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Aquino VH, Fumagalli MJ, Silva A, de Moura Negrini BV, Rojas A, Guillen Y, Bernal C, Figueiredo LTM. Linear epitope mapping in the E and NS1 proteins of dengue and Zika viruses: Prospection of peptides for vaccines and diagnostics. PLoS One 2023; 18:e0292451. [PMID: 37788262 PMCID: PMC10547212 DOI: 10.1371/journal.pone.0292451] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2023] [Accepted: 09/20/2023] [Indexed: 10/05/2023] Open
Abstract
The arrival of the Zika virus (ZIKV) in dengue virus (DENV)-endemic areas has posed challenges for both differential diagnosis and vaccine development. Peptides have shown promise in addressing these issues. The aim of this study was to identify the linear epitope profile recognized by serum samples from dengue and Zika patients in the E and NS1 proteins of DENV and ZIKV. This cross-sectional study included individuals of all ages with laboratory-confirmed DENV and ZIKV infections, who were selected through convenience sampling. The serum samples from dengue and Zika patients detected epitopes evenly distributed across the viral proteins in a peptide microarray platform. However, several epitopes were located within "epitope hotspots", characterized by clusters of peptides recognized in more than 30% of the sub-arrays analyzed using individual or pooled serum samples. The serum samples from dengue and Zika patients showed a high level of cross-reactivity with peptides in the DENV and ZIKV proteins. Analysis using an additional peptide microarray platform, which contained peptides selected based on the results of the initial screening, revealed that two DENV and one ZIKV peptide, highly specific to their related viruses, were located within the epitope hotspots; however, they presented low detection rates (32.5, 35.0, and 28.6%, respectively). In addition, two DENV peptides detected at similarly high rates by both dengue and Zika patients were also found within the epitope hotspots. These hotspots contain several immunodominant epitopes that are recognized by a larger number of individuals when compared to 15-amino acid (aa) sequence peptides. Thus, epitope hotspots may have greater potential to serve as antigens in diagnostic tests and vaccine development than peptides composed of only 15 amino acids.
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Affiliation(s)
- Victor Hugo Aquino
- Immunology Department, Research Institute for Health Sciences, National University of Asuncion, San Lorenzo, Central, Paraguay
- Department of Clinical Analyses, Toxicology and Food Sciences, School of Pharmaceutical Sciences, University of Sao Paulo, Ribeirao Preto, Sao Paulo, Brazil
| | - Marcilio J. Fumagalli
- Virology Research Center, Ribeirao Preto Medical School, University of Sao Paulo, Ribeirao Preto, Sao Paulo, Brazil
| | - Angélica Silva
- Virology Research Center, Ribeirao Preto Medical School, University of Sao Paulo, Ribeirao Preto, Sao Paulo, Brazil
| | | | - Alejandra Rojas
- Production Department, Research Institute for Health Sciences, National University of Asuncion, San Lorenzo, Central, Paraguay
| | - Yvalena Guillen
- Production Department, Research Institute for Health Sciences, National University of Asuncion, San Lorenzo, Central, Paraguay
| | - Cynthia Bernal
- Production Department, Research Institute for Health Sciences, National University of Asuncion, San Lorenzo, Central, Paraguay
| | - Luiz Tadeu Moraes Figueiredo
- Virology Research Center, Ribeirao Preto Medical School, University of Sao Paulo, Ribeirao Preto, Sao Paulo, Brazil
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2
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Lee JH, Hu JK, Georgeson E, Nakao C, Groschel B, Dileepan T, Jenkins MK, Seumois G, Vijayanand P, Schief WR, Crotty S. Modulating the quantity of HIV Env-specific CD4 T cell help promotes rare B cell responses in germinal centers. J Exp Med 2021; 218:e20201254. [PMID: 33355623 PMCID: PMC7769167 DOI: 10.1084/jem.20201254] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2020] [Revised: 09/23/2020] [Accepted: 11/13/2020] [Indexed: 01/17/2023] Open
Abstract
Immunodominance to nonneutralizing epitopes is a roadblock in designing vaccines against several diseases of high interest. One hypothetical possibility is that limited CD4 T cell help to B cells in a normal germinal center (GC) response results in selective recruitment of abundant, immunodominant B cells. This is a central issue in HIV envelope glycoprotein (Env) vaccine designs, because precursors to broadly neutralizing epitopes are rare. Here, we sought to elucidate whether modulating the quantity of T cell help can influence recruitment and competition of broadly neutralizing antibody precursor B cells at a physiological precursor frequency in response to Env trimer immunization. To do so, two new Env-specific CD4 transgenic (Tg) T cell receptor (TCR) mouse lines were generated, carrying TCR pairs derived from Env-protein immunization. Our results suggest that CD4 T cell help quantitatively regulates early recruitment of rare B cells to GCs.
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Affiliation(s)
- Jeong Hyun Lee
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, CA
- Consortium for HIV/AIDS Vaccine Development, The Scripps Research Institute, La Jolla, CA
| | - Joyce K. Hu
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, CA
| | - Erik Georgeson
- Consortium for HIV/AIDS Vaccine Development, The Scripps Research Institute, La Jolla, CA
- International AIDS Vaccine Initiative Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA
| | - Catherine Nakao
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, CA
| | - Bettina Groschel
- Consortium for HIV/AIDS Vaccine Development, The Scripps Research Institute, La Jolla, CA
- International AIDS Vaccine Initiative Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA
| | - Thamotharampillai Dileepan
- Department of Microbiology and Immunology, Center for Immunology, University of Minnesota Medical School, Minneapolis, MN
| | - Marc K. Jenkins
- Department of Microbiology and Immunology, Center for Immunology, University of Minnesota Medical School, Minneapolis, MN
| | - Gregory Seumois
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, CA
| | - Pandurangan Vijayanand
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, CA
- Clinical and Experimental Sciences, National Institute for Health Research Southampton, Respiratory Biomedical Research Unit, University of Southampton, Southampton, UK
| | - William R. Schief
- Consortium for HIV/AIDS Vaccine Development, The Scripps Research Institute, La Jolla, CA
- International AIDS Vaccine Initiative Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology and Harvard University, Cambridge, MA
| | - Shane Crotty
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, CA
- Consortium for HIV/AIDS Vaccine Development, The Scripps Research Institute, La Jolla, CA
- Department of Medicine, Division of Infectious Diseases and Global Public Health, University of California, San Diego, La Jolla, CA
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3
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Klasse PJ, Ozorowski G, Sanders RW, Moore JP. Env Exceptionalism: Why Are HIV-1 Env Glycoproteins Atypical Immunogens? Cell Host Microbe 2020; 27:507-518. [PMID: 32272076 PMCID: PMC7187920 DOI: 10.1016/j.chom.2020.03.018] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2020] [Revised: 03/17/2020] [Accepted: 03/22/2020] [Indexed: 11/24/2022]
Abstract
Recombinant HIV-1 envelope (Env) glycoproteins of ever-increasing sophistication have been evaluated as vaccine candidates for over 30 years. Structurally defined mimics of native trimeric Env glycoproteins (e.g., SOSIP trimers) present multiple epitopes for broadly neutralizing antibodies (bNAbs) and their germline precursors, but elicitation of bNAbs remains elusive. Here, we argue that the interactions between Env and the immune system render it exceptional among viral vaccine antigens and hinder its immunogenicity in absolute and comparative terms. In other words, Env binds to CD4 on key immune cells and transduces signals that can compromise their function. Moreover, the extensive array of oligomannose glycans on Env shields peptidic B cell epitopes, impedes the presentation of T helper cell epitopes, and attracts mannose binding proteins, which could affect the antibody response. We suggest lines of research for assessing how to overcome obstacles that the exceptional features of Env impose on the creation of a successful HIV-1 vaccine.
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Affiliation(s)
- P J Klasse
- Department of Microbiology and Immunology, Weill Cornell Medicine, Cornell University, New York, NY 10065, USA
| | - Gabriel Ozorowski
- Department of Integrative Structural and Computational Biology, Consortium for HIV Vaccine Development, Scripps Research Institute, La Jolla, CA 92037, USA
| | - Rogier W Sanders
- Department of Medical Microbiology, Academic Medical Center, University of Amsterdam, Amsterdam, the Netherlands
| | - John P Moore
- Department of Microbiology and Immunology, Weill Cornell Medicine, Cornell University, New York, NY 10065, USA.
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4
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Koblischke M, Spitzer FS, Florian DM, Aberle SW, Malafa S, Fae I, Cassaniti I, Jungbauer C, Knapp B, Laferl H, Fischer G, Baldanti F, Stiasny K, Heinz FX, Aberle JH. CD4 T Cell Determinants in West Nile Virus Disease and Asymptomatic Infection. Front Immunol 2020; 11:16. [PMID: 32038660 PMCID: PMC6989424 DOI: 10.3389/fimmu.2020.00016] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2019] [Accepted: 01/07/2020] [Indexed: 12/30/2022] Open
Abstract
West Nile (WN) virus infection of humans is frequently asymptomatic, but can also lead to WN fever or neuroinvasive disease. CD4 T cells and B cells are critical in the defense against WN virus, and neutralizing antibodies, which are directed against the viral glycoprotein E, are an accepted correlate of protection. For the efficient production of these antibodies, B cells interact directly with CD4 helper T cells that recognize peptides from E or the two other structural proteins (capsid-C and membrane-prM/M) of the virus. However, the specific protein sites yielding such helper epitopes remain unknown. Here, we explored the CD4 T cell response in humans after WN virus infection using a comprehensive library of overlapping peptides covering all three structural proteins. By measuring T cell responses in 29 individuals with either WN virus disease or asymptomatic infection, we showed that CD4 T cells focus on peptides in specific structural elements of C and at the exposed surface of the pre- and postfusion forms of the E protein. Our data indicate that these immunodominant epitopes are recognized in the context of multiple different HLA molecules. Furthermore, we observed that immunodominant antigen regions are structurally conserved and similarly targeted in other mosquito-borne flaviviruses, including dengue, yellow fever, and Zika viruses. Together, these findings indicate a strong impact of virion protein structure on epitope selection and antigenicity, which is an important issue to consider in future vaccine design.
