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González N, McKee K, Lynch RM, Georgiev IS, Jimenez L, Grau E, Yuste E, Kwong PD, Mascola JR, Alcamí J. Characterization of broadly neutralizing antibody responses to HIV-1 in a cohort of long term non-progressors. PLoS One 2018; 13:e0193773. [PMID: 29558468 PMCID: PMC5860703 DOI: 10.1371/journal.pone.0193773] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2017] [Accepted: 02/16/2018] [Indexed: 12/21/2022] Open
Abstract
Background Only a small fraction of HIV-1-infected patients develop broadly neutralizing antibodies (bNAbs), a process generally associated to chronic antigen stimulation. It has been described that rare aviremic HIV-1-infected patients can generate bNAbs but this issue remains controversial. To address this matter we have assessed bNAb responses in a large cohort of long-term non-progressors (LTNPs) with low or undetectable viremia. Methods Samples from the LTNP cohort of the Spanish AIDS Research Network (87 elite and 42 viremic controllers) and a control population of 176 viremic typical-progressors (TPs) were screened for bNAbs using Env-recombinant viruses. bNAb specificities were studied by ELISA using mutated gp120, neutralization assays with mutated viruses, and peptide competition. Epitope specificities were also elucidated from the serum pattern of neutralization against a panel of diverse HIV-1 isolates. Results Broadly neutralizing sera were found among 9.3% LTNPs, both elite (7%) and viremic controllers (14%). Within the broadly neutralizing sera, CD4 binding site antibodies were detected by ELISA in 4/12 LTNPs (33%), and 16/33 of TPs (48%). Anti-MPER antibodies were detected in 6/12 LTNPs (50%) and 14/33 TPs (42%) whereas glycan-dependent HIV-1 bNAbs were more frequent in LTNPs (11/12, 92%) as compared to TPs (12/33, 36%). A good concordance between standard serum mapping and neutralization-based mapping was observed. Conclusion LTNPs, both viremic and elite controllers, showed broad humoral immune responses against HIV-1, including activity against many major epitopes involved in bNAbs-mediated protection.
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Affiliation(s)
- Nuria González
- AIDS Immunopathology Unit, Instituto de Salud Carlos III, Madrid, Spain
- * E-mail: (NG); (JA)
| | - Krisha McKee
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, Washington, United States of America
| | - Rebecca M. Lynch
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, Washington, United States of America
| | - Ivelin S. Georgiev
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, Washington, United States of America
| | - Laura Jimenez
- AIDS Immunopathology Unit, Instituto de Salud Carlos III, Madrid, Spain
| | - Eulalia Grau
- IrsiCaixa Foundation, Hospital Universitari Germans Trias i Pujol, Universitat Autònoma de Barcelona, Badalona, Barcelona, Spain
| | - Eloísa Yuste
- Retrovirology and Viral Immunopathology Laboratory, IDIBAPS, Hospital Clínic, University of Barcelona, Barcelona, Spain
| | - Peter D. Kwong
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, Washington, United States of America
| | - John R. Mascola
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, Washington, United States of America
| | - José Alcamí
- AIDS Immunopathology Unit, Instituto de Salud Carlos III, Madrid, Spain
- * E-mail: (NG); (JA)
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2
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Villabona Arenas CJ, Vidal N, Ahuka Mundeke S, Muwonga J, Serrano L, Muyembe JJ, Boillot F, Delaporte E, Peeters M. Divergent HIV-1 strains (CRF92_C2U and CRF93_cpx) co-circulating in the Democratic Republic of the Congo: Phylogenetic insights on the early evolutionary history of subtype C. Virus Evol 2017; 3:vex032. [PMID: 29250430 PMCID: PMC5724398 DOI: 10.1093/ve/vex032] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Molecular epidemiological studies revealed that the epicenter of the HIV pandemic was Kinshasa, the capital city of the Democratic Republic of the Congo (DRC) in Central Africa. All known subtypes and numerous complex recombinant strains co-circulate in the DRC. Moreover, high intra-subtype diversity has been also documented. During two previous surveys