - Bapi Pahar
- Tulane National Primate Research Center, Covington, Louisiana, United States of America
| | - Pyone P. Aye
- Tulane National Primate Research Center, Covington, Louisiana, United States of America
| | - Faith Schiro
- Tulane National Primate Research Center, Covington, Louisiana, United States of America
| | - Dawn Szeltner
- Tulane National Primate Research Center, Covington, Louisiana, United States of America
| | - Lara A. Doyle-Meyers
- Tulane National Primate Research Center, Covington, Louisiana, United States of America
| | - Beth S. Haggarty
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Andrea P. O. Jordan
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Josephine Romano
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - George J. Leslie
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Xavier Alvarez
- Tulane National Primate Research Center, Covington, Louisiana, United States of America
| | - David H. O’Connor
- Wisconsin National Primate Research Center, Madison, Wisconsin, United States of America
| | - Roger W. Wiseman
- Wisconsin National Primate Research Center, Madison, Wisconsin, United States of America
| | - Christine M. Fennessey
- AIDS and Cancer Virus Program, Frederick National Laboratory for Cancer Research, Frederick, Maryland, United States of America
| | - Yuan Li
- AIDS and Cancer Virus Program, Frederick National Laboratory for Cancer Research, Frederick, Maryland, United States of America
| | - Michael Piatak
- AIDS and Cancer Virus Program, Frederick National Laboratory for Cancer Research, Frederick, Maryland, United States of America
| | - Jeffrey D. Lifson
- AIDS and Cancer Virus Program, Frederick National Laboratory for Cancer Research, Frederick, Maryland, United States of America
| | - Celia C. LaBranche
- Duke University Medical Center, Durham, North Carolina, United States of America
| | - Andrew A. Lackner
- Tulane National Primate Research Center, Covington, Louisiana, United States of America
| | - Brandon F. Keele
- AIDS and Cancer Virus Program, Frederick National Laboratory for Cancer Research, Frederick, Maryland, United States of America
| | - Nicholas J. Maness
- Tulane National Primate Research Center, Covington, Louisiana, United States of America
| | - Mark Marsh
- MRC Laboratory for Molecular Cell Biology, University College London, London, United Kingdom
| | - James A. Hoxie
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
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22
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Pegu A, Xu L, DeMouth ME, Fabozzi G, March K, Almasri CG, Cully MD, Wang K, Yang ES, Dias J, Fennessey CM, Hataye J, Wei RR, Rao E, Casazza JP, Promsote W, Asokan M, McKee K, Schmidt SD, Chen X, Liu C, Shi W, Geng H, Foulds KE, Kao SF, Noe A, Li H, Shaw GM, Zhou T, Petrovas C, Todd JP, Keele BF, Lifson JD, Doria-Rose N, Koup RA, Yang ZY, Nabel GJ, Mascola JR. Potent anti-viral activity of a trispecific HIV neutralizing antibody in SHIV-infected monkeys. Cell Rep 2022; 38:110199. [PMID: 34986348 PMCID: PMC8767641 DOI: 10.1016/j.celrep.2021.110199] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2021] [Revised: 10/20/2021] [Accepted: 12/10/2021] [Indexed: 01/07/2023] Open
Abstract
Broadly neutralizing antibodies (bNAbs) represent an alternative to drug therapy for the treatment of HIV-1 infection. Immunotherapy with single bNAbs often leads to emergence of escape variants, suggesting a potential benefit of combination bNAb therapy. Here, a trispecific bNAb reduces viremia 100- to 1000-fold in viremic SHIV-infected macaques. After treatment discontinuation, viremia rebounds transiently and returns to low levels, through CD8-mediated immune control. These viruses remain sensitive to the trispecific antibody, despite loss of sensitivity to one of the parental bNAbs. Similarly, the trispecific bNAb suppresses the emergence of resistance in viruses derived from HIV-1-infected subjects, in contrast to parental bNAbs. Trispecific HIV-1 neutralizing antibodies, therefore, mediate potent antiviral activity in vivo and may minimize the potential for immune escape.
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Affiliation(s)
- Amarendra Pegu
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), Bethesda, MD, USA
| | - Ling Xu
- Sanofi, 640 Memorial Dr., Cambridge MA, USA
| | - Megan E. DeMouth
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), Bethesda, MD, USA
| | - Giulia Fabozzi
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), Bethesda, MD, USA
| | - Kylie March
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), Bethesda, MD, USA
| | - Cassandra G. Almasri
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), Bethesda, MD, USA
| | - Michelle D. Cully
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), Bethesda, MD, USA
| | - Keyun Wang
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), Bethesda, MD, USA
| | - Eun Sung Yang
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), Bethesda, MD, USA
| | - Joana Dias
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), Bethesda, MD, USA
| | - Christine M. Fennessey
- AIDS and Cancer Virus Program, Leidos Biomedical Research Inc., Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Jason Hataye
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), Bethesda, MD, USA
| | | | - Ercole Rao
- Sanofi, 640 Memorial Dr., Cambridge MA, USA
| | - Joseph P. Casazza
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), Bethesda, MD, USA
| | - Wanwisa Promsote
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), Bethesda, MD, USA
| | - Mangaiarkarasi Asokan
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), Bethesda, MD, USA
| | - Krisha McKee
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), Bethesda, MD, USA
| | - Stephen D. Schmidt
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), Bethesda, MD, USA
| | - Xuejun Chen
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), Bethesda, MD, USA
| | - Cuiping Liu
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), Bethesda, MD, USA
| | - Wei Shi
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), Bethesda, MD, USA
| | - Hui Geng
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), Bethesda, MD, USA
| | - Kathryn E. Foulds
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), Bethesda, MD, USA
| | - Shing-Fen Kao
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), Bethesda, MD, USA
| | - Amy Noe
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), Bethesda, MD, USA
| | - Hui Li
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - George M. Shaw
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Tongqing Zhou
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), Bethesda, MD, USA
| | - Constantinos Petrovas
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), Bethesda, MD, USA
| | - John-Paul Todd
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), Bethesda, MD, USA
| | - Brandon F. Keele
- AIDS and Cancer Virus Program, Leidos Biomedical Research Inc., Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Jeffrey D. Lifson
- AIDS and Cancer Virus Program, Leidos Biomedical Research Inc., Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Nicole Doria-Rose
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), Bethesda, MD, USA
| | - Richard A. Koup
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), Bethesda, MD, USA
| | | | - Gary J. Nabel
- Sanofi, 640 Memorial Dr., Cambridge MA, USA,To whom correspondence should be addressed: G.J.N: , phone: 857-233-9936; J.R.M. ; 301-496-1852
| | - John R. Mascola
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), Bethesda, MD, USA,Lead contact,To whom correspondence should be addressed: G.J.N: , phone: 857-233-9936; J.R.M. ; 301-496-1852
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23
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Kleinman AJ, Sivanandham R, Sette P, Brocca-Cofano E, McAndrews C, Keele BF, Pandrea I, Apetrei C. Lack of Specific Regulatory T Cell Depletion and Cytoreduction Associated with Extensive Toxicity After Administration of Low and High Doses of Cyclophosphamide. AIDS Res Hum Retroviruses 2022; 38:45-49. [PMID: 33957772 PMCID: PMC8785720 DOI: 10.1089/aid.2021.0036] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [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: 01/03/2023] Open
Abstract
Up to 93% of the human immunodeficiency virus (HIV) latent reservoir comprised defective proviruses, suggesting that a functional cure is possible through the elimination of a small population of cells containing intact virus, instead of the entire reservoir. Cyclophosphamide (Cy) is an established chemotherapeutic agent for immune cell cancers. In high doses, Cy is a nonselective cytoreductor, used in allogeneic stem-cell transplantation, while in a low dose, metronomic schedule, Cy selectively depletes regulatory T cells (Tregs). We administered low and high doses to simian immunodeficiency virus (SIV)-infected rhesus macaques (RM) to assess their effects on the SIV reservoirs. As a Treg-depleting agent, Cy unselectively depleted Treg and total lymphocytes, resulting in minimal immune activation and no viral reactivation. As a cytoreductive agent, Cy induced massive viral reactivation in elite controller RMs without ART. However, when administered with antiretroviral therapy (ART), Cy had substantial adverse effects, including mortality. Our study thus dissuades further investigation of Cy as an HIV cure agent.
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Affiliation(s)
- Adam J. Kleinman
- Division of Infectious Diseases, DOM, School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Ranjit Sivanandham
- Division of Infectious Diseases, DOM, School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, USA.,Department of Pathology, School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Paola Sette
- Division of Infectious Diseases, DOM, School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, USA.,Department of Pathology, School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Egidio Brocca-Cofano
- Department of Pathology, School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Colin McAndrews
- Department of Pathology, School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Brandon F. Keele
- AIDS and Cancer Virus Program, Frederick National Laboratory for Cancer Research, Frederick, Maryland, USA
| | - Ivona Pandrea
- Department of Pathology, School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, USA.,Department of Infectious Diseases and Immunology, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Cristian Apetrei
- Division of Infectious Diseases, DOM, School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, USA.,Department of Infectious Diseases and Immunology, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, Pennsylvania, USA.,Address correspondence to: Cristian Apetrei, Division of Infectious Diseases, DOM, School of Medicine, University of Pittsburgh, S634 Scaife Hall, 3550 Terrace Street, Pittsburgh, PA 15261, USA
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24
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Moriarty RV, Golfinos AE, Gellerup DD, Schweigert H, Mathiaparanam J, Balgeman AJ, Weiler AM, Friedrich TC, Keele BF, Davenport MP, Venturi V, O’Connor SL. The mucosal barrier and anti-viral immune responses can eliminate portions of the viral population during transmission and early viral growth. PLoS One 2021; 16:e0260010. [PMID: 34855793 PMCID: PMC8639003 DOI: 10.1371/journal.pone.0260010] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2021] [Accepted: 11/01/2021] [Indexed: 11/18/2022] Open
Abstract
Little is known about how specific individual viral lineages replicating systemically during acute Human Immunodeficiency Virus or Simian Immunodeficiency Virus (HIV/SIV) infection persist into chronic infection. In this study, we use molecularly barcoded SIV (SIVmac239M) to track distinct viral lineages for 12 weeks after intravenous (IV) or intrarectal (IR) challenge in macaques. Two Mafa-A1*063+ cynomolgus macaques (Macaca fascicularis, CM) were challenged IV, and two Mamu-A1*001+ rhesus macaques (Macaca mulatta, RM) were challenged IR with 200,000 Infectious Units (IU) of SIVmac239M. We sequenced the molecular barcode of SIVmac239M from all animals over the 12 weeks of the study to characterize the diversity and persistence of virus lineages. During the first three weeks post-infection, we found ~70–560 times more unique viral lineages circulating in the animals challenged IV compared to those challenged IR, which is consistent with the hypothesis that the challenge route is the primary driver restricting the transmission of individual viral lineages. We also characterized the sequences of T cell epitopes targeted during acute SIV infection, and found that the emergence of escape variants in acutely targeted epitopes can occur on multiple virus templates simultaneously, but that elimination of some of these templates is likely a consequence of additional host factors. These data imply that virus lineages present during acute infection can still be eliminated from the systemic virus population even after initial selection.
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Affiliation(s)
- Ryan V. Moriarty
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
- Microbiology Doctoral Training Program, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Athena E. Golfinos
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Dane D. Gellerup
- Wisconsin National Primate Research Center, Madison, Wisconsin, United States of America
| | - Hannah Schweigert
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Jaffna Mathiaparanam
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Alexis J. Balgeman
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Andrea M. Weiler
- Wisconsin National Primate Research Center, Madison, Wisconsin, United States of America
- Department of Pathobiological Sciences, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Thomas C. Friedrich
- Wisconsin National Primate Research Center, Madison, Wisconsin, United States of America
- Department of Pathobiological Sciences, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Brandon F. Keele
- AIDS and Cancer Virus Program, Frederick National Laboratory, Frederick, MD, United States of America
| | - Miles P. Davenport
- Infection Analytics Program, Kirby Institute for Infection and Immunity, UNSW Sydney, Sydney, NSW, Australia
| | - Vanessa Venturi
- Infection Analytics Program, Kirby Institute for Infection and Immunity, UNSW Sydney, Sydney, NSW, Australia
| | - Shelby L. O’Connor
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
- Wisconsin National Primate Research Center, Madison, Wisconsin, United States of America
- * E-mail:
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25
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Frank I, Cigoli M, Arif MS, Fahlberg MD, Maldonado S, Calenda G, Pegu A, Yang ES, Rawi R, Chuang GY, Geng H, Liu C, Zhou T, Kwong PD, Arthos J, Cicala C, Grasperge BF, Blanchard JL, Gettie A, Fennessey CM, Keele BF, Vaccari M, Hope TJ, Fauci AS, Mascola JR, Martinelli E. Blocking α 4β 7 integrin delays viral rebound in SHIV SF162P3-infected macaques treated with anti-HIV broadly neutralizing antibodies. Sci Transl Med 2021; 13:eabf7201. [PMID: 34408080 PMCID: PMC8977869 DOI: 10.1126/scitranslmed.abf7201] [Citation(s) in RCA: 3] [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: 11/14/2020] [Revised: 03/30/2021] [Accepted: 07/30/2021] [Indexed: 12/20/2022]
Abstract
Anti-HIV broadly neutralizing antibodies (bNAbs) may favor development of antiviral immunity by engaging the immune system during immunotherapy. Targeting integrin α4β7 with an anti-α4β7 monoclonal antibody (Rh-α4β7) affects immune responses in SIV/SHIV-infected macaques. To explore the therapeutic potential of combining bNAbs with α4β7 integrin blockade, SHIVSF162P3-infected, viremic rhesus macaques were treated with bNAbs only (VRC07-523LS and PGT128 anti-HIV antibodies) or a combination of bNAbs and Rh-α4β7 or were left untreated as a control. Treatment with bNAbs alone decreased viremia below 200 copies/ml in all macaques, but seven of eight macaques (87.5%) in the bNAbs-only group rebounded within a median of 3 weeks (95% CI: 2 to 9). In contrast, three of six macaques treated with a combination of Rh-α4β7 and bNAbs (50%) maintained a viremia below 200 copies/ml until the end of the follow-up period; viremia in the other three macaques rebounded within a median of 6 weeks (95% CI: 5 to 11). Thus, there was a modest delay in viral rebound in the macaques treated with the combination antibody therapy compared to bNAbs alone. Our study suggests that α4β7 integrin blockade may prolong virologic control by bNAbs in SHIVSF162P3-infected macaques.