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Affiliation(s)
| | | | - David M Florian
- Center for Virology, Medical University of Vienna, Vienna, Austria
| | - Stephan W Aberle
- Center for Virology, Medical University of Vienna, Vienna, Austria
| | - Stefan Malafa
- Center for Virology, Medical University of Vienna, Vienna, Austria
| | - Ingrid Fae
- Department of Blood Group Serology and Transfusion Medicine, Medical University of Vienna, Vienna, Austria
| | - Irene Cassaniti
- Molecular Virology Unit, Microbiology and Virology Department, Fondazione IRCCS Policlinico San Matteo, Pavia, Italy.,Department of Clinical, Surgical, Diagnostic and Pediatric Sciences, University of Pavia, Pavia, Italy
| | - Christof Jungbauer
- Blood Service for Vienna, Lower Austria and Burgenland, Austrian Red Cross, Vienna, Austria
| | | | - Hermann Laferl
- Sozialmedizinisches Zentrum Süd, Kaiser-Franz-Josef-Spital, Vienna, Austria
| | - Gottfried Fischer
- Department of Blood Group Serology and Transfusion Medicine, Medical University of Vienna, Vienna, Austria
| | - Fausto Baldanti
- Molecular Virology Unit, Microbiology and Virology Department, Fondazione IRCCS Policlinico San Matteo, Pavia, Italy.,Department of Clinical, Surgical, Diagnostic and Pediatric Sciences, University of Pavia, Pavia, Italy
| | - Karin Stiasny
- Center for Virology, Medical University of Vienna, Vienna, Austria
| | - Franz X Heinz
- Center for Virology, Medical University of Vienna, Vienna, Austria
| | - Judith H Aberle
- Center for Virology, Medical University of Vienna, Vienna, Austria
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5
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Koblischke M, Mackroth MS, Schwaiger J, Fae I, Fischer G, Stiasny K, Heinz FX, Aberle JH. Protein structure shapes immunodominance in the CD4 T cell response to yellow fever vaccination. Sci Rep 2017; 7:8907. [PMID: 28827760 PMCID: PMC5566484 DOI: 10.1038/s41598-017-09331-w] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2017] [Accepted: 07/17/2017] [Indexed: 12/25/2022] Open
Abstract
The live attenuated yellow fever (YF) vaccine is a highly effective human vaccine and induces long-term protective neutralizing antibodies directed against the viral envelope protein E. The generation of such antibodies requires the help of CD4 T cells which recognize peptides derived from proteins in virus particles internalized and processed by E-specific B cells. The CD4 T helper cell response is restricted to few immunodominant epitopes, but the mechanisms of their selection are largely unknown. Here, we report that CD4 T cell responses elicited by the YF-17D vaccine are focused to hotspots of two helices of the viral capsid protein and to exposed strands and loops of E. We found that the locations of immunodominant epitopes within three-dimensional protein structures exhibit a high degree of overlap between YF virus and the structurally homologous flavivirus tick-borne encephalitis virus, although amino acid sequence identity of the epitope regions is only 15-45%. The restriction of epitopes to exposed E protein surfaces and their strikingly similar positioning within proteins of distantly related flaviviruses are consistent with a strong influence of protein structure that shapes CD4 T cell responses and provide leads for a rational design of immunogens for vaccination.
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Affiliation(s)
| | - Maria S Mackroth
- Department of Medicine I, Division of Infectious Diseases and Tropical Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Julia Schwaiger
- Center for Virology, Medical University of Vienna, Vienna, Austria
| | - Ingrid Fae
- Department of Blood Group Serology and Transfusion Medicine, Medical University of Vienna, Vienna, Austria
| | - Gottfried Fischer
- Department of Blood Group Serology and Transfusion Medicine, Medical University of Vienna, Vienna, Austria
| | - Karin Stiasny
- Center for Virology, Medical University of Vienna, Vienna, Austria
| | - Franz X Heinz
- Center for Virology, Medical University of Vienna, Vienna, Austria
| | - Judith H Aberle
- Center for Virology, Medical University of Vienna, Vienna, Austria.
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6
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Chen W, Crawford RB, Kaplan BLF, Kaminski NE. Modulation of HIVGP120 Antigen-Specific Immune Responses In Vivo by Δ9-Tetrahydrocannabinol. J Neuroimmune Pharmacol 2015; 10:344-55. [PMID: 25900076 DOI: 10.1007/s11481-015-9597-x] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2014] [Accepted: 03/04/2015] [Indexed: 11/25/2022]
Abstract
Approximately 25 % of HIV patients use marijuana for its putative therapeutic benefit; however, it is unknown how cannabinoids affect the immune status of HIV patients. Previously, a surrogate in vitro mouse model was established, which induced CD8(+) T cell proliferation and gp120-specific IFNγ production. ∆(9)-Tetrahydrocannabinol (THC), the predominant psychoactive compound in marijuana, suppressed or enhanced the responses depending on the magnitude of cellular activation. The purpose of the current study was to investigate whether THC produced similar effects in vivo and therefore a mouse model to induce HIVgp120-specific immune responses was established. A gp120-expressing plasmid, pVRCgp120, or a vector plasmid, pVRC2000, was injected intramuscularly into mice, which were also dosed with THC orally. The gp120-specific IFNγ and IL-2 responses were detected when splenocytes were restimulated with gp120-derived peptide 81 (IIGDIRQAHCNISRA), which was identified as being immunodominant. Various cellular populations were activated in response to pVRCgp120 stimulation followed by peptide restimulation, as evidenced by increased expression levels of activation markers (e.g., CD69, CD80, and major histocompatibility complex II [MHC II]). The IFNγ response and cellular activation were enhanced by THC in C57Bl/6 wild type (WT) mice but suppressed or not affected by THC in cannabinoid receptor 1 (CB1) and 2 (CB2) knockout (CB1 (-/-)CB2 (-/-)) mice. Furthermore, CB1 (-/-)CB2 (-/-) mice exhibited augmented IFNγ production when compared to WT mice in the absence of THC. Collectively, our findings demonstrate that under certain conditions, THC enhances HIV antigen-specific immune responses, which occurs through CB1/CB2-dependent and -independent mechanisms.
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MESH Headings
- Animals
- Dronabinol/pharmacology
- Female
- HIV Envelope Protein gp120/pharmacology
- HIV Envelope Protein gp120/physiology
- Histocompatibility Antigens Class II/immunology
- Mice
- Mice, Inbred C57BL
- Mice, Knockout
- Receptor, Cannabinoid, CB1/agonists
- Receptor, Cannabinoid, CB1/deficiency
- Receptor, Cannabinoid, CB1/immunology
- Receptor, Cannabinoid, CB2/agonists
- Receptor, Cannabinoid, CB2/deficiency
- Receptor, Cannabinoid, CB2/immunology
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Affiliation(s)
- Weimin Chen
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI, USA
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7
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Pavlović MD, Jandrlić DR, Mitić NS. Epitope distribution in ordered and disordered protein regions. Part B — Ordered regions and disordered binding sites are targets of T- and B-cell immunity. J Immunol Methods 2014; 407:90-107. [DOI: 10.1016/j.jim.2014.03.027] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2013] [Revised: 03/31/2014] [Accepted: 03/31/2014] [Indexed: 01/04/2023]
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8
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Specificities of human CD4+ T cell responses to an inactivated flavivirus vaccine and infection: correlation with structure and epitope prediction. J Virol 2014; 88:7828-42. [PMID: 24789782 DOI: 10.1128/jvi.00196-14] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Tick-borne encephalitis (TBE) virus is endemic in large parts of Europe and Central and Eastern Asia and causes more than 10,000 annual cases of neurological disease in humans. It is closely related to the mosquito-borne yellow fever, dengue, Japanese encephalitis, and West Nile viruses, and vaccination with an inactivated whole-virus vaccine can effectively prevent clinical disease. Neutralizing antibodies are directed to the viral envelope protein (E) and an accepted correlate of immunity. However, data on the specificities of CD4(+) T cells that recognize epitopes in the viral structural proteins and thus can provide direct help to the B cells producing E-specific antibodies are lacking. We therefore conducted a study on the CD4(+) T cell response against the virion proteins in vaccinated people in comparison to TBE patients. The data obtained with overlapping peptides in interleukin-2 (IL-2) enzyme-linked immunosorbent spot (ELISpot) assays were analyzed in relation to the three-dimensional structures of the capsid (C) and E proteins as well as to epitope predictions based on major histocompatibility complex (MHC) class II peptide affinities. In the C protein, peptides corresponding to two out of four alpha helices dominated the response in both vaccinees and patients, whereas in the E protein concordance of immunodominance was restricted to peptides of a single domain (domain III). Epitope predictions were much better for C than for E and were especially erroneous for the transmembrane regions. Our data provide evidence for a strong impact of protein structural features that influence peptide processing, contributing to the discrepancies observed between experimentally determined and computer-predicted CD4(+) T cell epitopes. Importance: Tick-borne encephalitis virus is endemic in large parts of Europe and Asia and causes more than 10,000 annual cases of neurological disease in humans. It is closely related to yellow fever, dengue, Japanese encephalitis, and West Nile viruses, and vaccination with an inactivated vaccine can effectively prevent disease. Both vaccination and natural infection induce the formation of antibodies to a viral surface protein that neutralize the infectivity of the virus and mediate protection. B lymphocytes synthesizing these antibodies require help from other lymphocytes (helper T cells) which recognize small peptides derived from proteins contained in the viral particle. Which of these peptides dominate immune responses to vaccination and infection, however, was unknown. In our study we demonstrate which parts of the proteins contribute most strongly to the helper T cell response, highlight specific weaknesses of currently available approaches for their prediction, and demonstrate similarities and differences between vaccination and infection.
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9
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Mitić NS, Pavlović MD, Jandrlić DR. Epitope distribution in ordered and disordered protein regions - part A. T-cell epitope frequency, affinity and hydropathy. J Immunol Methods 2014; 406:83-103. [PMID: 24614036 DOI: 10.1016/j.jim.2014.02.012] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2013] [Revised: 02/27/2014] [Accepted: 02/27/2014] [Indexed: 02/08/2023]
Abstract
Highly disordered protein regions are prevalently hydrophilic, extremely sensitive to proteolysis in vitro, and are expected to be under-represented as T-cell epitopes. The aim of this research was to find out whether disorder and hydropathy prediction methods could help in understanding epitope processing and presentation. According to the pan-specific T-cell epitope predictors NetMHCpan and NetMHCIIpan and 9 publicly available disorder predictors, frequency of epitopes presented by human leukocyte antigens (HLA) class-I or -II was found to be more than 2.5 times higher in ordered than in disordered protein regions (depending on the disorder predictor). Both HLA class-I and HLA class-II binding epitopes are prevalently hydrophilic in disordered and prevalently hydrophobic in ordered protein regions, whereas epitopes recognized by HLA class-II alleles are more hydrophobic than those recognized by HLA class-I. As regards both classes of HLA molecules, high-affinity binding epitopes display more hydrophobicity than low affinity-binding epitopes (in both ordered and disordered regions). Epitopes belonging to disordered protein regions were not predicted to have poor affinity to HLA class-II molecules, as expected from disorder intrinsic proteolytic instability. The relation of epitope hydrophobicity and order/disorder location was also valid if alleles were grouped according to the HLA class-I and HLA class-II supertypes, except for the class-I supertype A3 in which the main part of recognized epitopes was prevalently hydrophilic. Regarding specific supertypes, the affinity of epitopes belonging to ordered regions varies only slightly (depending on the disorder predictor) compared to the affinity of epitopes in corresponding disordered regions. The distribution of epitopes in ordered and disordered protein regions has revealed that the curves of order-epitope distribution were convex-like while the curves of disorder-epitope distribution were concave-like. The percentage of prevalently hydrophobic epitopes increases with the enhancement of epitope promiscuity level and moving from disordered to ordered regions. These data suggests that reverse vaccinology, oriented towards promiscuous and high-affinity epitopes, is also oriented towards prevalently hydrophobic, ordered regions. The analysis of predicted and experimentally evaluated epitopes of cancer-testis antigen MAGE-A3 has confirmed that the majority of T-cell epitopes, particularly those that are promiscuous or naturally processed, was located in ordered and disorder/order boundary protein regions overlapping hydrophobic regions.
