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Witney MJ, Tscharke DC. BMX-A and BMX-S: Accessible cell-free methods to estimate peptide-MHC-I affinity and stability. Mol Immunol 2023; 161:1-10. [PMID: 37478775 DOI: 10.1016/j.molimm.2023.07.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Revised: 06/12/2023] [Accepted: 07/11/2023] [Indexed: 07/23/2023]
Abstract
The affinity and stability of peptide binding to Major Histocompatibility Complex Class I (MHC-I) molecules are fundamental parameters that underpin the specificity and magnitude of CD8+ T cell responses. These parameters can be estimated in some cases by computational tools, but experimental validation remains valuable, especially for stability. Methods to measure peptide binding can be broadly categorised into either cell-based assays using TAP-deficient cell lines such as RMA/S, or cell-free strategies, such as peptide competition-binding assays and surface plasmon resonance. Cell-based assays are subject to confounding biological activity, including peptide trimming by peptidases and dilution of peptide-loaded MHC-I on the surface of cells through cell division. Current cell-free methods require in-house production and purification of MHC-I. In this study, we present the development of new cell-free assays to estimate the relative affinity and dissociation kinetics of peptide binding to MHC-I. These assays, which we have called BMX-A (relative affinity) and BMX-S (kinetic stability), are reliable, scalable and accessible, in that they use off-the-shelf commercial reagents and standard flow cytometry techniques.
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Affiliation(s)
- Matthew J Witney
- John Curtin School of Medical Research, The Australian National University, Canberra, ACT, Australia
| | - David C Tscharke
- John Curtin School of Medical Research, The Australian National University, Canberra, ACT, Australia.
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2
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Brito Baleeiro R, Liu P, Chard Dunmall LS, Di Gioia C, Nagano A, Cutmore L, Wang J, Chelala C, Nyambura LW, Walden P, Lemoine N, Wang Y. Personalized neoantigen viro-immunotherapy platform for triple-negative breast cancer. J Immunother Cancer 2023; 11:e007336. [PMID: 37586771 PMCID: PMC10432671 DOI: 10.1136/jitc-2023-007336] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/21/2023] [Indexed: 08/18/2023] Open
Abstract
BACKGROUND Triple-negative breast cancer (TNBC) corresponds to approximately 20% of all breast tumors, with a high propensity for metastasis and a poor prognosis. Because TNBC displays a high mutational load compared with other breast cancer types, a neoantigen-based immunotherapy strategy could be effective. One major bottleneck in the development of a neoantigen-based vaccine for TNBC is the selection of the best targets, that is, tumor-specific neoantigens which are presented at the surface of tumor cells and capable of eliciting robust immune responses. In this study, we aimed to set up a platform for identification and delivery of immunogenic neoantigens in a vaccine regimen for TNBC using oncolytic vaccinia virus (VV). METHODS We used bioinformatic tools and cell-based assays to identify immunogenic neoantigens in TNBC patients' samples, human and murine cell lines. Immunogenicity of the neoantigens was tested in vitro (human) and ex vivo (murine) in T-cell assays. To assess the efficacy of our regimen, we used a preclinical model of TNBC where we treated tumor-bearing mice with neoantigens together with oncolytic VV and evaluated the effect on induction of neoantigen-specific CD8+T cells, tumor growth and survival. RESULTS We successfully identified immunogenic neoantigens and generated neoantigen-specific CD8+T cells capable of recognizing a human TNBC cell line expressing the mutated gene. Using a preclinical model of TNBC, we showed that our tumor-specific oncolytic VV was able to change the tumor microenvironment, attracting and maintaining mature cross-presenting CD8α+dendritic cells and effector T-cells. Moreover, when delivered in a prime/boost regimen together with oncolytic VV, long peptides encompassing neoantigens were able to induce neoantigen-specific CD8+T cells, slow tumor growth and increase survival. CONCLUSIONS Our study provides a promising approach for the development of neoantigen-based immunotherapies for TNBC. By identifying immunogenic neoantigens and developing a delivery system through tumor-specific oncolytic VV, we have demonstrated that neoantigen-based vaccines could be effective in inducing neoantigen-specific CD8+T cells response with significant impact on tumor growth. Further studies are needed to determine the safety and efficacy of this approach in clinical trials.
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Affiliation(s)
- Renato Brito Baleeiro
- Centre for Cancer Biomarkers and Biotherapeutics, Queen Mary University of London, London, UK
| | - Peng Liu
- Centre for Cancer Biomarkers and Biotherapeutics, Queen Mary University of London, London, UK
| | - Louisa S Chard Dunmall
- Centre for Cancer Biomarkers and Biotherapeutics, Queen Mary University of London, London, UK
| | - Carmela Di Gioia
- Centre for Cancer Biomarkers and Biotherapeutics, Queen Mary University of London, London, UK
| | - Ai Nagano
- Centre for Cancer Biomarkers and Biotherapeutics, Queen Mary University of London, London, UK
| | - Lauren Cutmore
- Centre for Cancer Biomarkers and Biotherapeutics, Queen Mary University of London, London, UK
| | - Jun Wang
- Centre for Cancer Biomarkers and Biotherapeutics, Queen Mary University of London, London, UK
| | - Claude Chelala
- Centre for Cancer Biomarkers and Biotherapeutics, Queen Mary University of London, London, UK
| | - Lydon Wainaina Nyambura
- Department of Dermatology, Venerology and Allergology, Charité Universitätsmedizin Berlin, Berlin, Germany
| | - Peter Walden
- Department of Dermatology, Venerology and Allergology, Charité Universitätsmedizin Berlin, Berlin, Germany
| | - Nicholas Lemoine
- Centre for Cancer Biomarkers and Biotherapeutics, Queen Mary University of London, London, UK
- Zhengzhou University, Zhengzhou, Henan, China
| | - Yaohe Wang
- Centre for Cancer Biomarkers and Biotherapeutics, Queen Mary University of London, London, UK
- Zhengzhou University, Zhengzhou, Henan, China
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3
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Baumgaertner P, Schmidt J, Costa-Nunes CM, Bordry N, Guillaume P, Luescher I, Speiser DE, Rufer N, Hebeisen M. CD8 T cell function and cross-reactivity explored by stepwise increased peptide-HLA versus TCR affinity. Front Immunol 2022; 13:973986. [PMID: 36032094 PMCID: PMC9399405 DOI: 10.3389/fimmu.2022.973986] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Accepted: 07/22/2022] [Indexed: 12/05/2022] Open
Abstract
Recruitment and activation of CD8 T cells occur through specific triggering of T cell receptor (TCR) by peptide-bound human leucocyte antigen (HLA) ligands. Within the generated trimeric TCR-peptide:HLA complex, the molecular binding affinities between peptide and HLA, and between TCR and peptide:HLA both impact T cell functional outcomes. However, how their individual and combined effects modulate immunogenicity and overall T cell responsiveness has not been investigated systematically. Here, we established two panels of human tumor peptide variants differing in their affinity to HLA. For precise characterization, we developed the “blue peptide assay”, an upgraded cell-based approach to measure the peptide:HLA affinity. These peptide variants were then used to investigate the cross-reactivity of tumor antigen-specific CD8 T cell clonotypes derived from blood of cancer patients after vaccination with either the native or an affinity-optimized Melan-A/MART-1 epitope, or isolated from tumor infiltrated lymph nodes (TILNs). Vaccines containing the native tumor epitope generated T cells with better functionality, and superior cross-reactivity against potential low affinity escape epitopes, as compared to T cells induced by vaccines containing an HLA affinity-optimized epitope. Comparatively, Melan-A/MART-1-specific TILN cells displayed functional and cross-reactive profiles that were heterogeneous and clonotype-dependent. Finally, we took advantage of a collection of T cells expressing affinity-optimized NY-ESO-1-specific TCRs to interrogate the individual and combined impact of peptide:HLA and TCR-pHLA affinities on overall CD8 T cell responses. We found profound and distinct effects of both biophysical parameters, with additive contributions and absence of hierarchical dominance. Altogether, the biological impact of peptide:HLA and TCR-pHLA affinities on T cell responses was carefully dissected in two antigenic systems, frequently targeted in human cancer immunotherapy. Our technology and stepwise comparison open new insights into the rational design and selection of vaccine-associated tumor-specific epitopes and highlight the functional and cross-reactivity profiles that endow T cells with best tumor control capacity.
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Affiliation(s)
- Petra Baumgaertner
- Department of Oncology, Lausanne University Hospital and University of Lausanne, Epalinges, Switzerland
- Ludwig Institute for Cancer Research, Lausanne Branch - University of Lausanne, Epalinges, Switzerland
- *Correspondence: Michael Hebeisen, ; Petra Baumgaertner,
| | - Julien Schmidt
- Department of Oncology, Lausanne University Hospital and University of Lausanne, Epalinges, Switzerland
- Ludwig Institute for Cancer Research, Lausanne Branch - University of Lausanne, Epalinges, Switzerland
| | - Carla-Marisa Costa-Nunes
- Department of Oncology, Lausanne University Hospital and University of Lausanne, Epalinges, Switzerland
- Ludwig Institute for Cancer Research, Lausanne Branch - University of Lausanne, Epalinges, Switzerland
| | - Natacha Bordry
- Department of Oncology, Lausanne University Hospital and University of Lausanne, Epalinges, Switzerland
- Ludwig Institute for Cancer Research, Lausanne Branch - University of Lausanne, Epalinges, Switzerland
| | - Philippe Guillaume
- Department of Oncology, Lausanne University Hospital and University of Lausanne, Epalinges, Switzerland
- Ludwig Institute for Cancer Research, Lausanne Branch - University of Lausanne, Epalinges, Switzerland
| | - Immanuel Luescher
- Department of Oncology, Lausanne University Hospital and University of Lausanne, Epalinges, Switzerland
- Ludwig Institute for Cancer Research, Lausanne Branch - University of Lausanne, Epalinges, Switzerland
| | - Daniel E. Speiser
- Department of Oncology, Lausanne University Hospital and University of Lausanne, Epalinges, Switzerland
- Ludwig Institute for Cancer Research, Lausanne Branch - University of Lausanne, Epalinges, Switzerland
| | - Nathalie Rufer
- Department of Oncology, Lausanne University Hospital and University of Lausanne, Epalinges, Switzerland
- Ludwig Institute for Cancer Research, Lausanne Branch - University of Lausanne, Epalinges, Switzerland
| | - Michael Hebeisen
- Department of Oncology, Lausanne University Hospital and University of Lausanne, Epalinges, Switzerland
- Ludwig Institute for Cancer Research, Lausanne Branch - University of Lausanne, Epalinges, Switzerland
- *Correspondence: Michael Hebeisen, ; Petra Baumgaertner,
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4
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Baleeiro RB, Dunmall LSC, Liu P, Lu S, Lone Y, Lemoine NR, Wang Y. Optimized Anchor-Modified Peptides Targeting Mutated RAS Are Promising Candidates for Immunotherapy. Front Immunol 2022; 13:902709. [PMID: 35720289 PMCID: PMC9204602 DOI: 10.3389/fimmu.2022.902709] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Accepted: 04/28/2022] [Indexed: 12/02/2022] Open
Abstract
RAS mutations occur in approximately 20% of all cancers and given their clonality, key role as driver mutation, association with poor prognosis and undruggability, they represent attractive targets for immunotherapy. We have identified immunogenic peptides derived from codon 12 mutant RAS (G12A, G12C, G12D, G12R, G12S and G12V), which bind to HLA-A*02:01 and HLA-A*03:01 and elicit strong peptide-specific CD8+ T cell responses, indicating that there is an effective CD8+ T-cell repertoire against these mutant RAS-derived peptides that can be mobilized. Alterations in anchor residues of these peptides enhanced their binding affinity to HLA-A*02:01 molecules and allowed generation of CD8+ T cells that responded to target cells pulsed with the anchor-modified and also with the original peptide. Cytotoxic T cells generated against these peptides specifically lysed tumor cells expressing mutant RAS. Vaccination of transgenic humanized HLA-A2/DR1 mice with a long peptide encompassing an anchor-modified 9-mer G12V epitope generated CD8+ T cells reactive to the original 9-mer and to a HLA-A*02:01-positive human cancer cell line harboring the G12V mutation. Our data provide strong evidence that mutant RAS can be targeted by immunotherapy.