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Affiliation(s)
- Ines Frank
- Center for Biomedical Research, Population Council, New York, NY, USA
| | - Mariasole Cigoli
- Center for Biomedical Research, Population Council, New York, NY, USA
| | - Muhammad S Arif
- Department of Cell and Developmental Biology, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Marissa D Fahlberg
- Tulane National Primate Research Center, Tulane University, Covington, LA, USA
| | | | - Giulia Calenda
- Center for Biomedical Research, Population Council, New York, NY, USA
| | - Amarendra Pegu
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, Bethesda, MD, USA
| | - Eun Sung Yang
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, Bethesda, MD, USA
| | - Reda Rawi
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, Bethesda, MD, USA
| | - Gwo-Yu Chuang
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, Bethesda, MD, USA
| | - Hui Geng
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, Bethesda, MD, USA
| | - Cuiping Liu
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, Bethesda, MD, USA
| | - Tongqing Zhou
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, Bethesda, MD, USA
| | - Peter D Kwong
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, Bethesda, MD, USA
| | - James Arthos
- Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Claudia Cicala
- Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Brooke F Grasperge
- Tulane National Primate Research Center, Tulane University, Covington, LA, USA
| | - James L Blanchard
- Tulane National Primate Research Center, Tulane University, Covington, LA, USA
| | - Agegnehu Gettie
- Aaron Diamond AIDS Research Center, Rockefeller University, New York, NY, USA
| | - Christine M Fennessey
- AIDS and Cancer Virus Program, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Brandon F Keele
- AIDS and Cancer Virus Program, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Monica Vaccari
- Tulane National Primate Research Center, Tulane University, Covington, LA, USA
| | - Thomas J Hope
- Department of Cell and Developmental Biology, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Anthony S Fauci
- Laboratory of Immunoregulation, 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, Bethesda, MD, USA
| | - Elena Martinelli
- Center for Biomedical Research, Population Council, New York, NY, USA.
- Department of Cell and Developmental Biology, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
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26
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Immonen TT, Fennessey CM, Lipkey L, Thorpe A, Del Prete GQ, Lifson JD, Davenport MP, Keele BF. Transient viral replication during analytical treatment interruptions in SIV infected macaques can alter the rebound-competent viral reservoir. PLoS Pathog 2021; 17:e1009686. [PMID: 34143853 PMCID: PMC8244872 DOI: 10.1371/journal.ppat.1009686] [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] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Revised: 06/30/2021] [Accepted: 06/02/2021] [Indexed: 02/07/2023] Open
Abstract
Analytical treatment interruptions (ATIs) of antiretroviral therapy (ART) play a central role in evaluating the efficacy of HIV-1 treatment strategies targeting virus that persists despite ART. However, it remains unclear if ATIs alter the rebound-competent viral reservoir (RCVR), the virus population that persists during ART and from which viral recrudescence originates after ART discontinuation. To assess the impact of ATIs on the RCVR, we used a barcode sequence tagged SIV to track individual viral lineages through a series of ATIs in Rhesus macaques. We demonstrate that transient replication of individual rebounding lineages during an ATI can lead to their enrichment in the RCVR, increasing their probability of reactivating again after treatment discontinuation. These data establish that the RCVR can be altered by uncontrolled replication during ATI.
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Affiliation(s)
- Taina T. Immonen
- AIDS and Cancer Virus Program, Frederick National Laboratory, Frederick, Maryland, United States of America
| | - Christine M. Fennessey
- AIDS and Cancer Virus Program, Frederick National Laboratory, Frederick, Maryland, United States of America
| | - Leslie Lipkey
- AIDS and Cancer Virus Program, Frederick National Laboratory, Frederick, Maryland, United States of America
| | - Abigail Thorpe
- AIDS and Cancer Virus Program, Frederick National Laboratory, Frederick, Maryland, United States of America
| | - Gregory Q. Del Prete
- AIDS and Cancer Virus Program, Frederick National Laboratory, Frederick, Maryland, United States of America
| | - Jeffrey D. Lifson
- AIDS and Cancer Virus Program, Frederick National Laboratory, Frederick, Maryland, United States of America
| | - Miles P. Davenport
- Infection Analytics Program, Kirby Institute for Infection and Immunity, University of New South Wales, Sydney, New South Wales, Australia
| | - Brandon F. Keele
- AIDS and Cancer Virus Program, Frederick National Laboratory, Frederick, Maryland, United States of America
- * E-mail:
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27
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Okoye AA, Duell DD, Fukazawa Y, Varco-Merth B, Marenco A, Behrens H, Chaunzwa M, Selseth AN, Gilbride RM, Shao J, Edlefsen PT, Geleziunas R, Pinkevych M, Davenport MP, Busman-Sahay K, Nekorchuk M, Park H, Smedley J, Axthelm MK, Estes JD, Hansen SG, Keele BF, Lifson JD, Picker LJ. CD8+ T cells fail to limit SIV reactivation following ART withdrawal until after viral amplification. J Clin Invest 2021; 131:141677. [PMID: 33630764 DOI: 10.1172/jci141677] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [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: 06/25/2020] [Accepted: 02/23/2021] [Indexed: 12/15/2022] Open
Abstract
To define the contribution of CD8+ T cell responses to control of SIV reactivation during and following antiretroviral therapy (ART), we determined the effect of long-term CD8+ T cell depletion using a rhesusized anti-CD8β monoclonal antibody on barcoded SIVmac239 dynamics on stable ART and after ART cessation in rhesus macaques (RMs). Among the RMs with full CD8+ T cell depletion in both blood and tissue, there were no significant differences in the frequency of viral blips in plasma, the number of SIV RNA+ cells and the average number of RNA copies/infected cell in tissue, and levels of cell-associated SIV RNA and DNA in blood and tissue relative to control-treated RMs during ART. Upon ART cessation, both CD8+ T cell-depleted and control RMs rebounded in fewer than 12 days, with no difference in the time to viral rebound or in either the number or growth rate of rebounding SIVmac239M barcode clonotypes. However, effectively CD8+ T cell-depleted RMs showed a stable, approximately 2-log increase in post-ART plasma viremia relative to controls. These results indicate that while potent antiviral CD8+ T cell responses can develop during ART-suppressed SIV infection, these responses effectively intercept post-ART SIV rebound only after systemic viral replication, too late to limit reactivation frequency or the early spread of reactivating SIV reservoirs.
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Affiliation(s)
- Afam A Okoye
- Vaccine and Gene Therapy Institute and.,Oregon National Primate Research Center, Oregon Health & Science University, Beaverton, Oregon, USA
| | - Derick D Duell
- Vaccine and Gene Therapy Institute and.,Oregon National Primate Research Center, Oregon Health & Science University, Beaverton, Oregon, USA
| | - Yoshinori Fukazawa
- Vaccine and Gene Therapy Institute and.,Oregon National Primate Research Center, Oregon Health & Science University, Beaverton, Oregon, USA
| | - Benjamin Varco-Merth
- Vaccine and Gene Therapy Institute and.,Oregon National Primate Research Center, Oregon Health & Science University, Beaverton, Oregon, USA
| | - Alejandra Marenco
- Vaccine and Gene Therapy Institute and.,Oregon National Primate Research Center, Oregon Health & Science University, Beaverton, Oregon, USA
| | - Hannah Behrens
- Vaccine and Gene Therapy Institute and.,Oregon National Primate Research Center, Oregon Health & Science University, Beaverton, Oregon, USA
| | - Morgan Chaunzwa
- Vaccine and Gene Therapy Institute and.,Oregon National Primate Research Center, Oregon Health & Science University, Beaverton, Oregon, USA
| | - Andrea N Selseth
- Vaccine and Gene Therapy Institute and.,Oregon National Primate Research Center, Oregon Health & Science University, Beaverton, Oregon, USA
| | - Roxanne M Gilbride
- Vaccine and Gene Therapy Institute and.,Oregon National Primate Research Center, Oregon Health & Science University, Beaverton, Oregon, USA
| | - Jason Shao
- Statistical Center for HIV/AIDS Research and Prevention, Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - Paul T Edlefsen
- Statistical Center for HIV/AIDS Research and Prevention, Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | | | - Mykola Pinkevych
- Kirby Institute for Infection and Immunity, University of New South Wales, Sydney, New South Wales, Australia
| | - Miles P Davenport
- Kirby Institute for Infection and Immunity, University of New South Wales, Sydney, New South Wales, Australia
| | - Kathleen Busman-Sahay
- Vaccine and Gene Therapy Institute and.,Oregon National Primate Research Center, Oregon Health & Science University, Beaverton, Oregon, USA
| | - Michael Nekorchuk
- Vaccine and Gene Therapy Institute and.,Oregon National Primate Research Center, Oregon Health & Science University, Beaverton, Oregon, USA
| | - Haesun Park
- Vaccine and Gene Therapy Institute and.,Oregon National Primate Research Center, Oregon Health & Science University, Beaverton, Oregon, USA
| | - Jeremy Smedley
- Vaccine and Gene Therapy Institute and.,Oregon National Primate Research Center, Oregon Health & Science University, Beaverton, Oregon, USA
| | - Michael K Axthelm
- Vaccine and Gene Therapy Institute and.,Oregon National Primate Research Center, Oregon Health & Science University, Beaverton, Oregon, USA
| | - Jacob D Estes
- Vaccine and Gene Therapy Institute and.,Oregon National Primate Research Center, Oregon Health & Science University, Beaverton, Oregon, USA
| | - Scott G Hansen
- Vaccine and Gene Therapy Institute and.,Oregon National Primate Research Center, Oregon Health & Science University, Beaverton, Oregon, USA
| | - Brandon F Keele
- AIDS and Cancer Virus Program, Frederick National Laboratory for Cancer Research, Frederick, Maryland, USA.,Leidos Biomedical Research, Inc., Frederick, Maryland, USA
| | - Jeffery D Lifson
- AIDS and Cancer Virus Program, Frederick National Laboratory for Cancer Research, Frederick, Maryland, USA.,Leidos Biomedical Research, Inc., Frederick, Maryland, USA
| | - Louis J Picker
- Vaccine and Gene Therapy Institute and.,Oregon National Primate Research Center, Oregon Health & Science University, Beaverton, Oregon, USA
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28
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Swanstrom AE, Immonen TT, Oswald K, Pyle C, Thomas JA, Bosche WJ, Silipino L, Hull M, Newman L, Coalter V, Wiles A, Wiles R, Kiser J, Morcock DR, Shoemaker R, Fast R, Breed MW, Kramer J, Donohue D, Malys T, Fennessey CM, Trubey CM, Deleage C, Estes JD, Lifson JD, Keele BF, Del Prete GQ. Antibody-mediated depletion of viral reservoirs is limited in SIV-infected macaques treated early with antiretroviral therapy. J Clin Invest 2021; 131:142421. [PMID: 33465055 DOI: 10.1172/jci142421] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [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: 07/20/2020] [Accepted: 01/13/2021] [Indexed: 12/22/2022] Open
Abstract
The effectiveness of virus-specific strategies, including administered HIV-specific mAbs, to target cells that persistently harbor latent, rebound-competent HIV genomes during combination antiretroviral therapy (cART) has been limited by inefficient induction of viral protein expression. To examine antibody-mediated viral reservoir targeting without a need for viral induction, we used an anti-CD4 mAb to deplete both infected and uninfected CD4+ T cells. Ten rhesus macaques infected with barcoded SIVmac239M received cART for 93 weeks starting 4 days after infection. During cART, 5 animals received 5 to 6 anti-CD4 antibody administrations and CD4+ T cell populations were then allowed 1 year on cART to recover. Despite profound CD4+ T cell depletion in blood and lymph nodes, time to viral rebound following cART cessation was not significantly delayed in anti-CD4-treated animals compared with controls. Viral reactivation rates, determined based on rebounding SIVmac239M clonotype proportions, also were not significantly different in CD4-depleted animals. Notably, antibody-mediated depletion was limited in rectal tissue and negligible in lymphoid follicles. These results suggest that, even if robust viral reactivation can be achieved, antibody-mediated viral reservoir depletion may be limited in key tissue sites.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - Duncan Donohue
- DMS Applied Information and Management Sciences, Frederick National Laboratory for Cancer Research, Frederick, Maryland, USA
| | - Tyler Malys
- DMS Applied Information and Management Sciences, Frederick National Laboratory for Cancer Research, Frederick, Maryland, USA
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Halvas EK, Joseph KW, Brandt LD, Guo S, Sobolewski MD, Jacobs JL, Tumiotto C, Bui JK, Cyktor JC, Keele BF, Morse GD, Bale MJ, Shao W, Kearney MF, Coffin JM, Rausch JW, Wu X, Hughes SH, Mellors JW. HIV-1 viremia not suppressible by antiretroviral therapy can originate from large T cell clones producing infectious virus. J Clin Invest 2021; 130:5847-5857. [PMID: 33016926 DOI: 10.1172/jci138099] [Citation(s) in RCA: 77] [Impact Index Per Article: 25.7] [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: 03/13/2020] [Accepted: 07/22/2020] [Indexed: 12/31/2022] Open
Abstract
BACKGROUNDHIV-1 viremia that is not suppressed by combination antiretroviral therapy (ART) is generally attributed to incomplete medication adherence and/or drug resistance. We evaluated individuals referred by clinicians for nonsuppressible viremia (plasma HIV-1 RNA above 40 copies/mL) despite reported adherence to ART and the absence of drug resistance to the current ART regimen.METHODSSamples were collected from at least 2 time points from 8 donors who had nonsuppressible viremia for more than 6 months. Single templates of HIV-1 RNA obtained from plasma and viral outgrowth of cultured cells and from proviral DNA were amplified by PCR and sequenced for evidence of clones of cells that produced infectious viruses. Clones were confirmed by host-proviral integration site analysis.RESULTSHIV-1 genomic RNA with identical sequences were identified in plasma samples from all 8 donors. The identical viral RNA sequences did not change over time and did not evolve resistance to the ART regimen. In 4 of the donors, viral RNA sequences obtained from plasma matched those sequences from viral outgrowth cultures, indicating that the viruses were replication competent. Integration sites for infectious proviruses from those 4 donors were mapped to the introns of the MATR3, ZNF268, ZNF721/ABCA11P, and ABCA11P genes. The sizes of the clones were estimated to be from 50 million to 350 million cells.CONCLUSIONThese findings show that clones of HIV-1-infected cells producing virus can cause failure of ART to suppress viremia. The mechanisms involved in clonal expansion and persistence need to be defined to effectively target viremia and the HIV-1 reservoir.FUNDINGNational Cancer Institute, NIH; Howard Hughes Medical Research Fellows Program, Howard Hughes Medical Institute; Bill and Melinda Gates Foundation; Office of AIDS Research; American Cancer Society; National Cancer Institute through a Leidos subcontract; National Institute for Allergy and Infectious Diseases, NIH, to the I4C Martin Delaney Collaboratory; University of Rochester Center for AIDS Research and University of Rochester HIV/AIDS Clinical Trials Unit.