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Affiliation(s)
- Nenad S Mitić
- University of Belgrade, Faculty of Mathematics, P.O.B. 550, Studentski trg 16, Belgrade, Serbia.
| | - Mirjana D Pavlović
- University of Belgrade, Institute of General and Physical Chemistry, Studentski trg 12/V, Belgrade, Serbia.
| | - Davorka R Jandrlić
- University of Belgrade, Faculty of Mechanical Engineering, Kraljice Marije 16, Belgrade, Serbia.
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10
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HIV-1 Env DNA vaccine plus protein boost delivered by EP expands B- and T-cell responses and neutralizing phenotype in vivo. PLoS One 2013; 8:e84234. [PMID: 24391921 PMCID: PMC3877240 DOI: 10.1371/journal.pone.0084234] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2013] [Accepted: 11/13/2013] [Indexed: 02/07/2023] Open
Abstract
An effective HIV vaccine will most likely require the induction of strong T-cell responses, broadly neutralizing antibodies (bNAbs), and the elicitation of antibody-dependent cellular cytotoxicity (ADCC). Previously, we demonstrated the induction of strong HIV/SIV cellular immune responses in macaques and humans using synthetic consensus DNA immunogens delivered via adaptive electroporation (EP). However, the ability of this improved DNA approach to prime for relevant antibody responses has not been previously studied. Here, we investigate the immunogenicity of consensus DNA constructs encoding gp140 sequences from HIV-1 subtypes A, B, C and D in a DNA prime-protein boost vaccine regimen. Mice and guinea pigs were primed with single- and multi-clade DNA via EP and boosted with recombinant gp120 protein. Sera were analyzed for gp120 binding and induction of neutralizing antibody activity. Immunization with recombinant Env protein alone induced low-titer binding antibodies with limited neutralization breath. In contrast, the synthetic DNA prime-protein boost protocol induced significantly higher antibody binding titers. Furthermore, sera from DNA prime-protein boost groups were able to neutralize a broader range of viruses in a panel of tier 1 clade B viruses as well as multiple tier 1 clade A and clade C viruses. Further investigation of synthetic DNA prime plus adaptive EP plus protein boost appears warranted.
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11
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Mann B, Thornton J, Heath R, Wade KR, Tweten RK, Gao G, El Kasmi K, Jordan JB, Mitrea DM, Kriwacki R, Maisonneuve J, Alderson M, Tuomanen EI. Broadly protective protein-based pneumococcal vaccine composed of pneumolysin toxoid-CbpA peptide recombinant fusion protein. J Infect Dis 2013; 209:1116-25. [PMID: 24041791 DOI: 10.1093/infdis/jit502] [Citation(s) in RCA: 60] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
BACKGROUND Pneumococcus, meningococcus, and Haemophilus influenzae cause a similar spectrum of infections in the ear, lung, blood, and brain. They share cross-reactive antigens that bind to the laminin receptor of the blood-brain barrier as a molecular basis for neurotropism, and this step in pathogenesis was addressed in vaccine design. METHODS Biologically active peptides derived from choline-binding protein A (CbpA) of pneumococcus were identified and then genetically fused to L460D pneumolysoid. The fusion construct was tested for vaccine efficacy in mouse models of nasopharyngeal carriage, otitis media, pneumonia, sepsis, and meningitis. RESULTS The CbpA peptide-L460D pneumolysoid fusion protein was more broadly immunogenic than pneumolysoid alone, and antibodies were active in vitro against Streptococcus pneumoniae, Neisseria meningitidis, and H. influenzae. Passive and active immunization protected mice from pneumococcal carriage, otitis media, pneumonia, bacteremia, meningitis, and meningococcal sepsis. CONCLUSIONS The CbpA peptide-L460D pneumolysoid fusion protein was broadly protective against pneumococcal infection, with the potential for additional protection against other meningeal pathogens.
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12
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Hurwitz JL, Zhan X, Brown SA, Bonsignori M, Stambas J, Lockey TD, Jones B, Surman S, Sealy R, Freiden P, Branum K, Slobod KS. A Multi-Vector, Multi-Envelope HIV-1 Vaccine. J Pediatr Pharmacol Ther 2013; 12:68-76. [PMID: 23055844 DOI: 10.5863/1551-6776-12.2.68] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
The St. Jude Children's Research Hospital (St. Jude) HIV-1 vaccine program is based on the observation that multiple antigenically distinct HIV-1 envelope protein structures are capable of mediating HIV-1 infection. A cocktail vaccine comprising representatives of these diverse structures (immunotypes) is therefore considered necessary to elicit lymphocyte populations that prevent HIV-1 infection. This strategy is reminiscent of that used to design a currently licensed and successful 23-valent pneumococcus vaccine. Three recombinant vector systems are used for the delivery of envelope cocktails (DNA, vaccinia virus, and purified protein), and each of these has been tested individually in phase I safety trials. A fourth FDA-approved clinical trial, in which diverse envelopes and vectors are combined in a prime-boost vaccination regimen, has recently begun. This trial will continue to test the hypothesis that a multi-vector, multi-envelope vaccine can elicit diverse B- and T-cell populations that can prevent HIV-1 infections in humans.
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Affiliation(s)
- Julia L Hurwitz
- Departments of Immunology ; Infectious Diseases, St. Jude Children's Research Hospital ; Departments of Pathology
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13
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Identification of an HLA-DPB1*0501 restricted Melan-A/MART-1 epitope recognized by CD4+ T lymphocytes: prevalence for immunotherapy in Asian populations. J Immunother 2011; 34:525-34. [PMID: 21760531 DOI: 10.1097/cji.0b013e318226bd45] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
CD4 T lymphocytes play a central role in orchestrating an efficient antitumor immune response. Much effort has been devoted in the identification of major histocompatibility complex class II eptiopes from different tumor-associated antigens. Melan-A/MART-1 is expressed specifically in normal melanocytes and tumor cells of 75% to 100% of melanoma patients. Melan-A/MART-1 is considered as an attractive target for cancer immunotherapy. In the past, several human leukocyte antigen (HLA) class II restricted epitopes have been identified and characterized, including Melan-A/MART-11-20 (HLA-DR11 restricted), Melan-A/MART-125-36 (HLA-DQ6 and HLA-DR3 restricted), Melan-A/MART-127-40 (HLA-DR1 restricted), Melan-A/MART-151-73 (HLA-DR4 restricted), Melan-A/MART-191-110 (HLA-DR52 restricted), and Melan-A/MART-1100-111 (HLA-DR1 restricted). Owing to the infrequent expression of the above HLA class II alleles in Asian populations, immunotherapy using these defined Melan-A/MART-1 peptides could potentially only benefit a very small percentage of Asian melanoma patients. In this study, we established several CD4 T-cell clones by in vitro stimulation of peripheral blood mononuclear cells from a healthy donor by a peptide pool of 28 to 30 amino acid long peptides spanning the entire Melan-A/MART-1 protein. These CD4 T-cell clones recognized a peptide that is embedded within Melan-A/MART-121-50, in a HLA-DPB1*0501 restricted manner. Finally, we demonstrated that this epitope is naturally processed and presented by dendritic cells. HLA-DPB1*0501 is frequently expressed in Asian population (44.9% to 73.1%). Therefore, this epitope could provide a new tool and could significantly increase the percentage of melanoma patients that can benefit from cancer immunotherapy.
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Zhao P, Ma DX, Yu S, Xue FZ, Zhu WW, Shao N, Zhang JR, Ji CY. The development of Chinese specific human cytomegalovirus polyepitope recombinant vaccine. Antiviral Res 2011; 93:260-269. [PMID: 22197248 PMCID: PMC7114286 DOI: 10.1016/j.antiviral.2011.12.005] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2011] [Revised: 11/10/2011] [Accepted: 12/07/2011] [Indexed: 11/24/2022]
Abstract
Human cytomegalovirus (HCMV) infection is a major cause of morbidity in the recipients of organ transplants and in the congenitally infected infants. HCMV vaccine has emerged as an effective approach to prevent HCMV infection particularly for the development of multiple viral antigens vaccination and human leukocyte antigen (HLA)-restricted polyepitope technology. As the Chinese population makes up more than one fifth of the population worldwide, it is important to develop HCMV vaccines more specific for the Chinese population by targeting Chinese-restricted HLA alleles and antigens. In the present study, we designed a novel chimeric polyepitope vaccine based on the replication-deficient adenovirus Ad5F35, which encodes 83 HCMV T cell epitopes from 15 different HCMV antigens, restricted to 14 HLA I and 7 HLA II alleles that cover 92% of the Chinese population. Our results show that the recombinant adenovirus vaccine Ad5F35-CTL·Th can be efficiently transfected and expressed in peripheral blood mononuclear cells (PBMCs) with little cytopathic activity. Ad5F35-CTL·Th can also be endogenously processed and presented by PBMCs. Ad5F35-CTL·Th-stimulated HCMV-specific cytotoxic T lymphocytes (CTLs) showed strong cytolytic activity against HCMV polyepitope-sensitized target cells. The CTL activity was accompanied by high levels of IFN-γ production after Ad5F35-CTL·Th stimulation. The specificity and vigorous response to the recombinant adenovirus vaccine in vitro makes it a potential candidate to be used for transplantation recipients or congenitally infected infants.