on HIV-1 antiretroviral drug resistance in the DRC, we identified two divergent subtype C lineages in the protease and partial reverse transcriptase gene regions. We sequenced eight near full-length genomes and classified them using bootscanning and likelihood-based phylogenetic analyses. Four strains are more closely related to subtype C although within the range of inter sub-subtype distances. However, these strains also have small unclassified fragments and thus were named CRF92_C2U. Another strain is a unique recombinant of CRF92_C2U with an additional small unclassified fragment and a small divergent subtype A fragment. The three remaining strains represent a complex mosaic named CRF93_cpx. CRF93_cpx have two fragments of divergent subtype C sequences, which are not conventional subtype C nor the above described C2, and multiple divergent subtype A-like fragments. We then inferred the time-scaled evolutionary history of subtype C following a Bayesian approach and a partitioned analysis using major genomic regions. CRF92_C2U and CRF93_cpx had the most recent common ancestor with conventional subtype C around 1932 and 1928, respectively. A Bayesian demographic reconstruction corroborated that the subtype C transition to a faster phase of exponential growth occurred during the 1950s. Our analysis showed considerable differences between the newly discovered early-divergent strains and the conventional subtype C and therefore suggested that this virus has been diverging in humans for several decades before the HIV/M diversity boom in the 1950s.
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Affiliation(s)
- C J Villabona Arenas
- Unité Mixte Internationale 233, Institut de Recherche pour le Développement, INSERM U1175, Université de Montpellier, 911 Avenue Agropolis, Montpellier, 34394, France
| | - N Vidal
- Unité Mixte Internationale 233, Institut de Recherche pour le Développement, INSERM U1175, Université de Montpellier, 911 Avenue Agropolis, Montpellier, 34394, France
| | - S Ahuka Mundeke
- Unité Mixte Internationale 233, Institut de Recherche pour le Développement, INSERM U1175, Université de Montpellier, 911 Avenue Agropolis, Montpellier, 34394, France.,Institut National de Recherche Biomédicale, Av. De la Démocratie 5345, Kinshasa, Democratic Republic of the Congo.,Cliniques Universitaires de Kinshasa, Route de Kimwenza, Kinshasa, Congo, Democratic Republic of Congo
| | - J Muwonga
- Cliniques Universitaires de Kinshasa, Route de Kimwenza, Kinshasa, Congo, Democratic Republic of Congo.,Laboratoire National de Référence du SIDA, Kinshasa, Democratic Republic of Congo
| | - L Serrano
- Unité Mixte Internationale 233, Institut de Recherche pour le Développement, INSERM U1175, Université de Montpellier, 911 Avenue Agropolis, Montpellier, 34394, France
| | - J J Muyembe
- Institut National de Recherche Biomédicale, Av. De la Démocratie 5345, Kinshasa, Democratic Republic of the Congo.,Cliniques Universitaires de Kinshasa, Route de Kimwenza, Kinshasa, Congo, Democratic Republic of Congo
| | - F Boillot
- Alter-Santé Internationale and Développement, Montpellier, 34090, France
| | - E Delaporte
- Unité Mixte Internationale 233, Institut de Recherche pour le Développement, INSERM U1175, Université de Montpellier, 911 Avenue Agropolis, Montpellier, 34394, France
| | - M Peeters
- Unité Mixte Internationale 233, Institut de Recherche pour le Développement, INSERM U1175, Université de Montpellier, 911 Avenue Agropolis, Montpellier, 34394, France
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3
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Freund NT, Horwitz JA, Nogueira L, Sievers SA, Scharf L, Scheid JF, Gazumyan A, Liu C, Velinzon K, Goldenthal A, Sanders RW, Moore JP, Bjorkman PJ, Seaman MS, Walker BD, Klein F, Nussenzweig MC. A New Glycan-Dependent CD4-Binding Site Neutralizing Antibody Exerts Pressure on HIV-1 In Vivo. PLoS Pathog 2015; 11:e1005238. [PMID: 26516768 PMCID: PMC4627763 DOI: 10.1371/journal.ppat.1005238] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2015] [Accepted: 09/28/2015] [Indexed: 11/18/2022] Open
Abstract