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Affiliation(s)
- Elias K Halvas
- Department of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Kevin W Joseph
- Department of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Leah D Brandt
- Department of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Shuang Guo
- Leidos Biomedical Research, Inc., Frederick, Maryland, USA
| | | | - Jana L Jacobs
- Department of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Camille Tumiotto
- Department of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - John K Bui
- New York-Presbyterian Hospital/Weill Cornell Medical Center, Weill Department of Medicine, New York, New York, USA
| | - Joshua C Cyktor
- Department of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Brandon F Keele
- AIDS and Cancer Virus Program, Frederick National Laboratory for Cancer Research, Frederick, Maryland, USA
| | - Gene D Morse
- NYS Center of Excellence in Bioinformatics and Life Sciences, Translational Pharmacology Research Core, University at Buffalo, Buffalo, New York, USA
| | - Michael J Bale
- HIV Dynamics and Replication Program, National Cancer Institute, Frederick, Maryland, USA
| | - Wei Shao
- Advanced Biomedical Computing Science, Frederick National Laboratory for Cancer Research (FNLCR), Frederick, Maryland, USA
| | - Mary F Kearney
- HIV Dynamics and Replication Program, National Cancer Institute, Frederick, Maryland, USA
| | - John M Coffin
- Department of Molecular Biology and Microbiology, Tufts University, Boston, Massachusetts, USA
| | - Jason W Rausch
- Basic Research Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, Maryland, USA
| | - Xiaolin Wu
- Leidos Biomedical Research, Inc., Frederick, Maryland, USA
| | - Stephen H Hughes
- HIV Dynamics and Replication Program, National Cancer Institute, Frederick, Maryland, USA
| | - John W Mellors
- Department of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
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30
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Silva de Castro I, Gorini G, Mason R, Gorman J, Bissa M, Rahman MA, Arakelyan A, Kalisz I, Whitney S, Becerra-Flores M, Ni E, Peachman K, Trinh HV, Read M, Liu MH, Van Ryk D, Paquin-Proulx D, Shubin Z, Tuyishime M, Peele J, Ahmadi MS, Verardi R, Hill J, Beddall M, Nguyen R, Stamos JD, Fujikawa D, Min S, Schifanella L, Vaccari M, Galli V, Doster MN, Liyanage NPM, Sarkis S, Caccuri F, LaBranche C, Montefiori DC, Tomaras GD, Shen X, Rosati M, Felber BK, Pavlakis GN, Venzon DJ, Magnanelli W, Breed M, Kramer J, Keele BF, Eller MA, Cicala C, Arthos J, Ferrari G, Margolis L, Robert-Guroff M, Kwong PD, Roederer M, Rao M, Cardozo TJ, Franchini G. Anti-V2 antibodies virus vulnerability revealed by envelope V1 deletion in HIV vaccine candidates. iScience 2021; 24:102047. [PMID: 33554060 PMCID: PMC7847973 DOI: 10.1016/j.isci.2021.102047] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Revised: 11/23/2020] [Accepted: 01/06/2021] [Indexed: 12/17/2022] Open
Abstract
The efficacy of ALVAC-based HIV and SIV vaccines in humans and macaques correlates with antibodies to envelope variable region 2 (V2). We show here that vaccine-induced antibodies to SIV variable region 1 (V1) inhibit anti-V2 antibody-mediated cytotoxicity and reverse their ability to block V2 peptide interaction with the α4β7 integrin. SIV vaccines engineered to delete V1 and favor an α helix, rather than a β sheet V2 conformation, induced V2-specific ADCC correlating with decreased risk of SIV acquisition. Removal of V1 from the HIV-1 clade A/E A244 envelope resulted in decreased binding to antibodies recognizing V2 in the β sheet conformation. Thus, deletion of V1 in HIV envelope immunogens may improve antibody responses to V2 virus vulnerability sites and increase the efficacy of HIV vaccine candidates. HIV vaccine candidate protects against SIVmac251 acquisition V1 deleted envelope immunogens with V2 in α-helical conformation are protective V2-specific ADCC as correlate of risk Anti-V1 antibodies interfere with V2-specific ADCC
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Affiliation(s)
- Isabela Silva de Castro
- Animal Models and Retroviral Vaccines Section, National Cancer Institute, Bethesda, MD 20892, USA
| | - Giacomo Gorini
- Animal Models and Retroviral Vaccines Section, National Cancer Institute, Bethesda, MD 20892, USA
| | - Rosemarie Mason
- ImmunoTechnology Section, Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Jason Gorman
- Structural Biology Section, Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Massimiliano Bissa
- Animal Models and Retroviral Vaccines Section, National Cancer Institute, Bethesda, MD 20892, USA
| | - Mohammad A Rahman
- Immune Biology of Retroviral Infection Section, National Cancer Institute, Bethesda, MD 20892, USA
| | - Anush Arakelyan
- Section on Intercellular Interactions, Eunice Kennedy-Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA
| | - Irene Kalisz
- Advanced Bioscience Laboratories, Rockville, MD 20850, USA
| | | | | | - Eric Ni
- New York University School of Medicine, NYU Langone Health, New York, NY 10016, USA
| | - Kristina Peachman
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD 20817, USA.,U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD 20910, USA
| | - Hung V Trinh
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD 20817, USA.,U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD 20910, USA
| | - Michael Read
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD 20910, USA
| | - Mei-Hue Liu
- Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Donald Van Ryk
- Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Dominic Paquin-Proulx
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD 20817, USA.,U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD 20910, USA
| | - Zhanna Shubin
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD 20817, USA.,U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD 20910, USA
| | - Marina Tuyishime
- Division of Surgical Sciences, Duke University School of Medicine, Durham, NC 27701, USA
| | - Jennifer Peele
- Division of Surgical Sciences, Duke University School of Medicine, Durham, NC 27701, USA
| | - Mohammed S Ahmadi
- Structural Biology Section, Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Raffaello Verardi
- Structural Biology Section, Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Juliane Hill
- ImmunoTechnology Section, Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Margaret Beddall
- ImmunoTechnology Section, Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Richard Nguyen
- ImmunoTechnology Section, Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - James D Stamos
- Animal Models and Retroviral Vaccines Section, National Cancer Institute, Bethesda, MD 20892, USA
| | - Dai Fujikawa
- Animal Models and Retroviral Vaccines Section, National Cancer Institute, Bethesda, MD 20892, USA
| | - Susie Min
- Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Luca Schifanella
- Animal Models and Retroviral Vaccines Section, National Cancer Institute, Bethesda, MD 20892, USA
| | - Monica Vaccari
- Animal Models and Retroviral Vaccines Section, National Cancer Institute, Bethesda, MD 20892, USA
| | - Veronica Galli
- Animal Models and Retroviral Vaccines Section, National Cancer Institute, Bethesda, MD 20892, USA
| | - Melvin N Doster
- Animal Models and Retroviral Vaccines Section, National Cancer Institute, Bethesda, MD 20892, USA
| | - Namal P M Liyanage
- Animal Models and Retroviral Vaccines Section, National Cancer Institute, Bethesda, MD 20892, USA
| | - Sarkis Sarkis
- Animal Models and Retroviral Vaccines Section, National Cancer Institute, Bethesda, MD 20892, USA
| | - Francesca Caccuri
- Animal Models and Retroviral Vaccines Section, National Cancer Institute, Bethesda, MD 20892, USA
| | - Celia LaBranche
- Division of Surgical Sciences, Duke University School of Medicine, Durham, NC 27701, USA
| | - David C Montefiori
- Division of Surgical Sciences, Duke University School of Medicine, Durham, NC 27701, USA
| | - Georgia D Tomaras
- Duke Human Vaccine Institute, Duke University, Durham, NC 27701, USA
| | - Xiaoying Shen
- Duke Human Vaccine Institute, Duke University, Durham, NC 27701, USA
| | - Margherita Rosati
- Human Retrovirus Section, National Cancer Institute, Frederick, MD 21702, USA
| | - Barbara K Felber
- Human Retrovirus Pathogenesis Section, National Cancer Institute, Frederick, MD 21702, USA
| | - George N Pavlakis
- Human Retrovirus Section, National Cancer Institute, Frederick, MD 21702, USA
| | - David J Venzon
- Biostatistics and Data Management Section, Center for Cancer Research, National Cancer Institute, Bethesda, MD 20892, USA
| | - William Magnanelli
- AIDS and Cancer Virus Program, Leidos Biomedical Research Inc., Frederick National Laboratory, Frederick, MD 21704, USA
| | - Matthew Breed
- AIDS and Cancer Virus Program, Leidos Biomedical Research Inc., Frederick National Laboratory, Frederick, MD 21704, USA
| | - Josh Kramer
- AIDS and Cancer Virus Program, Leidos Biomedical Research Inc., Frederick National Laboratory, Frederick, MD 21704, USA
| | - Brandon F Keele
- AIDS and Cancer Virus Program, Leidos Biomedical Research Inc., Frederick National Laboratory, Frederick, MD 21704, USA
| | - Michael A Eller
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD 20817, USA.,U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD 20910, USA
| | - Claudia Cicala
- Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - James Arthos
- Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Guido Ferrari
- Division of Surgical Sciences, Duke University School of Medicine, Durham, NC 27701, USA
| | - Leonid Margolis
- Section on Intercellular Interactions, Eunice Kennedy-Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA
| | - Marjorie Robert-Guroff
- Immune Biology of Retroviral Infection Section, National Cancer Institute, Bethesda, MD 20892, USA
| | - Peter D Kwong
- Structural Biology Section, Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Mario Roederer
- ImmunoTechnology Section, Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Mangala Rao
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD 20910, USA
| | - Timothy J Cardozo
- New York University School of Medicine, NYU Langone Health, New York, NY 10016, USA
| | - Genoveffa Franchini
- Animal Models and Retroviral Vaccines Section, National Cancer Institute, Bethesda, MD 20892, USA
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Redd AD, Doria-Rose NA, Weiner JA, Nason M, Seivers M, Schmidt SD, Laeyendecker O, Martens C, Bruno D, Keele BF, Raju N, Georgiev IS, Lamers SL, Astemborski J, Kirk GD, Mascola JR, Ackerman ME, Mehta SH, Quinn TC. Longitudinal Antibody Responses in People Who Inject Drugs Infected With Similar Human Immunodeficiency Virus Strains. J Infect Dis 2020; 221:756-765. [PMID: 31581292 DOI: 10.1093/infdis/jiz503] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [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: 05/03/2019] [Accepted: 09/30/2019] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND Multiple factors influence the human immunodeficiency virus (HIV) antibody response produced during natural infection, leading to responses that can vary in specificity, strength, and breadth. METHODS People who inject drugs identified as recently infected with HIV (n = 23) were analyzed for clustering of their viral sequences (genetic distance, <2%). Longitudinal antibody responses were identified for neutralizing antibody (Nab) potential, and differences in antibody subclass, specificity, and Fc receptor ligation using pseudovirus entry and multiplexed Fc array assays, respectively. Responses were analyzed for differences between subject groups, defined by similarity in the sequence of the infecting virus. RESULTS Viral sequences from infected individuals were grouped into 3 distinct clusters with 7 unclustered individuals. Subjects in cluster 1 generally had lower antibody response magnitudes, except for antibodies targeting the V1/V2 region. Subjects in clusters 2 and 3 typically had higher antibody response magnitudes, with the Fv specificity of cluster 2 favoring gp140 recognition. NAb responses differed significantly between clusters for 3 of 18 pseudoviruses examined (P < .05), but there were no differences in overall NAb breadth (P = .62). DISCUSSION These data demonstrate that individuals infected with similar viral strains can generate partially similar antibody responses, but these do not drastically differ from those in individuals infected with relatively unrelated strains.