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Affiliation(s)
- Ping Zhao
- Department of Hematology, Qilu Hospital, Shandong University, Jinan 250012, PR China; Department of Pediatrics, Provincial Hospital Affiliated to Shandong University, Jinan 250021, PR China
| | - Dao-Xin Ma
- Department of Hematology, Qilu Hospital, Shandong University, Jinan 250012, PR China.
| | - Shuang Yu
- Department of Hematology, Qilu Hospital, Shandong University, Jinan 250012, PR China
| | - Fu-Zhong Xue
- Institute of Epidemiology and Health Statistics, School of Public Health of Shandong University, Jinan 250012, PR China
| | - Wei-Wei Zhu
- Department of Pediatrics, Jinan Central Hospital Affiliated to Shandong University, Jinan 250013, PR China
| | - Na Shao
- Department of Hematology, Qilu Hospital, Shandong University, Jinan 250012, PR China
| | - Jing-Ru Zhang
- Department of Hematology, Qilu Hospital, Shandong University, Jinan 250012, PR China
| | - Chun-Yan Ji
- Department of Hematology, Qilu Hospital, Shandong University, Jinan 250012, PR China.
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Zvi A, Rotem S, Bar-Haim E, Cohen O, Shafferman A. Whole-genome immunoinformatic analysis of F. tularensis: predicted CTL epitopes clustered in hotspots are prone to elicit a T-cell response. PLoS One 2011; 6:e20050. [PMID: 21625462 PMCID: PMC3098878 DOI: 10.1371/journal.pone.0020050] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2011] [Accepted: 04/13/2011] [Indexed: 12/21/2022] Open
Abstract
The cellular arm of the immune response plays a central role in the defense against intracellular pathogens, such as F. tularensis. To date, whole genome immunoinformatic analyses were limited either to relatively small genomes (e.g. viral) or to preselected subsets of proteins in complex pathogens. Here we present, for the first time, an unbiased bacterial global immunoinformatic screen of the 1740 proteins of F. tularensis subs. holarctica (LVS), aiming at identification of immunogenic peptides eliciting a CTL response. The very large number of predicted MHC class I binders (about 100,000, IC50 of 1000 nM or less) required the design of a strategy for further down selection of CTL candidates. The approach developed focused on mapping clusters rich in overlapping predicted epitopes, and ranking these “hotspot” regions according to the density of putative binding epitopes. Limited by the experimental load, we selected to screen a library of 1240 putative MHC binders derived from 104 top-ranking highly dense clusters. Peptides were tested for their ability to stimulate IFNγ secretion from splenocytes isolated from LVS vaccinated C57BL/6 mice. The majority of the clusters contained one or more CTL responder peptides and altogether 127 novel epitopes were identified, of which 82 are non-redundant. Accordingly, the level of success in identification of positive CTL responders was 17–25 fold higher than that found for a randomly selected library of 500 predicted MHC binders (IC50 of 500 nM or less). Most proteins (ca. 2/3) harboring the highly dense hotspots are membrane-associated. The approach for enrichment of true positive CTL epitopes described in this study, which allowed for over 50% increase in the dataset of known T-cell epitopes of F. tularensis, could be applied in immunoinformatic analyses of many other complex pathogen genomes.
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Affiliation(s)
- Anat Zvi
- Department of Biochemistry and Molecular Genetics, Israel Institute for Biological Research, Ness Ziona, Israel
| | - Shahar Rotem
- Department of Biochemistry and Molecular Genetics, Israel Institute for Biological Research, Ness Ziona, Israel
| | - Erez Bar-Haim
- Department of Biochemistry and Molecular Genetics, Israel Institute for Biological Research, Ness Ziona, Israel
| | - Ofer Cohen
- Department of Biochemistry and Molecular Genetics, Israel Institute for Biological Research, Ness Ziona, Israel
| | - Avigdor Shafferman
- Department of Biochemistry and Molecular Genetics, Israel Institute for Biological Research, Ness Ziona, Israel
- * E-mail:
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MULTIPRED2: a computational system for large-scale identification of peptides predicted to bind to HLA supertypes and alleles. J Immunol Methods 2010; 374:53-61. [PMID: 21130094 PMCID: PMC3090484 DOI: 10.1016/j.jim.2010.11.009] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2010] [Revised: 10/29/2010] [Accepted: 11/18/2010] [Indexed: 02/07/2023]
Abstract
MULTIPRED2 is a computational system for facile prediction of peptide binding to multiple alleles belonging to human leukocyte antigen (HLA) class I and class II DR molecules. It enables prediction of peptide binding to products of individual HLA alleles, combination of alleles, or HLA supertypes. NetMHCpan and NetMHCIIpan are used as prediction engines. The 13 HLA Class I supertypes are A1, A2, A3, A24, B7, B8, B27, B44, B58, B62, C1, and C4. The 13 HLA Class II DR supertypes are DR1, DR3, DR4, DR6, DR7, DR8, DR9, DR11, DR12, DR13, DR14, DR15, and DR16. In total, MULTIPRED2 enables prediction of peptide binding to 1077 variants representing 26 HLA supertypes. MULTIPRED2 has visualization modules for mapping promiscuous T-cell epitopes as well as those regions of high target concentration – referred to as T-cell epitope hotspots. Novel graphic representations are employed to display the predicted binding peptides and immunological hotspots in an intuitive manner and also to provide a global view of results as heat maps. Another function of MULTIPRED2, which has direct relevance to vaccine design, is the calculation of population coverage. Currently it calculates population coverage in five major groups in North America. MULTIPRED2 is an important tool to complement wet-lab experimental methods for identification of T-cell epitopes. It is available at http://cvc.dfci.harvard.edu/multipred2/.
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Surman SL, Brown SA, Jones BG, Woodland DL, Hurwitz JL. Clearance of HIV type 1 envelope recombinant sendai virus depends on CD4+ T cells and interferon-gamma but not B cells, CD8+ T cells, or perforin. AIDS Res Hum Retroviruses 2010; 26:783-93. [PMID: 20623995 DOI: 10.1089/aid.2009.0266] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
T cell-mediated viral clearance is classically attributed to the CD8(+) T cell subset, but CD4(+) T cells can sometimes assume this role. One such instance was illustrated by the immunization of C57BL/6 mice with HIV-1 envelope, followed by challenge with a recombinant Sendai virus (rSeV-env) carrying a gene for secreted HIV-1 envelope protein. Vaccinated mice that lacked both B cells (microMT) and CD8(+) T cells controlled virus, but control was lost when CD4(+) T cells were depleted. To explain this activity, we questioned whether CD4(+) T cells might utilize perforin for killing of MHC class II-positive targets. We also asked if the process might depend on IFN-gamma, which can upregulate MHC expression and enhance T cell recruitment to sites of virus challenge. To address these possibilities, we vaccinated perforin-KO mice with HIV-1 envelope and challenged them with rSeV-env. We found that perforin was not required for (1) CD4(+) T cell homing to the site of virus challenge, (2) expression of Th1 and Th2 cytokines (including IFN-gamma), or (3) virus clearance. To determine if IFN-gamma was required for protection, we repeated experiments in IFN-gamma-KO animals. In this case, significant protection was lost, although the CD4(+) T cells trafficked readily to the site of infection. In fact, local CD4(+) T cell numbers in vaccinated IFN-gamma- KO mice exceeded those in wild type animals. In both cases, cells were alphass TCR(+), NK-1.1(-), and CD44(+), typifying an activated CD4(+) T cell subset. Taken together, our results showed that HIV-1 envelope recombinant virus clearance was dependent on CD4(+) T cells and IFN-gamma, but occurred in the absence of B cells, CD8(+) T cells, or perforin.
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Affiliation(s)
- Sherri L. Surman
- Department of Infectious Diseases, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Scott A. Brown
- Department of Infectious Diseases, St. Jude Children's Research Hospital, Memphis, Tennessee
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Bart G. Jones
- Department of Infectious Diseases, St. Jude Children's Research Hospital, Memphis, Tennessee
| | | | - Julia L. Hurwitz
- Department of Infectious Diseases, St. Jude Children's Research Hospital, Memphis, Tennessee
- Department of Pediatrics, University of Tennessee, Memphis, Tennessee
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Maree L, van Zyl GU, Lotter SL, de Beer C, Esser MM, Preiser W. Young age a predictor of weak reactivity in a rapid antibody test in infants infected with HIV. J Med Virol 2010; 82:1314-7. [DOI: 10.1002/jmv.21832] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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Saffari B, Mohabatkar H. Computational analysis of cysteine proteases (Clan CA, Family Cl) of Leishmania major to find potential epitopic regions. GENOMICS PROTEOMICS & BIOINFORMATICS 2010; 7:87-95. [PMID: 19944381 PMCID: PMC5054412 DOI: 10.1016/s1672-0229(08)60037-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Abstract
Leishmania is associated with a broad spectrum of diseases, ranging from simple cutaneous to invasive visceral leishmaniasis. Here, the sequences of ten cysteine proteases of types A, B and C of Leishmania major were obtained from GeneDB database. Prediction of MHC class I epitopes of these cysteine proteases was performed by NetCTL program version 1.2. In addition, by using BcePred server, different structural properties of the proteins were predicted to find out their potential B cell epitopes. According to this computational analysis, nine regions were predicted as B cell epitopes. The results provide useful information for designing peptide-based vaccines.
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Affiliation(s)
- Babak Saffari
- Department of Biology, College of Sciences, Shiraz University, Shiraz, Iran
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20
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Brown SA, Surman SL, Sealy R, Jones BG, Slobod KS, Branum K, Lockey TD, Howlett N, Freiden P, Flynn P, Hurwitz JL. Heterologous Prime-Boost HIV-1 Vaccination Regimens in Pre-Clinical and Clinical Trials. Viruses 2010; 2:435-467. [PMID: 20407589 PMCID: PMC2855973 DOI: 10.3390/v2020435] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2009] [Revised: 01/12/2010] [Accepted: 01/22/2010] [Indexed: 12/21/2022] Open
Abstract
Currently, there are more than 30 million people infected with HIV-1 and thousands more are infected each day. Vaccination is the single most effective mechanism for prevention of viral disease, and after more than 25 years of research, one vaccine has shown somewhat encouraging results in an advanced clinical efficacy trial. A modified intent-to-treat analysis of trial results showed that infection was approximately 30% lower in the vaccine group compared to the placebo group. The vaccine was administered using a heterologous prime-boost regimen in which both target antigens and delivery vehicles were changed during the course of inoculations. Here we examine the complexity of heterologous prime-boost immunizations. We show that the use of different delivery vehicles in prime and boost inoculations can help to avert the inhibitory effects caused by vector-specific immune responses. We also show that the introduction of new antigens into boost inoculations can be advantageous, demonstrating that the effect of `original antigenic sin' is not absolute. Pre-clinical and clinical studies are reviewed, including our own work with a three-vector vaccination regimen using recombinant DNA, virus (Sendai virus or vaccinia virus) and protein. Promising preliminary results suggest that the heterologous prime-boost strategy may possibly provide a foundation for the future prevention of HIV-1 infections in humans.