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Affiliation(s)
- Renato B Baleeiro
- Centre for Cancer Biomarkers and Biotherapeutics, Barts Cancer Institute, Queen Mary University of London, London, United Kingdom
| | - Louisa S Chard Dunmall
- Centre for Cancer Biomarkers and Biotherapeutics, Barts Cancer Institute, Queen Mary University of London, London, United Kingdom
| | - Peng Liu
- Centre for Cancer Biomarkers and Biotherapeutics, Barts Cancer Institute, Queen Mary University of London, London, United Kingdom
| | - Shuangshuang Lu
- Sino-British Research Centre for Molecular Oncology, National Centre for International Research in Cell and Gene Therapy, School of Basic Medical Sciences, Academy of Medical Sciences, Zhengzhou University, Zhengzhou, China
| | - Yuchun Lone
- Centre National de la Recherche Scientifique (CNRS), Transgénèse et Archivage d'Animaux Modèles (TAAM), Orleans, France
| | - Nicholas R Lemoine
- Centre for Cancer Biomarkers and Biotherapeutics, Barts Cancer Institute, Queen Mary University of London, London, United Kingdom.,Sino-British Research Centre for Molecular Oncology, National Centre for International Research in Cell and Gene Therapy, School of Basic Medical Sciences, Academy of Medical Sciences, Zhengzhou University, Zhengzhou, China
| | - Yaohe Wang
- Centre for Cancer Biomarkers and Biotherapeutics, Barts Cancer Institute, Queen Mary University of London, London, United Kingdom.,Sino-British Research Centre for Molecular Oncology, National Centre for International Research in Cell and Gene Therapy, School of Basic Medical Sciences, Academy of Medical Sciences, Zhengzhou University, Zhengzhou, China
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5
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Mass spectrometric identification of immunogenic SARS-CoV-2 epitopes and cognate TCRs. Proc Natl Acad Sci U S A 2021; 118:2111815118. [PMID: 34725257 PMCID: PMC8609653 DOI: 10.1073/pnas.2111815118] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/20/2021] [Indexed: 12/24/2022] Open
Abstract
Durable protection against COVID-19 infection may be achieved by generating robust T cell responses to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and emerging SARS-CoV-2 variants; for those infected, effective treatments are urgently needed. For these strategies to be successful, accurate identification of T cell epitopes is critical. In this study, we used major histocompatibility complex immune precipitation, acid elution, and tandem mass spectrometry to define the SARS-CoV-2 immunopeptidome for membrane glycoprotein (MGP) and the nonstructural protein. Furthermore, taking advantage of a highly robust endogenous T cell workflow, we verify the immunogenicity of these MS-defined peptides by in vitro generation of MGP and NSP13 peptide-specific T cells and confirm T cell recognition of MGP or NSP13 endogenously expressing cell lines. Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infections elicit both humoral and cellular immune responses. For the prevention and treatment of COVID-19, the disease caused by SARS-CoV-2, it has become increasingly apparent that T cell responses are equally if not more important than humoral responses in mediating recovery and immune protection. One major challenge in developing T cell–based therapies for infectious and malignant diseases has been the identification of immunogenic epitopes that can elicit a meaningful T cell response. Traditionally, this has been achieved using sophisticated in silico methods to predict putative epitopes deduced from binding affinities. Our studies find that, in contrast to current convention, “immunodominant” SARS-CoV-2 peptides defined by such in silico methods often fail to elicit T cell responses recognizing naturally presented SARS-CoV-2 epitopes. We postulated that immunogenic epitopes for SARS-CoV-2 are best defined empirically by directly analyzing peptides eluted from the naturally processed peptide–major histocompatibility complex (MHC) and then validating immunogenicity by determining whether such peptides can elicit T cells recognizing SARS-CoV-2 antigen-expressing cells. Using a tandem mass spectrometry approach, we identified epitopes derived from not only structural but also nonstructural genes in regions highly conserved among SARS-CoV-2 strains, including recently recognized variants. Finally, there are no reported T cell receptor–engineered T cell technology that can redirect T cell specificity to recognize and kill SARS-CoV-2 target cells. We report here several SARS-CoV-2 epitopes defined by mass spectrometric analysis of MHC-eluted peptides, provide empiric evidence for their immunogenicity, and demonstrate engineered TCR-redirected killing.
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6
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Pan K, Chiu Y, Huang E, Chen M, Wang J, Lai I, Singh S, Shaw R, MacCoss M, Yee C. Immunogenic SARS-CoV2 Epitopes Defined by Mass Spectrometry. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2021. [PMID: 34312620 DOI: 10.1101/2021.07.20.453160] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
SARS-CoV-2 infections elicit both humoral and cellular immune responses. For the prevention and treatment of COVID19, the disease caused by SARS-CoV-2, T cell responses are important in mediating recovery and immune-protection. The identification of immunogenic epitopes that can elicit a meaningful T cell response can be elusive. Traditionally, this has been achieved using sophisticated in silico methods to predict putative epitopes; however, our previous studies find that 'immunodominant' SARS-CoV-2 peptides defined by such in silico methods often fail to elicit T cell responses recognizing SARS-CoV-2. We postulated that immunogenic epitopes for SARS-CoV-2 are best defined by directly analyzing peptides eluted from the peptide-MHC complex and then validating immunogenicity empirically by determining if such peptides can elicit T cells recognizing SARS-CoV-2 antigen-expressing cells. Using a tandem mass spectrometry approach, we identified epitopes of SARS-CoV-2 derived not only from structural but also non-structural genes in regions highly conserved among SARS-CoV-2 strains including recently recognized variants. We report here, for the first time, several novel SARS-CoV-2 epitopes from membrane glycol-protein (MGP) and non-structure protein-13 (NSP13) defined by mass-spectrometric analysis of MHC-eluted peptides, provide empiric evidence for their immunogenicity to induce T cell response. Significance Statement Current state of the art uses putative epitope peptides based on in silico prediction algorithms to evaluate the T cell response among COVID-19 patients. However, none of these peptides have been tested for immunogenicity, i.e. the ability to elicit a T cell response capable of recognizing endogenously presented peptide. In this study, we used MHC immune-precipitation, acid elution and tandem mass spectrometry to define the SARS-CoV-2 immunopeptidome for membrane glycol-protein and the non-structural protein. Furthermore, taking advantage of a highly robust endogenous T cell (ETC) workflow, we verify the immunogenicity of these MS-defined peptides by in vitro generation of MGP and NSP13 peptide-specific T cells and confirm T cell recognition of MGP or NSP13 endogenously expressing cell lines.
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7
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Jurewicz MM, Willis RA, Ramachandiran V, Altman JD, Stern LJ. MHC-I peptide binding activity assessed by exchange after cleavage of peptide covalently linked to β2-microglobulin. Anal Biochem 2019; 584:113328. [PMID: 31201791 DOI: 10.1016/j.ab.2019.05.017] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2019] [Revised: 05/14/2019] [Accepted: 05/31/2019] [Indexed: 10/26/2022]
Abstract
A common approach to measuring binding constants involves combining receptor and ligand and measuring the distribution of bound and free states after equilibration. For class I major histocompatibility (MHC-I) proteins, which bind short peptides for presentation to T cells, this approach is precluded by instability of peptide-free protein. Here we develop a method wherein a weakly-binding peptide covalently attached to the N-terminus of the MHC-I β2m subunit is released from the peptide binding site after proteolytic cleavage of the linker. The resultant protein is able to bind added peptide. A direct binding assay and method for estimation of peptide binding constant (Kd) are described, in which fluorescence polarization is used to follow peptide binding. A competition binding assay and method for estimation of inhibitor binding constant (Ki) using the same principle also are also described. The method uses a cubic equation to relate observed binding to probe concentration, probe Kd, inhibitor concentration, and inhibitor Ki under general reaction conditions without assumptions relating to relative binding affinities or concentrations. We also delineate advantages of this approach compared to the Cheng-Prusoff and Munson-Rodbard approaches for estimation of Ki using competition binding data.
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Affiliation(s)
- Mollie M Jurewicz
- Program in Immunology and Microbiology, University of Massachusetts Medical School, Worcester, MA, 01605, United States; Department of Pathology, University of Massachusetts Medical School, Worcester, MA, 01605, United States
| | - Richard A Willis
- Emory Vaccine Center, Yerkes National Primate Research Center, Atlanta, GA, 30329, United States
| | - Vasanthi Ramachandiran
- Emory Vaccine Center, Yerkes National Primate Research Center, Atlanta, GA, 30329, United States
| | - John D Altman
- Emory Vaccine Center, Yerkes National Primate Research Center, Atlanta, GA, 30329, United States; Department of Microbiology and Immunology, Emory Vaccine Center at Yerkes, Emory University School of Medicine, Atlanta, GA, 30329, United States
| | - Lawrence J Stern
- Program in Immunology and Microbiology, University of Massachusetts Medical School, Worcester, MA, 01605, United States; Department of Pathology, University of Massachusetts Medical School, Worcester, MA, 01605, United States; Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA, 01605, United States.
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8
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Bonsack M, Hoppe S, Winter J, Tichy D, Zeller C, Küpper MD, Schitter EC, Blatnik R, Riemer AB. Performance Evaluation of MHC Class-I Binding Prediction Tools Based on an Experimentally Validated MHC–Peptide Binding Data Set. Cancer Immunol Res 2019; 7:719-736. [DOI: 10.1158/2326-6066.cir-18-0584] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2018] [Revised: 12/19/2018] [Accepted: 03/18/2019] [Indexed: 11/16/2022]
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9
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Kinloch NN, Lee GQ, Carlson JM, Jin SW, Brumme CJ, Byakwaga H, Muzoora C, Bwana MB, Cobarrubias KD, Hunt PW, Martin JN, Carrington M, Bangsberg DR, Harrigan PR, Brockman MA, Brumme ZL. Genotypic and Mechanistic Characterization of Subtype-Specific HIV Adaptation to Host Cellular Immunity. J Virol 2019; 93:e01502-18. [PMID: 30305354 PMCID: PMC6288327 DOI: 10.1128/jvi.01502-18] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2018] [Accepted: 09/28/2018] [Indexed: 11/20/2022] Open
Abstract
The extent to which viral genetic context influences HIV adaptation to human leukocyte antigen (HLA) class I-restricted immune pressures remains incompletely understood. The Ugandan HIV epidemic, where major pandemic group M subtypes A1 and D cocirculate in a single host population, provides an opportunity to investigate this question. We characterized plasma HIV RNA gag, pol, and nef sequences, along with host HLA genotypes, in 464 antiretroviral-naive individuals chronically infected with HIV subtype A1 or D. Using phylogenetically informed statistical approaches, we identified HLA-associated polymorphisms and formally compared their strengths of selection between viral subtypes. A substantial number (32%) of HLA-associated polymorphisms identified in subtype A1 and/or D had previously been reported in subtype B, C, and/or circulating recombinant form 01_AE (CRF01_AE), confirming the shared nature of many HLA-driven escape pathways regardless of viral genetic context. Nevertheless, 34% of the identified HLA-associated polymorphisms were significantly differentially selected between subtypes A1 and D. Experimental investigation of select examples of subtype-specific escape revealed distinct underlying mechanisms with important implications for vaccine design: whereas some were attributable to subtype-specific sequence variation that influenced epitope-HLA binding, others were attributable to differential mutational barriers to immune escape. Overall, our results confirm that HIV genetic context is a key modulator of viral adaptation to host cellular immunity and highlight the power of combined bioinformatic and mechanistic studies, paired with knowledge of epitope immunogenicity, to identify appropriate viral regions for inclusion in subtype-specific and universal HIV vaccine strategies.IMPORTANCE The identification of HIV polymorphisms reproducibly selected under pressure by specific HLA alleles and the elucidation of their impact on viral function can help identify immunogenic viral regions where immune escape incurs a fitness cost. However, our knowledge of HLA-driven escape pathways and their functional costs is largely limited to HIV subtype B and, to a lesser extent, subtype C. Our study represents the first characterization of HLA-driven adaptation pathways in HIV subtypes A1 and D, which dominate in East Africa, and the first statistically rigorous characterization of differential HLA-driven escape across viral subtypes. The results support a considerable impact of viral genetic context on HIV adaptation to host HLA, where HIV subtype-specific sequence variation influences both epitope-HLA binding and the fitness costs of escape. Integrated bioinformatic and mechanistic characterization of these and other instances of differential escape could aid rational cytotoxic T-lymphocyte-based vaccine immunogen selection for both subtype-specific and universal HIV vaccines.