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Affiliation(s)
- Andrew D Redd
- Laboratory of Immunoregulation, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA.,Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Nicole A Doria-Rose
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | | | - Martha Nason
- Biostatistics Research Branch, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland
| | - Matthew Seivers
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Stephen D Schmidt
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Oliver Laeyendecker
- Laboratory of Immunoregulation, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA.,Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Craig Martens
- Genomics Unit, Research Technologies Branch, Rocky Mountain Laboratories, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, Montana, USA
| | - Daniel Bruno
- Genomics Unit, Research Technologies Branch, Rocky Mountain Laboratories, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, Montana, USA
| | - Brandon F Keele
- AIDS and Cancer Virus Program, Frederick National Laboratory for Cancer Research, Fredrick, Maryland, USA
| | - Nagarajan Raju
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, Tennessee, USA.,Department of Electrical Engineering and Computer Science, Vanderbilt University, Nashville, Tennessee, USA.,Vanderbilt Vaccine Center, Nashville, Tennessee, USA
| | - Ivelin S Georgiev
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, Tennessee, USA.,Department of Electrical Engineering and Computer Science, Vanderbilt University, Nashville, Tennessee, USA.,Vanderbilt Vaccine Center, Nashville, Tennessee, USA
| | | | - Jacquie Astemborski
- Department of Epidemiology, Bloomberg of School of Public Health, Johns Hopkins University, Baltimore, Maryland, USA
| | - Gregory D Kirk
- Department of Epidemiology, Bloomberg of School of Public Health, Johns Hopkins University, Baltimore, Maryland, USA
| | - John R Mascola
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | | | - Shruti H Mehta
- Department of Epidemiology, Bloomberg of School of Public Health, Johns Hopkins University, Baltimore, Maryland, USA
| | - Thomas C Quinn
- Laboratory of Immunoregulation, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA.,Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
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Wei Q, Hargett AA, Knoppova B, Duverger A, Rawi R, Shen CH, Farney SK, Hall S, Brown R, Keele BF, Heath SL, Saag MS, Kutsch O, Chuang GY, Kwong PD, Moldoveanu Z, Raska M, Renfrow MB, Novak J. Glycan Positioning Impacts HIV-1 Env Glycan-Shield Density, Function, and Recognition by Antibodies. iScience 2020; 23:101711. [PMID: 33205023 PMCID: PMC7649354 DOI: 10.1016/j.isci.2020.101711] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2020] [Revised: 08/12/2020] [Accepted: 10/16/2020] [Indexed: 11/24/2022] Open
Abstract
HIV-1 envelope (Env) N-glycosylation impact virus-cell entry and immune evasion. How each glycan interacts to shape the Env-protein-sugar complex and affects Env function is not well understood. Here, analysis of two Env variants from the same donor, with differing functional characteristics and N-glycosylation-site composition, revealed that changes to key N-glycosylation sites affected the Env structure at distant locations and had a ripple effect on Env-wide glycan processing, virus infectivity, antibody recognition, and virus neutralization. Specifically, the N262 glycan, although not in the CD4-binding site, modulated Env binding to the CD4 receptor, affected Env recognition by several glycan-dependent neutralizing antibodies, and altered site-specific glycosylation heterogeneity, with, for example, N448 displaying limited glycan processing. Molecular-dynamic simulations visualized differences in glycan density and how specific oligosaccharide positions can move to compensate for a glycan loss. This study demonstrates how changes in individual glycans can alter molecular dynamics, processing, and function of the Env-glycan shield. Two HIV-1 envelopes (Env) that differ in N-glycan composition were investigated Changes in N-glycosylation had ripple effect on Env-wide glycan processing Glycan changes impacted virus infectivity, antibody binding, and neutralization These data revealed a functional role of glycan clusters in Env glycan shield
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Affiliation(s)
- Qing Wei
- Department of Microbiology, University of Alabama at Birmingham, 845 19th Street S, Birmingham, AL 35294, USA
| | - Audra A Hargett
- Department of Biochemistry and Molecular Genetics, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Barbora Knoppova
- Department of Microbiology, University of Alabama at Birmingham, 845 19th Street S, Birmingham, AL 35294, USA
| | - Alexandra Duverger
- Department of Medicine, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Reda Rawi
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Chen-Hsiang Shen
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - S Katie Farney
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Stacy Hall
- Department of Microbiology, University of Alabama at Birmingham, 845 19th Street S, Birmingham, AL 35294, USA
| | - Rhubell Brown
- Department of Microbiology, University of Alabama at Birmingham, 845 19th Street S, Birmingham, AL 35294, USA
| | - Brandon F Keele
- AIDS and Cancer Virus Program, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Sonya L Heath
- Department of Medicine, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Michael S Saag
- Department of Medicine, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Olaf Kutsch
- Department of Medicine, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Gwo-Yu Chuang
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Peter D Kwong
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Zina Moldoveanu
- Department of Microbiology, University of Alabama at Birmingham, 845 19th Street S, Birmingham, AL 35294, USA
| | - Milan Raska
- Department of Microbiology, University of Alabama at Birmingham, 845 19th Street S, Birmingham, AL 35294, USA.,Department of Immunology, Palacky University Olomouc, Olomouc, Czech Republic
| | - Matthew B Renfrow
- Department of Biochemistry and Molecular Genetics, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Jan Novak
- Department of Microbiology, University of Alabama at Birmingham, 845 19th Street S, Birmingham, AL 35294, USA
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Wu Y, Pinkevych M, Xu Z, Keele BF, Davenport MP, Cromer D. Impact of fluctuation in frequency of human immunodeficiency virus/simian immunodeficiency virus reactivation during antiretroviral therapy interruption. Proc Biol Sci 2020; 287:20200354. [PMID: 32811309 DOI: 10.1098/rspb.2020.0354] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [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: 12/11/2022] Open
Abstract
Antiretroviral therapy (ART) provides effective control of human immunodeficiency virus (HIV) replication and maintains viral loads of HIV at undetectable levels. Interruption of ART causes rapid recrudescence of HIV plasma viremia due to reactivation of latently HIV-infected cells. Here, we characterize the timing of both the initial and subsequent successful viral reactivations following ART interruption in macaques infected with simian immunodeficiency virus (SIV). We compare these to previous results from HIV-infected patients. We find that on average the time until the first successful viral reactivation event is longer than the time between subsequent reactivations. Based on this result, we hypothesize that the reactivation frequency of both HIV and SIV may fluctuate over time, and that this may impact the treatment of HIV. We develop a stochastic model incorporating fluctuations in the frequency of viral reactivation following ART interruption that shows behaviours consistent with the observed data. Furthermore, we show that one of the impacts of a fluctuating reactivation frequency would be to significantly reduce the efficacy of 'anti-latency' interventions for HIV that aim to reduce the frequency of reactivation. It is therefore essential to consider the possibility of a fluctuating reactivation frequency when assessing the impact of such intervention strategies.
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Affiliation(s)
- Yuhuang Wu
- Infection Analytics Program, Kirby Institute for Infection and Immunity, University of New South Wales, Sydney, NSW, Australia
| | - Mykola Pinkevych
- Infection Analytics Program, Kirby Institute for Infection and Immunity, University of New South Wales, Sydney, NSW, Australia
| | - Zhuang Xu
- School of Physics, University of New South Wales, Sydney, NSW, Australia
| | - Brandon F Keele
- AIDS and Cancer Virus Program, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Miles P Davenport
- Infection Analytics Program, Kirby Institute for Infection and Immunity, University of New South Wales, Sydney, NSW, Australia
| | - Deborah Cromer
- Infection Analytics Program, Kirby Institute for Infection and Immunity, University of New South Wales, Sydney, NSW, Australia.,School of Mathematics and Statistics, University of New South Wales, Sydney, NSW, Australia
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Cornejo Castro EM, Marshall V, Lack J, Lurain K, Immonen T, Labo N, Fisher NC, Ramaswami R, Polizzotto MN, Keele BF, Yarchoan R, Uldrick TS, Whitby D. Dual infection and recombination of Kaposi sarcoma herpesvirus revealed by whole-genome sequence analysis of effusion samples. Virus Evol 2020; 6:veaa047. [PMID: 34211736 DOI: 10.1093/ve/veaa047] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Kaposi sarcoma herpesvirus (KSHV) is the etiological agent of three malignancies, Kaposi sarcoma (KS), primary effusion lymphoma (PEL) and KSHV-associated multicentric Castelman disease. KSHV infected patients may also have an interleukin six-related KSHV-associated inflammatory cytokine syndrome. KSHV-associated diseases occur in only a minority of chronically KSHV-infected individuals and often in the setting of immunosuppression. Mechanisms by which KSHV genomic variations and systemic co-infections may affect the pathogenic pathways potentially leading to these diseases have not been well characterized in vivo. To date, the majority of comparative genetic analyses of KSHV have been focused on a few regions scattered across the viral genome. We used next-generation sequencing techniques to investigate the taxonomic groupings of viruses from malignant effusion samples from fourteen participants with advanced KSHV-related malignancies, including twelve with PEL and two with KS and elevated KSHV viral load in effusions. The genomic diversity and evolutionary characteristics of nine isolated, near full-length KSHV genomes revealed extensive evidence of mosaic patterns across all these genomes. Further, our comprehensive NGS analysis allowed the identification of two distinct KSHV genome sequences in one individual, consistent with a dual infection. Overall, our results provide significant evidence for the contribution of KSHV phylogenomics to the origin of KSHV subtypes. This report points to a wider scope of studies to establish genome-wide patterns of sequence diversity and define the possible pathogenic role of sequence variations in KSHV-infected individuals.
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Affiliation(s)
- Elena M Cornejo Castro
- Viral Oncology Section, AIDS and Cancer Virus Program, Frederick National Laboratory for Cancer Research, P.O. Box B, Frederick, MD 21702, USA
| | - Vickie Marshall
- Viral Oncology Section, AIDS and Cancer Virus Program, Frederick National Laboratory for Cancer Research, P.O. Box B, Frederick, MD 21702, USA
| | - Justin Lack
- Advanced Biomedical Computing Center, Leidos Biomedical Research, Inc., Frederick, MD 21702, USA
| | - Kathryn Lurain
- HIV and AIDS Malignancy Branch, National Cancer Institute, 10 Center Dr, Bethesda, MD 20814, USA
| | - Taina Immonen
- Retroviral Evolution Section, AIDS and Cancer Virus Program, Frederick National Laboratory for Cancer Research, P.O. Box B, Frederick, MD 21702, USA
| | - Nazzarena Labo
- Viral Oncology Section, AIDS and Cancer Virus Program, Frederick National Laboratory for Cancer Research, P.O. Box B, Frederick, MD 21702, USA
| | - Nicholas C Fisher
- Viral Oncology Section, AIDS and Cancer Virus Program, Frederick National Laboratory for Cancer Research, P.O. Box B, Frederick, MD 21702, USA
| | - Ramya Ramaswami
- HIV and AIDS Malignancy Branch, National Cancer Institute, 10 Center Dr, Bethesda, MD 20814, USA
| | - Mark N Polizzotto
- HIV and AIDS Malignancy Branch, National Cancer Institute, 10 Center Dr, Bethesda, MD 20814, USA
| | - Brandon F Keele
- Retroviral Evolution Section, AIDS and Cancer Virus Program, Frederick National Laboratory for Cancer Research, P.O. Box B, Frederick, MD 21702, USA
| | - Robert Yarchoan
- HIV and AIDS Malignancy Branch, National Cancer Institute, 10 Center Dr, Bethesda, MD 20814, USA
| | - Thomas S Uldrick
- HIV and AIDS Malignancy Branch, National Cancer Institute, 10 Center Dr, Bethesda, MD 20814, USA
| | - Denise Whitby
- Viral Oncology Section, AIDS and Cancer Virus Program, Frederick National Laboratory for Cancer Research, P.O. Box B, Frederick, MD 21702, USA
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Berzofsky JA, Keele BF, Miller CJ, Sui Y. Vaccine-induced protection against intrarectal AIDS virus transmission in the absence of anti-Env antibodies mediated by trained innate immunity. The Journal of Immunology 2020. [DOI: 10.4049/jimmunol.204.supp.167.12] [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
Although anti-Envelope antibodies have been viewed as the primary means of protection against SIV or SHIV acquisition, we have found in two distinct vaccine studies that protection against intrarectal SHIV or SIV acquisition in repeated low-dose challenge can be achieved in the absence of anti-Env antibodies (Vaccine efficacy = 44% in one study and 81% in the other). Specific CD8+ T cells were induced but did not correlate with protection, and in one of the studies, CD8+ depletion experiments excluded any CD8-dependence of the protection. Rather, protection correlated with protective myeloid cells and inversely with suppressive myeloid-derived suppressor cells. Trained innate immunity of monocytes lasting at least 7 weeks after vaccination was confirmed by demonstrating the ability of monocytes from vaccinated animals to produce more IL-6, TNFa and/or Mip1a when re-exposed to virus than those from control animals. This trained innate response correlated with the number of exposures required to achieve infection. Trained innate immunity has been shown to be mediated by epigenetic changes in monocytes, and indeed, we have been able to detect such epigenetic changes. Thus, vaccine protection against rectal acquisition of SHIV or SIV can be achieved in the absence of anti-Env antibodies and even of CD8+ T cells, and can be mediated by trained innate monocyte immunity. These findings suggest a new mode of vaccine protection that needs to be investigated in future AIDS vaccine clinical trials.