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Affiliation(s)
- Scott A. Brown
- Department of Immunology, St. Jude Children’s Research Hospital, 262 Danny Thomas Place, Memphis, TN, USA; E-Mail: (S.A.B.)
- Department of Infectious Diseases, St. Jude Children’s Research Hospital, 262 Danny Thomas Place, Memphis, TN, USA; E-Mails: (S.L.S.); (R.S.); (B.G.J.); (K.B.); (N.H.); (P.F.); (P.F.)
| | - Sherri L. Surman
- Department of Infectious Diseases, St. Jude Children’s Research Hospital, 262 Danny Thomas Place, Memphis, TN, USA; E-Mails: (S.L.S.); (R.S.); (B.G.J.); (K.B.); (N.H.); (P.F.); (P.F.)
| | - Robert Sealy
- Department of Infectious Diseases, St. Jude Children’s Research Hospital, 262 Danny Thomas Place, Memphis, TN, USA; E-Mails: (S.L.S.); (R.S.); (B.G.J.); (K.B.); (N.H.); (P.F.); (P.F.)
| | - Bart G. Jones
- Department of Infectious Diseases, St. Jude Children’s Research Hospital, 262 Danny Thomas Place, Memphis, TN, USA; E-Mails: (S.L.S.); (R.S.); (B.G.J.); (K.B.); (N.H.); (P.F.); (P.F.)
| | - Karen S. Slobod
- Early Development, Novartis Vaccines and Diagnostics, 350 Mass Ave. Cambridge, MA 02139, USA; E-Mail: (K.S.S.)
| | - Kristen Branum
- Department of Infectious Diseases, St. Jude Children’s Research Hospital, 262 Danny Thomas Place, Memphis, TN, USA; E-Mails: (S.L.S.); (R.S.); (B.G.J.); (K.B.); (N.H.); (P.F.); (P.F.)
| | - Timothy D. Lockey
- Department of Therapeutics, Production and Quality, St. Jude Children’s Research Hospital, 262 Danny Thomas Place, Memphis, TN, USA; E-Mail: (T.D.L.)
| | - Nanna Howlett
- Department of Infectious Diseases, St. Jude Children’s Research Hospital, 262 Danny Thomas Place, Memphis, TN, USA; E-Mails: (S.L.S.); (R.S.); (B.G.J.); (K.B.); (N.H.); (P.F.); (P.F.)
| | - Pamela Freiden
- Department of Infectious Diseases, St. Jude Children’s Research Hospital, 262 Danny Thomas Place, Memphis, TN, USA; E-Mails: (S.L.S.); (R.S.); (B.G.J.); (K.B.); (N.H.); (P.F.); (P.F.)
| | - Patricia Flynn
- Department of Infectious Diseases, St. Jude Children’s Research Hospital, 262 Danny Thomas Place, Memphis, TN, USA; E-Mails: (S.L.S.); (R.S.); (B.G.J.); (K.B.); (N.H.); (P.F.); (P.F.)
- Department of Pediatrics, University of Tennessee, Memphis, TN 38163, USA
| | - Julia L. Hurwitz
- Department of Immunology, St. Jude Children’s Research Hospital, 262 Danny Thomas Place, Memphis, TN, USA; E-Mail: (S.A.B.)
- Department of Infectious Diseases, St. Jude Children’s Research Hospital, 262 Danny Thomas Place, Memphis, TN, USA; E-Mails: (S.L.S.); (R.S.); (B.G.J.); (K.B.); (N.H.); (P.F.); (P.F.)
- Department of Pathology, University of Tennessee, Memphis, TN 38163, USA
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Influence of disulfide-stabilized structure on the specificity of helper T-cell and antibody responses to HIV envelope glycoprotein gp120. J Virol 2010; 84:3303-11. [PMID: 20089653 DOI: 10.1128/jvi.02242-09] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
CD4(+) helper T cells specific for human immunodeficiency virus type 1 (HIV-1) are associated with control of viremia. Nevertheless, vaccines have had limited effectiveness thus far, in part because sequence variability and other structural features of the HIV envelope glycoprotein deflect the immune response. Previous studies indicated that CD4(+) T-cell epitope dominance is controlled by antigen three-dimensional structure through its influence on antigen processing and presentation. In this work, three disulfide bonds in the outer domain of gp120 were individually deleted in order to destabilize the local three-dimensional structure and enhance the presentation of nearby weakly immunogenic epitopes. However, upon immunization of groups of BALB/c mice, the CD4(+) T-cell response was broadly reduced for all three variants, and distinct epitope profiles emerged. For one variant, antibody titers were sharply increased, and the antibody exhibited significant CD4-blocking activity.
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Surman SL, Sealy R, Jones BG, Hurwitz JL. HIV-1 vaccine design: harnessing diverse lymphocytes to conquer a diverse pathogen. HUMAN VACCINES 2009; 5:268-71. [PMID: 19684481 DOI: 10.4161/hv.5.4.7706] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
In the fall of 2007, the HIV-1 research field received news that their front-runner vaccine was not protective. In response to this disappointment, scientists are now reviewing the intricacies of the immune response toward HIV-1 to develop new and better strategies for vaccine development. Decades ago, researchers recognized the impressive amino acid and carbohydrate diversity of HIV-1, and the associated obstacles to vaccine development. At first glance, the diversity and other unique features of HIV-1 may seem insurmountable, but attention to vaccine successes in other fields serves to renew optimism. The newly-licensed rotavirus and papillomavirus cocktail vaccines remind scientists that diverse pathogens can be conquered and that the chronic nature of a virus infection need not thwart successful vaccine design. Here we describe current efforts to gain insights from other vaccine fields and to adopt a cocktail vaccine approach for the prevention of HIV-1 infections in humans.
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Affiliation(s)
- Sherri L Surman
- Department of Infectious Diseases, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
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Weaver JM, Sant AJ. Understanding the focused CD4 T cell response to antigen and pathogenic organisms. Immunol Res 2009; 45:123-43. [PMID: 19198764 DOI: 10.1007/s12026-009-8095-8] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Immunodominance is a term that reflects the final, very limited peptide specificity of T cells that are elicited during an immune response. Recent experiments in our laboratory compel us to propose a new paradigm for the control of immunodominance in CD4 T cell responses, stating that immunodominance is peptide-intrinsic and is dictated by the off-rate of peptides from MHC class II molecules. Our studies have revealed that persistence of peptide:class II complexes both predicts and controls CD4 T cell immunodominance and that this parameter can be rationally manipulated to either promote or eliminate immune responses. Mechanistically, we have determined that DM editing in APC is a key event that is influenced by the kinetic stability of class II:peptide complexes and that differential persistence of complexes also impacts the expansion phase of the immune response. These studies have important implications for rational vaccine design and for understanding the immunological mechanisms that limit the specificity of CD4 T cell responses.
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Affiliation(s)
- Jason M Weaver
- David H. Smith Center for Vaccine Biology and Immunology, AaB Institute of Biomedical Sciences, Department of Microbiology and Immunology, University of Rochester, NY 14642, USA
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Lubong Sabado R, Kavanagh DG, Kaufmann DE, Fru K, Babcock E, Rosenberg E, Walker B, Lifson J, Bhardwaj N, Larsson M. In vitro priming recapitulates in vivo HIV-1 specific T cell responses, revealing rapid loss of virus reactive CD4 T cells in acute HIV-1 infection. PLoS One 2009; 4:e4256. [PMID: 19165342 PMCID: PMC2626278 DOI: 10.1371/journal.pone.0004256] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2008] [Accepted: 12/13/2008] [Indexed: 01/08/2023] Open
Abstract
BACKGROUND The requirements for priming of HIV-specific T cell responses initially seen in infected individuals remain to be defined. Activation of T cell responses in lymph nodes requires cell-cell contact between T cells and DCs, which can give concurrent activation of T cells and HIV transmission. METHODOLOGY The study aim was to establish whether DCs pulsed with HIV-1 could prime HIV-specific T cell responses and to characterize these responses. Both infectious and aldrithiol-2 inactivated noninfectious HIV-1 were compared to establish efficiencies in priming and the type of responses elicited. FINDINGS Our findings show that both infectious and inactivated HIV-1 pulsed DCs can prime HIV-specific responses from naïve T cells. Responses included several CD4(+) and CD8(+) T cell epitopes shown to be recognized in vivo by acutely and chronically infected individuals and some CD4(+) T cell epitopes not identified previously. Follow up studies of acute and recent HIV infected samples revealed that these latter epitopes are among the earliest recognized in vivo, but the responses are lost rapidly, presumably through activation-induced general CD4(+) T cell depletion which renders the newly activated HIV-specific CD4(+) T cells prime targets for elimination. CONCLUSION Our studies highlight the ability of DCs to efficiently prime naïve T cells and induce a broad repertoire of HIV-specific responses and also provide valuable insights to the pathogenesis of HIV-1 infection in vivo.
