1
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Tano-Menka R, Singh NK, Muzhingi I, Li X, Mandanas MV, Kaseke C, Crain CR, Zhang A, Ogunshola FJ, Vecchiarello L, Piechocka-Trocha A, Bashirova A, Birnbaum ME, Carrington M, Walker BD, Gaiha GD. Polymorphic residues in HLA-B that mediate HIV control distinctly modulate peptide interactions with both TCR and KIR molecules. Structure 2024; 32:1121-1136.e5. [PMID: 38733995 PMCID: PMC11329236 DOI: 10.1016/j.str.2024.04.015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2023] [Revised: 02/27/2024] [Accepted: 04/16/2024] [Indexed: 05/13/2024]
Abstract
Immunogenetic studies have shown that specific HLA-B residues (67, 70, 97, and 156) mediate the impact of HLA class I on HIV infection, but the molecular basis is not well understood. Here we evaluate the function of these residues within the protective HLA-B∗5701 allele. While mutation of Met67, Ser70, and Leu156 disrupt CD8+ T cell recognition, substitution of Val97 had no significant impact. Thermal denaturation of HLA-B∗5701-peptide complexes revealed that Met67 and Leu156 maintain HLA-peptide stability, while Ser70 and Leu156 facilitate T cell receptor (TCR) interactions. Analyses of existing structures and structural models suggested that Val97 mediates HLA-peptide binding to inhibitory KIR3DL1 molecules, which was confirmed by experimental assays. These data thereby demonstrate that the genetic basis by which host immunity impacts HIV outcomes occurs by modulating HLA-B-peptide stability and conformation for interaction with TCR and killer immunoglobulin receptor (KIR) molecules. Moreover, they indicate a key role for epitope specificity and HLA-KIR interactions to HIV control.
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MESH Headings
- Humans
- HLA-B Antigens/chemistry
- HLA-B Antigens/metabolism
- HLA-B Antigens/genetics
- HLA-B Antigens/immunology
- Protein Binding
- Receptors, Antigen, T-Cell/metabolism
- Receptors, Antigen, T-Cell/chemistry
- Receptors, Antigen, T-Cell/immunology
- HIV-1/immunology
- HIV-1/metabolism
- HIV Infections/immunology
- HIV Infections/virology
- Models, Molecular
- Receptors, KIR3DL1/metabolism
- Receptors, KIR3DL1/chemistry
- Receptors, KIR3DL1/genetics
- Peptides/chemistry
- Peptides/metabolism
- Binding Sites
- CD8-Positive T-Lymphocytes/immunology
- CD8-Positive T-Lymphocytes/metabolism
- Polymorphism, Genetic
- Protein Stability
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Affiliation(s)
- Rhoda Tano-Menka
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA
| | - Nishant K Singh
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA; Koch Institute for Integrative Cancer Research at MIT, Cambridge, MA 02142, USA; Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA
| | - Itai Muzhingi
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA
| | - Xiaolong Li
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA; The First Affiliated School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui 230027, China
| | - Michael V Mandanas
- Koch Institute for Integrative Cancer Research at MIT, Cambridge, MA 02142, USA
| | - Clarety Kaseke
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA
| | - Charles R Crain
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA
| | - Angela Zhang
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA
| | - Funsho J Ogunshola
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA; Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA
| | | | - Alicja Piechocka-Trocha
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA; Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA
| | - Arman Bashirova
- Basic Science Program, Frederick National Laboratory for Cancer Research, National Cancer Institute, Frederick, MD 21702, USA; Laboratory of Integrative Cancer Immunology, Center for Cancer Research, National Cancer Institute, Bethesda, MD 20892, USA
| | - Michael E Birnbaum
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA; Koch Institute for Integrative Cancer Research at MIT, Cambridge, MA 02142, USA; Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Mary Carrington
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA; Basic Science Program, Frederick National Laboratory for Cancer Research, National Cancer Institute, Frederick, MD 21702, USA; Laboratory of Integrative Cancer Immunology, Center for Cancer Research, National Cancer Institute, Bethesda, MD 20892, USA
| | - Bruce D Walker
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA; Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA; Institute for Medical Engineering and Science and Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Gaurav D Gaiha
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA; Division of Gastroenterology, Massachusetts General Hospital, Boston, MA 02114, USA.
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2
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Fonseca JA, King AC, Chahroudi A. More than the Infinite Monkey Theorem: NHP Models in the Development of a Pediatric HIV Cure. Curr HIV/AIDS Rep 2024; 21:11-29. [PMID: 38227162 PMCID: PMC10859349 DOI: 10.1007/s11904-023-00686-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/29/2023] [Indexed: 01/17/2024]
Abstract
PURPOSE OF REVIEW An HIV cure that eliminates the viral reservoir or provides viral control without antiretroviral therapy (ART) is an urgent need in children as they face unique challenges, including lifelong ART adherence and the deleterious effects of chronic immune activation. This review highlights the importance of nonhuman primate (NHP) models in developing an HIV cure for children as these models recapitulate the viral pathogenesis and persistence. RECENT FINDINGS Several cure approaches have been explored in infant NHPs, although knowledge gaps remain. Broadly neutralizing antibodies (bNAbs) show promise for controlling viremia and delaying viral rebound after ART interruption but face administration challenges. Adeno-associated virus (AAV) vectors hold the potential for sustained bNAb expression. Therapeutic vaccination induces immune responses against simian retroviruses but has yet to impact the viral reservoir. Combining immunotherapies with latency reversal agents (LRAs) that enhance viral antigen expression should be explored. Current and future cure approaches will require adaptation for the pediatric immune system and unique features of virus persistence, for which NHP models are fundamental to assess their efficacy.
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Affiliation(s)
- Jairo A Fonseca
- Department of Pediatrics, Emory University School of Medicine, Atlanta, GA, USA
| | - Alexis C King
- Department of Pediatrics, Emory University School of Medicine, Atlanta, GA, USA
| | - Ann Chahroudi
- Department of Pediatrics, Emory University School of Medicine, Atlanta, GA, USA.
- Emory National Primate Research Center, Emory University, Atlanta, GA, USA.
- Emory+Children's Center for Childhood Infections and Vaccines, Atlanta, GA, USA.
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Dragoni F, Kwaa AK, Traut CC, Veenhuis RT, Woldemeskel BA, Camilo-Contreras A, Raymond HE, Dykema AG, Scully EP, Rosecrans AM, Smith KN, Bushman FD, Simonetti FR, Blankson JN. Proviral location affects cognate peptide-induced virus production and immune recognition of HIV-1-infected T cell clones. J Clin Invest 2023; 133:e171097. [PMID: 37698927 PMCID: PMC10617777 DOI: 10.1172/jci171097] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Accepted: 09/06/2023] [Indexed: 09/14/2023] Open
Abstract
BACKGROUNDHIV-1-infected CD4+ T cells contribute to latent reservoir persistence by proliferating while avoiding immune recognition. Integration features of intact proviruses in elite controllers (ECs) and people on long-term therapy suggest that proviruses in specific chromosomal locations can evade immune surveillance. However, direct evidence of this mechanism is missing.METHODSIn this case report, we characterized integration sites and full genome sequences of expanded T cell clones in an EC before and after chemoradiation. We identified the cognate peptide of infected clones to investigate cell proliferation and virus production induced by T cell activation, and susceptibility to autologous CD8+ T cells.RESULTSThe proviral landscape was dominated by 2 large clones with replication-competent proviruses integrated into zinc finger (ZNF) genes (ZNF470 and ZNF721) in locations previously associated with deeper latency. A third nearly intact provirus, with a stop codon in Pol, was integrated into an intergenic site. Upon stimulation with cognate Gag peptides, infected clones proliferated extensively and produced virus, but the provirus in ZNF721 was 200-fold less inducible. While autologous CD8+ T cells decreased the proliferation of cells carrying the intergenic provirus, they had no effect on cells with the provirus in the ZNF721 gene.CONCLUSIONSWe provide direct evidence that upon activation of infected clones by cognate antigen, the lower inducibility of intact proviruses in ZNF genes can result in immune evasion and persistence.FUNDINGOffice of the NIH Director and National Institute of Dental & Craniofacial Research; NIAID, NIH; Johns Hopkins University Center for AIDS Research.
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Affiliation(s)
| | | | | | - Rebecca T. Veenhuis
- Department of Molecular and Comparative Pathobiology, and
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | | | | | - Hayley E. Raymond
- Department of Microbiology, University of Pennsylvania, Perelman School of Medicine, Philadelphia, Pennsylvania, USA
| | - Arbor G. Dykema
- Bloomberg~Kimmel Institute for Cancer Immunotherapy, and
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | | | | | - Kellie N. Smith
- Bloomberg~Kimmel Institute for Cancer Immunotherapy, and
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Frederic D. Bushman
- Department of Microbiology, University of Pennsylvania, Perelman School of Medicine, Philadelphia, Pennsylvania, USA
| | | | - Joel N. Blankson
- Department of Medicine
- Department of Molecular and Comparative Pathobiology, and
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4
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Navarrete-Muñoz MA, Ramos R, Holguín Á, Cabello A, Górgolas M, Benito JM, Rallón N. High frequency of CD8 escape mutations in elite controllers as new obstacle for HIV cure. Virulence 2022; 13:1713-1719. [PMID: 36190143 PMCID: PMC9543107 DOI: 10.1080/21505594.2022.2129353] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/30/2022] Open
Abstract
Accumulation of mutations in epitopes of cytolytic-T-lymphocytes immune response (CTL) in HIV-reservoir seems to be one of the reasons for shock-and-kill strategy failure. Ten non-controller patients on successful cART (TX) and seven elite controllers (EC) were included. HIV-Gag gene from purified resting memory CD4+ T-cells was sequenced by Next-Generation-Sequencing. HLA class-I alleles were typed to predict optimal HIV-Gag CTL epitopes. For each subject, the frequency of mutated epitopes in the HIV-Gag gene, the proportion of them considered as CTL-escape variants as well as their effect on antigen recognition by HLA were assessed. The proportion (%) of mutated HIV-Gag CTL epitopes in the reservoir was high and similar in EC and TX (86%[50-100] and 57%[48-82] respectively, p=0.315). Many of them were predicted to negatively impact antigen recognition. Moreover, the proportion of mutated epitopes considered to be CTL-escape variants was also similar in TX and EC (77%[49-92] vs. 50%[33-75] respectively, p=0.117). Thus, the most relevant finding of our study was the high and similar proportions of HIV-Gag CTL-escape mutations in the reservoir of both HIV-noncontroller patients with cART (TX) and patients with spontaneous HIV-control (EC). Our findings suggest that escape mutations of CTL-response may be another obstacle to eliminate the HIV reservoir and constitute a proof of concept that challenges HIV cure strategies focused on the reactivation of reservoirs. Due to the small sample size that could impact the robustness of the study, further studies with larger cohorts of elite controller patients are needed to confirm these results.