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Affiliation(s)
- Jay A Berzofsky
- 1Center for Cancer Research, National Cancer Institute, National Institutes of Health
| | - Brandon F Keele
- 2Leidos Biomedical Research Inc, Frederick National Laboratory for Cancer Research
| | | | - Yongjun Sui
- 1Center for Cancer Research, National Cancer Institute, National Institutes of Health
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36
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Raehtz KD, Barrenäs F, Xu C, Busman-Sahay K, Valentine A, Law L, Ma D, Policicchio BB, Wijewardana V, Brocca-Cofano E, Trichel A, Gale M, Keele BF, Estes JD, Apetrei C, Pandrea I. African green monkeys avoid SIV disease progression by preventing intestinal dysfunction and maintaining mucosal barrier integrity. PLoS Pathog 2020; 16:e1008333. [PMID: 32119719 PMCID: PMC7077871 DOI: 10.1371/journal.ppat.1008333] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [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: 08/30/2019] [Revised: 03/17/2020] [Accepted: 01/18/2020] [Indexed: 12/12/2022] Open
Abstract
Unlike HIV infection, SIV infection is generally nonpathogenic in natural hosts, such as African green monkeys (AGMs), despite life-long high viral replication. Lack of disease progression was reportedly based on the ability of SIV-infected AGMs to prevent gut dysfunction, avoiding microbial translocation and the associated systemic immune activation and chronic inflammation. Yet, the maintenance of gut integrity has never been documented, and the mechanism(s) by which gut integrity is preserved are unknown. We sought to investigate the early events of SIV infection in AGMs, specifically examining the impact of SIVsab infection on the gut mucosa. Twenty-nine adult male AGMs were intrarectally infected with SIVsab92018 and serially sacrificed at well-defined stages of SIV infection, preramp-up (1-3 days post-infection (dpi)), ramp-up (4-6 dpi), peak viremia (9-12 dpi), and early chronic SIV infection (46-55 dpi), to assess the levels of immune activation, apoptosis, epithelial damage and microbial translocation in the GI tract and peripheral lymph nodes. Tissue viral loads, plasma cytokines and plasma markers of gut dysfunction were also measured throughout the course of early infection. While a strong, but transient, interferon-based inflammatory response was observed, the levels of plasma markers linked to enteropathy did not increase. Accordingly, no significant increases in apoptosis of either mucosal enterocytes or lymphocytes, and no damage to the mucosal epithelium were documented during early SIVsab infection of AGMs. These findings were supported by RNAseq of the gut tissue, which found no significant alterations in gene expression that would indicate microbial translocation. Thus, for the first time, we confirmed that gut epithelial integrity is preserved, with no evidence of microbial translocation, in AGMs throughout early SIVsab infection. This might protect AGMs from developing intestinal dysfunction and the subsequent chronic inflammation that drives both HIV disease progression and HIV-associated comorbidities.
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Affiliation(s)
- Kevin D. Raehtz
- Division of Infectious Diseases, Department of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Fredrik Barrenäs
- Department of Microbiology, University of Washington, Seattle, Washington, United States of America
- Department of Cell and Molecular Biology, Uppsala University, Uppsala, Sweden
| | - Cuiling Xu
- Division of Infectious Diseases, Department of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
- Department of Pathology, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Kathleen Busman-Sahay
- Vaccine and Gene Therapy Institute, Oregon Health and Science University, Portland, Oregon, United States of America
- Oregon National Primate Research Center, Oregon Health and Science University, Portland, Oregon, United States of America
| | - Audrey Valentine
- Division of Infectious Diseases, Department of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Lynn Law
- Department of Immunology, University of Washington, Seattle, Washington, United States of America
- Center for Innate Immunity and Immune Diseases, University of Washington, Washington, United States of America
| | - Dongzhu Ma
- Department of Orthopedic Surgery, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Benjamin B. Policicchio
- Department of Infectious Diseases and Microbiology, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Viskam Wijewardana
- Department of Pathology, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Egidio Brocca-Cofano
- Department of Pathology, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Anita Trichel
- Division of Laboratory Animal Resources, School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Michael Gale
- Department of Immunology, University of Washington, Seattle, Washington, United States of America
- Center for Innate Immunity and Immune Diseases, University of Washington, Washington, United States of America
- Washington National Primate Research Center, University of Washington, Seattle, Washington, United States of America
| | - Brandon F. Keele
- AIDS and Cancer Virus Program, Frederick National Laboratory of Cancer Research, Frederick, Maryland, United States of America
| | - Jacob D. Estes
- Vaccine and Gene Therapy Institute, Oregon Health and Science University, Portland, Oregon, United States of America
- Oregon National Primate Research Center, Oregon Health and Science University, Portland, Oregon, United States of America
| | - Cristian Apetrei
- Division of Infectious Diseases, Department of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
- Department of Infectious Diseases and Microbiology, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Ivona Pandrea
- Department of Pathology, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
- Department of Infectious Diseases and Microbiology, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
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37
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Nixon CC, Mavigner M, Sampey GC, Brooks AD, Spagnuolo RA, Irlbeck DM, Mattingly C, Ho PT, Schoof N, Cammon CG, Tharp GK, Kanke M, Wang Z, Cleary RA, Upadhyay AA, De C, Wills SR, Falcinelli SD, Galardi C, Walum H, Schramm NJ, Deutsch J, Lifson JD, Fennessey CM, Keele BF, Jean S, Maguire S, Liao B, Browne EP, Ferris RG, Brehm JH, Favre D, Vanderford TH, Bosinger SE, Jones CD, Routy JP, Archin NM, Margolis DM, Wahl A, Dunham RM, Silvestri G, Chahroudi A, Garcia JV. Systemic HIV and SIV latency reversal via non-canonical NF-κB signalling in vivo. Nature 2020; 578:160-165. [PMID: 31969707 PMCID: PMC7111210 DOI: 10.1038/s41586-020-1951-3] [Citation(s) in RCA: 181] [Impact Index Per Article: 45.3] [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: 04/12/2019] [Accepted: 12/16/2019] [Indexed: 01/27/2023]
Abstract
Long-lasting, latently infected resting CD4+ T cells are the greatest obstacle to obtaining a cure for HIV infection, as these cells can persist despite decades of treatment with antiretroviral therapy (ART). Estimates indicate that more than 70 years of continuous, fully suppressive ART are needed to eliminate the HIV reservoir1. Alternatively, induction of HIV from its latent state could accelerate the decrease in the reservoir, thus reducing the time to eradication. Previous attempts to reactivate latent HIV in preclinical animal models and in clinical trials have measured HIV induction in the peripheral blood with minimal focus on tissue reservoirs and have had limited effect2-9. Here we show that activation of the non-canonical NF-κB signalling pathway by AZD5582 results in the induction of HIV and SIV RNA expression in the blood and tissues of ART-suppressed bone-marrow-liver-thymus (BLT) humanized mice and rhesus macaques infected with HIV and SIV, respectively. Analysis of resting CD4+ T cells from tissues after AZD5582 treatment revealed increased SIV RNA expression in the lymph nodes of macaques and robust induction of HIV in almost all tissues analysed in humanized mice, including the lymph nodes, thymus, bone marrow, liver and lung. This promising approach to latency reversal-in combination with appropriate tools for systemic clearance of persistent HIV infection-greatly increases opportunities for HIV eradication.
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Affiliation(s)
- Christopher C Nixon
- International Center for the Advancement of Translational Science, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Division of Infectious Diseases, Department of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Center for AIDS Research, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Maud Mavigner
- Department of Pediatrics, Emory University School of Medicine, Atlanta, GA, USA
| | - Gavin C Sampey
- Division of Infectious Diseases, Department of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Center for AIDS Research, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- UNC HIV Cure Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Qura Therapeutics, Chapel Hill, NC, USA
| | - Alyssa D Brooks
- Department of Pediatrics, Emory University School of Medicine, Atlanta, GA, USA
| | - Rae Ann Spagnuolo
- International Center for the Advancement of Translational Science, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Division of Infectious Diseases, Department of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Center for AIDS Research, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - David M Irlbeck
- Qura Therapeutics, Chapel Hill, NC, USA
- HIV Drug Discovery, ViiV Healthcare, Research Triangle Park, NC, USA
| | - Cameron Mattingly
- Department of Pediatrics, Emory University School of Medicine, Atlanta, GA, USA
| | - Phong T Ho
- International Center for the Advancement of Translational Science, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Division of Infectious Diseases, Department of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Center for AIDS Research, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Nils Schoof
- Department of Pediatrics, Emory University School of Medicine, Atlanta, GA, USA
| | - Corinne G Cammon
- International Center for the Advancement of Translational Science, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Division of Infectious Diseases, Department of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Center for AIDS Research, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Greg K Tharp
- Yerkes National Primate Research Center, Emory University, Atlanta, GA, USA
| | - Matthew Kanke
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Zhang Wang
- GlaxoSmithKline Research and Development, Collegeville, PA, USA
| | - Rachel A Cleary
- International Center for the Advancement of Translational Science, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Division of Infectious Diseases, Department of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Center for AIDS Research, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Amit A Upadhyay
- Yerkes National Primate Research Center, Emory University, Atlanta, GA, USA
| | - Chandrav De
- International Center for the Advancement of Translational Science, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Division of Infectious Diseases, Department of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Center for AIDS Research, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Saintedym R Wills
- Division of Infectious Diseases, Department of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Center for AIDS Research, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- UNC HIV Cure Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Qura Therapeutics, Chapel Hill, NC, USA
| | - Shane D Falcinelli
- Division of Infectious Diseases, Department of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Center for AIDS Research, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- UNC HIV Cure Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Department of Microbiology and Immunology, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Cristin Galardi
- Qura Therapeutics, Chapel Hill, NC, USA
- HIV Drug Discovery, ViiV Healthcare, Research Triangle Park, NC, USA
| | - Hasse Walum
- Yerkes National Primate Research Center, Emory University, Atlanta, GA, USA
| | - Nathaniel J Schramm
- International Center for the Advancement of Translational Science, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Division of Infectious Diseases, Department of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Center for AIDS Research, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | | | - Jeffrey D Lifson
- 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
| | - Brandon F Keele
- AIDS and Cancer Virus Program, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Sherrie Jean
- Yerkes National Primate Research Center, Emory University, Atlanta, GA, USA
| | - Sean Maguire
- GlaxoSmithKline Research and Development, Collegeville, PA, USA
| | - Baolin Liao
- International Center for the Advancement of Translational Science, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Division of Infectious Diseases, Department of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Center for AIDS Research, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Department of Infectious Diseases, Guangzhou Eighth People's Hospital, Guangzhou Medical University, Guangzhou, China
| | - Edward P Browne
- Division of Infectious Diseases, Department of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Center for AIDS Research, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- UNC HIV Cure Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Robert G Ferris
- Qura Therapeutics, Chapel Hill, NC, USA
- HIV Drug Discovery, ViiV Healthcare, Research Triangle Park, NC, USA
| | - Jessica H Brehm
- Qura Therapeutics, Chapel Hill, NC, USA
- HIV Drug Discovery, ViiV Healthcare, Research Triangle Park, NC, USA
| | - David Favre
- Qura Therapeutics, Chapel Hill, NC, USA
- GlaxoSmithKline Research and Development, Collegeville, PA, USA
| | | | - Steven E Bosinger
- Yerkes National Primate Research Center, Emory University, Atlanta, GA, USA
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, GA, USA
| | - Corbin D Jones
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Jean-Pierre Routy
- Chronic Viral Infection Service, McGill University Health Centre, Montreal, Quebec, Canada
- Division of Hematology, McGill University Health Centre, Montreal, Quebec, Canada
| | - Nancie M Archin
- Division of Infectious Diseases, Department of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Center for AIDS Research, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- UNC HIV Cure Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - David M Margolis
- Division of Infectious Diseases, Department of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Center for AIDS Research, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- UNC HIV Cure Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Qura Therapeutics, Chapel Hill, NC, USA
- Department of Microbiology and Immunology, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Department of Epidemiology, Gillings School of Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Angela Wahl
- International Center for the Advancement of Translational Science, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Division of Infectious Diseases, Department of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Center for AIDS Research, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Richard M Dunham
- Division of Infectious Diseases, Department of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
- Center for AIDS Research, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
- UNC HIV Cure Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
- Qura Therapeutics, Chapel Hill, NC, USA.
- HIV Drug Discovery, ViiV Healthcare, Research Triangle Park, NC, USA.
| | - Guido Silvestri
- Yerkes National Primate Research Center, Emory University, Atlanta, GA, USA
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, GA, USA
| | - Ann Chahroudi
- Department of Pediatrics, Emory University School of Medicine, Atlanta, GA, USA.
- Yerkes National Primate Research Center, Emory University, Atlanta, GA, USA.
