1
|
Jesus-Oliveira P, Silva-Couto L, Pinho N, Da Silva-Ferreira AT, Saboia-Vahia L, Cuervo P, Da-Cruz AM, Gomes-Silva A, Pinto EF. Identification of Immunodominant Proteins of the Leishmania (Viannia) naiffi SubProteome as Pan-Specific Vaccine Targets against Leishmaniasis. Vaccines (Basel) 2023; 11:1129. [PMID: 37514945 PMCID: PMC10386316 DOI: 10.3390/vaccines11071129] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Revised: 03/22/2023] [Accepted: 04/10/2023] [Indexed: 07/30/2023] Open
Abstract
Leishmaniasis is a wide-spectrum disease caused by parasites from Leishmania genus. A well-modulated immune response that is established after the long-lasting clinical cure of leishmaniasis can represent a standard requirement for a vaccine. Previous studies demonstrated that Leishmania (Viannia) naiffi causes benign disease and its antigens induce well-modulated immune responses in vitro. In this work we aimed to identify the immunodominant proteins present in the soluble extract of L. naiffi (sLnAg) as candidates for composing a pan-specific anti-leishmaniasis vaccine. After immunoblotting using cured patients of cutaneous leishmaniasis sera and proteomics approaches, we identified a group of antigenic proteins from the sLnAg. In silico analyses allowed us to select mildly similar proteins to the host; in addition, we evaluated the binding potential and degree of promiscuity of the protein epitopes to HLA molecules and to B-cell receptors. We selected 24 immunodominant proteins from a sub-proteome with 328 proteins. Homology analysis allowed the identification of 13 proteins with the most orthologues among seven Leishmania species. This work demonstrated the potential of these proteins as promising vaccine targets capable of inducing humoral and cellular pan-specific immune responses in humans, which may in the future contribute to the control of leishmaniasis.
Collapse
Affiliation(s)
- Prisciliana Jesus-Oliveira
- Laboratório Interdisciplinar de Pesquisas Médicas, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro 21040-360, Brazil
| | - Luzinei Silva-Couto
- Laboratório Interdisciplinar de Pesquisas Médicas, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro 21040-360, Brazil
| | - Nathalia Pinho
- Laboratório de Pesquisa em Leishmanioses, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro 21040-360, Brazil
- Rede de Pesquisas de Neuroinflamação do Rio de Janeiro, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro 21040-360, Brazil
| | | | - Leonardo Saboia-Vahia
- Laboratório de Vírus Respiratórios e Sarampo, Laboratório de Referência para COVID-19 (World Health Organization), Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro 21040-360, Brazil
| | - Patricia Cuervo
- Laboratório de Pesquisa em Leishmanioses, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro 21040-360, Brazil
- Rede de Pesquisas de Neuroinflamação do Rio de Janeiro, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro 21040-360, Brazil
| | - Alda Maria Da-Cruz
- Laboratório Interdisciplinar de Pesquisas Médicas, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro 21040-360, Brazil
- Rede de Pesquisas em Saúde, Fundação de Amparo à Pesquisa do Estado do Rio de Janeiro, Rio de Janeiro 20020-000, Brazil
- Disciplina de Parasitologia, Departamento de Microbiologia, Imunologia e Parasitologia, Faculdade de Ciências Médicas, Universidade Estadual do Rio de Janeiro, Rio de Janeiro 20550-170, Brazil
- Instituto Nacional de Ciência e Tecnologia em Neuroimunomodulação (INCT-NIM), Rio de Janeiro 21040-900, Brazil
| | - Adriano Gomes-Silva
- Laboratório Interdisciplinar de Pesquisas Médicas, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro 21040-360, Brazil
- Laboratório de Pesquisa Clínica em Micobacterioses, Instituto Nacional de Infectologia Evandro Chagas, Fundação Oswaldo Cruz, Rio de Janeiro 21040-360, Brazil
| | - Eduardo Fonseca Pinto
- Laboratório Interdisciplinar de Pesquisas Médicas, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro 21040-360, Brazil