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Affiliation(s)
- Natalie N Kinloch
- Faculty of Health Sciences, Simon Fraser University, Burnaby, British Columbia, Canada
| | - Guinevere Q Lee
- Ragon Institute of Massachusetts General Hospital, MIT and Harvard, Cambridge, Massachusetts, USA
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, British Columbia, Canada
| | | | - Steven W Jin
- Faculty of Health Sciences, Simon Fraser University, Burnaby, British Columbia, Canada
| | - Chanson J Brumme
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, British Columbia, Canada
| | - Helen Byakwaga
- Mbarara University of Science and Technology, Mbarara, Uganda
- University of California, San Francisco, San Francisco, California, USA
| | - Conrad Muzoora
- Mbarara University of Science and Technology, Mbarara, Uganda
| | - Mwebesa B Bwana
- Mbarara University of Science and Technology, Mbarara, Uganda
| | - Kyle D Cobarrubias
- Faculty of Health Sciences, Simon Fraser University, Burnaby, British Columbia, Canada
| | - Peter W Hunt
- University of California, San Francisco, San Francisco, California, USA
| | - Jeff N Martin
- University of California, San Francisco, San Francisco, California, USA
| | - Mary Carrington
- Cancer and Inflammation Program, Frederick National Laboratory for Cancer Research, Frederick, Maryland, USA
| | - David R Bangsberg
- Oregon Health and Science University-Portland State University School of Public Health, Portland, Oregon, USA
| | - P Richard Harrigan
- Department of Medicine, University of British Columbia, Vancouver, British Columbia, Canada
| | - Mark A Brockman
- Faculty of Health Sciences, Simon Fraser University, Burnaby, British Columbia, Canada
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, British Columbia, Canada
| | - Zabrina L Brumme
- Faculty of Health Sciences, Simon Fraser University, Burnaby, British Columbia, Canada
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, British Columbia, Canada
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10
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MHCflurry: Open-Source Class I MHC Binding Affinity Prediction. Cell Syst 2018; 7:129-132.e4. [DOI: 10.1016/j.cels.2018.05.014] [Citation(s) in RCA: 218] [Impact Index Per Article: 36.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2017] [Revised: 03/30/2018] [Accepted: 05/21/2018] [Indexed: 12/30/2022]
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11
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Blatnik R, Mohan N, Bonsack M, Falkenby LG, Hoppe S, Josef K, Steinbach A, Becker S, Nadler WM, Rucevic M, Larsen MR, Salek M, Riemer AB. A Targeted LC-MS Strategy for Low-Abundant HLA Class-I-Presented Peptide Detection Identifies Novel Human Papillomavirus T-Cell Epitopes. Proteomics 2018; 18:e1700390. [PMID: 29603667 PMCID: PMC6033010 DOI: 10.1002/pmic.201700390] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2017] [Revised: 03/16/2018] [Indexed: 12/12/2022]
Abstract
For rational design of therapeutic vaccines, detailed knowledge about target epitopes that are endogenously processed and truly presented on infected or transformed cells is essential. Many potential target epitopes (viral or mutation-derived), are presented at low abundance. Therefore, direct detection of these peptides remains a challenge. This study presents a method for the isolation and LC-MS3 -based targeted detection of low-abundant human leukocyte antigen (HLA) class-I-presented peptides from transformed cells. Human papillomavirus (HPV) was used as a model system, as the HPV oncoproteins E6 and E7 are attractive therapeutic vaccination targets and expressed in all transformed cells, but present at low abundance due to viral immune evasion mechanisms. The presented approach included preselection of target antigen-derived peptides by in silico predictions and in vitro binding assays. The peptide purification process was tailored to minimize contaminants after immunoprecipitation of HLA-peptide complexes, while keeping high isolation yields of low-abundant target peptides. The subsequent targeted LC-MS3 detection allowed for increased sensitivity, which resulted in successful detection of the known HLA-A2-restricted epitope E711-19 and ten additional E7-derived peptides on the surface of HPV16-transformed cells. T-cell reactivity was shown for all the 11 detected peptides in ELISpot assays, which shows that detection by our approach has high predictive value for immunogenicity. The presented strategy is suitable for validating even low-abundant candidate epitopes to be true immunotherapy targets.
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Affiliation(s)
- Renata Blatnik
- Immunotherapy and ImmunopreventionGerman Cancer Research Center (DKFZ)Im Neuenheimer Feld 28069120 HeidelbergGermany
- Molecular Vaccine DesignGerman Center for Infection Research (DZIF)Partner Site HeidelbergHeidelbergGermany
| | - Nitya Mohan
- Immunotherapy and ImmunopreventionGerman Cancer Research Center (DKFZ)Im Neuenheimer Feld 28069120 HeidelbergGermany
| | - Maria Bonsack
- Immunotherapy and ImmunopreventionGerman Cancer Research Center (DKFZ)Im Neuenheimer Feld 28069120 HeidelbergGermany
- Molecular Vaccine DesignGerman Center for Infection Research (DZIF)Partner Site HeidelbergHeidelbergGermany
| | - Lasse G. Falkenby
- Department of Biochemistry and Molecular BiologyUniversity of Southern DenmarkOdense MDenmark
| | - Stephanie Hoppe
- Immunotherapy and ImmunopreventionGerman Cancer Research Center (DKFZ)Im Neuenheimer Feld 28069120 HeidelbergGermany
- Molecular Vaccine DesignGerman Center for Infection Research (DZIF)Partner Site HeidelbergHeidelbergGermany
| | - Kathrin Josef
- Immunotherapy and ImmunopreventionGerman Cancer Research Center (DKFZ)Im Neuenheimer Feld 28069120 HeidelbergGermany
- Molecular Vaccine DesignGerman Center for Infection Research (DZIF)Partner Site HeidelbergHeidelbergGermany
| | - Alina Steinbach
- Immunotherapy and ImmunopreventionGerman Cancer Research Center (DKFZ)Im Neuenheimer Feld 28069120 HeidelbergGermany
- Molecular Vaccine DesignGerman Center for Infection Research (DZIF)Partner Site HeidelbergHeidelbergGermany
| | - Sara Becker
- Immunotherapy and ImmunopreventionGerman Cancer Research Center (DKFZ)Im Neuenheimer Feld 28069120 HeidelbergGermany
| | - Wiebke M. Nadler
- Division of Stem Cells and CancerGerman Cancer Research Center (DKFZ) and Heidelberg Institute for Stem Cell Technology and Experimental Medicine (HI‐STEM)HeidelbergGermany
| | - Marijana Rucevic
- Massachusetts General HospitalCenter for Cancer ResearchCharlestownMAUSA
| | - Martin R. Larsen
- Department of Biochemistry and Molecular BiologyUniversity of Southern DenmarkOdense MDenmark
| | - Mogjiborahman Salek
- Immunotherapy and ImmunopreventionGerman Cancer Research Center (DKFZ)Im Neuenheimer Feld 28069120 HeidelbergGermany
- Molecular Vaccine DesignGerman Center for Infection Research (DZIF)Partner Site HeidelbergHeidelbergGermany
| | - Angelika B. Riemer
- Immunotherapy and ImmunopreventionGerman Cancer Research Center (DKFZ)Im Neuenheimer Feld 28069120 HeidelbergGermany
- Molecular Vaccine DesignGerman Center for Infection Research (DZIF)Partner Site HeidelbergHeidelbergGermany
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12
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Nitschke NJ, Bjoern J, Iversen TZ, Andersen MH, Svane IM. Indoleamine 2,3-dioxygenase and survivin peptide vaccine combined with temozolomide in metastatic melanoma. Stem Cell Investig 2017; 4:77. [PMID: 29057249 DOI: 10.21037/sci.2017.08.06] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2017] [Accepted: 04/25/2017] [Indexed: 11/06/2022]
Abstract
BACKGROUND Indoleamine 2,3-dioxygenase (IDO) and survivin have been identified as potential targets for cancer vaccination. In this phase II study a vaccine using the peptides Sur1M2 and IDO5 was combined with the chemotherapy temozolomide (TMZ) for treatment of metastatic melanoma patients. The aim was to simultaneously target several immune inhibiting mechanisms and the highly malignant cells expressing survivin. METHODS HLA-A2 positive patients with advanced malignant melanoma were treated biweekly with 150 mg/m2 TMZ daily for 7 days followed by subcutaneous vaccination with 250 µg of each peptide in 500 µL Montanide solution at day 8. Granulocyte-macrophage colony-stimulating factor was used as an adjuvant and topical imiquimod was applied prior to vaccination. Treatment was continued until disease progression. Clinical response was evaluated by PET-CT and immunological outcome was assessed by ELISPOT and flow cytometry. RESULTS In total, 17 patients were treated with a clinical benefit rate of 18% including one patient with partial tumor regression. Immune analyses revealed a vaccine specific response in 8 (67%) of 12 patients tested, a significant decrease in the frequency of CD4+ T-cells during treatment, a tendency towards decreasing frequencies of naïve CD4+ and CD8+ T-cells, and increasing frequencies of memory CD4+ and CD8+ T-cells. CONCLUSIONS These results demonstrate that vaccine-induced immunity towards survivin and IDO-derived peptides can be achieved in combination with TMZ in patients mainly suffering from grade M1c melanoma including patients with brain metastases. A significant clinical activity could not be proven in this small study and a larger setup is needed to properly assess clinical efficacy.
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Affiliation(s)
- Nikolaj Juul Nitschke
- Center for Cancer Immune Therapy, Department of Hematology, Herlev Hospital, University of Copenhagen, Herlev, Denmark
| | - Jon Bjoern
- Center for Cancer Immune Therapy, Department of Hematology, Herlev Hospital, University of Copenhagen, Herlev, Denmark.,Department of Oncology, Herlev Hospital, University of Copenhagen, Herlev, Denmark
| | | | - Mads Hald Andersen
- Center for Cancer Immune Therapy, Department of Hematology, Herlev Hospital, University of Copenhagen, Herlev, Denmark
| | - Inge Marie Svane
- Center for Cancer Immune Therapy, Department of Hematology, Herlev Hospital, University of Copenhagen, Herlev, Denmark.,Department of Oncology, Herlev Hospital, University of Copenhagen, Herlev, Denmark
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13
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Rosenberg AS, Sauna ZE. Immunogenicity assessment during the development of protein therapeutics. J Pharm Pharmacol 2017; 70:584-594. [DOI: 10.1111/jphp.12810] [Citation(s) in RCA: 70] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2017] [Accepted: 07/26/2017] [Indexed: 12/29/2022]
Abstract
Abstract
Objective
Here we provide a critical review of the state of the art with respect to non-clinical assessments of immunogenicity for therapeutic proteins.
Key findings
The number of studies on immunogenicity published annually has more than doubled in the last 5 years. The science and technology, which have reached a critical mass, provide multiple of non-clinical approaches (computational, in vitro, ex vivo and animal models) to first predict and then to modify or eliminate T-cell or B-cell epitopes via de-immunization strategies. We discuss how these may be used in the context of drug development in assigning the immunogenicity risk of new and marketed therapeutic proteins.
Summary
Protein therapeutics represents a large share of the pharma market and provide medical interventions for some of the most complex and intractable diseases. Immunogenicity (the development of antibodies to therapeutic proteins) is an important concern for both the safety and efficacy of protein therapeutics as immune responses may neutralize the activity of life-saving and highly effective protein therapeutics and induce hypersensitivity responses including anaphylaxis. The non-clinical computational tools and experimental technologies that offer a comprehensive and increasingly accurate estimation of immunogenic potential are surveyed here. This critical review also discusses technologies which are promising but are not as yet ready for routine use.