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Affiliation(s)
- Rachel Lubong Sabado
- New York University School of Medicine, New York, New York, United States of America
| | - Daniel G. Kavanagh
- Partners AIDS Research Center (PARC), Massachusetts General Hospital, Harvard Medical School, Charlestown, Massachusetts, United States of America
| | - Daniel E. Kaufmann
- Partners AIDS Research Center (PARC), Massachusetts General Hospital, Harvard Medical School, Charlestown, Massachusetts, United States of America
| | - Karlhans Fru
- Molecular Virology, Department of Clinical and Experimental Medicine, Linköping University, Linköping, Sweden
| | - Ethan Babcock
- New York University School of Medicine, New York, New York, United States of America
| | - Eric Rosenberg
- Partners AIDS Research Center (PARC), Massachusetts General Hospital, Harvard Medical School, Charlestown, Massachusetts, United States of America
| | - Bruce Walker
- Partners AIDS Research Center (PARC), Massachusetts General Hospital, Harvard Medical School, Charlestown, Massachusetts, United States of America
| | - Jeffrey Lifson
- SAIC Fredrick, Inc., National Cancer Institute, Fredrick, Frederick, Maryland, United States of America
| | - Nina Bhardwaj
- New York University School of Medicine, New York, New York, United States of America
| | - Marie Larsson
- Molecular Virology, Department of Clinical and Experimental Medicine, Linköping University, Linköping, Sweden
- * E-mail:
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Khan AM, Miotto O, Nascimento EJM, Srinivasan KN, Heiny AT, Zhang GL, Marques ET, Tan TW, Brusic V, Salmon J, August JT. Conservation and variability of dengue virus proteins: implications for vaccine design. PLoS Negl Trop Dis 2008; 2:e272. [PMID: 18698358 PMCID: PMC2491585 DOI: 10.1371/journal.pntd.0000272] [Citation(s) in RCA: 72] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2008] [Accepted: 07/10/2008] [Indexed: 12/27/2022] Open
Abstract
Background Genetic variation and rapid evolution are hallmarks of RNA viruses, the result of high mutation rates in RNA replication and selection of mutants that enhance viral adaptation, including the escape from host immune responses. Variability is uneven across the genome because mutations resulting in a deleterious effect on viral fitness are restricted. RNA viruses are thus marked by protein sites permissive to multiple mutations and sites critical to viral structure-function that are evolutionarily robust and highly conserved. Identification and characterization of the historical dynamics of the conserved sites have relevance to multiple applications, including potential targets for diagnosis, and prophylactic and therapeutic purposes. Methodology/Principal Findings We describe a large-scale identification and analysis of evolutionarily highly conserved amino acid sequences of the entire dengue virus (DENV) proteome, with a focus on sequences of 9 amino acids or more, and thus immune-relevant as potential T-cell determinants. DENV protein sequence data were collected from the NCBI Entrez protein database in 2005 (9,512 sequences) and again in 2007 (12,404 sequences). Forty-four (44) sequences (pan-DENV sequences), mainly those of nonstructural proteins and representing ∼15% of the DENV polyprotein length, were identical in 80% or more of all recorded DENV sequences. Of these 44 sequences, 34 (∼77%) were present in ≥95% of sequences of each DENV type, and 27 (∼61%) were conserved in other Flaviviruses. The frequencies of variants of the pan-DENV sequences were low (0 to ∼5%), as compared to variant frequencies of ∼60 to ∼85% in the non pan-DENV sequence regions. We further showed that the majority of the conserved sequences were immunologically relevant: 34 contained numerous predicted human leukocyte antigen (HLA) supertype-restricted peptide sequences, and 26 contained T-cell determinants identified by studies with HLA-transgenic mice and/or reported to be immunogenic in humans. Conclusions/Significance Forty-four (44) pan-DENV sequences of at least 9 amino acids were highly conserved and identical in 80% or more of all recorded DENV sequences, and the majority were found to be immune-relevant by their correspondence to known or putative HLA-restricted T-cell determinants. The conservation of these sequences through the entire recorded DENV genetic history supports their possible value for diagnosis, prophylactic and/or therapeutic applications. The combination of bioinformatics and experimental approaches applied herein provides a framework for large-scale and systematic analysis of conserved and variable sequences of other pathogens, in particular, for rapidly mutating viruses, such as influenza A virus and HIV. Dengue viruses (DENVs) circulate in nature as a population of 4 distinct types, each with multiple genotypes and variants, and represent an increasing global public health issue with no prophylactic and therapeutic formulations currently available. Viral genomes contain sites that are evolutionarily stable and therefore highly conserved, presumably because changes in these sites have deleterious effects on viral fitness and survival. The identification and characterization of the historical dynamics of these sites in DENV have relevance to several applications such as diagnosis and drug and vaccine development. In this study, we have identified sequence fragments that were conserved across the majority of available DENV sequences, analyzed their historical dynamics, and evaluated their relevance as candidate vaccine targets, using various bioinformatics-based methods and immune assay in human leukocyte antigen (HLA) transgenic mice. This approach provides a framework for large-scale and systematic analysis of other human pathogens.
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Affiliation(s)
- Asif M. Khan
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Olivo Miotto
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
- Institute of Systems Science, National University of Singapore, Singapore
| | - Eduardo J. M. Nascimento
- Department of Medicine, Division of Infectious Diseases, The Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
| | - K. N. Srinivasan
- Department of Pharmacology and Molecular Sciences, The Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
- Product Evaluation and Registration Division, Centre for Drug Administration, Health Sciences Authority, Singapore
| | - A. T. Heiny
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Guang Lan Zhang
- Cancer Vaccine Center, Dana-Farber Cancer Institute, Boston, Massachusetts, United States of America
| | - E. T. Marques
- Department of Medicine, Division of Infectious Diseases, The Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
- Department of Pharmacology and Molecular Sciences, The Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
| | - Tin Wee Tan
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Vladimir Brusic
- Cancer Vaccine Center, Dana-Farber Cancer Institute, Boston, Massachusetts, United States of America
| | - Jerome Salmon
- Department of Pharmacology and Molecular Sciences, The Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
| | - J. Thomas August
- Department of Pharmacology and Molecular Sciences, The Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
- * E-mail:
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26
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Mirano-Bascos D, Tary-Lehmann M, Landry SJ. Antigen structure influences helper T-cell epitope dominance in the human immune response to HIV envelope glycoprotein gp120. Eur J Immunol 2008; 38:1231-7. [PMID: 18398933 DOI: 10.1002/eji.200738011] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
The development of an effective vaccine against HIV/AIDS has been hampered, in part, by a poor understanding of the rules governing helper T-cell epitope immunodominance. Studies in mice have shown that antigen structure modulates epitope immunodominance by affecting the processing and subsequent presentation of helper T-cell epitopes. Previous epitope mapping studies showed that the immunodominant helper T-cell epitopes in mice immunized with gp120 were found flanking flexible loops of the protein. In this report, we show that helper T-cell epitopes against gp120 in humans infected with HIV are also found flanking flexible loops. Immunodominant epitopes were found to be located primarily in the outer domain, an average of 12 residues C-terminal to flexible loops. In the less immunogenic inner domain, epitopes were found an average of five residues N-terminal to conserved regions of the protein, once again placing the epitopes C-terminal to flexible loops. These results show that antigen structure plays a significant role in the shaping of the helper T-cell response against HIV gp120 in humans. This relationship between antigen structure and helper T-cell epitope immunodominance may prove to be useful in the development of rationally designed vaccines against pathogens such as HIV.
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Affiliation(s)
- Denise Mirano-Bascos
- Interdisciplinary Program in the Biomedical Sciences, Tulane University, New Orleans, LA 70112, USA
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27
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Target peptide sequence within infectious human immunodeficiency virus type 1 does not ensure envelope-specific T-helper cell reactivation: influences of cysteine protease and gamma interferon-induced thiol reductase activities. CLINICAL AND VACCINE IMMUNOLOGY : CVI 2008; 15:713-9. [PMID: 18235043 DOI: 10.1128/cvi.00412-07] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Recent clinical trials have shown that the presence of a robust human immunodeficiency virus type 1 (HIV-1)-specific T-cell response may not be sufficient to prevent or control HIV-1 infection. Studies of antigen processing in the context of infectious HIV-1 are therefore warranted. Envelope-specific, major histocompatibility complex class II-restricted murine T-cell hybridomas were tested for responsiveness to splenic antigen-presenting cells exposed to HIV-1-infected GHOST cells. Interleukin-2 assays showed that the presence of a peptide within HIV-1 did not ensure the reactivation of peptide-specific T cells. Further experiments defined the impact of gamma interferon-induced thiol reductase and cysteine proteases on the processing of HIV-1 peptides. The results highlight potential influences of peptide context on T-cell reactivation by HIV-1 and encourage the continued study of antigen processing as support for improved vaccine design.
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28
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Zhang GL, Khan AM, Srinivasan KN, Heiny AT, Lee KX, Kwoh CK, August JT, Brusic V. Hotspot Hunter: a computational system for large-scale screening and selection of candidate immunological hotspots in pathogen proteomes. BMC Bioinformatics 2008; 9 Suppl 1:S19. [PMID: 18315850 PMCID: PMC2259420 DOI: 10.1186/1471-2105-9-s1-s19] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
BACKGROUND T-cell epitopes that promiscuously bind to multiple alleles of a human leukocyte antigen (HLA) supertype are prime targets for development of vaccines and immunotherapies because they are relevant to a large proportion of the human population. The presence of clusters of promiscuous T-cell epitopes, immunological hotspots, has been observed in several antigens. These clusters may be exploited to facilitate the development of epitope-based vaccines by selecting a small number of hotspots that can elicit all of the required T-cell activation functions. Given the large size of pathogen proteomes, including of variant strains, computational tools are necessary for automated screening and selection of immunological hotspots. RESULTS Hotspot Hunter is a web-based computational system for large-scale screening and selection of candidate immunological hotspots in pathogen proteomes through analysis of antigenic diversity. It allows screening and selection of hotspots specific to four common HLA supertypes, namely HLA class I A2, A3, B7 and class II DR. The system uses Artificial Neural Network and Support Vector Machine methods as predictive engines. Soft computing principles were employed to integrate the prediction results produced by both methods for robust prediction performance. Experimental validation of the predictions showed that Hotspot Hunter can successfully identify majority of the real hotspots. Users can predict hotspots from a single protein sequence, or from a set of aligned protein sequences representing pathogen proteome. The latter feature provides a global view of the localizations of the hotspots in the proteome set, enabling analysis of antigenic diversity and shift of hotspots across protein variants. The system also allows the integration of prediction results of the four supertypes for identification of hotspots common across multiple supertypes. The target selection feature of the system shortlists candidate peptide hotspots for the formulation of an epitope-based vaccine that could be effective against multiple variants of the pathogen and applicable to a large proportion of the human population. CONCLUSION Hotspot Hunter is publicly accessible at http://antigen.i2r.a-star.edu.sg/hh/. It is a new generation computational tool aiding in epitope-based vaccine design.