- Rede de Pesquisas em Saúde, Fundação de Amparo à Pesquisa do Estado do Rio de Janeiro, Rio de Janeiro 20020-000, Brazil
| |
Collapse
|
2
|
James CA, Ronning P, Cullinan D, Cotto KC, Barnell EK, Campbell KM, Skidmore ZL, Sanford DE, Goedegebuure SP, Gillanders WE, Griffith OL, Hawkins WG, Griffith M. In silico epitope prediction analyses highlight the potential for distracting antigen immunodominance with allogeneic cancer vaccines. CANCER RESEARCH COMMUNICATIONS 2021; 1:115-126. [PMID: 35611186 PMCID: PMC9126504 DOI: 10.1158/2767-9764.crc-21-0029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Allogeneic cancer vaccines are designed to induce antitumor immune responses with the goal of impacting tumor growth. Typical allogeneic cancer vaccines are produced by expansion of established cancer cell lines, transfection with vectors encoding immunostimulatory cytokines, and lethal irradiation. More than 100 clinical trials have investigated the clinical benefit of allogeneic cancer vaccines in various cancer types. Results show limited therapeutic benefit in clinical trials and currently there are no FDA approved allogeneic cancer vaccines. We used recently developed bioinformatics tools including the pVAC-seq suite of software tools to analyze DNA/RNA sequencing data from the TCGA to examine the repertoire of antigens presented by a typical allogeneic cancer vaccine, and to simulate allogeneic cancer vaccine clinical trials. Specifically, for each simulated clinical trial we modeled the repertoire of antigens presented by allogeneic cancer vaccines consisting of three hypothetical cancer cell lines to 30 patients with the same cancer type. Simulations were repeated ten times for each cancer type. Each tumor sample in the vaccine and the vaccine recipient was subjected to HLA typing, differential expression analyses for tumor associated antigens (TAAs), germline variant calling, and neoantigen prediction. These analyses provided a robust, quantitative comparison between potentially beneficial TAAs and neoantigens versus distracting antigens present in the allogeneic cancer vaccines. We observe that distracting antigens greatly outnumber shared TAAs and neoantigens, providing one potential explanation for the lack of observed responses to allogeneic cancer vaccines. This analysis provides additional rationale for the redirection of efforts towards a personalized cancer vaccine approach.
Collapse
Affiliation(s)
- C. Alston James
- Department of Surgery, Washington University School of Medicine, St. Louis, Missouri
| | - Peter Ronning
- Department of Medicine, Washington University School of Medicine, St. Louis, Missouri.,McDonnell Genome Institute, Washington University School of Medicine, St. Louis, Missouri
| | - Darren Cullinan
- Department of Surgery, Washington University School of Medicine, St. Louis, Missouri
| | - Kelsy C. Cotto
- Department of Medicine, Washington University School of Medicine, St. Louis, Missouri
| | - Erica K. Barnell
- Department of Medicine, Washington University School of Medicine, St. Louis, Missouri.,McDonnell Genome Institute, Washington University School of Medicine, St. Louis, Missouri
| | - Katie M. Campbell
- Department of Medicine, Washington University School of Medicine, St. Louis, Missouri
| | - Zachary L. Skidmore
- Department of Medicine, Washington University School of Medicine, St. Louis, Missouri
| | - Dominic E. Sanford
- Department of Surgery, Washington University School of Medicine, St. Louis, Missouri.,Siteman Cancer Center, Washington University School of Medicine, St. Louis, Missouri
| | - S. Peter Goedegebuure
- Department of Surgery, Washington University School of Medicine, St. Louis, Missouri
| | - William E. Gillanders
- Department of Surgery, Washington University School of Medicine, St. Louis, Missouri.,Siteman Cancer Center, Washington University School of Medicine, St. Louis, Missouri
| | - Obi L. Griffith