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Affiliation(s)
- María A Navarrete-Muñoz
- HIV and Viral Hepatitis Research Laboratory, Instituto de Investigación Sanitaria Fundación Jiménez Díaz, Universidad Autónoma de Madrid (IIS-FJD, UAM), Madrid, Spain.,Hospital Universitario Rey Juan Carlos, Móstoles, Spain
| | - Ricardo Ramos
- Unidad de Genómica, Scientific Park of Madrid, Madrid, Spain
| | - África Holguín
- HIV-1 Molecular Epidemiology Laboratory, Instituto Ramón y Cajal de Investigación Sanitaria(IRYCIS), Madrid, Spain
| | - Alfonso Cabello
- Division of Infectious Diseases, Hospital Universitario Fundación Jiménez Díaz, Madrid, Spain
| | - Miguel Górgolas
- Division of Infectious Diseases, Hospital Universitario Fundación Jiménez Díaz, Madrid, Spain
| | - José M Benito
- HIV and Viral Hepatitis Research Laboratory, Instituto de Investigación Sanitaria Fundación Jiménez Díaz, Universidad Autónoma de Madrid (IIS-FJD, UAM), Madrid, Spain.,Hospital Universitario Rey Juan Carlos, Móstoles, Spain
| | - Norma Rallón
- HIV and Viral Hepatitis Research Laboratory, Instituto de Investigación Sanitaria Fundación Jiménez Díaz, Universidad Autónoma de Madrid (IIS-FJD, UAM), Madrid, Spain.,Hospital Universitario Rey Juan Carlos, Móstoles, Spain
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5
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Immunological Control of HIV-1 Disease Progression by Rare Protective HLA Allele. J Virol 2022; 96:e0124822. [DOI: 10.1128/jvi.01248-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
HLA-B57 is a relatively rare allele around world and the strongest protective HLA allele in Caucasians and African black individuals infected with HIV-1. Previous studies suggested that the advantage of this allele in HIV-1 disease progression is due to a strong functional ability of HLA-B57-restricted Gag-specific T cells and lower fitness of mutant viruses selected by the T cells.
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6
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Control of HIV-1 Replication by CD8 + T Cells Specific for Two Novel Pol Protective Epitopes in HIV-1 Subtype A/E Infection. J Virol 2022; 96:e0081122. [PMID: 36154612 PMCID: PMC9555181 DOI: 10.1128/jvi.00811-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Although many HIV-1-specific CD8+ T cell epitopes have been identified and used in various HIV-1 studies, most of these epitopes were derived from HIV-1 subtypes B and C. Only 17 well-defined epitopes, none of which were protective, have been identified for subtype A/E infection. The roles of HIV-1-specific T cells have been rarely analyzed for subtype A/E infection. In this study, we identified six novel HLA-B*15:02-restricted optimal HIV-1 subtype A/E epitopes and then analyzed the presentation of these epitopes by HIV-1 subtype A/E virus-infected cells and the T cell responses to these epitopes in treatment-naive HIV-1 subtype A/E-infected HLA-B*15:02+ Vietnamese individuals. Responders to the PolTY9 or PolLF10 epitope had a significantly lower plasma viral load (pVL) than nonresponders among HLA-B*15:02+ individuals, whereas no significant difference in pVL was found between responders to four other epitopes and nonresponders. The breadth of T cell responses to these two Pol epitopes correlated inversely with pVL. These findings suggest that HLA-B*15:02-restricted T cells specific for PolTY9 and PolLF10 contribute to the suppression of HIV-1 replication in HLA-B*15:02+ individuals. The HLA-B*15:02-associated mutation Pol266I reduced the recognition of PolTY9-specific T cells in vitro but did not affect HIV-1 replication by PolTY9-specific T cells in Pol266I mutant virus-infected individuals. These findings indicate that PolTY9-specific T cells suppress replication of the Pol266I mutant virus even though the T cells selected this mutant. This study demonstrates the effective role of T cells specific for these Pol epitopes to control circulating viruses in HIV-1 subtype A/E infection. IMPORTANCE It is expected that HIV-1-specific CD8+ T cells that effectively suppress HIV-1 replication will contribute to HIV-1 vaccine development and therapy to achieve an HIV cure. T cells specific for protective epitopes were identified in HIV-1 subtype B and C infections but not in subtype A/E infection, which is epidemic in Southeast Asia. In the present study, we identified six T cell epitopes derived from the subtype A/E virus and demonstrated that T cells specific for two Pol epitopes effectively suppressed HIV-1 replication in treatment-naive Vietnamese individuals infected with HIV-1 subtype A/E. One of these Pol protective epitopes was conserved among circulating viruses, and one escape mutation was accumulated in the other epitope. This mutation did not critically affect HIV-1 control by specific T cells in HIV-1 subtype A/E-infected individuals. This study identified two protective Pol epitopes and characterized them in cases of HIV-1 subtype A/E infection.
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7
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Abstract
PURPOSE OF REVIEW Immunological studies of spontaneous HIV and simian virus (SIV) controllers have identified virus-specific CD8 + T cells as a key immune mechanism of viral control. The purpose of this review is to consider how knowledge about the mechanisms that are associated with CD8 + T cell control of HIV/SIV in natural infection can be harnessed in HIV remission strategies. RECENT FINDINGS We discuss characteristics of CD8 + T-cell responses that may be critical for suppressing HIV replication in spontaneous controllers comprising HIV antigen recognition including specific human leukocyte antigen types, broadly cross-reactive T cell receptors and epitope targeting, enhanced expansion and antiviral functions, and localization of virus-specific T cells near sites of reservoir persistence. We also discuss the need to better understand the timing of CD8 + T-cell responses associated with viral control of HIV/SIV during acute infection and after treatment interruption as well as the mechanisms by which HIV/SIV-specific CD8 + T cells coordinate with other immune responses to achieve control. SUMMARY We propose implications as to how this knowledge from natural infection can be applied in the design and evaluation of CD8 + T-cell-based remission strategies and offer questions to consider as these strategies target distinct CD8 + T-cell-dependent mechanisms of viral control.
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8
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Lian X, Gao C, Sun X, Jiang C, Einkauf KB, Seiger KW, Chevalier JM, Yuki Y, Martin M, Hoh R, Peluso MJ, Carrington M, Ruiz-Mateos E, Deeks SG, Rosenberg ES, Walker BD, Lichterfeld M, Yu XG. Signatures of immune selection in intact and defective proviruses distinguish HIV-1 elite controllers. Sci Transl Med 2021; 13:eabl4097. [PMID: 34910552 PMCID: PMC9202005 DOI: 10.1126/scitranslmed.abl4097] [Citation(s) in RCA: 50] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Increasing evidence suggests that durable drug-free control of HIV-1 replication is enabled by effective cellular immune responses that may induce an attenuated viral reservoir configuration with a weaker ability to drive viral rebound. Here, we comprehensively tracked effects of antiviral immune responses on intact and defective proviral sequences from elite controllers (ECs), analyzing both classical escape mutations and HIV-1 chromosomal integration sites as biomarkers of antiviral immune selection pressure. We observed that, within ECs, defective proviruses were commonly located in permissive genic euchromatin positions, which represented an apparent contrast to autologous intact proviruses that were frequently located in heterochromatin regions; this suggests differential immune selection pressure on intact versus defective proviruses in ECs. In comparison to individuals receiving antiretroviral therapy, intact and defective proviruses from ECs showed reduced frequencies of escape mutations in cytotoxic T cell epitopes and antibody contact regions, possibly due to the small and poorly inducible reservoir that may be insufficient to drive effective viral escape in ECs. About 15% of ECs harbored nef deletions in intact proviruses, consistent with increased viral vulnerability to host immunity in the setting of nef dysfunction. Together, these results suggest a distinct signature of immune footprints in proviral sequences from ECs.