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Affiliation(s)
- Guang Lan Zhang
- Institute for Infocomm Research, 21 Heng Mui Keng Terrace, Singapore 119613
- School of Computer Engineering, Nanyang Technological University, Singapore 639798
| | - Asif M Khan
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117597
- Department of Microbiology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117597
| | - Kellathur N Srinivasan
- Department of Pharmacology and Molecular Sciences, Johns Hopkins School of Medicine, Baltimore, MD 21205, USA
- Product Evaluation and Registration Division, Centre for Drug Administration, Health Sciences Authority, 11 Biopolis Way, #011-03 Helios, Singapore 138667
| | - AT Heiny
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117597
| | - KX Lee
- Department of Microbiology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117597
| | - Chee Keong Kwoh
- School of Computer Engineering, Nanyang Technological University, Singapore 639798
| | - J Thomas August
- Department of Pharmacology and Molecular Sciences, Johns Hopkins School of Medicine, Baltimore, MD 21205, USA
| | - Vladimir Brusic
- Cancer Vaccine Center, Dana-Farber Cancer Institute, Boston, MA 02115, USA
- School of Land, Crop, and Food Sciences, University of Queensland, Brisbame 4072, Australia
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29
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Brown SA, Hurwitz JL, Zirkel A, Surman S, Takimoto T, Alymova I, Coleclough C, Portner A, Doherty PC, Slobod KS. A recombinant Sendai virus is controlled by CD4+ effector T cells responding to a secreted human immunodeficiency virus type 1 envelope glycoprotein. J Virol 2007; 81:12535-42. [PMID: 17652379 PMCID: PMC2168998 DOI: 10.1128/jvi.00197-07] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
The importance of antigen-specific CD4(+) helper T cells in virus infections is well recognized, but their possible role as direct mediators of virus clearance is less well characterized. Here we describe a recombinant Sendai virus strategy for probing the effector role(s) of CD4(+) T cells. Mice were vaccinated with DNA and vaccinia virus recombinant vectors encoding a secreted human immunodeficiency virus type 1 (HIV-1) envelope protein and then challenged with a Sendai virus carrying a homologous HIV-1 envelope gene. The primed mice showed (i) prompt homing of numerous envelope-primed CD4(+) T cell populations to the virus-infected lung, (ii) substantial production of gamma interferon, and interleukin-2 (IL-2), IL-4, and IL-5 in that site, and (iii) significantly reduced pulmonary viral load. The challenge experiments were repeated with immunoglobulin(-/-) microMT mice in the presence or absence of CD8(+) and/or CD4(+) T cells. These selectively immunodeficient mice were protected by primed CD4(+) T cells in the absence of antibody or CD8(+) T cells. Together, these results highlight the role of CD4(+) T cells as direct effectors in vivo and, because this protocol gives such a potent response, identify an outstanding experimental model for further dissecting CD4(+) T-cell-mediated immunity in the lung.
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30
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Zhan X, Hurwitz JL, Brown SA, Slobod KS. HIV-1 envelope T cell epitope "hotspots " among mice and humans and among CD4+ and CD8+ T cell subpopulations. AIDS Res Hum Retroviruses 2007; 23:471-6. [PMID: 17411381 DOI: 10.1089/aid.2006.0241] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
HIV-1-specific T cell responses correlate with control of infection and disease, thus encouraging a full understanding of the peptides and antigen-processing mechanisms that govern T cell activation. We have previously demonstrated that CD4(+) T cell epitopes cluster nonrandomly within envelope protein "hotspot" regions. The current study was initiated to determine whether envelope-specific CD8(+) T cells might share epitope "hotspots" with the CD4(+) T cell population. Identification of CD8(+) T cell determinants by ELISPOT assays with peripheral blood mononuclear cells from four HIV-1-infected individuals, in conjunction with a survey of determinants in the Los Alamos database, revealed similarities among "hotspot" positions for CD4(+) and CD8T(+) cells within mice and humans. These results emphasized the important influence that envelope peptide position may have on antigen processing, and the consequent impact such processing may have on HIV-1-specific CD4(+) and CD8(+) T-cell activities.
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Affiliation(s)
- Xiaoyan Zhan
- Department of Infectious Diseases, St. Jude Children's Research Hospital, 332 N. Lauderdale, Memphis, Tennessee 38105, USA
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31
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Khan AM, Miotto O, Heiny A, Salmon J, Srinivasan K, Nascimento E, Marques ET, Brusic V, Tan TW, August JT. A systematic bioinformatics approach for selection of epitope-based vaccine targets. Cell Immunol 2006; 244:141-7. [PMID: 17434154 PMCID: PMC2041846 DOI: 10.1016/j.cellimm.2007.02.005] [Citation(s) in RCA: 69] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2007] [Accepted: 02/06/2007] [Indexed: 11/24/2022]
Abstract
Epitope-based vaccines provide a new strategy for prophylactic and therapeutic application of pathogen-specific immunity. A critical requirement of this strategy is the identification and selection of T-cell epitopes that act as vaccine targets. This study describes current methodologies for the selection process, with dengue virus as a model system. A combination of publicly available bioinformatics algorithms and computational tools are used to screen and select antigen sequences as potential T-cell epitopes of supertype human leukocyte antigen (HLA) alleles. The selected sequences are tested for biological function by their activation of T-cells of HLA transgenic mice and of pathogen infected subjects. This approach provides an experimental basis for the design of pathogen specific, T-cell epitope-based vaccines that are targeted to majority of the genetic variants of the pathogen, and are effective for a broad range of differences in human leukocyte antigens among the global human population.
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Affiliation(s)
- Asif M. Khan
- Department of Microbiology, Yong Loo Lin School of Medicine, National University of Singapore, 5 Science Drive 2, Singapore 117597, Singapore
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, 8 Medical Drive, Singapore 117597, Singapore
| | - Olivo Miotto
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, 8 Medical Drive, Singapore 117597, Singapore
- Institute of Systems Science, National University of Singapore, 25 Heng Mui Keng Terrace, Singapore 119615, Singapore
| | - A.T. Heiny
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, 8 Medical Drive, Singapore 117597, Singapore
| | - Jerome Salmon
- Department of Pharmacology and Molecular Sciences, The Johns Hopkins University School of Medicine, 725 North Wolfe Street, Baltimore, MD 21205, United States of America
| | - K.N. Srinivasan
- Department of Pharmacology and Molecular Sciences, The Johns Hopkins University School of Medicine, 725 North Wolfe Street, Baltimore, MD 21205, United States of America
- Product Evaluation & Registration Division, Centre for Drug Administration, Health Sciences Authority, 11 Biopolis Way, Singapore 138667, Singapore
| | - Eduardo Nascimento
- Department of Pharmacology and Molecular Sciences, The Johns Hopkins University School of Medicine, 725 North Wolfe Street, Baltimore, MD 21205, United States of America
| | - Ernesto T. Marques
- Department of Pharmacology and Molecular Sciences, The Johns Hopkins University School of Medicine, 725 North Wolfe Street, Baltimore, MD 21205, United States of America
| | - Vladimir Brusic
- Department of Microbiology, Yong Loo Lin School of Medicine, National University of Singapore, 5 Science Drive 2, Singapore 117597, Singapore
- School of Land and Food Sciences, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Tin Wee Tan
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, 8 Medical Drive, Singapore 117597, Singapore
| | - J. Thomas August
- Department of Pharmacology and Molecular Sciences, The Johns Hopkins University School of Medicine, 725 North Wolfe Street, Baltimore, MD 21205, United States of America
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32
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Weaver EA, Lu Z, Camacho ZT, Moukdar F, Liao HX, Ma BJ, Muldoon M, Theiler J, Nabel GJ, Letvin NL, Korber BT, Hahn BH, Haynes BF, Gao F. Cross-subtype T-cell immune responses induced by a human immunodeficiency virus type 1 group m consensus env immunogen. J Virol 2006; 80:6745-56. [PMID: 16809280 PMCID: PMC1489064 DOI: 10.1128/jvi.02484-05] [Citation(s) in RCA: 58] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The genetic diversity among globally circulating human immunodeficiency virus type 1 (HIV-1) strains is a serious challenge for HIV-1 vaccine design. We have generated a synthetic group M consensus env gene (CON6) for induction of cross-subtype immune responses and report here a comparative study of T-cell responses to this and natural strain env immunogens in a murine model. Three different strains of mice were immunized with CON6 as well as subtype A, B, or C env immunogens, using a DNA prime-recombinant vaccinia virus boost strategy. T-cell epitopes were mapped by gamma interferon enzyme-linked immunospot analysis using five overlapping Env peptide sets from heterologous subtype A, B, and C viruses. The CON6-derived vaccine was immunogenic and induced a greater number of T-cell epitope responses than any single wild-type subtype A, B, and C env immunogen and similar T-cell responses to a polyvalent vaccine. The responses were comparable to within-clade responses but significantly more than between-clade responses. The magnitude of the T-cell responses induced by CON6 (measured by individual epitope peptides) was also greater than the magnitude of responses induced by individual wild-type env immunogens. Though the limited major histocompatibility complex repertoire in inbred mice does not necessarily predict responses in nonhuman primates and humans, these results suggest that synthetic centralized env immunogens represent a promising approach for HIV-1 vaccine design that merits further characterization.
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MESH Headings
- AIDS Vaccines/genetics
- AIDS Vaccines/immunology
- AIDS Vaccines/pharmacology
- Animals
- Epitopes, T-Lymphocyte/genetics
- Epitopes, T-Lymphocyte/immunology
- Epitopes, T-Lymphocyte/pharmacology
- Gene Products, env/genetics
- Gene Products, env/immunology
- Gene Products, env/pharmacology
- Genetic Variation
- HIV Antigens/genetics
- HIV Antigens/immunology
- HIV Antigens/pharmacology
- HIV Infections/genetics
- HIV Infections/immunology
- HIV Infections/prevention & control
- HIV-1/genetics
- HIV-1/immunology
- Histocompatibility Antigens/immunology
- Humans
- Interferon-gamma/immunology
- Mice
- Mice, Inbred BALB C
- Peptides/genetics
- Peptides/immunology
- Peptides/pharmacology
- Species Specificity
- T-Lymphocytes/immunology
- Vaccines, DNA/genetics
- Vaccines, DNA/immunology
- Vaccines, DNA/pharmacology
- Vaccines, Synthetic/genetics
- Vaccines, Synthetic/immunology
- Vaccines, Synthetic/pharmacology
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Affiliation(s)
- Eric A Weaver
- Duke Human Vaccine Institute, Duke University Medical Center, 112 RPIII, Research Drive, Box 3347, DUMC, Durham, NC 27710, USA
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Gupta V, Tabiin TM, Sun K, Chandrasekaran A, Anwar A, Yang K, Chikhlikar P, Salmon J, Brusic V, Marques ET, Kellathur SN, August TJ. SARS coronavirus nucleocapsid immunodominant T-cell epitope cluster is common to both exogenous recombinant and endogenous DNA-encoded immunogens. Virology 2006; 347:127-39. [PMID: 16387339 PMCID: PMC7111852 DOI: 10.1016/j.virol.2005.11.042] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2005] [Revised: 09/22/2005] [Accepted: 11/22/2005] [Indexed: 01/12/2023]
Abstract
Correspondence between the T-cell epitope responses of vaccine immunogens and those of pathogen antigens is critical to vaccine efficacy. In the present study, we analyzed the spectrum of immune responses of mice to three different forms of the SARS coronavirus nucleocapsid (N): (1) exogenous recombinant protein (N-GST) with Freund's adjuvant; (2) DNA encoding unmodified N as an endogenous cytoplasmic protein (pN); and (3) DNA encoding N as a LAMP-1 chimera targeted to the lysosomal MHC II compartment (p-LAMP-N). Lysosomal trafficking of the LAMP/N chimera in transfected cells was documented by both confocal and immunoelectron microscopy. The responses of the immunized mice differed markedly. The strongest T-cell IFN-γ and CTL responses were to the LAMP-N chimera followed by the pN immunogen. In contrast, N-GST elicited strong T cell IL-4 but minimal IFN-γ responses and a much greater antibody response. Despite these differences, however, the immunodominant T-cell ELISpot responses to each of the three immunogens were elicited by the same N peptides, with the greatest responses being generated by a cluster of five overlapping peptides, N76–114, each of which contained nonameric H2d binding domains with high binding scores for both class I and, except for N76–93, class II alleles. These results demonstrate that processing and presentation of N, whether exogenously or endogenously derived, resulted in common immunodominant epitopes, supporting the usefulness of modified antigen delivery and trafficking forms and, in particular, LAMP chimeras as vaccine candidates. Nevertheless, the profiles of T-cell responses were distinctly different. The pronounced Th-2 and humoral response to N protein plus adjuvant are in contrast to the balanced IFN-γ and IL-4 responses and strong memory CTL responses to the LAMP-N chimera.