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Affiliation(s)
- Amy S Rosenberg
- Laboratory of Immunology, Division of Biotechnology Product Review and Research 3, Office of Biotechnology Products, Center for Drugs Evaluation and Research, U.S. Food and Drug Administration, Silver Spring, MD, USA
| | - Zuben E Sauna
- Hemostasis Branch, Division of Plasma Protein Therapeutics, Office of Tissues and Advanced Therapeutics, Center for Biologics Evaluation and Research, U.S. Food and Drug Administration, Silver Spring, MD, USA
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14
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Human leukemia antigen-A*0201-restricted epitopes of human endogenous retrovirus W family envelope (HERV-W env) induce strong cytotoxic T lymphocyte responses. Virol Sin 2017; 32:280-289. [PMID: 28840564 DOI: 10.1007/s12250-017-3984-9] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2017] [Accepted: 07/20/2017] [Indexed: 12/29/2022] Open
Abstract
Human endogenous retrovirus W family (HERV-W) envelope (env) has been reported to be related to several human diseases, including autoimmune disorders, and it could activate innate immunity. However, there are no reports investigating whether human leukemia antigen (HLA)-A*0201+ restriction is involved in the immune response caused by HERV-W env in neuropsychiatric diseases. In the present study, HERV-W env-derived epitopes presented by HLA-A*0201 are described with the potential for use in adoptive immunotherapy. Five peptides displaying HLA-A*0201-binding motifs were predicted using SYFEPITHI and BIMAS, and synthesized. A CCK-8 assay showed peptides W, Q and T promoted lymphocyte proliferation. Stimulation of peripheral blood mononuclear cells from HLA-A*0201+ donors with each of these peptides induced peptide-specific CD8+ T cells. High numbers of IFN-γ-secreting T cells were also detectable after several weekly stimulations with W, Q and T. Besides lysis of HERV-W env-loaded target cells, specific apoptosis was also observed. These data demonstrate that human T cells can be sensitized toward HERV-W env peptides (W, Q and T) and, moreover, pose a high killing potential toward HERV-W env-expressing U251 cells. In conclusion, peptides W Q and T, which are HERV-W env antigenic epitopes, have both antigenicity and immunogenicity, and can cause strong T cell immune responses. Our data strengthen the view that HERV-W env should be considered as an autoantigen that can induce autoimmunity in neuropsychiatric diseases, such as multiple sclerosis and schizophrenia. These data might provide an experimental foundation for a HERV-W env peptide vaccine and new insight into the treatment of neuropsychiatric diseases.
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15
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Vukmanović S, Sadrieh N. Skin sensitizers in cosmetics and beyond: potential multiple mechanisms of action and importance of T-cell assays for in vitro screening. Crit Rev Toxicol 2017; 47:415-432. [DOI: 10.1080/10408444.2017.1288025] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Stanislav Vukmanović
- Cosmetics Division, Office of Cosmetics and Colors (OCAC), Center for Food Safety and Applied Nutrition (CFSAN), Food and Drug Administration (FDA), MD, USA
| | - Nakissa Sadrieh
- Cosmetics Division, Office of Cosmetics and Colors (OCAC), Center for Food Safety and Applied Nutrition (CFSAN), Food and Drug Administration (FDA), MD, USA
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16
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Aberrant Glycosylation of Anchor-Optimized MUC1 Peptides Can Enhance Antigen Binding Affinity and Reverse Tolerance to Cytotoxic T Lymphocytes. Biomolecules 2016; 6:biom6030031. [PMID: 27367740 PMCID: PMC5039417 DOI: 10.3390/biom6030031] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2016] [Revised: 06/07/2016] [Accepted: 06/07/2016] [Indexed: 12/22/2022] Open
Abstract
Cancer vaccines have often failed to live up to their promise, although recent results with checkpoint inhibitors are reviving hopes that they will soon fulfill their promise. Although mutation-specific vaccines are under development, there is still high interest in an off-the-shelf vaccine to a ubiquitous antigen, such as MUC1, which is aberrantly expressed on most solid and many hematological tumors, including more than 90% of breast carcinomas. Clinical trials for MUC1 have shown variable success, likely because of immunological tolerance to a self-antigen and to poor immunogenicity of tandem repeat peptides. We hypothesized that MUC1 peptides could be optimized, relying on heteroclitic optimizations of potential anchor amino acids with and without tumor-specific glycosylation of the peptides. We have identified novel MUC1 class I peptides that bind to HLA-A*0201 molecules with significantly higher affinity and function than the native MUC1 peptides. These peptides elicited CTLs from normal donors, as well as breast cancer patients, which were highly effective in killing MUC1-expressing MCF-7 breast cancer cells. Each peptide elicited lytic responses in greater than 6/8 of normal individuals and 3/3 breast cancer patients. The CTLs generated against the glycosylated-anchor modified peptides cross reacted with the native MUC1 peptide, STAPPVHNV, suggesting these analog peptides may offer substantial improvement in the design of epitope-based vaccines.
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17
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Tang B, Zhou W, Du J, He Y, Li Y. Identification of human leukemia antigen A*0201-restricted epitopes derived from epidermal growth factor pathway substrate number 8. Mol Med Rep 2015; 12:1741-52. [PMID: 25936538 PMCID: PMC4463842 DOI: 10.3892/mmr.2015.3673] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2014] [Accepted: 03/12/2015] [Indexed: 12/12/2022] Open
Abstract
T-cell-mediated immunotherapy of hematological malignancies requires selection of targeted tumor-associated antigens and T-cell epitopes contained in these tumor proteins. Epidermal growth factor receptor pathway substrate 8 (EPS8), whose function is pivotal for tumor proliferation, progression and metastasis, has been found to be overexpressed in most human tumor types, while its expression in normal tissue is low. The aim of the present study was to identify human leukemia antigen (HLA)-A*0201-restricted epitopes of EPS8 by using a reverse immunology approach. To achieve this, computer algorithms were used to predict HLA-A*0201 molecular binding, proteasome cleavage patterns as well as translocation of transporters associated with antigen processing. Candidate peptides were experimentally validated by T2 binding affinity assay and brefeldin-A decay assay. The functional avidity of peptide-specific cytotoxic T lymphocytes (CTLs) induced from peripheral blood mononuclear cells of healthy volunteers were evaluated by using an enzyme-linked immunosorbent spot assay and a cytotoxicity assay. Four peptides, designated as P455, P92, P276 and P360, had high affinity and stability of binding towards the HLA-A*0201 molecule, and specific CTLs induced by them significantly responded to the corresponding peptides and secreted IFN-γ. At the same time, the CTLs were able to specifically lyse EPS8-expressing cell lines in an HLA-A*0201-restricted manner. The present study demon-strated that P455, P92, P276 and P360 were CTL epitopes of EPS8, and were able to be used for epitope-defined adoptive T-cell transfer and multi-epitope-based vaccine design.
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Affiliation(s)
- Baishan Tang
- Department of Hematology, Zhujiang Hospital, Southern Medical University, Guangzhou, Guangdong 510280, P.R. China
| | - Weijun Zhou
- Department of Hematology, Zhujiang Hospital, Southern Medical University, Guangzhou, Guangdong 510280, P.R. China
| | - Jingwen Du
- Department of Hematology, Zhujiang Hospital, Southern Medical University, Guangzhou, Guangdong 510280, P.R. China
| | - Yanjie He
- Department of Hematology, Zhujiang Hospital, Southern Medical University, Guangzhou, Guangdong 510280, P.R. China
| | - Yuhua Li
- Department of Hematology, Zhujiang Hospital, Southern Medical University, Guangzhou, Guangdong 510280, P.R. China
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18
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Duan Z, Guo J, Huang X, Liu H, Chen X, Jiang M, Wen J. Identification of cytotoxic T lymphocyte epitopes in dengue virus serotype 1. J Med Virol 2015; 87:1077-89. [PMID: 25777343 DOI: 10.1002/jmv.24167] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/20/2015] [Indexed: 11/12/2022]
Abstract
Dengue virus (DENV) has a serious and growing impact on global health and the exact role of DENV-specific CD8(+) T-cells in DENV infection is still uncertain. In the present study, SYFPEITHI algorithm was used to screen the amino acid sequence of Dengue virus serotype 1 (DENV-1) for potential epitopes, and seven putative HLA-A*1101-restricted and five putative HLA-A*2402-restricted epitopes conserved in hundreds of DENV-1 strains were synthesized. The binding affinity of these epitope candidates to corresponding HLA molecules was evaluated using competitive peptide-binding assay. The immunogenicity and specificity of peptides were further tested in HLA-A*1101 transgenic mice, HLA-A*2402 transgenic mice and peripheral blood mononuclear cells (PBMCs) of patients infected with DENV-1. Percentage inhibition (PI) values calculated in competitive peptide-binding assay showed that six peptides (E39-47 PTLDIELLK, NS5(505-513) GVEGEGLHK, NS2b(15-23) SILLSSLLK, NS5(561-569) ALLATSIFK, NS3(99-107) AVEPGKNPK, and NS4b(159-167) VVYDAKFEK) could bind to HLA-A*1101 molecule with high affinity and five peptides (NS3472-480 QYIYMGQPL, NS4a40-48 AYRHAMEEL, NS5(880-888) DYMTSMKRF, NS3(548-556) SYKVASEGF, and NS3(22-30) IYRILQRGL) have a high affinity for HLA-A*2402 molecule. Enzyme-linked immunospot (ELISPOT) results indicated that these high-affinity peptides were recognized by splenocytes of DENV-1-infected transgenic mice and high-affinity peptide-immunized transgenic mice displayed high levels of peptide-specific IFN-γ-secreting cells. In addition, both peptide-pulsed splenocytes and DENV-1-infected splenic monocytes were efficiently killed by these peptide-specific cytotoxic T lymphocytes. Finally, except NS2b(15-23), 10 high-affinity peptides were recognized by PBMCs of patients infected with DENV-1. These identified epitopes would contribute to the understanding of the function of DENV-specific CD8(+) T-cells.
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Affiliation(s)
- Zhiliang Duan
- Department of Microbiology and Immunology, School of Basic Medical Sciences, Wenzhou Medical University, Wenzhou, China; Department of Clinical Laboratory, The Second Affiliated Hospital & Yuying Children's Hospital of Wenzhou Medical University, Wenzhou, China
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19
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Vincent K, Hardy MP, Trofimov A, Laumont CM, Sriranganadane D, Hadj-Mimoune S, Salem Fourati I, Soudeyns H, Thibault P, Perreault C. Rejection of leukemic cells requires antigen-specific T cells with high functional avidity. Biol Blood Marrow Transplant 2013; 20:37-45. [PMID: 24161924 DOI: 10.1016/j.bbmt.2013.10.020] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2013] [Accepted: 10/21/2013] [Indexed: 12/31/2022]
Abstract
In a context where injection of antigen (Ag)-specific T cells probably represents the future of leukemia immunotherapy, identification of optimal target Ags is crucial. We therefore sought to discover a reliable marker for selection of the most potent Ags. To this end, (1) we immunized mice against 8 individual Ags: 4 minor histocompatibility Ags (miHAs) and 4 leukemia-associated Ags (LAAs) that were overexpressed on leukemic relative to normal thymocytes; (2) we assessed their ability to reject EL4 leukemic cells; and (3) we correlated the properties of our Ags (and their cognate T cells) with their ability to induce protective antileukemic responses. Overall, individual miHAs instigated more potent antileukemic responses than LAAs. Three features had no influence on the ability of primed T cells to reject leukemic cells: (1) MHC-peptide affinity; (2) the stability of MHC-peptide complexes; and (3) epitope density at the surface of leukemic cells, as assessed using mass spectrometry. The cardinal feature of successful Ags is that they were recognized by high-avidity CD8 T cells that proliferated extensively in vivo. Our work suggests that in vitro evaluation of functional avidity represents the best criterion for selection of Ags, which should be prioritized in clinical trials of leukemia immunotherapy.
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Affiliation(s)
- Krystel Vincent
- Institute for Research in Immunology and Cancer, Université de Montréal, Montréal, Quebec, Canada; Department of Medicine, Université de Montréal, Montréal, Quebec, Canada
| | - Marie-Pierre Hardy
- Institute for Research in Immunology and Cancer, Université de Montréal, Montréal, Quebec, Canada; Department of Medicine, Université de Montréal, Montréal, Quebec, Canada
| | - Assya Trofimov
- Institute for Research in Immunology and Cancer, Université de Montréal, Montréal, Quebec, Canada; Department of Medicine, Université de Montréal, Montréal, Quebec, Canada
| | - Céline M Laumont
- Institute for Research in Immunology and Cancer, Université de Montréal, Montréal, Quebec, Canada; Department of Medicine, Université de Montréal, Montréal, Quebec, Canada
| | - Dev Sriranganadane
- Institute for Research in Immunology and Cancer, Université de Montréal, Montréal, Quebec, Canada; Department of Chemistry, Université de Montréal, Montréal, Quebec, Canada
| | - Sarah Hadj-Mimoune
- Institute for Research in Immunology and Cancer, Université de Montréal, Montréal, Quebec, Canada; Department of Medicine, Université de Montréal, Montréal, Quebec, Canada
| | - Insaf Salem Fourati
- Department of Microbiology, Infectiology and Immunology, Université de Montréal, Montréal, Quebec, Canada
| | - Hugo Soudeyns
- Department of Microbiology, Infectiology and Immunology, Université de Montréal, Montréal, Quebec, Canada
| | - Pierre Thibault
- Institute for Research in Immunology and Cancer, Université de Montréal, Montréal, Quebec, Canada; Department of Chemistry, Université de Montréal, Montréal, Quebec, Canada
| | - Claude Perreault
- Institute for Research in Immunology and Cancer, Université de Montréal, Montréal, Quebec, Canada; Department of Medicine, Université de Montréal, Montréal, Quebec, Canada.