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Affiliation(s)
- Xiaodong Lian
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA
- Infectious Disease Division, Brigham and Women’s Hospital, Boston, MA 02115, USA
| | - Ce Gao
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA
- Infectious Disease Division, Brigham and Women’s Hospital, Boston, MA 02115, USA
| | - Xiaoming Sun
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA
| | - Chenyang Jiang
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA
- Infectious Disease Division, Brigham and Women’s Hospital, Boston, MA 02115, USA
| | - Kevin B. Einkauf
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA
- Infectious Disease Division, Brigham and Women’s Hospital, Boston, MA 02115, USA
| | - Kyra W. Seiger
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA
- Infectious Disease Division, Brigham and Women’s Hospital, Boston, MA 02115, USA
| | - Joshua M. Chevalier
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA
- Infectious Disease Division, Brigham and Women’s Hospital, Boston, MA 02115, USA
| | - Yuko Yuki
- Basic Science Program, Frederick National Laboratory for Cancer Research, National Cancer Institute, Frederick, MD and Laboratory of Integrative Cancer Immunology, Center for Cancer Research, National Cancer Institute, Bethesda, MD 20892, USA
| | - Maureen Martin
- Basic Science Program, Frederick National Laboratory for Cancer Research, National Cancer Institute, Frederick, MD and Laboratory of Integrative Cancer Immunology, Center for Cancer Research, National Cancer Institute, Bethesda, MD 20892, USA
| | - Rebecca Hoh
- University of California at San Francisco, San Francisco, CA 94143, USA
| | - Michael J. Peluso
- University of California at San Francisco, San Francisco, CA 94143, USA
| | - Mary Carrington
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA
- Basic Science Program, Frederick National Laboratory for Cancer Research, National Cancer Institute, Frederick, MD and Laboratory of Integrative Cancer Immunology, Center for Cancer Research, National Cancer Institute, Bethesda, MD 20892, USA
| | - Ezequiel Ruiz-Mateos
- Clinical Unit of Infectious Diseases, Microbiology and Preventive Medicine, Institute of Biomedicine of Seville (IBiS), Virgen del Rocío University Hospital, CSIC, University of Seville, Seville 41013, Spain
| | - Steven G. Deeks
- University of California at San Francisco, San Francisco, CA 94143, USA
| | - Eric S. Rosenberg
- Infectious Disease Division, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Bruce D. Walker
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA
- Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA
- Institute for Medical Engineering and Sciences and Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Mathias Lichterfeld
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA
- Infectious Disease Division, Brigham and Women’s Hospital, Boston, MA 02115, USA
| | - Xu G. Yu
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA
- Infectious Disease Division, Brigham and Women’s Hospital, Boston, MA 02115, USA
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9
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Collins DR, Urbach JM, Racenet ZJ, Arshad U, Power KA, Newman RM, Mylvaganam GH, Ly NL, Lian X, Rull A, Rassadkina Y, Yanez AG, Peluso MJ, Deeks SG, Vidal F, Lichterfeld M, Yu XG, Gaiha GD, Allen TM, Walker BD. Functional impairment of HIV-specific CD8 + T cells precedes aborted spontaneous control of viremia. Immunity 2021; 54:2372-2384.e7. [PMID: 34496223 PMCID: PMC8516715 DOI: 10.1016/j.immuni.2021.08.007] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2021] [Revised: 06/21/2021] [Accepted: 08/09/2021] [Indexed: 12/14/2022]
Abstract
Spontaneous control of HIV infection has been repeatedly linked to antiviral CD8+ T cells but is not always permanent. To address mechanisms of durable and aborted control of viremia, we evaluated immunologic and virologic parameters longitudinally among 34 HIV-infected subjects with differential outcomes. Despite sustained recognition of autologous virus, HIV-specific proliferative and cytolytic T cell effector functions became selectively and intrinsically impaired prior to aborted control. Longitudinal transcriptomic profiling of functionally impaired HIV-specific CD8+ T cells revealed altered expression of genes related to activation, cytokine-mediated signaling, and cell cycle regulation, including increased expression of the antiproliferative transcription factor KLF2 but not of genes associated with canonical exhaustion. Lymphoid HIV-specific CD8+ T cells also exhibited poor functionality during aborted control relative to durable control. Our results identify selective functional impairment of HIV-specific CD8+ T cells as prognostic of impending aborted HIV control, with implications for clinical monitoring and immunotherapeutic strategies.
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Affiliation(s)
- David R Collins
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, USA; Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | | | | | - Umar Arshad
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, USA
| | - Karen A Power
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, USA
| | - Ruchi M Newman
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, USA
| | - Geetha H Mylvaganam
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, USA; Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | - Ngoc L Ly
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, USA
| | - Xiaodong Lian
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, USA; Division of Infectious Diseases, Brigham and Women's Hospital, Boston, MA, USA
| | - Anna Rull
- Joan XXIII University Hospital, Pere Virgili Institute (IISPV), Rovira i Virgili University, Tarragona, Spain
| | - Yelizaveta Rassadkina
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, USA; Division of Infectious Diseases, Brigham and Women's Hospital, Boston, MA, USA
| | - Adrienne G Yanez
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, USA; Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | - Michael J Peluso
- Division of HIV, Infectious Diseases and Global Medicine, University of California, San Francisco, CA, USA
| | - Steven G Deeks
- Division of HIV, Infectious Diseases and Global Medicine, University of California, San Francisco, CA, USA
| | - Francesc Vidal
- Joan XXIII University Hospital, Pere Virgili Institute (IISPV), Rovira i Virgili University, Tarragona, Spain
| | - Mathias Lichterfeld
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, USA; Division of Infectious Diseases, Brigham and Women's Hospital, Boston, MA, USA
| | - Xu G Yu
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, USA; Division of Infectious Diseases, Brigham and Women's Hospital, Boston, MA, USA
| | - Gaurav D Gaiha
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, USA; Division of Gastroenterology, Massachusetts General Hospital, Boston, MA, USA
| | - Todd M Allen
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, USA
| | - Bruce D Walker
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, USA; Howard Hughes Medical Institute, Chevy Chase, MD, USA; Institute for Medical Engineering and Sciences and Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA.
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10
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Lunardi LW, Bragatte MADS, Vieira GF. The influence of HLA/HIV genetics on the occurrence of elite controllers and a need for therapeutics geotargeting view. Braz J Infect Dis 2021; 25:101619. [PMID: 34562387 PMCID: PMC9392165 DOI: 10.1016/j.bjid.2021.101619] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Revised: 08/09/2021] [Accepted: 08/13/2021] [Indexed: 11/02/2022] Open
Abstract
The interaction of HIV-1, human leukocyte antigen (HLA), and elite controllers (EC) compose a still intricate triad. Elite controllers maintain a very low viral load and a normal CD4 count, even without antiretrovirals. There is a lot of diversity in HIV subtypes and HLA alleles. The most common subtype in each country varies depending on its localization and epidemiological history. As we know EC appears to maintain an effective CD8 response against HIV. In this phenomenon, some alleles of HLAs are associated with a slow progression of HIV infection, others with a rapid progression. This relationship also depends on the virus subtype. Epitopes of Gag protein-restricted by HLA-B*57 generated a considerable immune response in EC. However, some mutations allow HIV to escape the CD8 response, while others do not. HLA protective alleles, like HLA-B*27, HLA-B*57 and HLA-B*58:01, that are common in Caucasians infected with HIV-1 Clade B, do not show the same protection in sub-Saharan Africans infected by HIV-1 Clade C. Endogenous pathway of antigen processing and presentation is used to present intracellular synthesized cellular peptides as well as viral protein fragments via the MHC class I molecule to the cytotoxic T-lymphocytes (CTLs). Some epitopes are immunodominant, which means that they drive the immune reaction to some virus. Mutation on an anchor residue of epitope necessary for binding on MHC class I is used by HIV to escape the immune system. Mutations inside or flanking an epitope may lead to T cell lack of recognition and CTL escape. Studying how immunodominance at epitopes drives the EC in a geographically dependent way with genetics and immunological elements orchestrating it may help future research on vaccines or immunotherapy for HIV.
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Affiliation(s)
- Luciano Werle Lunardi
- Universidade Federal do Rio Grande do Sul, Programa de Pós-Graduação em Genética e Biologia Molecular, Porto Alegre, RS, Brazil
| | - Marcelo Alves de Souza Bragatte
- Universidade Federal do Rio Grande do Sul, Programa de Pós-Graduação em Genética e Biologia Molecular, Porto Alegre, RS, Brazil
| | - Gustavo Fioravanti Vieira
- Universidade Federal do Rio Grande do Sul, Programa de Pós-Graduação em Genética e Biologia Molecular, Porto Alegre, RS, Brazil; Universidade La Salle Canoas, Programa de Pós-Graduação em Saúde e Desenvolvimento Humano, Canoas, RS, Brazil.
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11
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Bansal A, Gehre MN, Qin K, Sterrett S, Ali A, Dang Y, Abraham S, Costanzo MC, Venegas LA, Tang J, Manjunath N, Brockman MA, Yang OO, Kan-Mitchell J, Goepfert PA. HLA-E-restricted HIV-1-specific CD8+ T cell responses in natural infection. J Clin Invest 2021; 131:148979. [PMID: 34228645 PMCID: PMC8363272 DOI: 10.1172/jci148979] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Accepted: 07/01/2021] [Indexed: 01/07/2023] Open
Abstract
CD8+ T cell responses restricted by MHC-E, a nonclassical MHC molecule, have been associated with protection in an SIV/rhesus macaque model. The biological relevance of HLA-E-restricted CD8+ T cell responses in HIV infection, however, remains unknown. In this study, CD8+ T cells responding to HIV-1 Gag peptides presented by HLA-E were analyzed. Using in vitro assays, we observed HLA-E-restricted T cell responses to what we believe to be a newly identified subdominant Gag-KL9 as well as a well-described immunodominant Gag-KF11 epitope in T cell lines derived from chronically HIV-infected patients and also primed from healthy donors. Blocking of the HLA-E/KF11 binding by the B7 signal peptide resulted in decreased CD8+ T cell responses. KF11 presented via HLA-E in HIV-infected cells was recognized by antigen-specific CD8+ T cells. Importantly, bulk CD8+ T cells obtained from HIV-infected individuals recognized infected cells via HLA-E presentation. Ex vivo analyses at the epitope level showed a higher responder frequency of HLA-E-restricted responses to KF11 compared with KL9. Taken together, our findings of HLA-E-restricted HIV-specific immune responses offer intriguing and possibly paradigm-shifting insights into factors that contribute to the immunodominance of CD8+ T cell responses in HIV infection.