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Affiliation(s)
- Vandana Gupta
- Division of Biomedical Sciences, Johns Hopkins in Singapore, 31 Biopolis Way, #02-01 The Nanos, Singapore 138669, Singapore
| | - Tani M. Tabiin
- Division of Biomedical Sciences, Johns Hopkins in Singapore, 31 Biopolis Way, #02-01 The Nanos, Singapore 138669, Singapore
| | - Kai Sun
- Division of Biomedical Sciences, Johns Hopkins in Singapore, 31 Biopolis Way, #02-01 The Nanos, Singapore 138669, Singapore
| | - Ananth Chandrasekaran
- Division of Biomedical Sciences, Johns Hopkins in Singapore, 31 Biopolis Way, #02-01 The Nanos, Singapore 138669, Singapore
| | - Azlinda Anwar
- Division of Biomedical Sciences, Johns Hopkins in Singapore, 31 Biopolis Way, #02-01 The Nanos, Singapore 138669, Singapore
| | - Kun Yang
- Department of Pharmacology and Molecular Sciences, The Johns Hopkins University School of Medicine, 725 N. Wolfe Street, Baltimore, MD 21205, USA
| | - Priya Chikhlikar
- Department of Pharmacology and Molecular Sciences, The Johns Hopkins University School of Medicine, 725 N. Wolfe Street, Baltimore, MD 21205, USA
| | - Jerome Salmon
- Department of Pharmacology and Molecular Sciences, The Johns Hopkins University School of Medicine, 725 N. Wolfe Street, Baltimore, MD 21205, USA
| | - Vladimir Brusic
- Institute for Infocomm Research, 21 Heng Mui Keng Terrace, Singapore 119613, Singapore
- School of Land and Food Sciences and the Institute for Molecular Bioscience, University of Queensland, Brisbane 4072, Australia
| | - Ernesto T.A. Marques
- Department of Pharmacology and Molecular Sciences, The Johns Hopkins University School of Medicine, 725 N. Wolfe Street, Baltimore, MD 21205, USA
- Department of Medicine, Division of Infectious Diseases, The Johns Hopkins University School of Medicine, 725 N. Wolfe Street, Baltimore, MD 21218, USA
- Virology and Experimental Therapy Laboratory, Aggeu Magalhaes Research Center, Recife, PE 50670-420, Brazil
| | - Srinivasan N. Kellathur
- Division of Biomedical Sciences, Johns Hopkins in Singapore, 31 Biopolis Way, #02-01 The Nanos, Singapore 138669, Singapore
- Department of Pharmacology and Molecular Sciences, The Johns Hopkins University School of Medicine, 725 N. Wolfe Street, Baltimore, MD 21205, USA
| | - Thomas J. August
- Division of Biomedical Sciences, Johns Hopkins in Singapore, 31 Biopolis Way, #02-01 The Nanos, Singapore 138669, Singapore
- Department of Pharmacology and Molecular Sciences, The Johns Hopkins University School of Medicine, 725 N. Wolfe Street, Baltimore, MD 21205, USA
- Corresponding author. Department of Pharmacology and Molecular Sciences, The Johns Hopkins University School of Medicine, 725 N. Wolfe Street, Baltimore, MD 21205, USA. Fax: +1 410 502 3066.
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Zhan X, Martin LN, Slobod KS, Coleclough C, Lockey TD, Brown SA, Stambas J, Bonsignori M, Sealy RE, Blanchard JL, Hurwitz JL. Multi-envelope HIV-1 vaccine devoid of SIV components controls disease in macaques challenged with heterologous pathogenic SHIV. Vaccine 2005; 23:5306-20. [PMID: 16095768 DOI: 10.1016/j.vaccine.2005.07.008] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2005] [Revised: 07/05/2005] [Accepted: 07/06/2005] [Indexed: 11/27/2022]
Abstract
A central obstacle to the design of a global HIV-1 vaccine is virus diversity. Pathogen diversity is not unique to HIV-1, and has been successfully conquered in other fields by the creation of vaccine cocktails. Here we describe the testing of an HIV-1 envelope cocktail vaccine. Six macaques received the vaccine, delivered by successive immunizations with recombinant DNA, recombinant vaccinia virus and recombinant envelope proteins. Following vaccination, animals developed a diversity of anti-envelope antibody binding and neutralizing activities toward proteins and viruses that were not represented by sequence in the vaccine. T-cells were also elicited, as measured by gamma-interferon production assays with envelope-derived peptide pools. Vaccinated and control animals were then challenged with the heterologous pathogenic SHIV, 89.6P. Vaccinated monkeys experienced significantly lower virus titers and better maintenance of CD4+ T-cells than unvaccinated controls. The B- and T-cell immune responses were far superior post-challenge in the vaccinated group. Four of six vaccinated animals and only one of six control animals survived a 44-week observation period post-challenge. The present report is the first to describe pathogenic SHIV disease control mediated by a heterologous HIV-1 vaccine, devoid of 89.6 or SIV derivatives.
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Affiliation(s)
- Xiaoyan Zhan
- Department of Infectious Diseases, St. Jude Children's Research Hospital, 332 N. Lauderdale, Memphis, TN 38105, USA
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35
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Stambas J, Brown SA, Gutierrez A, Sealy R, Yue W, Jones B, Lockey TD, Zirkel A, Freiden P, Brown B, Surman S, Coleclough C, Slobod KS, Doherty PC, Hurwitz JL. Long lived multi-isotype anti-HIV antibody responses following a prime-double boost immunization strategy. Vaccine 2005; 23:2454-64. [PMID: 15752831 DOI: 10.1016/j.vaccine.2004.10.030] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2004] [Revised: 10/10/2004] [Accepted: 10/28/2004] [Indexed: 10/26/2022]
Abstract
Despite decades of work, an effective HIV vaccine remains elusive. In an effort to elicit protective immunity, investigators have sought to define vaccines able to elicit durable HIV-specific B-cell and T-cell activities. Additionally, vaccines are sought which can induce antibodies of a variety of isotypes, as each isotype possesses unique attributes in terms of opsonization, Fc receptor binding capacity, complement fixation and location. One prominent new vaccine strategy, applied to numerous distinct antigenic systems is the prime boost-regimen, with DNA, vaccinia virus (VV), and/or purified recombinant protein. To examine the durability, location and isotype distribution of responses induced by prime-boost regimens, we tested successive immunizations with DNA, VV and protein (D-V-P), comparing three forms of protein inoculations: (i) purified protein administered intramuscularly with complete Freunds adjuvant, (ii) purified protein administered intranasally, and (iii) purified protein conjugated to oxidized mannan, administered intranasally. We found that all three protocols elicited serum antibodies of multiple isotypes, with serum IgA being most prominent among mice immunized with mannan-conjugated protein. All D-V-P protocols, regardless of protein form or route, also elicited antibody responses at mucosal surfaces. In bronchoalveolar lavage, a tendency toward IgA production was again most prominent in mice boosted with the protein-mannan conjugate. Both B-cell and T-cell responses were sustained for more than 1 year post-immunization following each form of vaccination. Contemporaneous with long-lasting serum and mucosal antibodies were antibody forming cells in the bone marrow of primed animals. Results highlight the D-V-P vaccination strategy as a promising approach for attaining durable, multi-isotype B-cell and T-cell activities toward HIV.
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Affiliation(s)
- J Stambas
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
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Brown SA, Lockey TD, Slaughter C, Slobod KS, Surman S, Zirkel A, Mishra A, Pagala VR, Coleclough C, Doherty PC, Hurwitz JL. T cell epitope "hotspots" on the HIV Type 1 gp120 envelope protein overlap with tryptic fragments displayed by mass spectrometry. AIDS Res Hum Retroviruses 2005; 21:165-70. [PMID: 15725756 DOI: 10.1089/aid.2005.21.165] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Our previous work has shown that immunodominant T-helper cell epitopes cluster within distinct fragments on a single face of the HIV envelope gp120 protein. We show in this report that the general positions of immunodominant epitopes are shared by T cells derived from BALB/c, C57BL/6, and CB6F1 mice, yet the precise peptides recognized by the responding T cell populations may differ. In addition, we find that gp120 peptides displayed by tryptic digestion and mass spectrometry of a purified HIV envelope protein share location with peptides defined as immunodominant T cell targets. Results are consistent with the suggestion that gp120 peptide location influences antigen processing, which, in turn, influences the specificity of immunodominant T cells.
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Affiliation(s)
- Scott A Brown
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, Tennessee 38105, USA
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Abstract
The ecology of pathogenic viruses can be considered both in the context of survival in the macro-environments of nature, the theme pursued generally by epidemiologists, and in the micro-environments of the infected host. The long-lived, complex, higher vertebrates have evolved specialized, adaptive immune systems designed to minimise the consequences of such parasitism. Through evolutionary time, the differential selective pressures exerted variously by the need for virus and host survival have shaped both the "one-host" viruses and vertebrate immunity. With the development of vaccines to protect us from many of our most familiar parasites, the most dangerous pathogens threatening us now tend to be those "emerging", or adventitious, infectious agents that sporadically enter human populations from avian or other wild-life reservoirs. Such incursions must, of course, have been happening through the millenia, and are likely to have led to the extraordinary diversity of recognition molecules, the breadth in effector functions, and the persistent memory that distinguishes the vertebrate, adaptive immune system from the innate response mechanisms that operate more widely through animal biology. Both are important to contemporary humans and, particularly in the period immediately following infection, we still rely heavily on an immediate response capacity, elements of which are shared with much simpler, and more primitive organisms. Perhaps we will now move forward to develop useful therapies that exploit, or mimic, such responses. At this stage, however, most of our hopes for minimizing the threat posed by viruses still focus on the manipulation of the more precisely targeted, adaptive immune system.
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Affiliation(s)
- P C Doherty
- Department of Microbiology and Immunology, University of Melbourne, Victoria, Australia.
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