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20
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Jawa V, Cousens LP, Awwad M, Wakshull E, Kropshofer H, De Groot AS. T-cell dependent immunogenicity of protein therapeutics: Preclinical assessment and mitigation. Clin Immunol 2013; 149:534-55. [PMID: 24263283 DOI: 10.1016/j.clim.2013.09.006] [Citation(s) in RCA: 181] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2013] [Revised: 09/13/2013] [Accepted: 09/14/2013] [Indexed: 02/07/2023]
Abstract
Protein therapeutics hold a prominent and rapidly expanding place among medicinal products. Purified blood products, recombinant cytokines, growth factors, enzyme replacement factors, monoclonal antibodies, fusion proteins, and chimeric fusion proteins are all examples of therapeutic proteins that have been developed in the past few decades and approved for use in the treatment of human disease. Despite early belief that the fully human nature of these proteins would represent a significant advantage, adverse effects associated with immune responses to some biologic therapies have become a topic of some concern. As a result, drug developers are devising strategies to assess immune responses to protein therapeutics during both the preclinical and the clinical phases of development. While there are many factors that contribute to protein immunogenicity, T cell- (thymus-) dependent (Td) responses appear to play a critical role in the development of antibody responses to biologic therapeutics. A range of methodologies to predict and measure Td immune responses to protein drugs has been developed. This review will focus on the Td contribution to immunogenicity, summarizing current approaches for the prediction and measurement of T cell-dependent immune responses to protein biologics, discussing the advantages and limitations of these technologies, and suggesting a practical approach for assessing and mitigating Td immunogenicity.
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21
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Lampen MH, Hassan C, Sluijter M, Geluk A, Dijkman K, Tjon JM, de Ru AH, van der Burg SH, van Veelen PA, van Hall T. Alternative peptide repertoire of HLA-E reveals a binding motif that is strikingly similar to HLA-A2. Mol Immunol 2013; 53:126-31. [PMID: 22898188 DOI: 10.1016/j.molimm.2012.07.009] [Citation(s) in RCA: 78] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2012] [Revised: 07/09/2012] [Accepted: 07/21/2012] [Indexed: 12/31/2022]
Abstract
The non-classical HLA-E is a conserved class I molecule that mainly presents monomorphic leader peptides derived from other HLA class I molecules. These leader peptides comprise an optimized sequence for tight and deep binding into the HLA-E groove. In a TAP-deficient environment, as it can be generated during viral infection or in tumor tissue, loading of the classical leader peptide sequences is hampered leading to an alternative HLA-E peptide repertoire. In this study, we characterized this alternative peptide repertoire using cells in which TAP activity is inhibited. We identified more than 500 unique peptide sequences carried by HLA-E and found that their binding motif is different from the dominant leader peptides. Hydrophobic amino acids were only found at positions 2 and 9, in close resemblance to the peptide binding motif of HLA-A*0201. HLA-E-eluted peptides were indeed able to bind this classical HLA class I molecule. Our findings suggest that the dominant leader peptides uniquely conform to HLA-E, but that in their absence a peptide pool is presented like that of HLA-A*0201.
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Affiliation(s)
- Margit H Lampen
- Department of Clinical Oncology, Leiden University Medical Center, The Netherlands
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22
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Chornoguz O, Gapeev A, O'Neill MC, Ostrand-Rosenberg S. Major histocompatibility complex class II+ invariant chain negative breast cancer cells present unique peptides that activate tumor-specific T cells from breast cancer patients. Mol Cell Proteomics 2012; 11:1457-67. [PMID: 22942358 DOI: 10.1074/mcp.m112.019232] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The major histocompatibility complex (MHC) class II-associated Invariant chain (Ii) is present in professional antigen presenting cells where it regulates peptide loading onto MHC class II molecules and the peptidome presented to CD4+ T lymphocytes. Because Ii prevents peptide loading in neutral subcellular compartments, we reasoned that Ii- cells may present peptides not presented by Ii+ cells. Based on the hypothesis that patients are tolerant to MHC II-restricted tumor peptides presented by Ii+ cells, but will not be tolerant to novel peptides presented by Ii- cells, we generated MHC II vaccines to activate cancer patients' T cells. The vaccines are Ii- tumor cells expressing syngeneic HLA-DR and the costimulatory molecule CD80. We used liquid chromatography coupled with mass spectrometry to sequence MHC II-restricted peptides from Ii+ and Ii- MCF10 human breast cancer cells transfected with HLA-DR7 or the MHC Class II transactivator CIITA to determine if Ii- cells present novel peptides. Ii expression was induced in the HLA-DR7 transfectants by transfection of Ii, and inhibited in the CIITA transfectants by RNA interference. Peptides were analyzed and binding affinity predicted by artificial neural net analysis. HLA-DR7-restricted peptides from Ii- and Ii+ cells do not differ in size or in subcellular location of their source proteins; however, a subset of HLA-DR7-restricted peptides of Ii- cells are not presented by Ii+ cells, and are derived from source proteins not used by Ii+ cells. Peptides from Ii- cells with the highest predicted HLA-DR7 binding affinity were synthesized, and activated tumor-specific HLA-DR7+ human T cells from healthy donors and breast cancer patients, demonstrating that the MS-identified peptides are bonafide tumor antigens. These results demonstrate that Ii regulates the repertoire of tumor peptides presented by MHC class II+ breast cancer cells and identify novel immunogenic MHC II-restricted peptides that are potential therapeutic reagents for cancer patients.
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Affiliation(s)
- Olesya Chornoguz
- Department of Biological Sciences, University of Maryland Baltimore County, Baltimore, Maryland, USA
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van Luijn MM, van de Loosdrecht AA, Lampen MH, van Veelen PA, Zevenbergen A, Kester MGD, de Ru AH, Ossenkoppele GJ, van Hall T, van Ham SM. Promiscuous binding of invariant chain-derived CLIP peptide to distinct HLA-I molecules revealed in leukemic cells. PLoS One 2012; 7:e34649. [PMID: 22563374 PMCID: PMC3338516 DOI: 10.1371/journal.pone.0034649] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2011] [Accepted: 03/05/2012] [Indexed: 01/20/2023] Open
Abstract
Antigen presentation by HLA class I (HLA-I) and HLA class II (HLA-II) complexes is achieved by proteins that are specific for their respective processing pathway. The invariant chain (Ii)-derived peptide CLIP is required for HLA-II-mediated antigen presentation by stabilizing HLA-II molecules before antigen loading through transient and promiscuous binding to different HLA-II peptide grooves. Here, we demonstrate alternative binding of CLIP to surface HLA-I molecules on leukemic cells. In HLA-II-negative AML cells, we found plasma membrane display of the CLIP peptide. Silencing Ii in AML cells resulted in reduced HLA-I cell surface display, which indicated a direct role of CLIP in the HLA-I antigen presentation pathway. In HLA-I-specific peptide eluates from B-LCLs, five Ii-derived peptides were identified, of which two were from the CLIP region. In vitro peptide binding assays strikingly revealed that the eluted CLIP peptide RMATPLLMQALPM efficiently bound to four distinct HLA-I supertypes (-A2, -B7, -A3, -B40). Furthermore, shorter length variants of this CLIP peptide also bound to these four supertypes, although in silico algorithms only predicted binding to HLA-A2 or -B7. Immunization of HLA-A2 transgenic mice with these peptides did not induce CTL responses. Together these data show a remarkable promiscuity of CLIP for binding to a wide variety of HLA-I molecules. The found participation of CLIP in the HLA-I antigen presentation pathway could reflect an aberrant mechanism in leukemic cells, but might also lead to elucidation of novel processing pathways or immune escape mechanisms.
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Affiliation(s)
- Marvin M van Luijn
- Department of Hematology, VU Institute for Cancer and Immunology, VU University Medical Center, Amsterdam, The Netherlands.
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Ebert LM, MacRaild SE, Davis ID, Cebon J, Chen W. A novel method for detecting antigen-specific human regulatory T cells. J Immunol Methods 2012; 377:56-61. [PMID: 22265970 DOI: 10.1016/j.jim.2012.01.004] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2011] [Revised: 12/06/2011] [Accepted: 01/05/2012] [Indexed: 02/01/2023]
Abstract
Antigenic epitopes recognized by FoxP3(+) regulatory T cells (Treg) are poorly defined, largely due to a lack of assays for determining Treg specificity. We have developed a novel approach for detecting human Treg specific to peptide antigen, utilizing down-regulation of surface CD3 as a read-out of antigen recognition. Culture conditions and re-stimulation time have been optimized, allowing the detection of even very rare Treg, such as those specific to tumor antigens.
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Affiliation(s)
- Lisa M Ebert
- Ludwig Institute for Cancer Research (Melbourne-Austin Branch), Melbourne, Australia
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25
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Chew SL, Or MY, Chang CXL, Gehring AJ, Bertoletti A, Grotenbreg GM. Stability screening of arrays of major histocompatibility complexes on combinatorially encoded flow cytometry beads. J Biol Chem 2011; 286:28466-75. [PMID: 21680737 DOI: 10.1074/jbc.m111.262691] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
The binding and stabilization capacity of potential T cell epitopes to class I MHC molecules form the basis for their immunogenicity and provide fundamental insight into factors that dictate cellular immune responses. We have developed a versatile high throughput cell-free method to measure MHC stability by capturing a variety of MHC products on the surface of streptavidin-coated particles followed by flow cytometry analysis. Arrays of peptide-MHC combinations, generated by exchanging conditional ligand-loaded MHC, could be probed in a single experiment, thus combining the molecular precision of biochemically purified MHCs with high content multiparametric flow cytometry-based assays. Semiquantitative determination of the peptide affinity for the restriction element could also be accomplished through competition experiments using this bead-based assay. Furthermore, the generated peptide-MHC reagents could directly be applied to antigen-specific CD8(+) T lymphocyte analysis. The combinatorial labeling of beads allowed straightforward identification by their unique fluorescent signatures and provided a convenient means for extended assay multiplexing.
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Affiliation(s)
- Shi Ling Chew
- Department of Microbiology, Department of Biological Sciences, and Immunology Programme, Life Sciences Institute, National University of Singapore, 117456 Singapore
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26
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Antigen processing by nardilysin and thimet oligopeptidase generates cytotoxic T cell epitopes. Nat Immunol 2010; 12:45-53. [PMID: 21151101 DOI: 10.1038/ni.1974] [Citation(s) in RCA: 84] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2010] [Accepted: 11/17/2010] [Indexed: 12/18/2022]
Abstract
Cytotoxic T lymphocytes (CTLs) recognize peptides presented by HLA class I molecules on the cell surface. The C terminus of these CTL epitopes is considered to be produced by the proteasome. Here we demonstrate that the cytosolic endopeptidases nardilysin and thimet oligopeptidase (TOP) complemented proteasome activity. Nardilysin and TOP were required, either together or alone, for the generation of a tumor-specific CTL epitope from PRAME, an immunodominant CTL epitope from Epstein-Barr virus protein EBNA3C, and a clinically important epitope from the melanoma protein MART-1. TOP functioned as C-terminal trimming peptidase in antigen processing, and nardilysin contributed to both the C-terminal and N-terminal generation of CTL epitopes. By broadening the antigenic peptide repertoire, nardilysin and TOP strengthen the immune defense against intracellular pathogens and cancer.
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27
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Roomp K, Antes I, Lengauer T. Predicting MHC class I epitopes in large datasets. BMC Bioinformatics 2010; 11:90. [PMID: 20163709 PMCID: PMC2836306 DOI: 10.1186/1471-2105-11-90] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2009] [Accepted: 02/17/2010] [Indexed: 11/10/2022] Open
Abstract
Background Experimental screening of large sets of peptides with respect to their MHC binding capabilities is still very demanding due to the large number of possible peptide sequences and the extensive polymorphism of the MHC proteins. Therefore, there is significant interest in the development of computational methods for predicting the binding capability of peptides to MHC molecules, as a first step towards selecting peptides for actual screening. Results We have examined the performance of four diverse MHC Class I prediction methods on comparatively large HLA-A and HLA-B allele peptide binding datasets extracted from the Immune Epitope Database and Analysis resource (IEDB). The chosen methods span a representative cross-section of available methodology for MHC binding predictions. Until the development of IEDB, such an analysis was not possible, as the available peptide sequence datasets were small and spread out over many separate efforts. We tested three datasets which differ in the IC50 cutoff criteria used to select the binders and non-binders. The best performance was achieved when predictions were performed on the dataset consisting only of strong binders (IC50 less than 10 nM) and clear non-binders (IC50 greater than 10,000 nM). In addition, robustness of the predictions was only achieved for alleles that were represented with a sufficiently large (greater than 200), balanced set of binders and non-binders. Conclusions All four methods show good to excellent performance on the comprehensive datasets, with the artificial neural networks based method outperforming the other methods. However, all methods show pronounced difficulties in correctly categorizing intermediate binders.