- Department of Medicine, Washington University School of Medicine, St. Louis, Missouri.,McDonnell Genome Institute, Washington University School of Medicine, St. Louis, Missouri.,Siteman Cancer Center, Washington University School of Medicine, St. Louis, Missouri.,Department of Genetics, Washington University School of Medicine, St. Louis, Missouri.,CorrespondingAuthor: Malachi Griffith, McDonnell Genome Institute, 4444 Forest Park Avenue, Campus Box 8501, St. Louis, MO 63108. Phone: 314-286-1274; E-mail: ; Obi L. Griffith, McDonnell Genome Institute, 4444 Forest Park Avenue, Campus Box 8501, St. Louis, MO 63108. E-mail: ; and William G. Hawkins, McDonnell Genome Institute, 4444 Forest Park Avenue, Campus Box 8501, St. Louis, MO 63108. E-mail:
| | - William G. Hawkins
- Department of Surgery, Washington University School of Medicine, St. Louis, Missouri.,Siteman Cancer Center, Washington University School of Medicine, St. Louis, Missouri.,CorrespondingAuthor: Malachi Griffith, McDonnell Genome Institute, 4444 Forest Park Avenue, Campus Box 8501, St. Louis, MO 63108. Phone: 314-286-1274; E-mail: ; Obi L. Griffith, McDonnell Genome Institute, 4444 Forest Park Avenue, Campus Box 8501, St. Louis, MO 63108. E-mail: ; and William G. Hawkins, McDonnell Genome Institute, 4444 Forest Park Avenue, Campus Box 8501, St. Louis, MO 63108. E-mail:
| | - Malachi Griffith
- Department of Medicine, Washington University School of Medicine, St. Louis, Missouri.,McDonnell Genome Institute, Washington University School of Medicine, St. Louis, Missouri.,Siteman Cancer Center, Washington University School of Medicine, St. Louis, Missouri.,Department of Genetics, Washington University School of Medicine, St. Louis, Missouri.,CorrespondingAuthor: Malachi Griffith, McDonnell Genome Institute, 4444 Forest Park Avenue, Campus Box 8501, St. Louis, MO 63108. Phone: 314-286-1274; E-mail: ; Obi L. Griffith, McDonnell Genome Institute, 4444 Forest Park Avenue, Campus Box 8501, St. Louis, MO 63108. E-mail: ; and William G. Hawkins, McDonnell Genome Institute, 4444 Forest Park Avenue, Campus Box 8501, St. Louis, MO 63108. E-mail:
| |
Collapse
|
3
|
Li M, Itoh A, Xi J, Yu C, Wu Y, Ridgway WM, Liu H. Enhancing Antigen Presentation and Inducing Antigen-Specific Immune Tolerance with Amphiphilic Peptides. THE JOURNAL OF IMMUNOLOGY 2021; 207:2051-2059. [PMID: 34526376 DOI: 10.4049/jimmunol.1901301] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/06/2019] [Accepted: 08/06/2021] [Indexed: 11/19/2022]
Abstract
Ag-specific immunotherapy to restore immune tolerance to self-antigens, without global immune suppression, is a long-standing goal in the treatment of autoimmune disorders such as type 1 diabetes (T1D). However, vaccination with autoantigens such as insulin or glutamic acid decarboxylase have largely failed in human T1D trials. Induction and maintenance of peripheral tolerance by vaccination requires efficient autoantigen presentation by APCs. In this study, we show that a lipophilic modification at the N-terminal end of CD4+ epitopes (lipo-peptides) dramatically improves peptide Ag presentation. We designed amphiphilic lipo-peptides to efficiently target APCs in the lymph nodes by binding and trafficking with endogenous albumin. Additionally, we show that lipophilic modification anchors the peptide into the membranes of APCs, enabling a bivalent cell-surface Ag presentation. The s.c. injected lipo-peptide accumulates in the APCs in the lymph node, enhances the potency and duration of peptide Ag presentation by APCs, and induces Ag-specific immune tolerance that controls both T cell- and B cell-mediated immunity. Immunization with an amphiphilic insulin B chain 9-23 peptide, an immunodominant CD4+ T cell epitope in NOD mice, significantly suppresses the activation of T cells, increases inhibitory cytokine production, induces regulatory T cells, and delays the onset and lowers the incidence of T1D. Importantly, treatment with a lipophilic β-cell peptide mixture delays progression to end-stage diabetes in acutely diabetic NOD mice, whereas the same doses of standard soluble peptides were not effective. Amphiphilic modification effectively enhances Ag presentation for peptide-based immune regulation of autoimmune diseases.