- Emory + Children's Center for Childhood Infections and Vaccines, Atlanta, GA, USA.
| | - J Victor Garcia
- International Center for the Advancement of Translational Science, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
- Division of Infectious Diseases, Department of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
- Center for AIDS Research, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
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Hataye JM, Casazza JP, Best K, Liang CJ, Immonen TT, Ambrozak DR, Darko S, Henry AR, Laboune F, Maldarelli F, Douek DC, Hengartner NW, Yamamoto T, Keele BF, Perelson AS, Koup RA. Principles Governing Establishment versus Collapse of HIV-1 Cellular Spread. Cell Host Microbe 2019; 26:748-763.e20. [PMID: 31761718 PMCID: PMC6948011 DOI: 10.1016/j.chom.2019.10.006] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [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: 03/25/2019] [Revised: 09/19/2019] [Accepted: 10/07/2019] [Indexed: 10/25/2022]
Abstract
A population at low census might go extinct or instead transition into exponential growth to become firmly established. Whether this pivotal event occurs for a within-host pathogen can be the difference between health and illness. Here, we define the principles governing whether HIV-1 spread among cells fails or becomes established by coupling stochastic modeling with laboratory experiments. Following ex vivo activation of latently infected CD4 T cells without de novo infection, stochastic cell division and death contributes to high variability in the magnitude of initial virus release. Transition to exponential HIV-1 spread often fails due to release of an insufficient amount of replication-competent virus. Establishment of exponential growth occurs when virus produced from multiple infected cells exceeds a critical population size. We quantitatively define the crucial transition to exponential viral spread. Thwarting this process would prevent HIV transmission or rebound from the latent reservoir.
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Affiliation(s)
- Jason M Hataye
- Immunology Section, Immunology Laboratory, Vaccine Research Center, National Institute of Allergy and Infectious Diseases, Bethesda, MD 20892, USA.
| | - Joseph P Casazza
- Immunology Section, Immunology Laboratory, Vaccine Research Center, National Institute of Allergy and Infectious Diseases, Bethesda, MD 20892, USA
| | - Katharine Best
- Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, NM 87545, USA
| | - C Jason Liang
- Biostatistics Research Branch, National Institute of Allergy and Infectious Diseases, Rockville, MD 20892, USA
| | - Taina T Immonen
- AIDS and Cancer Virus Program, Frederick National Laboratory for Cancer Research, National Cancer Institute, Frederick, MD 21702, USA
| | - David R Ambrozak
- Immunology Section, Immunology Laboratory, Vaccine Research Center, National Institute of Allergy and Infectious Diseases, Bethesda, MD 20892, USA
| | - Samuel Darko
- Human Immunology Section, Immunology Laboratory, Vaccine Research Center, National Institute of Allergy and Infectious Diseases, Bethesda, MD 20892, USA
| | - Amy R Henry
- Human Immunology Section, Immunology Laboratory, Vaccine Research Center, National Institute of Allergy and Infectious Diseases, Bethesda, MD 20892, USA
| | - Farida Laboune
- Human Immunology Section, Immunology Laboratory, Vaccine Research Center, National Institute of Allergy and Infectious Diseases, Bethesda, MD 20892, USA
| | - Frank Maldarelli
- HIV Dynamics and Replication Program, Frederick National Laboratory for Cancer Research, National Cancer Institute, Frederick, MD 21702, USA
| | - Daniel C Douek
- Human Immunology Section, Immunology Laboratory, Vaccine Research Center, National Institute of Allergy and Infectious Diseases, Bethesda, MD 20892, USA
| | - Nicolas W Hengartner
- Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, NM 87545, USA
| | - Takuya Yamamoto
- Laboratory of Immunosenescence, National Institutes of Biomedical Innovation, Health, and Nutrition, Osaka 567-0085, Japan
| | - Brandon F Keele
- AIDS and Cancer Virus Program, Frederick National Laboratory for Cancer Research, National Cancer Institute, Frederick, MD 21702, USA
| | - Alan S Perelson
- Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, NM 87545, USA
| | - Richard A Koup
- Immunology Section, Immunology Laboratory, Vaccine Research Center, National Institute of Allergy and Infectious Diseases, Bethesda, MD 20892, USA.
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39
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Pinkevych M, Fennessey CM, Cromer D, Reid C, Trubey CM, Lifson JD, Keele BF, Davenport MP. Predictors of SIV recrudescence following antiretroviral treatment interruption. eLife 2019; 8:e49022. [PMID: 31650954 PMCID: PMC6917497 DOI: 10.7554/elife.49022] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [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: 06/04/2019] [Accepted: 10/24/2019] [Indexed: 12/26/2022] Open
Abstract
There is currently a need for proxy measures of the HIV rebound competent reservoir (RCR) that can predict viral rebound after combined antiretroviral treatment (cART) interruption. In this study, macaques infected with a barcoded SIVmac239 virus received cART beginning between 4- and 27 days post-infection, leading to the establishment of different levels of viral dissemination and persistence. Later treatment initiation led to higher SIV DNA levels maintained during treatment, which was significantly associated with an increased frequency of SIV reactivation and production of progeny capable of causing rebound viremia following treatment interruption. However, a 100-fold increase in SIV DNA in PBMCs was associated with only a 2-fold increase in the frequency of reactivation. These data suggest that the RCR can be established soon after infection, and that a large fraction of persistent viral DNA that accumulates after this time makes relatively little contribution to viral rebound.
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Affiliation(s)
- Mykola Pinkevych
- Infection Analytics ProgramKirby Institute for Infection and Immunity, UNSW AustraliaSydneyAustralia
| | - Christine M Fennessey
- AIDS and Cancer Virus ProgramFrederick National Laboratory for Cancer ResearchFrederickUnited States
| | - Deborah Cromer
- Infection Analytics ProgramKirby Institute for Infection and Immunity, UNSW AustraliaSydneyAustralia
| | - Carolyn Reid
- AIDS and Cancer Virus ProgramFrederick National Laboratory for Cancer ResearchFrederickUnited States
| | - Charles M Trubey
- AIDS and Cancer Virus ProgramFrederick National Laboratory for Cancer ResearchFrederickUnited States
| | - Jeffrey D Lifson
- AIDS and Cancer Virus ProgramFrederick National Laboratory for Cancer ResearchFrederickUnited States
| | - Brandon F Keele
- AIDS and Cancer Virus ProgramFrederick National Laboratory for Cancer ResearchFrederickUnited States
| | - Miles P Davenport
- Infection Analytics ProgramKirby Institute for Infection and Immunity, UNSW AustraliaSydneyAustralia
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40
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Musick A, Spindler J, Boritz E, Pérez L, Crespo-Vélez D, Patro SC, Sobolewski MD, Bale MJ, Reid C, Keele BF, Capoferri A, Shao W, Wiegand A, Simonetti FR, Mellors JW, Hughes SH, Coffin JM, Maldarelli F, Kearney MF. HIV Infected T Cells Can Proliferate in vivo Without Inducing Expression of the Integrated Provirus. Front Microbiol 2019; 10:2204. [PMID: 31632364 PMCID: PMC6781911 DOI: 10.3389/fmicb.2019.02204] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [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: 06/04/2019] [Accepted: 09/09/2019] [Indexed: 12/27/2022] Open
Abstract
BACKGROUND HIV-1 proviruses can persist during ART in clonally-expanded populations of CD4+ T cells. To date, few examples of an expanded clones containing replication-competent proviruses exist, although it is suspected to be common. One such clone, denoted AMBI-1 (Maldarelli et al., 2014), was also a source of persistent viremia on ART, begging the question of how the AMBI-1 clone can survive despite infection with a replication-competent, actively-expressing provirus. We hypothesized that only a small fraction of cells within the AMBI-1 clone are activated to produce virus particles during cell division while the majority remain latent despite division, ensuring their survival. To address this question, we determined the fraction of HIV-1 proviruses within the AMBI-1 clone that expresses unspliced cell-associated RNA during ART and compared this fraction to 33 other infected T cell clones within the same individual. RESULTS In total, 34 different clones carrying either intact or defective proviruses in "Patient 1" from Maldarelli et al. (2014) were assessed. We found that 2.3% of cells within the AMBI-1 clone contained unspliced HIV-1 RNA. Highest levels of HIV-1 RNA were found in the effector memory (EM) T cell subset. The fraction of cells within clones that contained HIV-1 RNA was not different in clones with intact (median 2.3%) versus defective (median 3.5%) proviruses (p = 0.2). However, higher fractions and levels of RNA were found in cells with proviruses containing multiple drug resistance mutations, including those contributing to rebound viremia. CONCLUSION These findings show that the vast majority of HIV-1 proviruses within expanded T cell clones, including intact proviruses, may be transcriptionally silent at any given time, implying that infected T cells may be able to be activated to proliferate without inducing the expression of the integrated provirus or, alternatelively, may be able to proliferate without cellular activation. The results of this study suggest that the long, presumed correlation between the level of cellular and proviral activation may not be accurate and, therefore, requires further investigation.
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Affiliation(s)
- Andrew Musick
- Human Immunodeficiency Virus (HIV) Dynamics and Replication Program, Center for Cancer Research (CCR), National Cancer Institute (NCI)-Frederick, Frederick, MD, United States
| | - Jonathan Spindler
- Human Immunodeficiency Virus (HIV) Dynamics and Replication Program, Center for Cancer Research (CCR), National Cancer Institute (NCI)-Frederick, Frederick, MD, United States
| | - Eli Boritz
- Virus Persistence and Dynamics Section, Vaccine Research Center, National Institute for Allergies and Infectious Diseases (NIAID), Bethesda, MD, United States
| | - Liliana Pérez
- Virus Persistence and Dynamics Section, Vaccine Research Center, National Institute for Allergies and Infectious Diseases (NIAID), Bethesda, MD, United States
| | - Daniel Crespo-Vélez
- Virus Persistence and Dynamics Section, Vaccine Research Center, National Institute for Allergies and Infectious Diseases (NIAID), Bethesda, MD, United States
| | - Sean C. Patro
- Human Immunodeficiency Virus (HIV) Dynamics and Replication Program, Center for Cancer Research (CCR), National Cancer Institute (NCI)-Frederick, Frederick, MD, United States
| | | | - Michael J. Bale
- Human Immunodeficiency Virus (HIV) Dynamics and Replication Program, Center for Cancer Research (CCR), National Cancer Institute (NCI)-Frederick, Frederick, MD, United States
| | - Carolyn Reid
- Frederick National Laboratory for Cancer Research, Aquired Immunodeficiency Syndrome (AIDS) and Cancer Virus Program, Leidos Biomedical Research Inc., Frederick, MD, United States
| | - Brandon F. Keele
- Frederick National Laboratory for Cancer Research, Aquired Immunodeficiency Syndrome (AIDS) and Cancer Virus Program, Leidos Biomedical Research Inc., Frederick, MD, United States
| | - Adam Capoferri
- Human Immunodeficiency Virus (HIV) Dynamics and Replication Program, Center for Cancer Research (CCR), National Cancer Institute (NCI)-Frederick, Frederick, MD, United States
| | - Wei Shao
- Frederick National Laboratory for Cancer Research, Advanced Biomedical Computing Center, Leidos Biomedical Research, Inc., Frederick, MD, United States
| | - Ann Wiegand
- Human Immunodeficiency Virus (HIV) Dynamics and Replication Program, Center for Cancer Research (CCR), National Cancer Institute (NCI)-Frederick, Frederick, MD, United States
| | - Francesco R. Simonetti
- Human Immunodeficiency Virus (HIV) Dynamics and Replication Program, Center for Cancer Research (CCR), National Cancer Institute (NCI)-Frederick, Frederick, MD, United States
| | - John W. Mellors
- Department of Medicine, University of Pittsburgh, Pittsburgh, PA, United States
| | - Stephen H. Hughes
- Human Immunodeficiency Virus (HIV) Dynamics and Replication Program, Center for Cancer Research (CCR), National Cancer Institute (NCI)-Frederick, Frederick, MD, United States
| | - John M. Coffin
- Department of Molecular Biology and Microbiology, Tufts University, Boston, MA, United States
| | - Frank Maldarelli
- Human Immunodeficiency Virus (HIV) Dynamics and Replication Program, Center for Cancer Research (CCR), National Cancer Institute (NCI)-Frederick, Frederick, MD, United States
| | - Mary F. Kearney
- Human Immunodeficiency Virus (HIV) Dynamics and Replication Program, Center for Cancer Research (CCR), National Cancer Institute (NCI)-Frederick, Frederick, MD, United States
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41
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Pham HT, Hassounah S, Keele BF, Van Rompay KKA, Mesplède T. Insertion as a Resistance Mechanism Against Integrase Inhibitors in Several Retroviruses. Clin Infect Dis 2019; 69:1460-1461. [PMID: 30753366 DOI: 10.1093/cid/ciz136] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2018] [Accepted: 02/07/2019] [Indexed: 12/21/2022] Open
Affiliation(s)
- Hanh Thi Pham
- McGill AIDS Centre, Lady Davis Institute for Medical Research, Jewish General Hospital.,Department of Microbiology and Immunology, Faculty of Medicine, McGill University, Montréal, Québec, Canada
| | - Said Hassounah
- McGill AIDS Centre, Lady Davis Institute for Medical Research, Jewish General Hospital
| | - Brandon F Keele
- AIDS and Cancer Virus Program, Frederick National Laboratory for Cancer Research, Maryland
| | - Koen K A Van Rompay
- California National Primate Research Center, University of California, Davis.,Department of Pathology, Microbiology and Immunology, School of Veterinary Medicine, University of California, Davis
| | - Thibault Mesplède
- McGill AIDS Centre, Lady Davis Institute for Medical Research, Jewish General Hospital.,Department of Microbiology and Immunology, Faculty of Medicine, McGill University, Montréal, Québec, Canada.,Department of Medicine, Division of Experimental Medicine, Montréal, Québec, Canada.,Department of Medicine, Division of Infectious Diseases, Jewish General Hospital, Faculty of Medicine, McGill University, Montréal, Québec, Canada
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42
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Iwamoto N, Mason RD, Song K, Gorman J, Welles HC, Arthos J, Cicala C, Min S, King HAD, Belli AJ, Reimann KA, Foulds KE, Kwong PD, Lifson JD, Keele BF, Roederer M. Blocking α 4β 7 integrin binding to SIV does not improve virologic control. Science 2019; 365:1033-1036. [PMID: 31488690 PMCID: PMC9513815 DOI: 10.1126/science.aaw7765] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [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: 02/01/2019] [Accepted: 06/26/2019] [Indexed: 07/31/2023]
Abstract
A study in nonhuman primates reported that infusions of an antibody against α4β7 integrin, in combination with antiretroviral therapy, showed consistent, durable control of simian immunodeficiency virus (SIV) in rhesus macaques. The antibody used has pleiotropic effects, so we set out to gain insight into the underlying mechanism by comparing this treatment to treatment with non-neutralizing monoclonal antibodies against the SIV envelope glycoprotein that only block α4β7 binding to SIV Env but have no other host-directed effects. Similar to the initial study, we used an attenuated strain of SIV containing a stop codon in nef. The study used 30 macaques that all began antiretroviral therapy and then were divided into five groups to receive different antibody treatments. Unlike the published report, we found no sustained virologic control by these treatments in vivo.