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Affiliation(s)
- Kirsten Roomp
- Department of Computational Biology and Applied Algorithmics, Max Planck Institute for Informatics, 66123 Saarbruecken, Germany
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28
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Warren RL, Holt RA. A census of predicted mutational epitopes suitable for immunologic cancer control. Hum Immunol 2010; 71:245-54. [PMID: 20035814 DOI: 10.1016/j.humimm.2009.12.007] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2009] [Revised: 12/09/2009] [Accepted: 12/17/2009] [Indexed: 11/25/2022]
Abstract
The adaptive immune system can protect against spontaneously arising tumors, and the potential exists to reduce cancer incidence by priming adaptive immune responses with vaccines. Immunologic cancer control has been implemented for cancers caused by infectious agents, but not for spontaneous cancers caused by mutation. This is largely due to the high cost of preventative clinical trials and the lack of validated tumor epitopes. Here we evaluate, computationally, all known somatic mutations in human tumors for their antigenic potential. All possible human leukocyte antigen (HLA) class I presented peptides containing recurrent somatic cancer mutations with frequency > 5% were screened by three independent epitope prediction algorithms (SYFPEITHI, BIMAS, and IEDB). Using stringent filters, a total of 20 genes, 35 mutations, and 159 candidate epitopes were identified, each presented by up to four distinct HLA class I alleles. The top-ranking gene from our survey was KRAS, which figures prominently because there are frequent hotspot mutations in numerous, prevalent cancers, and mutant peptides are predicted to be presented by several common HLA alleles. From our data, we estimate that prophylactic vaccination could provide meaningful levels of prevention of tumors associated with common recurrent mutations.
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Affiliation(s)
- René L Warren
- British Columbia Cancer Agency, Genome Sciences Centre, Vancouver, British Columbia, Canada
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29
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Jarmalavicius S, Trefzer U, Walden P. Differential arginine methylation of the G‐protein pathway suppressor GPS‐2 recognized by tumor‐specific T cells in melanoma. FASEB J 2009; 24:937-46. [DOI: 10.1096/fj.09-136283] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Saulius Jarmalavicius
- Clinical Research Group Tumor ImmunologyDepartment of DermatologyCharité‐Universitätsmedizin BerlinBerlinGermany
| | - Uwe Trefzer
- Clinical Research Group Tumor ImmunologyDepartment of DermatologyCharité‐Universitätsmedizin BerlinBerlinGermany
| | - Peter Walden
- Clinical Research Group Tumor ImmunologyDepartment of DermatologyCharité‐Universitätsmedizin BerlinBerlinGermany
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30
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Proteomic identification of an MHC-binding peptidome from pancreas and breast cancer cell lines. Mol Immunol 2009; 46:2931-7. [DOI: 10.1016/j.molimm.2009.06.021] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2009] [Revised: 06/10/2009] [Accepted: 06/18/2009] [Indexed: 11/23/2022]
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31
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Kessler JH, Benckhuijsen WE, Mutis T, Melief CJM, van der Burg SH, Drijfhout JW. Competition-based cellular peptide binding assay for HLA class I. ACTA ACUST UNITED AC 2008; Chapter 18:Unit 18.12. [PMID: 18432926 DOI: 10.1002/0471142735.im1812s61] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
This unit describes a competition assay to determine binding of unlabeled test peptides to thirteen of the most prevalent HLA class I molecules. It uses cells expressing the HLA class I molecule of interest on their surface, fluorescently labeled reference peptides, and unlabeled test peptides. Cells of interest are stripped from their natural HLA-bound peptides using acid treatment and subsequently incubated with a mixture of labeled reference peptide and titrating concentrations of test peptide. Subsequently, FACS analysis is performed to determine the amount of bound reference peptide, which is a measure of the ability of test peptide to compete for binding to HLA. The assay provides IC50 values for binding of test peptides to HLA molecules. It can be performed in a normally equipped cellular laboratory, requires no additional equipment besides a flow cytometer (FACS), and is relatively easy to perform. Assay-specific parameters for several HLA alleles are provided.
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Affiliation(s)
- Jan H Kessler
- Leiden University Medical Center, Leiden, Netherlands
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32
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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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33
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De Groot AS, Rivera DS, McMurry JA, Buus S, Martin W. Identification of immunogenic HLA-B7 "Achilles' heel" epitopes within highly conserved regions of HIV. Vaccine 2007; 26:3059-71. [PMID: 18206276 DOI: 10.1016/j.vaccine.2007.12.004] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2007] [Accepted: 12/01/2007] [Indexed: 10/22/2022]
Abstract
Genetic polymorphisms in class I human leukocyte antigen molecules (HLA) have been shown to determine susceptibility to HIV infection as well as the rate of progression to AIDS. In particular, the HLA-B7 supertype has been shown to be associated with high viral loads and rapid progression to disease. Using a multiplatform in silico/in vitro approach, we have prospectively identified 45 highly conserved, putative HLA-B7 restricted HIV CTL epitopes and evaluated them in HLA binding and ELISpot assays. All 45 epitopes (100%) bound to HLA-B7 in cell-based HLA binding assays: 28 (62%) bound with high affinity, 6 (13%) peptides bound with medium affinity and 11 (24%) bound with low affinity. Forty of the 45 peptides (88%) stimulated a IFN-gamma response in PBMC from at least one subject. Eighteen of these 40 epitopes have not been previously described; an additional eight epitopes have not been previously described as restricted by B7. The HLA-B7 restricted epitopes discovered using this in silico screening approach are highly conserved across strains and clades of HIV as well as conserved in the HIV genome over the 20 years since HIV-1 isolates were first sequenced. This study demonstrates that it is possible to select a broad range of HLA-B7 restricted epitopes that comprise stable elements in the rapidly mutating HIV genome. The most immunogenic of these epitopes will be included in the GAIA multi-epitope vaccine.
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34
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Santegoets SJAM, Schreurs MWJ, Reurs AW, Lindenberg JJ, Kueter EWM, van den Eertwegh AJM, Hooijberg E, Brandwijk RJ, Hufton SE, Hoogenboom HR, Scheper RJ, Somers VA, de Gruijl TD. Identification and characterization of ErbB-3-binding protein-1 as a target for immunotherapy. THE JOURNAL OF IMMUNOLOGY 2007; 179:2005-12. [PMID: 17641068 DOI: 10.4049/jimmunol.179.3.2005] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Based on immune reactivity in response to a whole-cell colon tumor vaccine and using serological identification of Ags by recombinant cDNA expression cloning, we here describe the molecular and functional identification of a novel human tumor Ag. By screening a cDNA expression library derived from the coloncarcinoma cell line HT-29 with pooled colorectal cancer patients' sera, 26 clones reactive with IgG Abs could be identified. Characterization of these cDNA clones by sequence analysis and alignment, and detailed serological analysis revealed cancer-related immunoreactivity for the ErbB-3-binding protein-1 (Ebp1). Immunohistochemical staining of colorectal tumors and neighboring normal colon tissue indicated the observed cancer-related immunogenicity of Ebp1 to be related to overexpression. Via reverse immunology, five potential HLA-A2-restricted T cell epitopes were identified, of which two (Ebp1(45-54) and Ebp1(59-67)) bound HLA-A2 with intermediate and high affinity, respectively. Analysis of their immunogenicity in vitro indicated that only the high-affinity Ebp1(59) epitope gave rise to CD8(+) T cells capable of recognizing both exogenously loaded Ebp1 peptide and endogenously expressed Ebp1 on target cells. In addition, in vivo CD8(+) T cell responsiveness against the Ebp1(59) epitope could be detected in two of nine and three of six cancer patients PBMC and tumor draining lymph nodes, respectively, but not in nine of nine healthy donors tested. These data confirm that Ebp1 is an immunogenic protein, capable of eliciting CD8-mediated responses in vivo and in vitro, providing a rationale for further exploration of Ebp1 as a possible target for anticancer immunotherapy.
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MESH Headings
- Adaptor Proteins, Signal Transducing/biosynthesis
- Adaptor Proteins, Signal Transducing/chemistry
- Adaptor Proteins, Signal Transducing/genetics
- Antigens, Neoplasm/biosynthesis
- Antigens, Neoplasm/chemistry
- Antigens, Neoplasm/genetics
- Breast Neoplasms/immunology
- Breast Neoplasms/pathology
- Cell Line
- Cell Line, Tumor
- Cloning, Molecular
- Colorectal Neoplasms/immunology
- Colorectal Neoplasms/pathology
- Colorectal Neoplasms/therapy
- Cytotoxicity Tests, Immunologic
- DNA, Complementary/biosynthesis
- Drug Delivery Systems
- Epitopes, T-Lymphocyte/immunology
- Epitopes, T-Lymphocyte/metabolism
- Gene Library
- HLA-A2 Antigen/immunology
- HT29 Cells
- Humans
- Immunization, Passive/methods
- RNA-Binding Proteins/biosynthesis
- RNA-Binding Proteins/chemistry
- RNA-Binding Proteins/genetics
- Receptor, ErbB-3/metabolism
- T-Lymphocytes, Cytotoxic/immunology
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35
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Abstract
The effectiveness of T-cell-mediated immunotherapy of cancer depends on both an optimal immunostimulatory context of the therapy and the proper selection with respect to quality and quantity of the targeted tumor-associated antigens (TAA), and, more precisely, the T-cell epitopes contained in these tumor proteins. Our progressing insight in human leukocyte antigen (HLA) class I and class II antigen processing and presentation mechanisms has improved the prediction by reverse immunology of novel cytotoxic T lymphocyte and T-helper cell epitopes within known antigens. Computer algorithms that in silico predict HLA class I and class II binding, proteasome cleavage patterns and transporter associated with antigen processing translocation are now available to expedite epitope identification. The advent of genomics allows a high-throughput screening for tumor-specific transcripts and mutations, with that identifying novel shared and unique TAA. The increasing power of mass spectrometry and proteomics will lead to the direct identification from the tumor cell surface of numerous novel tumor-specific HLA class I and class II presented ligands. Together, the expanded repertoire of tumor-specific T-cell epitopes will enable more precise immunomonitoring and the development of effective epitope-defined adoptive T-cell transfer and multi-epitope-based vaccination strategies targeting epitopes derived from a wider diversity of TAA presented in a broader array of HLA molecules.
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Affiliation(s)
- J H Kessler
- Department of Immunohematology and Blood Transfusion, Leiden University Medical Center, Leiden, The Netherlands.
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36
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Wahl A, Weidanz J, Hildebrand W. Direct class I HLA antigen discovery to distinguish virus-infected and cancerous cells. Expert Rev Proteomics 2007; 3:641-52. [PMID: 17181478 DOI: 10.1586/14789450.3.6.641] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Class I human leukocyte antigen molecules are nature's proteome-scanning chips, presenting thousands of endogenously loaded peptides on the surface of virtually every cell in the body. Cytotoxic T cells survey the class I human leukocyte antigen peptide cargo presented, recognize peptides unique to unhealthy cells and destroy diseased cells. A precise understanding of how class I molecules distinguish diseased cells is positioned to drive immune-based diagnostics, therapies and vaccines. When identifying epitopes unique to unhealthy cells, the most experimentally direct approach is to examine the class I-presented peptides of infected/cancerous cells. Here we discuss the strategies adapted for protein production, protein/peptide purification, peptide separation and for maintaining experimental reproducibility during the direct characterization of class I human leukocyte antigen peptides.
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Affiliation(s)
- Angela Wahl
- University of Oklahoma, Department of Microbiology and Immunology, University of Oklahoma Health Sciences Center, 975 NE, 10 Street, BRC Room 317, Oklahoma City, OK 73104, USA.