The CD4 binding site (CD4bs) on the envelope glycoprotein is a major site of vulnerability that is conserved among different HIV-1 isolates. Many broadly neutralizing antibodies (bNAbs) to the CD4bs belong to the VRC01 class, sharing highly restricted origins, recognition mechanisms and viral escape pathways. We sought to isolate new anti-CD4bs bNAbs with different origins and mechanisms of action. Using a gp120 2CC core as bait, we isolated antibodies encoded by IGVH3-21 and IGVL3-1 genes with long CDRH3s that depend on the presence of the N-linked glycan at position-276 for activity. This binding mode is similar to the previously identified antibody HJ16, however the new antibodies identified herein are more potent and broad. The most potent variant, 179NC75, had a geometric mean IC80 value of 0.42 μg/ml against 120 Tier-2 HIV-1 pseudoviruses in the TZM.bl assay. Although this group of CD4bs glycan-dependent antibodies can be broadly and potently neutralizing in vitro, their in vivo activity has not been tested to date. Here, we report that 179NC75 is highly active when administered to HIV-1-infected humanized mice, where it selects for escape variants that lack a glycan site at position-276. The same glycan was absent from the virus isolated from the 179NC75 donor, implying that the antibody also exerts selection pressure in humans. CD4bs is a central viral vulnerability site and isolation of new anti-HIV-1 CD4bs broadly neutralizing antibodies (bNAbs) provides information about viral escape mechanisms. Here we describe a new anti-HIV-1 bNAb that was isolated from an HIV-1 infected donor. The antibody, 179NC75, targets the CD4 binding site in a glycan-dependent manner. Although many CD4bs antibodies have been already described, a glycan-dependent mode of recognition is unusual for anti-HIV-1 CD4bs bNAbs. The glycan-dependent CD4bs antibodies have never been tested for their ability to neutralize HIV-1 in vivo. We infected humanized mice with HIV-1YU2 and treated them with 179NC75 three weeks after infection. We observed a drop in viral load immediately after treatment followed by a viral rebound. The viral rebound was associated with specific escape mutations in the plasma virus envelope, resulting in a deletion of N276 glycan, and in some cases a glycan shift from position 276 to position 460. Similar signature mutations were found in the envelope of the autologous virus cloned from patient’s plasma. This defines the escape pathways from 179NC75, and shows that they are the same in humans and in HIV-1YU2 infected humanized mice.
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Affiliation(s)
- Natalia T. Freund
- Laboratory of Molecular Immunology, The Rockefeller University, New York, New York, United States of America
- * E-mail:
| | - Joshua A. Horwitz
- Laboratory of Molecular Immunology, The Rockefeller University, New York, New York, United States of America
| | - Lilian Nogueira
- Laboratory of Molecular Immunology, The Rockefeller University, New York, New York, United States of America
| | - Stuart A. Sievers
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, California, United States of America
| | - Louise Scharf
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, California, United States of America
| | - Johannes F. Scheid
- Laboratory of Molecular Immunology, The Rockefeller University, New York, New York, United States of America
| | - Anna Gazumyan
- Laboratory of Molecular Immunology, The Rockefeller University, New York, New York, United States of America
| | - Cassie Liu
- Laboratory of Molecular Immunology, The Rockefeller University, New York, New York, United States of America
| | - Klara Velinzon
- Laboratory of Molecular Immunology, The Rockefeller University, New York, New York, United States of America
| | - Ariel Goldenthal
- Ragon Institute of MGH, MIT and Harvard, Cambridge, Massachusetts, United States of America
| | - Rogier W. Sanders
- Department of Medical Microbiology, Academic Medical Center, University of Amsterdam, Amsterdam, The Netherlands
| | - John P. Moore
- Department of Microbiology and Immunology, Weill Medical College, Cornell University, New York, New York, United States of America
| | - Pamela J. Bjorkman
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, California, United States of America
| | - Michael S. Seaman
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Bruce D. Walker