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Affiliation(s)
- Anju Bansal
- Department of Medicine, University of Alabama at Birmingham School of Medicine, Birmingham, Alabama, USA
| | - Mika N. Gehre
- Department of Biological Sciences, University of Texas at El Paso, El Paso, Texas, USA
| | - Kai Qin
- Department of Medicine, University of Alabama at Birmingham School of Medicine, Birmingham, Alabama, USA
| | - Sarah Sterrett
- Department of Medicine, University of Alabama at Birmingham School of Medicine, Birmingham, Alabama, USA
| | - Ayub Ali
- Department of Medicine and AIDS Institute, UCLA, Los Angeles, California, USA
| | - Ying Dang
- Department of Biomedical Sciences, Texas Tech University Health Sciences Center, Paul L. Foster School of Medicine, El Paso, Texas, USA
| | - Sojan Abraham
- Department of Biomedical Sciences, Texas Tech University Health Sciences Center, Paul L. Foster School of Medicine, El Paso, Texas, USA
| | - Margaret C. Costanzo
- Department of Biological Sciences, University of Texas at El Paso, El Paso, Texas, USA
| | - Leon A. Venegas
- Department of Biological Sciences, University of Texas at El Paso, El Paso, Texas, USA
| | - Jianming Tang
- Department of Medicine, University of Alabama at Birmingham School of Medicine, Birmingham, Alabama, USA
| | - N. Manjunath
- Department of Biomedical Sciences, Texas Tech University Health Sciences Center, Paul L. Foster School of Medicine, El Paso, Texas, USA
| | | | - Otto O. Yang
- Department of Medicine and AIDS Institute, UCLA, Los Angeles, California, USA
| | - June Kan-Mitchell
- Department of Biological Sciences, University of Texas at El Paso, El Paso, Texas, USA
| | - Paul A. Goepfert
- Department of Medicine, University of Alabama at Birmingham School of Medicine, Birmingham, Alabama, USA
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12
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Role of Escape Mutant-Specific T Cells in Suppression of HIV-1 Replication and Coevolution with HIV-1. J Virol 2020; 94:JVI.01151-20. [PMID: 32699092 PMCID: PMC7495385 DOI: 10.1128/jvi.01151-20] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2020] [Accepted: 07/18/2020] [Indexed: 12/20/2022] Open
Abstract
Escape mutant-specific CD8+ T cells were elicited in some individuals infected with escape mutants, but it is still unknown whether these CD8+ T cells can suppress HIV-1 replication. We clarified that Gag280V mutation were selected by HLA-B*52:01-restricted CD8+ T cells specific for the GagRI8 protective epitope, whereas the Gag280V virus could frequently elicit GagRI8-6V mutant-specific CD8+ T cells. GagRI8-6V mutant-specific T cells had a strong ability to suppress the replication of the Gag280V mutant virus both in vitro and in vivo. In addition, these T cells contributed to the selection of wild-type virus in HLA-B*52:01+ Japanese individuals. We for the first time demonstrated that escape mutant-specific CD8+ T cells can suppress HIV-1 replication and play an important role in the coevolution with HIV-1. Thus, the present study highlighted an important role of escape mutant-specific T cells in the control of HIV-1 and coevolution with HIV-1. The accumulation of HIV-1 escape mutations affects HIV-1 control by HIV-1-specific T cells. Some of these mutations can elicit escape mutant-specific T cells, but it still remains unclear whether they can suppress the replication of HIV-1 mutants. It is known that HLA-B*52:01-restricted RI8 (Gag 275 to 282; RMYSPTSI) is a protective T cell epitope in HIV-1 subtype B-infected Japanese individuals, though 3 Gag280A/S/V mutations are found in 26% of them. Gag280S and Gag280A were HLA-B*52:01-associated mutations, whereas Gag280V was not, implying a different mechanism for the accumulation of Gag280 mutations. In this study, we investigated the coevolution of HIV-1 with RI8-specific T cells and suppression of HIV-1 replication by its escape mutant-specific T cells both in vitro and in vivo. HLA-B*52:01+ individuals infected with Gag280A/S mutant viruses failed to elicit these mutant epitope-specific T cells, whereas those with the Gag280V mutant one effectively elicited RI8-6V mutant-specific T cells. These RI8-6V-specific T cells suppressed the replication of Gag280V virus and selected wild-type virus, suggesting a mechanism affording no accumulation of the Gag280V mutation in the HLA-B*52:01+ individuals. The responders to wild-type (RI8-6T) and RI8-6V mutant peptides had significantly higher CD4 counts than nonresponders, indicating that the existence of not only RI8-6T-specific T cells but also RI8-6V-specific ones was associated with a good clinical outcome. The present study clarified the role of escape mutant-specific T cells in HIV-1 evolution and in the control of HIV-1. IMPORTANCE Escape mutant-specific CD8+ T cells were elicited in some individuals infected with escape mutants, but it is still unknown whether these CD8+ T cells can suppress HIV-1 replication. We clarified that Gag280V mutation were selected by HLA-B*52:01-restricted CD8+ T cells specific for the GagRI8 protective epitope, whereas the Gag280V virus could frequently elicit GagRI8-6V mutant-specific CD8+ T cells. GagRI8-6V mutant-specific T cells had a strong ability to suppress the replication of the Gag280V mutant virus both in vitro and in vivo. In addition, these T cells contributed to the selection of wild-type virus in HLA-B*52:01+ Japanese individuals. We for the first time demonstrated that escape mutant-specific CD8+ T cells can suppress HIV-1 replication and play an important role in the coevolution with HIV-1. Thus, the present study highlighted an important role of escape mutant-specific T cells in the control of HIV-1 and coevolution with HIV-1.
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13
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Chan HY, Zhang J, Garliss CC, Kwaa AK, Blankson JN, Smith KN. A T Cell Receptor Sequencing-Based Assay Identifies Cross-Reactive Recall CD8 + T Cell Clonotypes Against Autologous HIV-1 Epitope Variants. Front Immunol 2020; 11:591. [PMID: 32318072 PMCID: PMC7154155 DOI: 10.3389/fimmu.2020.00591] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2020] [Accepted: 03/13/2020] [Indexed: 12/31/2022] Open
Abstract
HIV-1 positive elite controllers or suppressors control viral replication without antiretroviral therapy, likely via CTL-mediated elimination of infected cells, and therefore represent a model of an HIV-1 functional cure. Efforts to cure HIV-1 accordingly rely on the existence or generation of antigen-specific cytotoxic T lymphocytes (CTL) to eradicate infected cells upon reversal of latency. Detecting and quantifying these HIV-1-specific CTL responses will be crucial for developing vaccine and T cell-based immunotherapies. A recently developed assay, called MANAFEST, uses T cell receptor (TCR) Vβ sequencing of peptide-stimulated cultures followed by a bioinformatic pipeline to identify neoantigen-specific T cells in cancer patients. This assay is more sensitive than conventional immune assays and therefore has the possibility to identify HIV-1 antigenic targets that have not been previously explored for vaccine or T cell immunotherapeutic strategies. Here we show that a modified version of the MANAFEST assay, called ViraFEST, can identify memory CD8+ T cell responses against autologous HIV-1 Gag and Nef epitope variants in an elite suppressor. Nine TCR Vβ clonotypes were identified and 6 of these were cross-reactive for autologous variants or known escape variants. Our findings are a proof of principle that the ViraFEST assay can be used to detect and monitor these responses for downstream use in immunotherapeutic treatment approaches.
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Affiliation(s)
- Hok Yee Chan
- Bloomberg-Kimmel Institute for Cancer Immunotherapy, Johns Hopkins School of Medicine, Baltimore, MD, United States.,Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins School of Medicine, Baltimore, MD, United States
| | - Jiajia Zhang
- Bloomberg-Kimmel Institute for Cancer Immunotherapy, Johns Hopkins School of Medicine, Baltimore, MD, United States.,Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins School of Medicine, Baltimore, MD, United States
| | - Caroline C Garliss
- Department of Medicine, Johns Hopkins School of Medicine, Baltimore, MD, United States
| | - Abena K Kwaa
- Department of Medicine, Johns Hopkins School of Medicine, Baltimore, MD, United States
| | - Joel N Blankson
- Department of Medicine, Johns Hopkins School of Medicine, Baltimore, MD, United States.,Department of Molecular and Comparative Pathobiology, Johns Hopkins School of Medicine, Baltimore, MD, United States
| | - Kellie N Smith
- Bloomberg-Kimmel Institute for Cancer Immunotherapy, Johns Hopkins School of Medicine, Baltimore, MD, United States.,Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins School of Medicine, Baltimore, MD, United States
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14
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May ME, Pohlmeyer CW, Kwaa AK, Mankowski MC, Bailey JR, Blankson JN. Combined Effects of HLA-B*57/5801 Elite Suppressor CD8+ T Cells and NK Cells on HIV-1 Replication. Front Cell Infect Microbiol 2020; 10:113. [PMID: 32266164 PMCID: PMC7098910 DOI: 10.3389/fcimb.2020.00113] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2019] [Accepted: 03/02/2020] [Indexed: 11/22/2022] Open
Abstract
Elite controllers or suppressors (ES) are HIV-1 infected individuals who maintain undetectable viral loads without anti-retroviral therapy. The HLA-B*57 allele is overrepresented in ES suggesting a role for HIV-specific CD8+ T cells in immune control. Natural killer (NK) cells also play a role in controlling viral replication, and genetic studies demonstrate that specific combinations of killer cell immunoglobulin-like receptor (KIR) alleles and HLA subtypes including HLA-B*57 correlate with delayed progression to AIDS. While prior studies have shown that both HIV-specific CD8+ T cells and NK cells can inhibit viral replication in vitro, the interaction between these two effector cells has not been studied. We performed in vitro suppression assays using CD8+ T cells and NK cells from HLA-B*57 ES either alone or in combination with each other. We found no evidence of antagonism or synergy between the CD8+ T cells and NK cells, suggesting that they have independent mechanisms of inhibition in vitro. Our data has implications for combined immunotherapy with CD8+ T cells and NK cells in HIV cure strategies.
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Affiliation(s)
- Megan E May
- Department of Medicine, Johns Hopkins Medicine, Baltimore, MD, United States
| | | | - Abena K Kwaa
- Department of Medicine, Johns Hopkins Medicine, Baltimore, MD, United States
| | | | - Justin R Bailey
- Department of Medicine, Johns Hopkins Medicine, Baltimore, MD, United States
| | - Joel N Blankson
- Department of Medicine, Johns Hopkins Medicine, Baltimore, MD, United States
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15
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Kovacs AAZ, Kono N, Wang CH, Wang D, Frederick T, Operskalski E, Tien PC, French AL, Minkoff H, Kassaye S, T. Golub E, Aouizerat BE, Kuniholm MH, Millstein J. Association of HLA Genotype With T-Cell Activation in Human Immunodeficiency Virus (HIV) and HIV/Hepatitis C Virus-Coinfected Women. J Infect Dis 2020; 221:1156-1166. [PMID: 31802115 PMCID: PMC7325713 DOI: 10.1093/infdis/jiz589] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2019] [Accepted: 11/06/2019] [Indexed: 01/15/2023] Open
Abstract
BACKGROUND Global immune activation and HLA alleles are each associated with the pathogenesis of human immunodeficiency virus (HIV) and hepatitis C virus . METHODS We evaluated the relationship between 44 HLA class I and 28 class II alleles and percentages of activated CD8 (CD8+CD38+DR+) and CD4 (CD4+CD38+DR+) T cells in 586 women who were naive to highly active antiretroviral therapy. We used linear generalized estimating equation regression models, adjusting for race/ethnicity, age, HIV load, and hepatitis C virus infection and controlling for multiplicity using a false discovery rate threshold of 0.10. RESULTS Ten HLA alleles were associated with CD8 and/or CD4 T-cell activation. Lower percentages of activated CD8 and/or CD4 T cells were associated with protective alleles B*57:03 (CD8 T cells, -6.6% [P = .002]; CD4 T cells, -2.7% [P = .007]), C*18:01 (CD8 T cells, -6.6%; P < .0008) and DRB1*13:01 (CD4 T cells, -2.7%; P < .0004), and higher percentages were found with B*18:01 (CD8 T cells, 6.2%; P < .0003), a detrimental allele. Other alleles/allele groups associated with activation included C*12:03, group DQA1*01:00, DQB1*03:01, DQB1*03:02, DQB1*06:02, and DQB1*06:03. CONCLUSION These findings suggest that a person's HLA type may play a role in modulating T-cell activation independent of viral load and sheds light on the relationship between HLA, T-cell activation, immune control, and HIV pathogenesis.