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37
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Zimbwa P, Milicic A, Frater J, Scriba TJ, Willis A, Goulder PJR, Pillay T, Gunthard H, Weber JN, Zhang HT, Phillips RE. Precise identification of a human immunodeficiency virus type 1 antigen processing mutant. J Virol 2006; 81:2031-8. [PMID: 17108020 PMCID: PMC1797578 DOI: 10.1128/jvi.00968-06] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
Human immunodeficiency virus type 1 (HIV-1) evokes a strong immune response, but the virus persists. Polymorphisms within known antigenic sites result in loss of immune recognition and can be positively selected. Amino acid variation outside known HLA class I restricted epitopes can also enable immune escape by interfering with the processing of the optimal peptide antigen. However, the lack of precise rules dictating epitope generation and the enormous genetic diversity of HIV make prediction of processing mutants very difficult. Polymorphism E169D in HIV-1 reverse transcriptase (RT) is significantly associated with HLA-B*0702 in HIV-1-infected individuals. This polymorphism does not map within a known HLA-B*0702 epitope; instead, it is located five residues downstream of a HLA-B*0702-restricted epitope SPAIFQSSM (SM9). Here we investigate the association between E169D and HLA-B*0702 for immune escape via the SM9 epitope. We show that this single amino acid variation prevents the immune recognition of the flanked SM9 epitope by cytotoxic T cells through lack of generation of the epitope, which is a result of aberrant proteasomal cleavage. The E169D polymorphism also maps within and abrogates the recognition of an HLA-A*03-restricted RT epitope MR9. This study highlights the potential for using known statistical associations as indicators for viral escape but also the complexity involved in interpreting the immunological consequences of amino acid changes in HIV sequences.
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Affiliation(s)
- Peter Zimbwa
- The James Martin 21st Century School at The Peter Medawar Building for Pathogen Research, Nuffield Department of Clinical Medicine, University of Oxford, South Parks Road, Oxford OX1 3SY, United Kingdom
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38
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Frater AJ, Edwards CTT, McCarthy N, Fox J, Brown H, Milicic A, Mackie N, Pillay T, Drijfhout JW, Dustan S, Clarke JR, Holmes EC, Zhang HT, Pfafferott K, Goulder PJ, McClure MO, Weber J, Phillips RE, Fidler S. Passive sexual transmission of human immunodeficiency virus type 1 variants and adaptation in new hosts. J Virol 2006; 80:7226-34. [PMID: 16809328 PMCID: PMC1489048 DOI: 10.1128/jvi.02014-05] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Human immunodeficiency virus type 1 (HIV-1) genetic diversity is a major obstacle for the design of a successful vaccine. Certain viral polymorphisms encode human leukocyte antigen (HLA)-associated immune escape, potentially overcoming limited vaccine protection. Although transmission of immune escape variants has been reported, the overall extent to which this phenomenon occurs in populations and the degree to which it contributes to HIV-1 viral evolution are unknown. Selection on the HIV-1 env gene at transmission favors neutralization-sensitive variants, but it is not known to what degree selection acts on the internal HIV-1 proteins to restrict or enhance the transmission of immune escape variants. Studies have suggested that HLA class I may determine susceptibility to HIV-1 infection, but a definitive role for HLA at transmission remains unproven. Comparing populations of acute seroconverters and chronically infected patients, we found no evidence of selection acting to restrict transmission of HIV-1 variants. We found that statistical associations previously reported in chronic infection between viral polymorphisms and HLA class I alleles are not present in acute infection, suggesting that the majority of viral polymorphisms in these patients are the result of transmission rather than de novo adaptation. Using four episodes of HIV-1 transmission in which the donors and recipients were both sampled very close to the time of infection we found that, despite a transmission bottleneck, genetic variants of HIV-1 infection are transmitted in a frequency-dependent manner. As HIV-1 infections are seeded by unique donor-adapted viral variants, each episode is a highly individual antigenic challenge. Host-specific, idiosyncratic HIV-1 antigenic diversity will seriously tax the efficacy of immunization based on consensus sequences.
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Affiliation(s)
- A J Frater
- The James Martin 21st Century School, Nuffield Department of Medicine, Peter Medawar Building for Pathogen Research, South Parks Road, Oxford OX1 3SY, United Kingdom
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39
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Kessler JH, Bres-Vloemans SA, van Veelen PA, de Ru A, Huijbers IJG, Camps M, Mulder A, Offringa R, Drijfhout JW, Leeksma OC, Ossendorp F, Melief CJM. BCR-ABL fusion regions as a source of multiple leukemia-specific CD8+ T-cell epitopes. Leukemia 2006; 20:1738-50. [PMID: 16932347 DOI: 10.1038/sj.leu.2404354] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
For immunotherapy of residual disease in patients with Philadelphia-positive leukemias, the BCR-ABL fusion regions are attractive disease-specific T-cell targets. We analyzed these regions for the prevalence of cytotoxic T lymphocyte (CTL) epitopes by an advanced reverse immunology procedure. Seventeen novel BCR-ABL fusion peptides were identified to bind efficiently to the human lymphocyte antigen (HLA)-A68, HLA-B51, HLA-B61 or HLA-Cw4 HLA class I molecules. Comprehensive enzymatic digestion analysis showed that 10 out of the 28 HLA class I binding fusion peptides were efficiently excised after their C-terminus by the proteasome, which is an essential requirement for efficient cell surface expression. Therefore, these peptides are prime vaccine candidates. The other peptides either completely lacked C-terminal liberation or were only inefficiently excised by the proteasome, rendering them inappropriate or less suitable for inclusion in a vaccine. CTL raised against the properly processed HLA-B61 epitope AEALQRPVA from the BCR-ABL e1a2 fusion region, expressed in acute lymphoblastic leukemia (ALL), specifically recognized ALL tumor cells, proving cell surface presentation of this epitope, its applicability for immunotherapy and underlining the accuracy of our epitope identification strategy. Our study provides a reliable basis for the selection of optimal peptides to be included in immunotherapeutic BCR-ABL vaccines against leukemia.
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MESH Headings
- Amino Acid Sequence
- CD8-Positive T-Lymphocytes/immunology
- Cancer Vaccines/immunology
- Cell Line, Tumor
- Epitope Mapping/methods
- Epitopes, T-Lymphocyte/immunology
- Fusion Proteins, bcr-abl/genetics
- Fusion Proteins, bcr-abl/immunology
- Fusion Proteins, bcr-abl/metabolism
- HLA-A Antigens/immunology
- HLA-A Antigens/metabolism
- HLA-A2 Antigen
- HLA-B Antigens/immunology
- HLA-B Antigens/metabolism
- HLA-B51 Antigen
- HLA-C Antigens/immunology
- HLA-C Antigens/metabolism
- Humans
- Immunotherapy/methods
- Leukemia, Myelogenous, Chronic, BCR-ABL Positive/immunology
- Leukemia, Myelogenous, Chronic, BCR-ABL Positive/therapy
- Molecular Sequence Data
- Peptide Fragments/genetics
- Peptide Fragments/immunology
- Peptide Fragments/metabolism
- Protein Binding/immunology
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Affiliation(s)
- J H Kessler
- Department of Immunohematology and Blood Transfusion, Leiden University Medical Center, Leiden, The Netherlands.
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40
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Viatte S, Alves PM, Romero P. Reverse immunology approach for the identification of CD8 T-cell-defined antigens: advantages and hurdles. Immunol Cell Biol 2006; 84:318-30. [PMID: 16681829 DOI: 10.1111/j.1440-1711.2006.01447.x] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
One of the challenges of tumour immunology remains the identification of strongly immunogenic tumour antigens for vaccination. Reverse immunology, that is, the procedure to predict and identify immunogenic peptides from the sequence of a gene product of interest, has been postulated to be a particularly efficient, high-throughput approach for tumour antigen discovery. Over one decade after this concept was born, we discuss the reverse immunology approach in terms of costs and efficacy: data mining with bioinformatic algorithms, molecular methods to identify tumour-specific transcripts, prediction and determination of proteasomal cleavage sites, peptide-binding prediction to HLA molecules and experimental validation, assessment of the in vitro and in vivo immunogenic potential of selected peptide antigens, isolation of specific cytolytic T lymphocyte clones and final validation in functional assays of tumour cell recognition. We conclude that the overall low sensitivity and yield of every prediction step often requires a compensatory up-scaling of the initial number of candidate sequences to be screened, rendering reverse immunology an unexpectedly complex approach.
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Affiliation(s)
- Sebastien Viatte
- Division of Clinical Onco-Immunology, Ludwig Institute for Cancer Research, Lausanne branch, University Hospital, CHUV, and National Center for Competence in Research, NCCR, Molecular Oncology, Lausanne, Switzerland
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41
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Buchli R, Vangundy RS, Giberson CF, Hildebrand WH. Critical factors in the development of fluorescence polarization-based peptide binding assays: an equilibrium study monitoring specific peptide binding to soluble HLA-A*0201. J Immunol Methods 2006; 314:38-53. [PMID: 16844138 DOI: 10.1016/j.jim.2006.05.010] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2005] [Revised: 04/19/2006] [Accepted: 05/12/2006] [Indexed: 01/12/2023]
Abstract
There is currently a significant interest in the identification and validation of HLA-restricted CTL epitopes, which are thought to have important implications for the development of preventive and/or therapeutic applications in bacterial or viral infections, autoimmune diseases, and cancer. To better facilitate epitope discovery and validation, we present a cell- and radioisotope-free HLA-A*0201 assay system which relies upon fluorescence polarization. The assay has the advantage of allowing real-time measurements in solution without separation steps. In this report, we directed our efforts towards enhancing the sensitivity and reproducibility of the assay by conducting an in-depth analysis of parameters critical for standardization. Initial experiments demonstrated that the attachment of a fluorescence moiety at positions 5 and 8 for 9-mers and positions 5 and 6 for 10-mers, respectively, does not interfere with ligand binding to soluble HLA-A*0201. In addition, it was found that their binding to HLA-A*0201 was very effective showing high affinity binding with K(d)'s between 10.7 to 21.8 nM and binding capacities of up to 37%. In order to deliver maximized responses, factors such as the regulation of thermal HLA activation parameters to initiate peptide exchange as well as the specific adjustment of assay components were identified. Overall, the results obtained clearly demonstrate high accuracy, sensitivity and reproducibility of the FP-based assay approach. With the need for both increased throughput and miniaturized volumes, this fully homogenous, fluorescent-type binding assay is expected to be useful for routine analysis of peptide binding to MHC class I as well as class II molecules.
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Affiliation(s)
- Rico Buchli
- Pure Protein L.L.C., Oklahoma City, OK 73104-3698, United States.
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Milicic A, Edwards CTT, Hué S, Fox J, Brown H, Pillay T, Drijfhout JW, Weber JN, Holmes EC, Fidler SJ, Zhang HT, Phillips RE. Sexual transmission of single human immunodeficiency virus type 1 virions encoding highly polymorphic multisite cytotoxic T-lymphocyte escape variants. J Virol 2006; 79:13953-62. [PMID: 16254331 PMCID: PMC1280182 DOI: 10.1128/jvi.79.22.13953-13962.2005] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Antigenic variation inherent in human immunodeficiency virus type 1 (HIV-1) virions that successfully instigate new infections transferred by sex has not been well defined. Yet this is the viral "challenge" which any vaccine-induced immunity must deal with. Closely timed comparisons of the virus circulating in the "donor" and that which initiates new infection are difficult to carry out rigorously, as suitable samples are very hard to get in the face of ethical hurdles. Here we investigate HIV-1 variation in four homosexual couples where we sampled blood from both parties within several weeks of the estimated transmission event. We analyzed variation within highly immunogenic HIV-1 internal proteins encoding epitopes recognized by cytotoxic T lymphocytes (CTLs). These responses are believed to be crucial as a means of containing viral replication. In the donors we detected virions capable of evading host CTL recognition at several linked epitopes of distinct HLA class I restriction. When a donor transmitted escape variants to a recipient with whom he had HLA class I molecules in common, the recipient's CTL response to those epitopes was prevented, thus impeding adequate viral control. In addition, we show that even when HLA class I alleles are disparate in the transmitting couple, a single polymorphism can abolish CTL recognition of an overlapping epitope of distinct restriction and so confer immune escape properties to the recipient's seroconversion virus. In donors who are themselves controlling an early, acute infection, the precise timing of onward transmission is a crucial determinant of the viral variants available to compose the inoculum.