- Ragon Institute of MGH, MIT and Harvard, Cambridge, Massachusetts, United States of America
- Howard Hughes Medical Institute, Chevy Chase, Maryland, United States of America
| | - Florian Klein
- First Department of Internal Medicine, University Hospital of Cologne, Cologne, Germany
- Center for Molecular Medicine Cologne (CMMC), University of Cologne, Germany
| | - Michel C. Nussenzweig
- Laboratory of Molecular Immunology, The Rockefeller University, New York, New York, United States of America
- Howard Hughes Medical Institute, Chevy Chase, Maryland, United States of America
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Palma P, Romiti ML, Montesano C, Santilli V, Mora N, Aquilani A, Dispinseri S, Tchidjou HK, Montano M, Eriksson LE, Baldassari S, Bernardi S, Scarlatti G, Wahren B, Rossi P. Therapeutic DNA vaccination of vertically HIV-infected children: report of the first pediatric randomised trial (PEDVAC). PLoS One 2013; 8:e79957. [PMID: 24312194 PMCID: PMC3842924 DOI: 10.1371/journal.pone.0079957] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2013] [Accepted: 09/26/2013] [Indexed: 01/09/2023] Open
Abstract
Subjects Twenty vertically HIV-infected children, 6–16 years of age, with stable viral load control and CD4+ values above 400 cells/mm3. Intervention Ten subjects continued their ongoing antiretroviral treatment (ART, Group A) and 10 were immunized with a HIV-DNA vaccine in addition to their previous therapy (ART and vaccine, Group B). The genetic vaccine represented HIV-1 subtypes A, B and C, encoded Env, Rev, Gag and RT and had no additional adjuvant. Immunizations took place at weeks 0, 4 and 12, with a boosting dose at week 36. Monitoring was performed until week 60 and extended to week 96. Results Safety data showed good tolerance of the vaccine. Adherence to ART remained high and persistent during the study and did not differ significantly between controls and vaccinees. Neither group experienced either virological failure or a decline of CD4+ counts from baseline. Higher HIV-specific cellular immune responses were noted transiently to Gag but not to other components of the vaccine. Lymphoproliferative responses to a virion antigen HIV-1 MN were higher in the vaccinees than in the controls (p = 0.047), whereas differences in reactivity to clade-specific Gag p24, RT or Env did not reach significance. Compared to baseline, the percentage of HIV-specific CD8+ lymphocytes releasing perforin in the Group B was higher after the vaccination schedule had been completed (p = 0.031). No increased CD8+ perforin levels were observed in control Group A. Conclusions The present study demonstrates the feasibility, safety and moderate immunogenicity of genetic vaccination in vertically HIV-infected children, paving the way for amplified immunotherapeutic approaches in the pediatric population. Trial registration clinicaltrialsregister.eu _2007-002359-18IT
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Affiliation(s)
- Paolo Palma
- University Department of Pediatrics, Unit of Immune and Infectious Diseases, Children's Hospital “Bambino Gesu”, Rome, Italy
- * E-mail:
| | - Maria Luisa Romiti
- Department of Medicine, Chair of Pediatrics, University of Rome “Tor Vergata”, Rome, Italy
| | - Carla Montesano
- Department of Biology, University of Rome “Tor Vergata”, Rome, Italy
| | - Veronica Santilli
- Department of Medicine, Chair of Pediatrics, University of Rome “Tor Vergata”, Rome, Italy
| | - Nadia Mora
- Department of Medicine, Chair of Pediatrics, University of Rome “Tor Vergata”, Rome, Italy
| | - Angela Aquilani
- Department of Medicine, Chair of Pediatrics, University of Rome “Tor Vergata”, Rome, Italy
| | - Stefania Dispinseri
- Unit of Viral Evolution and Transmission, San Raffaele Scientific Institute, Milan, Italy
| | - Hyppolite K. Tchidjou
- University Department of Pediatrics, Unit of Immune and Infectious Diseases, Children's Hospital “Bambino Gesu”, Rome, Italy
| | - Marco Montano
- Chair of Infectious Diseases, University of Rome “Tor Vergata”, Rome, Italy
| | - Lars E. Eriksson
- Department of Neurobiology, Care Sciences and Society, Karolinska Institutet and Department of Infectious Diseases, Karolinska University Hospital, Huddinge, Sweden