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Affiliation(s)
- Andrea A Z Kovacs
- Department of Pediatrics, Maternal, Child and Adolescent Center for Infectious Diseases and Virology, Keck School of Medicine, University of Southern California, Los Angeles, California
| | - Naoko Kono
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, California
| | - Chia-Hao Wang
- Department of Pediatrics, Maternal, Child and Adolescent Center for Infectious Diseases and Virology, Keck School of Medicine, University of Southern California, Los Angeles, California
- City of Hope National Medical Center, Duarte, California
| | - Daidong Wang
- Department of Pediatrics, Maternal, Child and Adolescent Center for Infectious Diseases and Virology, Keck School of Medicine, University of Southern California, Los Angeles, California
| | - Toni Frederick
- Department of Pediatrics, Maternal, Child and Adolescent Center for Infectious Diseases and Virology, Keck School of Medicine, University of Southern California, Los Angeles, California
| | - Eva Operskalski
- Department of Pediatrics, Maternal, Child and Adolescent Center for Infectious Diseases and Virology, Keck School of Medicine, University of Southern California, Los Angeles, California
| | - Phyllis C Tien
- Department of Medicine, University of California, San Francisco and Department of Veterans Affairs, San Francisco, California
| | - Audrey L French
- Department of Medicine, Stroger Hospital of Cook County/CORE Center, Rush Medical School, Chicago, Illinois
| | - Howard Minkoff
- Departments of Obstetrics and Gynecology Maimonides Medical Center and SUNY Downstate, Brooklyn, New York
| | - Seble Kassaye
- Department of Medicine, Georgetown University School of Medicine, Washington, DC
| | - Elizabeth T. Golub
- Johns Hopkins Bloomberg School of Public Health, Department of Epidemiology, Baltimore, Maryland
| | - Bradley E Aouizerat
- Bluestone Center for Clinical Research, New York University, New York, New York
- Department of Oral and Maxillofacial Surgery, New York University, New York, New York
| | - Mark H Kuniholm
- Department of Epidemiology and Biostatistics, University at Albany, State University of New York, Rensselaer, New York
| | - Joshua Millstein
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, California
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16
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Arora J, Pierini F, McLaren PJ, Carrington M, Fellay J, Lenz TL. HLA Heterozygote Advantage against HIV-1 Is Driven by Quantitative and Qualitative Differences in HLA Allele-Specific Peptide Presentation. Mol Biol Evol 2020; 37:639-650. [PMID: 31651980 PMCID: PMC7038656 DOI: 10.1093/molbev/msz249] [Citation(s) in RCA: 45] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Pathogen-mediated balancing selection is regarded as a key driver of host immunogenetic diversity. A hallmark for balancing selection in humans is the heterozygote advantage at genes of the human leukocyte antigen (HLA), resulting in improved HIV-1 control. However, the actual mechanism of the observed heterozygote advantage is still elusive. HLA heterozygotes may present a broader array of antigenic viral peptides to immune cells, possibly resulting in a more efficient cytotoxic T-cell response. Alternatively, heterozygosity may simply increase the chance to carry the most protective HLA alleles, as individual HLA alleles are known to differ substantially in their association with HIV-1 control. Here, we used data from 6,311 HIV-1-infected individuals to explore the relative contribution of quantitative and qualitative aspects of peptide presentation in HLA heterozygote advantage against HIV. Screening the entire HIV-1 proteome, we observed that heterozygous individuals exhibited a broader array of HIV-1 peptides presented by their HLA class I alleles. In addition, viral load was negatively correlated with the breadth of the HIV-1 peptide repertoire bound by an individual's HLA variants, particularly at HLA-B. This suggests that heterozygote advantage at HLA-B is at least in part mediated by quantitative peptide presentation. We also observed higher HIV-1 sequence diversity among HLA-B heterozygous individuals, suggesting stronger evolutionary pressure from HLA heterozygosity. However, HLA heterozygotes were also more likely to carry certain HLA alleles, including the highly protective HLA-B*57:01 variant, indicating that HLA heterozygote advantage ultimately results from a combination of quantitative and qualitative effects in antigen presentation.
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Affiliation(s)
- Jatin Arora
- Research Group for Evolutionary Immunogenomics, Max Planck Institute for Evolutionary Biology, Plön, Germany
| | - Federica Pierini
- Research Group for Evolutionary Immunogenomics, Max Planck Institute for Evolutionary Biology, Plön, Germany
| | - Paul J McLaren
- JC Wilt Infectious Diseases Research Center, National HIV and Retrovirology Laboratory, Public Health Agency of Canada, Winnipeg, MB, Canada
- Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Winnipeg, MB, Canada
| | - Mary Carrington
- Basic Science Program, Frederick National Laboratory for Cancer Research, Frederick, MD
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology and Harvard University, Cambridge, MA
| | - Jacques Fellay
- Global Health Institute, School of Life Sciences, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
- Precision Medicine Unit, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland
| | - Tobias L Lenz
- Research Group for Evolutionary Immunogenomics, Max Planck Institute for Evolutionary Biology, Plön, Germany
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17
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Abstract
HIV infection can be effectively treated by lifelong administration of combination antiretroviral therapy, but an effective vaccine will likely be required to end the HIV epidemic. Although the majority of current vaccine strategies focus on the induction of neutralizing antibodies, there is substantial evidence that cellular immunity mediated by CD8+ T cells can sustain long-term disease-free and transmission-free HIV control and may be harnessed to induce both therapeutic and preventive antiviral effects. In this Review, we discuss the increasing evidence derived from individuals who spontaneously control infection without antiretroviral therapy as well as preclinical immunization studies that provide a clear rationale for renewed efforts to develop a CD8+ T cell-based HIV vaccine in conjunction with B cell vaccine efforts. Further, we outline the remaining challenges in translating these findings into viable HIV prevention, treatment and cure strategies. Recently, antibody-mediated control of HIV infection has received considerable attention. Here, the authors discuss the importance of CD8+ T cells in HIV infection and suggest that efforts to develop vaccines that target these cells in conjunction with B cells should be renewed.
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18
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Broad Recognition of Circulating HIV-1 by HIV-1-Specific Cytotoxic T-Lymphocytes with Strong Ability to Suppress HIV-1 Replication. J Virol 2018; 93:JVI.01480-18. [PMID: 30333175 DOI: 10.1128/jvi.01480-18] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2018] [Accepted: 10/10/2018] [Indexed: 11/20/2022] Open
Abstract
HIV-1-specific cytotoxic T-lymphocytes (CTLs) with strong abilities to suppress HIV-1 replication and recognize most circulating HIV-1 strains are candidates for effector T cells for cure treatment and prophylactic AIDS vaccine. Previous studies demonstrated that the existence of CTLs specific for 11 epitopes was significantly associated with good clinical outcomes in Japan, although CTLs specific for one of these epitopes select for escape mutations. However, it remains unknown whether the CTLs specific for the remaining 10 epitopes suppress HIV-1 replication in vitro and recognize circulating HIV-1. Here, we investigated the abilities of these CTLs to suppress HIV-1 replication and to recognize variants in circulating HIV-1. CTL clones specific for 10 epitopes had strong abilities to suppress HIV-1 replication in vitro The ex vivo and in vitro analyses of T-cell responses to variant epitope peptides showed that the T cells specific for 10 epitopes recognized mutant peptides which are detected in 84.1% to 98.8% of the circulating HIV-1 strains found in HIV-1-infected Japanese individuals. In addition, the T cells specific for 5 epitopes well recognized target cells infected with 7 mutant viruses that had been detected in >5% of tested individuals. Taken together, these results suggest that CTLs specific for the 10 epitopes effectively suppress HIV-1 replication and broadly recognize the circulating HIV-1 strains in the HIV-1-infected individuals. This study suggests the use of these T cells in clinical trials.IMPORTANCE In recent T-cell AIDS vaccine trials, the vaccines did not prevent HIV-1 infection, although HIV-1-specific T cells were induced in the vaccinated individuals, suggesting that the T cells have a weak ability to suppress HIV-1 replication and fail to recognize circulating HIV-1. We previously demonstrated that the T-cell responses to 10 epitopes were significantly associated with good clinical outcome. However, there is no direct evidence that these T cells have strong abilities to suppress HIV-1 replication and recognize circulating HIV-1. Here, we demonstrated that the T cells specific for the 10 epitopes had strong abilities to suppress HIV-1 replication in vitro Moreover, the T cells cross-recognized most of the circulating HIV-1 in HIV-1-infected individuals. This study suggests the use of T cells specific for these 10 epitopes in clinical trials of T-cell vaccines as a cure treatment.
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19
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Abstract
In this brief review and perspective, we address the question of whether the immune responses that bring about immune control of acute HIV infection are the same as, or distinct from, those that maintain long-term viral suppression once control of viremia has been achieved. To this end, we describe the natural history of elite and post-treatment control, noting the lack of data regarding what happens acutely. We review the evidence suggesting that the two clinical phenotypes may differ in terms of the mechanisms required to achieve and maintain control, as well as the level of inflammation that persists once a steady state is achieved. We then describe the evidence from longitudinal studies of controllers who fail and studies of biologic sex (male versus female), age (children versus adults), and simian immunodeficiency virus (SIV) (pathogenic/experimental versus nonpathogenic/natural infection). Collectively, these studies demonstrate that the battle between the inflammatory and anti-inflammatory pathways during acute infection has long-term consequences, both for the degree to which control is maintained and the health of the individual. Potent and stringent control of HIV may be required acutely, but once control is established, the chronic inflammatory response can be detrimental. Interventional approaches designed to bring about HIV cure and/or remission should be nuanced accordingly.