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Affiliation(s)
- Anita Milicic
- The Peter Medawar Building for Pathogen Research and The James Martin 21st Century School, Nuffield Department of Clinical Medicine, University of Oxford, South Parks Road, Oxford OX1 3SY, United Kingdom
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43
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Anchor profiles of HLA-specific peptides: analysis by a novel affinity scoring method and experimental validation. Proteins 2006; 58:53-69. [PMID: 15526297 DOI: 10.1002/prot.20302] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
The study of intermolecular interactions is a fundamental research subject in biology. Here we report on the development of a quantitative structure-based affinity scoring method for peptide-protein complexes, named PepScope. The method operates on the basis of a highly specific force field function (CHARMM) that is applied to all-atom structural representations of peptide-receptor complexes. Peptide side-chain contributions to total affinity are scored after detailed rotameric sampling followed by controlled energy refinement. A de novo approach to estimate dehydration energies was developed, based on the simulation of individual amino acids in a solvent box filled with explicit water molecules. Transferability of the method was demonstrated by its application to the hydrophobic HLA-A2 and -A24 receptors, the polar HLA-A1, and the sterically ruled HLA-B7 receptor. A combined theoretical and experimental study on 39 anchor substitutions in FxSKQYMTx/HLA-A2 and -A24 complexes indicated a prediction accuracy of about two thirds of a log-unit in Kd. Analysis of free energy contributions identified a great role of desolvation and conformational strain effects in establishing a given specificity profile. Interestingly, the method rightly predicted that most anchor profiles are less specific than so far assumed. This suggests that many potential T-cell epitopes could be missed with current prediction methods. The results presented in this work may therefore significantly affect T-cell epitope discovery programs applied in the field of peptide vaccine development.
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Bontkes HJ, Ruizendaal JJ, Kramer D, Meijer CJLM, Schreurs MWJ, Hooijberg E. Interleukin-12 Increases Proliferation and Interferon-γ Production but Not Cytolytic Activity of Human Antigen-Specific Effector Memory Cytotoxic T Lymphocytes: Power of the Effect Depends on the Functional Avidity of the T Cell and the Antigen Concentration. Hum Immunol 2005; 66:1137-45. [PMID: 16571414 DOI: 10.1016/j.humimm.2006.02.002] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2005] [Indexed: 12/21/2022]
Abstract
Cytotoxic T lymphocytes (CTLs) play an important role in the defense against viral infections and malignant diseases. Interleukin (IL)-12 plays a crucial role in induction of antigen-specific primary CTL responses and enhances proliferation, interferon-gamma (IFN-gamma) production, and cytolytic activity of mitogen-stimulated T cells. However, the effects of IL-12 on proliferation and effector functions of previously in vitro or in vivo primed antigen-specific CTLs are less clear. Our results show that IL-12 induces an increase in proliferation of and IFN-gamma production by influenza peptide-specific CTLs, but no increase in cytolytic activity on a per cell basis was observed in bulk cultures. Stimulation of a CTL clone confirmed these results; IL-12 supported an increase in IFN-gamma production, but did not increase cytolytic activity. The extent of the effect of IL-12 on IFN-gamma production differs per CTL clone and depends on the avidity of the clone and the peptide concentration on its target. Our data suggest that IL-12 is a good adjuvant for boosting CTL responses, in terms of proliferation and IFN-gamma production, the latter particularly for CTLs with low to intermediate avidity, such as tumor-associated self-antigen-specific CTLs.
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Affiliation(s)
- Hetty J Bontkes
- Department of Pathology, VU University Medical Center, Amsterdam, The Netherlands.
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Pillay T, Zhang HT, Drijfhout JW, Robinson N, Brown H, Khan M, Moodley J, Adhikari M, Pfafferott K, Feeney ME, St John A, Holmes EC, Coovadia HM, Klenerman P, Goulder PJR, Phillips RE. Unique acquisition of cytotoxic T-lymphocyte escape mutants in infant human immunodeficiency virus type 1 infection. J Virol 2005; 79:12100-5. [PMID: 16140787 PMCID: PMC1212591 DOI: 10.1128/jvi.79.18.12100-12105.2005] [Citation(s) in RCA: 37] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The role of cytotoxic T-lymphocyte (CTL) escape in rapidly progressive infant human immunodeficiency virus type 1 (HIV-1) infection is undefined. The data presented here demonstrate that infant HIV-1-specific CTL can select for viral escape variants very early in life. These variants, furthermore, may be selected specifically in the infant, despite the same CTL specificity being present in the mother. Additionally, pediatric CTL activity may be compromised both by the transmission of maternal escape variants and by mother-to-child transmission of escape variants that originally arose in the father. The unique acquisition of these CTL escape forms may help to explain the severe nature of some pediatric HIV infections.
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Affiliation(s)
- Thillagavathie Pillay
- The Peter Medawar Building for Pathogen Research and Nuffield Department of Medicine, John Radcliffe Hospital, Oxford, United Kingdom
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Bernardeau K, Gouard S, David G, Ruellan AL, Devys A, Barbet J, Bonneville M, Chérel M, Davodeau F. Assessment of CD8 involvement in T cell clone avidity by direct measurement of HLA-A2/Mage3 complex density using a high-affinity TCR like monoclonal antibody. Eur J Immunol 2005; 35:2864-75. [PMID: 16163672 DOI: 10.1002/eji.200526307] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Peptide affinity for MHC molecules determines the number of MHC/peptide complexes stabilized at the cell surface in in vitro tests or in vaccination protocols. We isolated a high affinity monoclonal antibody specific for the HLA-A2/Mage3 complex that enables an equilibrium binding assay to be performed on T2 cell line loaded with a range of Mage3 peptides. Binding of Mage3 to the HLA-A2 molecule can be modeled by a standard receptor-ligand interaction characterized by an affinity constant. This model enables the measurement of the affinity of other immunogenic peptides for HLA-A2 by a competition test and the calculation of the density of complexes stabilized at the T2 cell surface for all peptide concentrations. Quantification of the HLA-A2/Mage3 complexes at target cell surfaces was used to estimate the number of complexes required to reach cytotoxicity ED50 of human T cell clones sorted from an unprimed repertoire. We confirm with this antibody the direct relationship between clone avidity and TCR affinity, and the moderate contribution of the CD8 co-receptor in the reinforcement of TCR-MHC/peptide contact. Nevertheless, CD8 plays a critical role in the amplification of the specific signal to establish an efficient T cell response at low specific complex densities found in physiological situations.
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Affiliation(s)
- Karine Bernardeau
- INSERM U601, Institut de Biologie, and Université Nantes, Nantes, France
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Schreurs MWJ, Kueter EWM, Scholten KBJ, Kramer D, Meijer CJLM, Hooijberg E. Identification of a potential human telomerase reverse transcriptase-derived, HLA-A1-restricted cytotoxic T-lymphocyte epitope. Cancer Immunol Immunother 2005; 54:703-12. [PMID: 15726360 PMCID: PMC11032920 DOI: 10.1007/s00262-004-0611-z] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2004] [Accepted: 08/23/2004] [Indexed: 12/18/2022]
Abstract
The catalytic subunit of human telomerase reverse transcriptase (hTERT) is expressed in the majority of tumor cells of different histological origins as opposed to most normal somatic cells. This implicates hTERT as a widely expressed tumor-associated antigen and an attractive candidate for antigen-specific tumor immunotherapy. T lymphocytes specific for hTERT-derived epitopes have been isolated and shown reactive with hTERT-expressing tumor cells. To further increase the applicability of hTERT as a target antigen for immunotherapy, we set out to identify potential hTERT-derived, HLA-A1-restricted cytotoxic T-lymphocyte (CTL) epitopes. The "reverse immunology" approach, involving computer-assisted epitope prediction, in vitro CTL induction, and tetramer-guided CTL isolation, resulted in specific CTLs against hTERT-derived, HLA-A1-binding peptides. Intermediate- to low-avidity CTLs were induced against the hTERT325-333 peptide and recognized endogenously processed hTERT. Recognition of endogenous hTERT depended on an increase of hTERT expression above normal levels in tumor cells through hTERT transduction, most probably as a result of limited CTL avidity. The altered peptide ligand hTERT699T-707 was designed to increase HLA-A1-binding affinity of the hTERT699-707 peptide and was used to induce CTLs. However, these CTLs poorly cross-recognized native hTERT699-707 and failed to recognize endogenously processed hTERT. In conclusion, our study has identified the hTERT325-333 peptide as a potential hTERT-derived epitope that may prove useful for induction and monitoring of hTERT-specific, HLA-A1-restricted CTL responses.
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Affiliation(s)
- Marco W. J. Schreurs
- Department of Pathology, VU University Medical Center, de Boelelaan 1117, 1081 HV Amsterdam, The Netherlands
| | - Esther W. M. Kueter
- Department of Pathology, VU University Medical Center, de Boelelaan 1117, 1081 HV Amsterdam, The Netherlands
| | - Kirsten B. J. Scholten
- Department of Pathology, VU University Medical Center, de Boelelaan 1117, 1081 HV Amsterdam, The Netherlands
| | - Duco Kramer
- Department of Pathology, VU University Medical Center, de Boelelaan 1117, 1081 HV Amsterdam, The Netherlands
| | - Chris J. L. M. Meijer
- Department of Pathology, VU University Medical Center, de Boelelaan 1117, 1081 HV Amsterdam, The Netherlands
| | - Erik Hooijberg
- Department of Pathology, VU University Medical Center, de Boelelaan 1117, 1081 HV Amsterdam, The Netherlands
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Ringhoffer M, Müller CR, Schenk A, Kirsche H, Schmitt M, Greiner J, Gschwend JE. Simultaneous expression of T-cell activating antigens in renal cell carcinoma: implications for specific immunotherapy. J Urol 2004; 171:2456-60. [PMID: 15126875 DOI: 10.1097/01.ju.0000118383.86684.38] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
PURPOSE The activation of antigen specific T cells by tumor associated antigens (TAA) might be a promising treatment strategy for patients with renal cell carcinoma (RCC). We analyzed TAA expression in patients with RCC as well as the prevalence of fitting HLA phenotypes and calculated the percent of patients eligible for peptide vaccination trials. MATERIALS AND METHODS A total of 41 RCC samples from primary tumors were analyzed for TAA expression by reverse transcriptase-polymerase chain reaction. Genes of interest were MAGE-1, MAGE-3, G250 and PRAME since peptides derived from these genes have been shown to activate antigen specific cytotoxic T lymphocytes. Results were combined with data on the HLA gene and haplotype frequencies in the German population as an example of a white population. RESULTS Tumor specific expression of at least 1 T-cell activating antigen was observed in all patients. Of the patients 80% expressed 2 or more TAAs simultaneously. HLA molecules suitable for presentation of the respective antigens were calculated to be expressed in 51% to 85% of white German patients. These results mirror with only minor variations most of the white populations in Europe and North America. CONCLUSIONS We noted that T-cell activating tumor associated antigens are frequently expressed in patients with RCC. Based on HLA expression analysis in a white population at least 30% of patients with RCC are eligible for monovalent specific immunotherapy and 41% are eligible for polyvalent specific immunotherapy. These data are a rational basis for future prospective vaccination trials in patients with RCC.
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Affiliation(s)
- Mark Ringhoffer
- Departments of Internal Medicine III, University Hospital and German National Bone Marrow Donor Registry, Ulm, Germany
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Andersen MH, Becker JC, Straten PT. Identification of an HLA-A3-restricted cytotoxic T lymphocyte (CTL) epitope from ML-IAP. J Invest Dermatol 2004; 122:1336-7. [PMID: 15140242 DOI: 10.1111/j.0022-202x.2004.22508.x] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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50
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Reker S, Becker JC, Svane IM, Ralfkiaer E, Straten PT, Andersen MH. HLA-B35-restricted immune responses against survivin in cancer patients. Int J Cancer 2004; 108:937-41. [PMID: 14712500 DOI: 10.1002/ijc.11634] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
Two HLA-A2 restricted epitopes have recently been identified from the broadly expressed tumor antigen survivin, and several vaccination trials in cancer patients based on these survivin-derived peptides have been initiated. Consequently, there is a crucial need for the identification of survivin epitopes restricted to other HLA-molecules in order to extend the proportion of patients that can enter these ongoing clinical trials. In the present study, we characterized 2 survivin-derived epitopes, which are restricted to HLA-B35. Specific T-cell reactivity against these survivin-derived epitopes was found in the peripheral blood from patients with different B-cell malignancies and melanoma. Substitution of the C-terminal anchor residue of the survivin-derived peptides improved the recognition by tumor-infiltrating lymphocytes from melanoma patients. Furthermore, we demonstrated spontaneous cytotoxic T-cell responses to survivin in a primary melanoma lesion. The characterization of these epitopes allows more patients can be included in the ongoing peptide-based survivin vaccination trials against cancer.
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Affiliation(s)
- Sine Reker
- Tumor Immunology Group, Division of Cancer Biology, Danish Cancer Society, Strandboulevarden 49, DK-2100 Copenhagen, Denmark
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