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Affiliation(s)
- Nami Iwamoto
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), Bethesda, MD, USA
| | - Rosemarie D Mason
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), Bethesda, MD, USA
| | - Kaimei Song
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), Bethesda, MD, USA
| | - Jason Gorman
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), Bethesda, MD, USA
| | - Hugh C Welles
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), Bethesda, MD, USA
| | - James Arthos
- Laboratory of Immunoregulation, NIAID, NIH, Bethesda, MD, USA
| | - Claudia Cicala
- Laboratory of Immunoregulation, NIAID, NIH, Bethesda, MD, USA
| | - Susie Min
- Laboratory of Immunoregulation, NIAID, NIH, Bethesda, MD, USA
| | - Hannah A D King
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), Bethesda, MD, USA
| | - Aaron J Belli
- MassBiologics, University of Massachusetts Medical School, Boston, MA, USA
| | - Keith A Reimann
- MassBiologics, University of Massachusetts Medical School, Boston, MA, USA
| | - Kathryn E Foulds
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), Bethesda, MD, USA
| | - Peter D Kwong
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), Bethesda, MD, USA
| | - Jeffrey D Lifson
- AIDS and Cancer Virus Program, Frederick National Laboratory, Frederick, MD, USA
| | - Brandon F Keele
- AIDS and Cancer Virus Program, Frederick National Laboratory, Frederick, MD, USA
| | - Mario Roederer
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), Bethesda, MD, USA.
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43
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Yu WH, Su D, Torabi J, Fennessey CM, Shiakolas A, Lynch R, Chun TW, Doria-Rose N, Alter G, Seaman MS, Keele BF, Lauffenburger DA, Julg B. Predicting the broadly neutralizing antibody susceptibility of the HIV reservoir. JCI Insight 2019; 4:130153. [PMID: 31484826 DOI: 10.1172/jci.insight.130153] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [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: 05/22/2019] [Accepted: 07/26/2019] [Indexed: 01/10/2023] Open
Abstract
Broadly neutralizing antibodies (bNAbs) against HIV-1 are under evaluation for both prevention and therapy. HIV-1 sequence diversity observed in most HIV-infected individuals and archived variations in critical bNAb epitopes present a major challenge for the clinical application of bNAbs, as preexistent resistant viral strains can emerge, resulting in bNAb failure to control HIV. In order to identify viral resistance in patients prior to antibody therapy and to guide the selection of effective bNAb combination regimens, we developed what we believe to be a novel Bayesian machine-learning model that uses HIV-1 envelope protein sequences and foremost approximated glycan occupancy information as variables to quantitatively predict the half-maximal inhibitory concentrations (IC50) of 126 neutralizing antibodies against a variety of cross clade viruses. We then applied this model to peripheral blood mononuclear cell-derived proviral Env sequences from 25 HIV-1-infected individuals mapping the landscape of neutralization resistance within each individual's reservoir and determined the predicted ideal bNAb combination to achieve 100% neutralization at IC50 values <1 μg/ml. Furthermore, predicted cellular viral reservoir neutralization signatures of individuals before an analytical antiretroviral treatment interruption were consistent with the measured neutralization susceptibilities of the respective plasma rebound viruses, validating our model as a potentially novel tool to facilitate the advancement of bNAbs into the clinic.
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Affiliation(s)
- Wen-Han Yu
- Ragon Institute of MGH, MIT and Harvard, Cambridge, Massachusetts, USA.,Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - David Su
- Ragon Institute of MGH, MIT and Harvard, Cambridge, Massachusetts, USA
| | - Julia Torabi
- Ragon Institute of MGH, MIT and Harvard, Cambridge, Massachusetts, USA
| | - Christine M Fennessey
- AIDS and Cancer Virus Program, Frederick National Laboratory for Cancer Research, Frederick, Maryland, USA
| | - Andrea Shiakolas
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, Maryland, USA
| | - Rebecca Lynch
- Department of Microbiology, Immunology and Tropical Medicine, School of Medicine and Health Sciences, The George Washington University, Washington, District of Columbia, USA
| | - Tae-Wook Chun
- Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, Maryland, USA
| | - Nicole Doria-Rose
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, Maryland, USA
| | - Galit Alter
- Ragon Institute of MGH, MIT and Harvard, Cambridge, Massachusetts, USA
| | - Michael S Seaman
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Boston, Massachusetts, USA
| | - Brandon F Keele
- AIDS and Cancer Virus Program, Frederick National Laboratory for Cancer Research, Frederick, Maryland, USA
| | - Douglas A Lauffenburger
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Boris Julg
- Ragon Institute of MGH, MIT and Harvard, Cambridge, Massachusetts, USA
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44
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Abbink P, Mercado NB, Nkolola JP, Peterson RL, Tuyishime H, McMahan K, Moseley ET, Borducchi EN, Chandrashekar A, Bondzie EA, Agarwal A, Belli AJ, Reimann KA, Keele BF, Geleziunas R, Lewis MG, Barouch DH. Lack of therapeutic efficacy of an antibody to α 4β 7 in SIVmac251-infected rhesus macaques. Science 2019; 365:1029-1033. [PMID: 31488689 DOI: 10.1126/science.aaw8562] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2019] [Accepted: 06/26/2019] [Indexed: 12/15/2022]
Abstract
Sustained virologic control of human immunodeficiency virus type 1 (HIV-1) infection after discontinuation of antiretroviral therapy (ART) is a major goal of the HIV-1 cure field. A recent study reported that administration of an antibody against α4β7 induced durable virologic control after ART discontinuation in 100% of rhesus macaques infected with an attenuated strain of simian immunodeficiency virus (SIV) containing a stop codon in nef We performed similar studies in 50 rhesus macaques infected with wild-type, pathogenic SIVmac251. In animals that initiated ART during either acute or chronic infection, anti-α4β7 antibody infusion had no detectable effect on the viral reservoir or viral rebound after ART discontinuation. These data demonstrate that anti-α4β7 antibody administration did not provide therapeutic efficacy in the model of pathogenic SIVmac251 infection of rhesus macaques.
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Affiliation(s)
- Peter Abbink
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA
| | - Noe B Mercado
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA
| | - Joseph P Nkolola
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA
| | - Rebecca L Peterson
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA
| | - Hubert Tuyishime
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA
| | - Katherine McMahan
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA
| | - Edward T Moseley
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA
| | - Erica N Borducchi
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA
| | - Abishek Chandrashekar
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA
| | - Esther A Bondzie
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA
| | - Arshi Agarwal
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA
| | - Aaron J Belli
- MassBiologics of the University of Massachusetts Medical School, Boston, MA 02126, USA
| | - Keith A Reimann
- MassBiologics of the University of Massachusetts Medical School, Boston, MA 02126, USA
| | - Brandon F Keele
- AIDS and Cancer Virus Program, Frederick National Laboratory, Frederick, MD 21702, USA
| | | | | | - Dan H Barouch
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA. .,Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology, and Harvard University, Cambridge, MA 02139, USA
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45
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Patro SC, Wu X, Guo S, Bale MJ, Wiegand A, Spindler J, Fennessey CM, Halvas EK, Keele BF, Hughes SH, Mellors JW, Coffin JM, Rausch JW, Kearney MF. A9 A method to obtain full-length HIV proviral sequences and their sites of integration. Virus Evol 2019. [PMCID: PMC6735837 DOI: 10.1093/ve/vez002.008] [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] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Abstract
Accurate definition of the HIV-1 reservoir on antiretroviral therapy (ART) is of paramount importance to the development of curative strategies. Much of this reservoir is derived from clonal expansion of latently infected CD4+ T cells. Methods used to characterize the reservoir include near full-length single-genome sequencing (NFL-SGS) and integration site analysis (ISA). However, current technologies do not link the intact proviruses detected by NFL-SGS to their sites of integration. Therefore, we developed a method to obtain both near full-length single-proviral sequences and their sites of integration. We call our method full-length integrated proviral single-genome sequencing (FLIP-SGS). Genomic DNA from ACH2 and CEM cells mixed at 1:1,000, or patient samples were diluted to a single proviral endpoint. An in-house, optimized whole genome amplification (WGA) method was performed on wells at the endpoint, generating multiple copies of all DNA molecules within each well. The number of proviral copies after WGA was determined by droplet digital PCR targeting the long terminal region (LTR). Forty per cent of each WGA reaction was used to obtain the provirus–host integration sites with ISA (linker ligation, nested PCR, and Illumina sequencing). The remaining fraction was used to amplify the full-length proviruses in four overlapping fragments (LTR-pol, gag-int, int-env, and env-LTR) for Sanger sequencing. WGA performed on the endpoint-diluted ACH2:CEM DNA amplified single-copy HIV-1 proviral templates greater than 500-fold, making it possible to obtain unique integration sites from single proviruses in ACH2 cells, including one that was previously reported (in the NT5C3A gene on chromosome 7) and two that were not previously reported (in the EIF4ENIF1 gene of chromosome 22 and an unknown region of chromosome 6). Near full-length PCR amplification and Sanger sequencing was performed on proviruses integrated in the NT5C3A gene. FLIP-SGS was applied to peripheral blood mononuclear cells from one HIV-1 infected donor with viremia suppressed on ART and yielded integration sites of four genomes that appear to contain large internal deletions. We report a method for near full-length HIV-1 single-genome sequencing combined with host integration site detection that we call FLIP-SGS. This assay will further define clonal expansion of infected CD4+ T cells as a mechanism that maintains the HIV-1 reservoir and as the source of identical sequences observed during therapy and rebound, rather than from ongoing replication.
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Affiliation(s)
- Sean C Patro
- HIV Dynamics and Replication Program, National Cancer Institute, Frederick, MD 21702, USA
| | - Xiaolin Wu
- Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA
| | - Shuang Guo
- Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA
| | - Michael J Bale
- HIV Dynamics and Replication Program, National Cancer Institute, Frederick, MD 21702, USA
| | - Ann Wiegand
- HIV Dynamics and Replication Program, National Cancer Institute, Frederick, MD 21702, USA
| | - Jonathan Spindler
- HIV Dynamics and Replication Program, National Cancer Institute, Frederick, MD 21702, USA
| | - Christine M Fennessey
- AIDS and Cancer Virus Program, Leidos Biomedical Research, Inc., Frederick National Laboratory, Frederick, MD 21702, USA
| | - Elias K Halvas
- Department of Medicine, University of Pittsburgh, Pittsburgh, PA 15213, USA
| | - Brandon F Keele
- AIDS and Cancer Virus Program, Leidos Biomedical Research, Inc., Frederick National Laboratory, Frederick, MD 21702, USA
| | - Stephen H Hughes
- HIV Dynamics and Replication Program, National Cancer Institute, Frederick, MD 21702, USA
| | - John W Mellors
- Department of Medicine, University of Pittsburgh, Pittsburgh, PA 15213, USA
| | - John M Coffin
- Department of Molecular Biology and Microbiology, Tufts University, Boston, MA 02111, USA
| | - Jason W Rausch
- Basic Research Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702, USA
| | - Mary F Kearney
- HIV Dynamics and Replication Program, National Cancer Institute, Frederick, MD 21702, USA
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46
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McManus WR, Bale MJ, Spindler J, Wiegand A, Musick A, Patro SC, Sobolewski MD, Musick VK, Anderson EM, Cyktor JC, Halvas EK, Shao W, Wells D, Wu X, Keele BF, Milush JM, Hoh R, Mellors JW, Hughes SH, Deeks SG, Coffin JM, Kearney MF. HIV-1 in lymph nodes is maintained by cellular proliferation during antiretroviral therapy. J Clin Invest 2019; 129:4629-4642. [PMID: 31361603 DOI: 10.1172/jci126714] [Citation(s) in RCA: 69] [Impact Index Per Article: 13.8] [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: 12/19/2022] Open
Abstract
To investigate the possibility that HIV-1 replication in lymph nodes sustains the reservoir during ART, we looked for evidence of viral replication in 5 donors after up to 13 years of viral suppression. We characterized proviral populations in lymph nodes and peripheral blood before and during ART, evaluated the levels of viral RNA expression in single lymph node and blood cells, and characterized the proviral integration sites in paired lymph node and blood samples. Proviruses with identical sequences, identical integration sites, and similar levels of RNA expression were found in lymph nodes and blood samples collected during ART, and no single sequence with significant divergence from the pretherapy population was present in either blood or lymph nodes. These findings show that all detectable persistent HIV-1 infection is consistent with maintenance in lymph nodes by clonal proliferation of cells infected before ART and not by ongoing viral replication during ART.