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Affiliation(s)
- Philip Goulder
- Department of Paediatrics, University of Oxford, Oxford, United Kingdom
- HIV Pathogenesis Programme, Doris Duke Medical Research Institute, University of KwaZulu-Natal, Durban, South Africa
- * E-mail:
| | - Steven G. Deeks
- Department of Medicine, University of California, San Francisco, California, United States of America
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20
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Caetano DG, Côrtes FH, Bello G, Teixeira SLM, Hoagland B, Grinsztejn B, Veloso VG, Guimarães ML, Morgado MG. Next-generation sequencing analyses of the emergence and maintenance of mutations in CTL epitopes in HIV controllers with differential viremia control. Retrovirology 2018; 15:62. [PMID: 30201008 PMCID: PMC6131818 DOI: 10.1186/s12977-018-0444-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2018] [Accepted: 09/05/2018] [Indexed: 01/10/2023] Open
Abstract
Background Despite the low level of viral replication in HIV controllers (HICs), studies have reported viral mutations related to escape from cytotoxic T-lymphocyte (CTL) response in HIV-1 plasma sequences. Thus, evaluating the dynamics of the emergence of CTL-escape mutants in HICs reservoirs is important for understanding viremia control. To analyze the HIV-1 mutational profile and dynamics of CTL-escape mutants in HICs, we selected 11 long-term non-progressor individuals and divided them into the following groups: (1) viremic controllers (VCs; n = 5) and (2) elite controllers (ECs; n = 6). For each individual, we used HIV-1 proviral DNA from PBMCs related to earliest (VE) and latest (VL) visits to obtain gag and nef sequences using the Illumina HiSeq system. The consensus of each mapped gene was used to assess viral divergence, and next-generation sequencing data were employed to identify SNPs and variations within and flanking CTL epitopes. Results Divergence analysis showed higher values for nef compared to gag among the HICs. EC and VC groups showed similar divergence rates for both genes. Analysis of the number of SNPs showed that VCs present more variability in both genes. Synonymous/non-synonymous mutation ratios were < 1 for gag among ECs and for nef among ECs and VCs, exhibiting a predominance of non-synonymous mutations. Such mutations were observed in regions encoding CTL-restricted epitopes in all individuals. All ECs presented non-synonymous mutations in CTL epitopes but generally at low frequency (< 1%); all VCs showed a high number of mutations, with significant frequency changes between VE and VL visits. A higher frequency of internal mutations was observed for gag epitopes, with significant changes across visits compared to Nef epitopes, indicating a pattern associated with differential genetic pressure. Conclusions The high genetic conservation of HIV-1 gag and nef among ECs indicates that the higher level of viremia control restricts the evolution of both genes. Although viral replication levels in HICs are low or undetectable, all individuals exhibited CTL epitope mutations in proviral gag and nef variants, indicating that potential CTL escape mutants are present in HIC reservoirs and that situations leading to a disequilibrium of the host-virus relationship can result in the spread of CTL-escape variants. Electronic supplementary material The online version of this article (10.1186/s12977-018-0444-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Diogo Gama Caetano
- Laboratório de Aids e Imunologia Molecular, Instituto Oswaldo Cruz -FIOCRUZ, Av. Brasil 4365, Rio de Janeiro, RJ, 21045-900, Brazil
| | - Fernanda Heloise Côrtes
- Laboratório de Aids e Imunologia Molecular, Instituto Oswaldo Cruz -FIOCRUZ, Av. Brasil 4365, Rio de Janeiro, RJ, 21045-900, Brazil
| | - Gonzalo Bello
- Laboratório de Aids e Imunologia Molecular, Instituto Oswaldo Cruz -FIOCRUZ, Av. Brasil 4365, Rio de Janeiro, RJ, 21045-900, Brazil
| | - Sylvia Lopes Maia Teixeira
- Laboratório de Aids e Imunologia Molecular, Instituto Oswaldo Cruz -FIOCRUZ, Av. Brasil 4365, Rio de Janeiro, RJ, 21045-900, Brazil
| | - Brenda Hoagland
- Laboratório de Pesquisa Clínica em DST e Aids, Instituto Nacional de Infectologia Evandro Chagas (INI)-FIOCRUZ, Rio de Janeiro, Brazil
| | - Beatriz Grinsztejn
- Laboratório de Pesquisa Clínica em DST e Aids, Instituto Nacional de Infectologia Evandro Chagas (INI)-FIOCRUZ, Rio de Janeiro, Brazil
| | - Valdilea Gonçalves Veloso
- Laboratório de Pesquisa Clínica em DST e Aids, Instituto Nacional de Infectologia Evandro Chagas (INI)-FIOCRUZ, Rio de Janeiro, Brazil
| | - Monick Lindenmeyer Guimarães
- Laboratório de Aids e Imunologia Molecular, Instituto Oswaldo Cruz -FIOCRUZ, Av. Brasil 4365, Rio de Janeiro, RJ, 21045-900, Brazil
| | - Mariza Gonçalves Morgado
- Laboratório de Aids e Imunologia Molecular, Instituto Oswaldo Cruz -FIOCRUZ, Av. Brasil 4365, Rio de Janeiro, RJ, 21045-900, Brazil.
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Abstract
HIV-infected individuals who maintain control of virus without antiretroviral therapy (ART) are called HIV controllers. The immune responses of these individuals suppress HIV viral replication to low levels or, in the case of elite controllers, to undetectable levels. Although some research indicates a role for inferior virulence of the infecting viral strain in natural control, perhaps by way of defective Nef protein function, we find that the majority of research in HIV controllers highlights CD8 T cells as the main suppressor of viral replication. The most convincing evidence for this argument lies in the strong correlation between certain HLA-I alleles, especially B*57, and HIV control status, a finding that has been replicated by many groups. However, natural control can also occur in individuals lacking these specific HLA alleles, and our understanding of what constitutes an effective CD8 T-cell response remains an incomplete picture. Recent research has broadened our understanding of natural HIV control by illustrating the interactions between different immune cells, including innate immune effectors and antigen-presenting cells. For many years, the immune responses of the natural HIV controllers have been studied for clues on how to achieve functional cure in the rest of the HIV-infected population. The goal of a future functional cure to HIV is one where HIV-infected individuals’ immune responses are able to suppress virus long-term without requiring ART. This review highlights recent advances in our understanding of how HIV controllers’ natural immune responses are able to suppress virus.
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Affiliation(s)
- Sushma Boppana
- Department of Medicine, University of Alabama at Birmingham, Birmingham, USA
| | - Paul Goepfert
- Department of Medicine, University of Alabama at Birmingham, Birmingham, USA
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Zhao Y, Tang H, Tan C, Zhao H, Liu Y. HLA-B27 Correlates with the Intracellular Elimination, Replication, and Trafficking of Salmonella Enteritidis Collected from Reactive Arthritis Patients. Med Sci Monit 2017; 23:5420-5429. [PMID: 29135969 PMCID: PMC5699175 DOI: 10.12659/msm.904681] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
BACKGROUND The aim of this study was to explore the correlation between HLA-B27 and the intracellular elimination, replication, and trafficking of Salmonella enteritidis (S. enteritidis) collected from patients with reactive arthritis. MATERIAL AND METHODS Confocal microscopy, flow cytometry, and sandwich enzyme-linked immunosorbent assay (ELISA) were employed in this study to evaluate the localization of proteins of interest, to assess the intracellular trafficking of S. enteritidis, and to measure the production of cytokines of interest. RESULTS HLA-B27 was negatively associated with intracellular S. enteritidis elimination in healthy human monocytes/macrophages. In S. enteritidis infected monocytes/macrophages, HLA-27B was also negatively correlated with bacteria elimination but positively related to bacteria replication. S. enteritidis did not co-localize with NRAMP1 and LAMP1/2 in HLA-B27 cells. S. enteritidis did not co-exist with transferrin or dextran within HLA-B27 and A2 cells. CONCLUSIONS HLA-B27 is closely associated with the intracellular elimination and replication of S. enteritidis. Replicated bacteria in HLA-B27 monocytic cells were located within unique vacuoles rather than disturbing host endocytosis.
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Affiliation(s)
- Yi Zhao
- Department of Rheumatology and Immunology, West China Hospital, Sichuan University, Chengdu, Sichuan, China (mainland)
| | - Honghu Tang
- Department of Rheumatology and Immunology, West China Hospital, Sichuan University, Chengdu, Sichuan, China (mainland)
| | - Chunyu Tan
- Department of Rheumatology and Immunology, West China Hospital, Sichuan University, Chengdu, Sichuan, China (mainland)
| | - Hua Zhao
- Department of Rheumatology and Immunology, West China Hospital, Sichuan University, Chengdu, Sichuan, China (mainland)
| | - Yi Liu
- Department of Rheumatology and Immunology, West China Hospital, Sichuan University, Chengdu, Sichuan, China (mainland)
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Walker-Sperling VE, Pohlmeyer CW, Veenhuis RT, May M, Luna KA, Kirkpatrick AR, Laeyendecker O, Cox AL, Carrington M, Bailey JR, Arduino RC, Blankson JN. Factors Associated With the Control of Viral Replication and Virologic Breakthrough in a Recently Infected HIV-1 Controller. EBioMedicine 2017; 16:141-149. [PMID: 28159573 PMCID: PMC5474502 DOI: 10.1016/j.ebiom.2017.01.034] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2016] [Revised: 01/18/2017] [Accepted: 01/25/2017] [Indexed: 01/08/2023] Open
Abstract
HIV-1 controllers are patients who control HIV-1 viral replication without antiretroviral therapy. Control is achieved very early in the course of infection, but the mechanisms through which viral replication is restricted are not fully understood. We describe a patient who presented with acute HIV-1 infection and was found to have an HIV-1 RNA level of < 100 copies/mL. She did not have any known protective HLA alleles, but significant immune activation of CD8 + T cells and natural killer (NK) cells was present, and both cell types inhibited viral replication. Virus cultured from this patient replicated as well in vitro as virus isolated from her partner, a patient with AIDS who was the source of transmission. Virologic breakthrough occurred 9 months after her initial presentation and was associated with an increase in CD4 + T cell activation levels and a significant decrease in NK cell inhibitory capacity. Remarkably, CD8 + T cell inhibitory capacity was preserved and there were no new escape mutations in targeted Gag epitopes. These findings suggest that fully replication-competent virus can be controlled in acute HIV-1 infection in some patients without protective HLA alleles and that NK cell responses may contribute to this early control of viral replication. We show that an HIV-1 controller was infected with pathogenic virus yet maintained low viral loads during primary infection. She had activated NK cells and CD8+ T cells and both cell types suppressed HIV-1 replication shortly after infection. She eventually lost control of viral replication, and this was associated with a reduction in NK cell suppressive activity.