- School of Health Science, City University, London, United Kingdom
| | - Stefania Baldassari
- University Department of Pediatrics, Unit of Immune and Infectious Diseases, Children's Hospital “Bambino Gesu”, Rome, Italy
| | - Stefania Bernardi
- University Department of Pediatrics, Unit of Immune and Infectious Diseases, Children's Hospital “Bambino Gesu”, Rome, Italy
| | - Gabriella Scarlatti
- Unit of Viral Evolution and Transmission, San Raffaele Scientific Institute, Milan, Italy
| | - Britta Wahren
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Paolo Rossi
- University Department of Pediatrics, Unit of Immune and Infectious Diseases, Children's Hospital “Bambino Gesu”, Rome, Italy
- Department of Medicine, Chair of Pediatrics, University of Rome “Tor Vergata”, Rome, Italy
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5
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Balla-Jhagjhoorsingh SS, Corti D, Heyndrickx L, Willems E, Vereecken K, Davis D, Vanham G. The N276 glycosylation site is required for HIV-1 neutralization by the CD4 binding site specific HJ16 monoclonal antibody. PLoS One 2013; 8:e68863. [PMID: 23874792 PMCID: PMC3714269 DOI: 10.1371/journal.pone.0068863] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2013] [Accepted: 05/31/2013] [Indexed: 11/19/2022] Open
Abstract
Immunogen design for HIV-1 vaccines could be based on epitope identification of naturally occurring neutralizing antibodies in infected patients. A tier 2 neutralizing monoclonal antibody (mAb), HJ16 recognizes a new epitope in the CD4 binding site (CD4bs) region that only partially overlaps with the b12 epitope. We aimed to identify the critical binding site by resistance induction in a sensitive primary CRF02_AG strain. In four independent dose-escalation studies, the N276D mutation was consistently the only alteration found and it was confirmed to be responsible for resistance to HJ16 by site-directed mutagenesis in envelopes (envs) of the homologous CRF02_AG, as well as of a subtype A and a subtype C primary isolate. This mutation removes an N-linked glycosylation site. The effect of N276D was very selective, as it failed to confer resistance to a range of other entry inhibitors. Remarkably, sensitivity to the CD4bs VRC01 and VRC03 mAbs was increased in the N276D mutated viruses. These data indicate that binding of the CD4bs specific HJ16 mAb critically depends on the interaction with the N276-glycan, thus indicating that HJ16 is the first glycan dependent CD4bs-specific mAb.
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Role of human immunodeficiency virus type 1 envelope structure in the induction of broadly neutralizing antibodies. J Virol 2012; 86:13152-63. [PMID: 23015715 DOI: 10.1128/jvi.01110-12] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Very soon after the discovery of neutralizing antibodies (NAbs) toward human immunodeficiency virus type 1 (HIV-1) infection, it became apparent that characterization of these NAbs would be an important step in finding a cure for or a vaccine to eradicate HIV-1. Since the initial description of broadly cross-clade NAbs naturally produced in HIV-1 patients, numerous studies have described new viral targets for these antibodies. More recently, studies concerning new groups of patients able to control their viremia, such as long-term nonprogressors (LTNPs) or elite controllers, have described the generation of numerous envelope-targeted NAbs. Recent studies have marked a new stage in research on NAbs with the description of antibodies obtained from a worldwide screening of HIV-positive patients. These studies have permitted the discovery of NAb families with great potential for both neutralization and neutralization breadth, such as PG, PGT, CH, and highly active agonistic anti-CD4 binding site antibodies (HAADs), of which VRC01 and its variants are members. These antibodies are able to neutralize more than 80% of circulating strains without any autoreactivity and can be rapidly integrated into clinical trials in order to test their protective potential. In this review, we will focus on new insights into HIV-1 envelope structure and their implications for the generation of potent NAbs.
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