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Affiliation(s)
- William R McManus
- HIV Dynamics and Replication Program, Center for Cancer Research, National Cancer Institute, Frederick, Maryland, USA
| | - Michael J Bale
- HIV Dynamics and Replication Program, Center for Cancer Research, National Cancer Institute, Frederick, Maryland, USA
| | - Jonathan Spindler
- HIV Dynamics and Replication Program, Center for Cancer Research, National Cancer Institute, Frederick, Maryland, USA
| | - Ann Wiegand
- HIV Dynamics and Replication Program, Center for Cancer Research, National Cancer Institute, Frederick, Maryland, USA
| | - Andrew Musick
- HIV Dynamics and Replication Program, Center for Cancer Research, National Cancer Institute, Frederick, Maryland, USA
| | - Sean C Patro
- HIV Dynamics and Replication Program, Center for Cancer Research, National Cancer Institute, Frederick, Maryland, USA
| | | | - Victoria K Musick
- HIV Dynamics and Replication Program, Center for Cancer Research, National Cancer Institute, Frederick, Maryland, USA
| | - Elizabeth M Anderson
- HIV Dynamics and Replication Program, Center for Cancer Research, National Cancer Institute, Frederick, Maryland, USA
| | - Joshua C Cyktor
- Department of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Elias K Halvas
- Department of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Wei Shao
- Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, Maryland, USA
| | - Daria Wells
- Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, Maryland, USA
| | - Xiaolin Wu
- Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, Maryland, USA
| | - Brandon F Keele
- Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, Maryland, USA
| | | | - Rebecca Hoh
- Department of Medicine, UCSF, San Francisco, California, USA
| | - John W Mellors
- Department of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Stephen H Hughes
- HIV Dynamics and Replication Program, Center for Cancer Research, National Cancer Institute, Frederick, Maryland, USA
| | - Steven G Deeks
- Department of Medicine, UCSF, San Francisco, California, USA
| | - John M Coffin
- Department of Molecular Biology and Microbiology, Tufts University, Boston, Massachusetts, USA
| | - Mary F Kearney
- HIV Dynamics and Replication Program, Center for Cancer Research, National Cancer Institute, Frederick, Maryland, USA
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47
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Asokan M, Maximova A, Dias J, Crowley AR, Pegu A, Ambrozak D, McKee K, Shi W, Todd JP, Ackerman ME, Gama L, Keele BF, Lifson JD, Perelson AS, Mascola JR, Koup R. Passive infusion of Fc-modified neutralizing antibodies does not affect the dynamics of plasma virus decay in SHIV-infected macaques. The Journal of Immunology 2019. [DOI: 10.4049/jimmunol.202.supp.72.6] [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
Passive neutralizing antibody (NAb) infusion leads to a reduction of HIV plasma viremia in infected people as well as in SHIV-infected rhesus macaques. Potential mechanisms of viral reduction include neutralization of free virus as well as Fc-dependent effector functions that can clear infected cells. We generated several Fc variants of the human IgG1 NAb VRC07-523LS and characterized them for neutralization, complement binding, ADCC, phagocytosis, and binding to rhesus FcgR. Based on these assays, we down selected two variants, LALA and DEL, that showed knock-out or increase in ADCC and phagocytosis respectively, with complement binding knocked out in both. The parental, LALA and DEL variants of VRC07-523LS were administered at a single dose of 20 mg/kg i.v. to rhesus macaques chronically infected with SHIV-SF162P3 for 6–14 weeks (n=6 to 10 per group). Animals were followed for rate of plasma virus decay and antibody PK. All groups showed similar characteristics: 1) plasma virus decay was delayed for 24h after NAb infusion 2) the rate of plasma virus decay was the same between day 1 and day 5, and 3) plasma virus decay was independent of FcgRIII genotype. Pharmacokinetic analysis showed that serum NAb concentrations in the VRC07-523LS, LALA and DEL groups were maintained at greater than ten-fold excess of the in vitro IC80 against SHIV SF162P3 throughout the period of investigation. Further, unlike VRC07-523LS-LALA, VRC07-523LS-DEL was able to engage natural killer cells and monocytes and mediate both HIV envelope-dependent ADCC and phagocytosis. These results show that the initial impact on plasma viremia by passive NAb therapy is predominantly mediated by virus neutralization rather than ADCC or phagocytosis.
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Deleage C, Immonen TT, Fennessey CM, Reynaldi A, Reid C, Newman L, Lipkey L, Schlub TE, Camus C, O’Brien S, Smedley J, Conway JM, Del Prete GQ, Davenport MP, Lifson JD, Estes JD, Keele BF. Defining early SIV replication and dissemination dynamics following vaginal transmission. Sci Adv 2019; 5:eaav7116. [PMID: 31149634 PMCID: PMC6541462 DOI: 10.1126/sciadv.aav7116] [Citation(s) in RCA: 24] [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] [Subscribe] [Scholar Register] [Received: 10/12/2018] [Accepted: 04/23/2019] [Indexed: 06/09/2023]
Abstract
Understanding HIV transmission is critical to guide the development of prophylactic interventions to prevent infection. We used a nonhuman primate (NHP) model with a synthetic swarm of sequence-tagged variants of SIVmac239 ("SIVmac239X") and scheduled necropsy during primary infection (days 3 to 14 after challenge) to study viral dynamics and host responses to the establishment and dissemination of infection following vaginal challenge. We demonstrate that local replication was initiated at multiple sites within the female genital tract (FGT), with each site having multiple viral variants. Local replication and spread in the FGT preceded lymphatic dissemination. Innate viral restriction factors were observed but appeared to follow viral replication and were ineffective at blocking initial viral establishment and dissemination. However, major delays were observed in time to dissemination in animals and among different viral variants within the same animal. It will be important to assess how phenotypic differences affect early viral dynamics.
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Affiliation(s)
- Claire Deleage
- AIDS and Cancer Virus Program, Leidos Biomedical Research, Inc. Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Taina T. Immonen
- AIDS and Cancer Virus Program, Leidos Biomedical Research, Inc. Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Christine M. Fennessey
- AIDS and Cancer Virus Program, Leidos Biomedical Research, Inc. Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Arnold Reynaldi
- Infection Analytics Program, Kirby Institute for Infection and Immunity, University of New South Wales, Sydney, Australia
| | - Carolyn Reid
- AIDS and Cancer Virus Program, Leidos Biomedical Research, Inc. Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Laura Newman
- AIDS and Cancer Virus Program, Leidos Biomedical Research, Inc. Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Leslie Lipkey
- AIDS and Cancer Virus Program, Leidos Biomedical Research, Inc. Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Timothy E. Schlub
- The University of Sydney, Faculty of Medicine and Health, Sydney School of Public Health, New South Wales, Australia
| | - Celine Camus
- AIDS and Cancer Virus Program, Leidos Biomedical Research, Inc. Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Sean O’Brien
- AIDS and Cancer Virus Program, Leidos Biomedical Research, Inc. Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Jeremy Smedley
- Laboratory Animal Sciences Program, Leidos Biomedical Research, Inc. Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Jessica M. Conway
- Department of Mathematics and Center for Infectious Disease Dynamics, Pennsylvania State University, State College, PA, USA
| | - Gregory Q. Del Prete
- AIDS and Cancer Virus Program, Leidos Biomedical Research, Inc. Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - 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, Leidos Biomedical Research, Inc. Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Jacob D. Estes
- AIDS and Cancer Virus Program, Leidos Biomedical Research, Inc. Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Brandon F. Keele
- AIDS and Cancer Virus Program, Leidos Biomedical Research, Inc. Frederick National Laboratory for Cancer Research, Frederick, MD, USA
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Fennessey CM, Camus C, Immonen TT, Reid C, Maldarelli F, Lifson JD, Keele BF. Low-level alternative tRNA priming of reverse transcription of HIV-1 and SIV in vivo. Retrovirology 2019; 16:11. [PMID: 30947720 PMCID: PMC6450007 DOI: 10.1186/s12977-019-0473-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2019] [Accepted: 04/01/2019] [Indexed: 01/19/2023] Open
Abstract
Background Reverse transcription (RT) of HIV and SIV is initiated by the binding of the acceptor stem of tRNALys3 to the primer binding site (PBS) of the viral RNA genome. Previous studies have suggested that this tRNALys3 is not the only molecule capable of priming reverse transcription, and that at least one other lysyl tRNA, tRNALys5, which has an acceptor stem sequence varying from tRNALys3 by only a single transition mutation resulting in the integration of a thymine (T) at position 8 of the PBS in the viral genome, can prime reverse transcription. Results We undertook an unbiased approach, evaluating the primer binding site by deep-sequencing of HIV and SIV directly from the plasma of 15 humans and 11 macaques. We found that in humans there are low but measurable levels of viral RNA genomes harboring a PBS containing the noncanonical T at position 8 (PBS-Lys5) corresponding to the tRNAlys5 sequence and representing an average of 0.52% (range 0.07–1.6%) of the total viral population. This value is remarkably consistent with the proportion of PBS-Lys5 we identified in a cross-sectional assessment of the LANL HIV database (0.51%). In macaques chronically infected with SIVmac239, the PBS-Lys5 was also detected but at a frequency 1-log less than seen for HIV, with an average of 0.056% (range 0.01–0.09%). At this proportion, PBS-Lys5 was comparable to other transition mutations, making it impossible to determine whether the mutation observed is a result of use of tRNALys5 as an RT primer at very low levels or merely the product of in vitro cDNA synthesis/PCR error. We also identified two novel PBS sequences in HIV and SIV at low levels in vivo corresponding to tRNALys6 and tRNALys1,2, suggesting that these tRNAs may rarely also be used to prime RT. In vivo reversion of the PBS-Lys5 found in SIVmac239 was rapid and reached background levels by 30 days post-infection. Conclusions We conclude that while alternative tRNAs can initiate reverse transcription of HIV and SIV in vivo, their overall contributions to the replicating viral population are small. Electronic supplementary material The online version of this article (10.1186/s12977-019-0473-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Christine M Fennessey
- AIDS and Cancer Virus Program, Frederick National Laboratory for Cancer Research, Frederick, MD, 21702, USA
| | - Celine Camus
- AIDS and Cancer Virus Program, Frederick National Laboratory for Cancer Research, Frederick, MD, 21702, USA
| | - Taina T Immonen
- AIDS and Cancer Virus Program, Frederick National Laboratory for Cancer Research, Frederick, MD, 21702, USA
| | - Carolyn Reid
- AIDS and Cancer Virus Program, Frederick National Laboratory for Cancer Research, Frederick, MD, 21702, USA
| | - Frank Maldarelli
- HIV Dynamics and Replication Program, National Cancer Institute, Frederick, MD, 21702, USA
| | - Jeffrey D Lifson
- AIDS and Cancer Virus Program, Frederick National Laboratory for Cancer Research, Frederick, MD, 21702, USA
| | - Brandon F Keele
- AIDS and Cancer Virus Program, Frederick National Laboratory for Cancer Research, Frederick, MD, 21702, USA.
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Martinez-Navio JM, Fuchs SP, Pantry SN, Lauer WA, Duggan NN, Keele BF, Rakasz EG, Gao G, Lifson JD, Desrosiers RC. Adeno-Associated Virus Delivery of Anti-HIV Monoclonal Antibodies Can Drive Long-Term Virologic Suppression. Immunity 2019; 50:567-575.e5. [PMID: 30850342 PMCID: PMC6457122 DOI: 10.1016/j.immuni.2019.02.005] [Citation(s) in RCA: 87] [Impact Index Per Article: 17.4] [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: 11/01/2018] [Revised: 12/10/2018] [Accepted: 02/08/2019] [Indexed: 01/03/2023]
Abstract
Long-term delivery of anti-HIV monoclonal antibodies (mAbs) using adeno-associated virus (AAV) vectors holds promise for the prevention and treatment of HIV infection. We describe a therapy trial in which four rhesus monkeys were infected with SHIV-AD8 for 86 weeks before receiving the AAV-encoded mAbs 3BNC117, 10-1074, and 10E8. Although anti-drug antibody (ADA) responses restricted mAb delivery, one monkey successfully maintained 50-150 μg/mL of 3BNC117 and 10-1074 for over 2 years. Delivery of these two mAbs to this monkey resulted in an abrupt decline in plasma viremia, which remained undetectable for 38 successive measurements over 3 years. We generated two more examples of virologic suppression using AAV delivery of a cocktail of four mAbs in a 12-monkey study. Our results provide proof of concept for AAV-delivered mAbs to produce a "functional cure." However, they also serve as a warning that ADAs may be a problem for practical application of this approach in humans.
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Affiliation(s)
- José M Martinez-Navio
- Department of Pathology, Miller School of Medicine, University of Miami, Miami, Florida, USA
| | - Sebastian P Fuchs
- Department of Pathology, Miller School of Medicine, University of Miami, Miami, Florida, USA
| | - Shara N Pantry
- Department of Pathology, Miller School of Medicine, University of Miami, Miami, Florida, USA
| | - William A Lauer
- Department of Pathology, Miller School of Medicine, University of Miami, Miami, Florida, USA
| | - Natasha N Duggan
- Department of Pathology, Miller School of Medicine, University of Miami, Miami, Florida, USA
| | - Brandon F Keele
- AIDS and Cancer Virus Program, Frederick National Laboratory for Cancer Research, Frederick, Maryland, USA
| | - Eva G Rakasz
- Wisconsin National Primate Research Center, University of Wisconsin, Madison, WI, USA
| | - Guangping Gao
- Gene Therapy Center, University of Massachusetts Medical School, Worcester, MA, USA
| | - Jeffrey D Lifson
- AIDS and Cancer Virus Program, Frederick National Laboratory for Cancer Research, Frederick, Maryland, USA
| | - Ronald C Desrosiers
- Department of Pathology, Miller School of Medicine, University of Miami, Miami, Florida, USA.
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