HIV-1 controllers are patients who control the virus without HIV-1 medications. These patients may teach us how to design a vaccine against HIV-1. Little is known about how the virus is controlled in the early phase of infection in these patients. Here we show that a recently infected HIV-1 controller had a strong natural killer cell response to the virus. Interestingly, she lost control of the virus 9 months later and her natural killer cell response to the virus was diminished. Our work suggests that natural killer cells may have contributed to viral control in the early phase of infection.
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Affiliation(s)
- Victoria E Walker-Sperling
- Department of Medicine, Center for AIDS Research, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Christopher W Pohlmeyer
- Department of Medicine, Center for AIDS Research, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Rebecca T Veenhuis
- Department of Medicine, Center for AIDS Research, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Megan May
- Department of Medicine, Center for AIDS Research, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Krystle A Luna
- Department of Medicine, University of Texas MD Anderson Cancer Center, Austin, TX, USA
| | - Allison R Kirkpatrick
- Laboratory of Immunoregulation, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, NIH, Baltimore, MD, USA
| | - Oliver Laeyendecker
- Department of Medicine, Center for AIDS Research, Johns Hopkins University School of Medicine, Baltimore, MD, USA; Laboratory of Immunoregulation, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, NIH, Baltimore, MD, USA
| | - Andrea L Cox
- Department of Medicine, Center for AIDS Research, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Mary Carrington
- Cancer and Inflammation Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD, USA; Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology and Harvard University, Cambridge, MA, USA
| | - Justin R Bailey
- Department of Medicine, Center for AIDS Research, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Roberto C Arduino
- Department of Internal Medicine, Division of Infectious Diseases, The University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Joel N Blankson
- Department of Medicine, Center for AIDS Research, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
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Arcia D, Acevedo-Sáenz L, Rugeles MT, Velilla PA. Role of CD8 + T Cells in the Selection of HIV-1 Immune Escape Mutations. Viral Immunol 2016; 30:3-12. [PMID: 27805477 DOI: 10.1089/vim.2016.0095] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Human immunodeficiency virus type-1 (HIV-1) infection represents one of the biggest public health problems worldwide. The immune response, mainly the effector mechanisms mediated by CD8+ T cells, induces the selection of mutations that allows the virus to escape the immune control. These mutations are generally selected within CD8+ T cell epitopes restricted to human leukocyte antigen class I (HLA-I), leading to a decrease in the presentation and recognition of the epitope, decreasing the activation of CD8+ T cells. However, these mutations may also affect cellular processing of the peptide or recognition by the T cell receptor. Escape mutations often carry a negative impact in viral fitness that is partially or totally compensated by the selection of compensatory mutations. The selection of either escape mutations or compensatory mutations may negatively affect the course of the infection. In addition, these mutations are a major barrier for the development of new therapeutic strategies focused on the induction of specific CD8+ T cell responses.
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Affiliation(s)
- David Arcia
- Grupo Inmunovirología, Facultad de Medicina, Universidad de Antioquia UdeA , Medellín, Colombia
| | - Liliana Acevedo-Sáenz
- Grupo Inmunovirología, Facultad de Medicina, Universidad de Antioquia UdeA , Medellín, Colombia
| | - María Teresa Rugeles
- Grupo Inmunovirología, Facultad de Medicina, Universidad de Antioquia UdeA , Medellín, Colombia
| | - Paula A Velilla
- Grupo Inmunovirología, Facultad de Medicina, Universidad de Antioquia UdeA , Medellín, Colombia
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Walker-Sperling VE, Pohlmeyer CW, Tarwater PM, Blankson JN. The Effect of Latency Reversal Agents on Primary CD8+ T Cells: Implications for Shock and Kill Strategies for Human Immunodeficiency Virus Eradication. EBioMedicine 2016; 8:217-229. [PMID: 27428432 PMCID: PMC4919475 DOI: 10.1016/j.ebiom.2016.04.019] [Citation(s) in RCA: 75] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2016] [Revised: 04/15/2016] [Accepted: 04/15/2016] [Indexed: 11/16/2022] Open
Abstract
Shock and kill strategies involving the use of small molecules to induce viral transcription in resting CD4 + T cells (shock) followed by immune mediated clearance of the reactivated cells (kill), have been proposed as a method of eliminating latently infected CD4 + T cells. The combination of the histone deacetylase (HDAC) inhibitor romidepsin and protein kinase C (PKC) agonist bryostatin-1 is very effective at reversing latency in vitro. However, we found that primary HIV-1 specific CD8 + T cells were not able to eliminate autologous resting CD4 + T cells that had been reactivated with these drugs. We tested the hypothesis that the drugs affected primary CD8 + T cell function and found that both agents had inhibitory effects on the suppressive capacity of HIV-specific CD8 + T cells from patients who control viral replication without antiretroviral therapy (elite suppressors/controllers). The inhibitory effect was additive and multi-factorial in nature. These inhibitory effects were not seen with prostratin, another PKC agonist, either alone or in combination with JQ1, a bromodomain-containing protein 4 inhibitor. Our results suggest that because of their adverse effects on primary CD8 + T cells, some LRAs may cause immune-suppression and therefore should be used with caution in shock and kill strategies. Latency reversal agents can reactivate HIV-1 expression in latently infected cells. CD8 T cells from HIV-1 infected patients did not eliminate reactivated latently infected cells. This finding can partially be explained by our data showing that latency reversal agents affect the function of CD8 + T cells.
Latently infected CD4 + T cells are a major barrier to the cure of HIV-1 infection. One strategy of eliminating these cells involves inducing viral transcription with small molecules (latency reversal agents or LRAs) which would result in the recognition of these cells by the immune system. We show here that CD8 + T cells were not able to eliminate CD4 + T cells from HIV-1-infected patients following stimulation with LRAs. Our data suggests that this may be partially because some LRAs affect the function of CD8 + T cells. Thus it will be critical to select LRAs that do not cause immune suppression.
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Affiliation(s)
| | - Christopher W Pohlmeyer
- Center for AIDS Research, Department of Medicine, Johns Hopkins University School of Medicine, USA
| | - Patrick M Tarwater
- Division of Biostatistics and Epidemiology, Paul L. Foster School of Medicine, El Paso, TX, USA
| | - Joel N Blankson
- Center for AIDS Research, Department of Medicine, Johns Hopkins University School of Medicine, USA.
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26
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Consequences of HLA-B*13-Associated Escape Mutations on HIV-1 Replication and Nef Function. J Virol 2015; 89:11557-71. [PMID: 26355081 DOI: 10.1128/jvi.01955-15] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2015] [Accepted: 08/31/2015] [Indexed: 01/05/2023] Open
Abstract
UNLABELLED HLA-B*13 is associated with superior in vivo HIV-1 viremia control. Protection is thought to be mediated by sustained targeting of key cytotoxic T lymphocyte (CTL) epitopes and viral fitness costs of CTL escape in Gag although additional factors may contribute. We assessed the impact of 10 published B*13-associated polymorphisms in Gag, Pol, and Nef, in 23 biologically relevant combinations, on HIV-1 replication capacity and Nef-mediated reduction of cell surface CD4 and HLA class I expression. Mutations were engineered into HIV-1NL4.3, and replication capacity was measured using a green fluorescent protein (GFP) reporter T cell line. Nef-mediated CD4 and HLA-A*02 downregulation was assessed by flow cytometry, and T cell recognition of infected target cells was measured via coculture with an HIV-specific luciferase reporter cell line. When tested individually, only Gag-I147L and Gag-I437L incurred replicative costs (5% and 17%, respectively), consistent with prior reports. The Gag-I437L-mediated replication defect was rescued to wild-type levels by the adjacent K436R mutation. A novel B*13 epitope, comprising 8 residues and terminating at Gag147, was identified in p24(Gag) (GQMVHQAIGag140-147). No other single or combination Gag, Pol, or Nef mutant impaired viral replication. Single Nef mutations did not affect CD4 or HLA downregulation; however, the Nef double mutant E24Q-Q107R showed 40% impairment in HLA downregulation with no evidence of Nef stability defects. Moreover, target cells infected with HIV-1-NefE24Q-Q107R were recognized better by HIV-specific T cells than those infected with HIV-1NL4.3 or single Nef mutants. Our results indicate that CTL escape in Gag and Nef can be functionally costly and suggest that these effects may contribute to long-term HIV-1 control by HLA-B*13. IMPORTANCE Protective effects of HLA-B*13 on HIV-1 disease progression are mediated in part by fitness costs of CTL escape mutations in conserved Gag epitopes, but other mechanisms remain incompletely known. We extend our knowledge of the impact of B*13-driven escape on HIV-1 replication by identifying Gag-K436R as a compensatory mutation for the fitness-costly Gag-I437L. We also identify Gag-I147L, the most rapidly and commonly selected B*13-driven substitution in HIV-1, as a putative C-terminal anchor residue mutation in a novel B*13 epitope. Most notably, we identify a novel escape-driven fitness defect: B*13-driven substitutions E24Q and Q107R in Nef, when present together, substantially impair this protein's ability to downregulate HLA class I. This, in turn, increases the visibility of infected cells to HIV-specific T cells. Our results suggest that B*13-associated escape mutations impair HIV-1 replication by two distinct mechanisms, that is, by reducing Gag fitness and dampening Nef immune evasion function.
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The Breadth of Expandable Memory CD8+ T Cells Inversely Correlates with Residual Viral Loads in HIV Elite Controllers. J Virol 2015; 89:10735-47. [PMID: 26269189 DOI: 10.1128/jvi.01527-15] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2015] [Accepted: 07/27/2015] [Indexed: 12/28/2022] Open
Abstract
UNLABELLED Previous studies have shown that elite controllers with minimal effector T cell responses harbor a low-frequency, readily expandable, highly functional, and broadly directed memory population. Here, we interrogated the in vivo relevance of this cell population by investigating whether the breadth of expandable memory responses is associated with the magnitude of residual viremia in individuals achieving durable suppression of HIV infection. HIV-specific memory CD8(+) T cells were expanded by using autologous epitopic and variant peptides. Viral load was measured by an ultrasensitive single-copy PCR assay. Following expansion, controllers showed a greater increase in the overall breadth of Gag responses than did untreated progressors (P = 0.01) as well as treated progressors (P = 0.0003). Nef- and Env-specific memory cells expanded poorly for all groups, and their expanded breadths were indistinguishable among groups (P = 0.9 for Nef as determined by a Kruskal-Wallis test; P = 0.6 for Env as determined by a Kruskal-Wallis test). More importantly, we show that the breadth of expandable, previously undetectable Gag-specific responses was inversely correlated with residual viral load (r = -0.6; P = 0.009). Together, these data reveal a direct link between the abundance of Gag-specific expandable memory responses and prolonged maintenance of low-level viremia. Our studies highlight a CD8(+) T cell feature that would be desirable in a vaccine-induced T cell response. IMPORTANCE Many studies have shown that the rare ability of some individuals to control HIV infection in the absence of antiretroviral therapy appears to be heavily dependent upon special HIV-specific killer T lymphocytes that are able to inhibit viral replication. The identification of key features of these immune cells has the potential to inform rational HIV vaccine design. This study shows that a special subset of killer lymphocytes, known as central memory CD8(+) T lymphocytes, is at least partially involved in the durable control of HIV replication. HIV controllers maintain a large proportion of Gag-specific expandable memory CD8(+) T cells involved in ongoing viral suppression. These data suggest that induction of this cell subset by future HIV vaccines may be important for narrowing possible routes of rapid escape from vaccine-induced CD8(+) T cell responses.
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Migueles SA, Mendoza D, Zimmerman MG, Martins KM, Toulmin SA, Kelly EP, Peterson BA, Johnson SA, Galson E, Poropatich KO, Patamawenu A, Imamichi H, Ober A, Rehm CA, Jones S, Hallahan CW, Follmann DA, Connors M. CD8(+) T-cell Cytotoxic Capacity Associated with Human Immunodeficiency Virus-1 Control Can Be Mediated through Various Epitopes and Human Leukocyte Antigen Types. EBioMedicine 2015; 2:46-58. [PMID: 26137533 PMCID: PMC4485486 DOI: 10.1016/j.ebiom.2014.12.009] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2014] [Revised: 12/18/2014] [Accepted: 12/19/2014] [Indexed: 12/16/2022] Open
Abstract
Understanding natural immunologic control over Human Immunodeficiency Virus (HIV)-1 replication, as occurs in rare long-term nonprogressors/elite controllers (LTNP/EC), should inform the design of efficacious HIV vaccines and immunotherapies. Durable control in LTNP/EC is likely mediated by highly functional virus-specific CD8(+) T-cells. Protective Human Leukocyte Antigen (HLA) class I alleles, like B*27 and B*57, are present in most, but not all LTNP/EC, providing an opportunity to investigate features shared by their HIV-specific immune responses. To better understand the contribution of epitope targeting and conservation to immune control, we compared the CD8(+) T-cell specificity and function of B*27/57(neg) LTNP/EC (n = 23), B*27/57(pos) LTNP/EC (n = 23) and B*27/57(neg) progressors (n = 13). Fine mapping revealed 11 previously unreported immunodominant responses. Although B*27/57(neg) LTNP/EC did not target more highly conserved epitopes, their CD8(+) T-cell cytotoxic capacity was significantly higher than progressors. Similar to B*27/57(pos) LTNP/EC, this superior cytotoxicity was mediated by preferential expansion of immunodominant responses and lysis through the predicted HLA. These findings suggest that increased CD8(+) T-cell cytotoxic capacity is a common mechanism of control in most LTNP/EC regardless of HLA type. They also suggest that potent cytotoxicity can be mediated through various epitopes and HLA molecules and could, in theory, be induced in most people.
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Affiliation(s)
- Stephen A. Migueles
- Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Daniel Mendoza
- Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Matthew G. Zimmerman
- Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Kelly M. Martins
- Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Sushila A. Toulmin
- Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Elizabeth P. Kelly
- Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Bennett A. Peterson
- Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Sarah A. Johnson
- Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Eric Galson
- Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Kate O. Poropatich
- Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Andy Patamawenu
- Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Hiromi Imamichi
- Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Alexander Ober
- Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Catherine A. Rehm
- Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Sara Jones
- Clinical Monitoring Research Program, Leidos Biomedical Research, Inc., Frederick, MD, USA
| | - Claire W. Hallahan
- Biostatistics Research Branch, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Dean A. Follmann
- Biostatistics Research Branch, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Mark Connors
- Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
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Yang W, Laeyendecker O, Wendel SK, Zhang B, Sun S, Zhou JY, Ao M, Moore RD, Jackson JB, Zhang H. Glycoproteomic study reveals altered plasma proteins associated with HIV elite suppressors. Theranostics 2014; 4:1153-63. [PMID: 25285165 PMCID: PMC4183994 DOI: 10.7150/thno.9510] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2014] [Accepted: 08/21/2014] [Indexed: 11/25/2022] Open
Abstract
HIV elite suppressors (ES) or controllers are individuals achieving control of viremia by their natural immunological mechanisms without highly active antiretroviral therapy (HAART). Study of the mechanisms responsible for the immunological suppression of viremia in ES may lead to the detection of individuals with ES and the effective control of HIV infection. We hypothesize that plasma glycoproteins play essential roles in the immune system of ES since plasma proteins are critical and highly relevant in anti-viral immunity and most plasma proteins are glycoproteins. To examine glycoproteins associated with ES, plasma samples from ES individuals (n=20), and from individuals on HAART (n=20), with AIDS (n=20), and no HIV infection (n=10) were analyzed by quantitative glycoproteomics. We found that a number of glycoproteins changed between ES versus HAART, AIDS and HIV- individuals. In sharp contrast, the level of plasma glycoproteins in the HAART cohort showed fewer changes compared with AIDS and HIV- individuals. These results showed that although both ES and HAART effectively suppress viremia, ES appeared to profoundly affect immunologically relevant glycoproteins in plasma as consequence of or support for anti-viral immunity. Bioinformatic analysis revealed that altered proteins in ES plasma were mainly associated with inflammation. This analysis suggests that overlapping, while distinguishable, glycoprotein profiles for inflammation and immune activation appeared to be present between ES and non-ES (HAART+AIDS) cohorts, indicating different triggers for inflammation and immune activation between natural and treatment-related viral suppression.
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Comparative analysis of the capacity of elite suppressor CD4+ and CD8+ T cells to inhibit HIV-1 replication in monocyte-derived macrophages. J Virol 2014; 88:9789-98. [PMID: 24942573 DOI: 10.1128/jvi.00860-14] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
UNLABELLED Elite controllers or suppressors (ESs) are HIV-1-infected individuals who are able to maintain viral loads below the limit of detection of clinical assays without antiretroviral therapy. The mechanisms of virologic control are not fully understood, but ESs have been shown to have a more effective CD8+ T cell response to infected CD4+ T cells than chronic progressors (CPs). While macrophages are another cell type productively infected by HIV-1, few studies have examined the ability of primary effector T cells to suppress HIV-1 replication in these target cells. Here, we compared the ability of unstimulated primary CD4+ and CD8+ effector T cells to suppress viral replication in monocyte-derived macrophages (MDMs) in ESs and CPs. While CD4+ effector T cells were capable of inhibiting viral replication in MDMs, the magnitude of this response was not significantly different between ESs and CPs. In contrast, the CD8+ T cells from ESs were significantly more effective than those from CPs at inhibiting viral replication in MDMs. The CD4+ T cell response was partially mediated by soluble factors, while the CD8+ T cell response required cell-to-cell interaction. Our results suggest that the individual contributions of various effector cells should be considered in rational vaccine design and in ongoing eradication efforts. IMPORTANCE Elite suppressors are individuals capable of maintaining low-level viremia in HIV-1 infection without antiretroviral drugs. Their T cell responses have been implicated in eliminating infected CD4+ T cells, and as such, elite suppressors may represent a model of a functional cure of HIV-1 infection. Here, we sought to determine whether the suppressive T cell responses against infected CD4+ T cells also apply to infected macrophages by comparing the responses of elite suppressors and HIV-1-positive individuals on highly active antiretroviral therapy (HAART). Our results show that the CD8+ cells but not CD4+ T cells from elite suppressors have a response against infected macrophages superior to the response of CD8+ cells from patients on HAART. Our results suggest that the induction of a CD8+ T cell response effective against infected macrophages is an outcome to consider in rational vaccine design.
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Buggert M, Norström MM, Salemi M, Hecht FM, Karlsson AC. Functional avidity and IL-2/perforin production is linked to the emergence of mutations within HLA-B*5701-restricted epitopes and HIV-1 disease progression. THE JOURNAL OF IMMUNOLOGY 2014; 192:4685-96. [PMID: 24740510 DOI: 10.4049/jimmunol.1302253] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Viral escape from HIV-1-specific CD8(+) T cells has been demonstrated in numerous studies previously. However, the qualitative features driving the emergence of mutations within epitopes are still unclear. In this study, we aimed to distinguish whether specific functional characteristics of HLA-B*5701-restricted CD8(+) T cells influence the emergence of mutations in high-risk progressors (HRPs) versus low-risk progressors (LRPs). Single-genome sequencing was performed to detect viral mutations (variants) within seven HLA-B*5701-restricted epitopes in Gag (n = 4) and Nef (n = 3) in six untreated HLA-B*5701 subjects followed from early infection up to 7 y. Several well-characterized effector markers (IFN-γ, IL-2, MIP-1β, TNF, CD107a, and perforin) were identified by flow cytometry following autologous (initial and emerging variant/s) epitope stimulations. This study demonstrates that specific functional attributes may facilitate the outgrowth of mutations within HLA-B*5701-restricted epitopes. A significantly lower fraction of IL-2-producing cells and a decrease in functional avidity and polyfunctional sensitivity were evident in emerging epitope variants compared with the initial autologous epitopes. Interestingly, the HRPs mainly drove these differences, whereas the LRPs maintained a directed and maintained functional response against emerging epitope variants. In addition, LRPs induced improved cell-cycle progression and perforin upregulation after autologous and emerging epitope variant stimulations in contrast to HRPs. The maintained quantitative and qualitative features of the CD8(+) T cell responses in LRPs toward emerging epitope variants provide insights into why HLA-B*5701 subjects have different risks of HIV-1 disease progression.
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Affiliation(s)
- Marcus Buggert
- Division of Clinical Microbiology, Department of Laboratory Medicine, Karolinska Institutet, Stockholm S-141 86, Sweden
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