Collapse
Affiliation(s)
- Meng Li
- Department of Chemical Engineering and Materials Science, Wayne State University, Detroit, MI
| | - Arata Itoh
- Division of Rheumatology, Allergy, and Clinical Immunology, University of California, Davis, Davis, CA
| | - Jingchao Xi
- Department of Chemical Engineering and Materials Science, Wayne State University, Detroit, MI
| | - Chunsong Yu
- Department of Chemical Engineering and Materials Science, Wayne State University, Detroit, MI
| | - Yuehong Wu
- Division of Rheumatology, Allergy, and Clinical Immunology, University of California, Davis, Davis, CA
| | - William M Ridgway
- Division of Rheumatology, Allergy, and Clinical Immunology, University of California, Davis, Davis, CA
| | - Haipeng Liu
- Department of Chemical Engineering and Materials Science, Wayne State University, Detroit, MI; .,Department of Oncology, Wayne State University, Detroit, MI; and.,Tumor Biology and Microenvironment Program, Barbara Ann Karmanos Cancer Institute, Detroit, MI
| |
Collapse
|
4
|
Brentville VA, Metheringham RL, Daniels I, Atabani S, Symonds P, Cook KW, Vankemmelbeke M, Choudhury R, Vaghela P, Gijon M, Meiners G, Krebber WJ, Melief CJM, Durrant LG. Combination vaccine based on citrullinated vimentin and enolase peptides induces potent CD4-mediated anti-tumor responses. J Immunother Cancer 2021; 8:jitc-2020-000560. [PMID: 32561639 PMCID: PMC7304843 DOI: 10.1136/jitc-2020-000560] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/26/2020] [Indexed: 11/03/2022] Open
Abstract
BACKGROUND Stress-induced post-translational modifications occur during autophagy and can result in generation of new epitopes and immune recognition. One such modification is the conversion of arginine to citrulline by peptidylarginine deiminase enzymes. METHODS We used Human leukocyte antigen (HLA) transgenic mouse models to assess the immunogenicity of citrullinated peptide vaccine by cytokine Enzyme linked immunosorbant spot (ELISpot) assay. Vaccine efficacy was assessed in tumor therapy studies using HLA-matched B16 melanoma and ID8 ovarian models expressing either constitutive or interferon-gamma (IFNγ) inducible Major Histocompatibility Complex (MHC) class II (MHC-II) as represented by most human tumors. To determine the importance of CD4 T cells in tumor therapy, we analyzed the immune cell infiltrate into murine tumors using flow cytometry and performed therapy studies in the presence of CD4 and CD8 T cell depletion. We assessed the T cell repertoire to citrullinated peptides in ovarian cancer patients and healthy donors using flow cytometry. RESULTS The combination of citrullinated vimentin and enolase peptides (Modi-1) stimulated strong CD4 T cell responses in mice. Responses resulted in a potent anti-tumor therapy against established tumors and generated immunological memory which protected against tumor rechallenge. Depletion of CD4, but not CD8 T cells, abrogated the primary anti-tumor response as well as the memory response to tumor rechallenge. This was further reinforced by successful tumor regression being associated with an increase in tumor-infiltrating CD4 T cells and a reduction in tumor-associated myeloid suppressor cells. The anti-tumor response also relied on direct CD4 T cell recognition as only tumors expressing MHC-II were rejected. A comparison of different Toll-like receptor (TLR)-stimulating adjuvants showed that Modi-1 induced strong Th1 responses when combined with granulocyte-macrophage colony-stimulating factor (GMCSF), TLR9/TLR4, TLR9, TLR3, TLR1/2 and TLR7 agonists. Direct linkage of the TLR1/2 agonist to the peptides allowed the vaccine dose to be reduced by 10-fold to 100-fold without loss of anti-tumor activity. Furthermore, a CD4 Th1 response to the citrullinated peptides was seen in ovarian cancer patients. CONCLUSIONS Modi-1 citrullinated peptide vaccine induces potent CD4-mediated anti-tumor responses in mouse models and a CD4 T cell repertoire is present in ovarian cancer patients to the citrullinated peptides suggesting that Modi-1 could be an effective vaccine for ovarian cancer patients.
Collapse
MESH Headings
- Adjuvants, Immunologic/administration & dosage
- Animals
- CD4-Positive T-Lymphocytes/immunology
- CD8-Positive T-Lymphocytes
- Cancer Vaccines/administration & dosage
- Cancer Vaccines/genetics
- Cancer Vaccines/immunology
- Cell Line, Tumor
- Citrullination/immunology
- Female
- HLA Antigens/genetics
- HLA Antigens/immunology
- Humans
- Immunogenicity, Vaccine
- Interferon-gamma/immunology
- Lymphocyte Depletion
- Male
- Melanoma, Experimental/immunology
- Melanoma, Experimental/therapy
- Mice
- Mice, Transgenic
- Phosphopyruvate Hydratase/genetics
- Phosphopyruvate Hydratase/immunology
- Vaccines, Combined/administration & dosage
- Vaccines, Combined/genetics
- Vaccines, Combined/immunology
- Vaccines, Subunit/administration & dosage
- Vaccines, Subunit/genetics
- Vaccines, Subunit/immunology
- Vimentin/genetics
- Vimentin/immunology
Collapse
Affiliation(s)
| | | | - Ian Daniels
- Scancell Ltd, University of Nottingham Biodiscovery Institute, Nottingham, UK
| | - Suha Atabani
- Biodiscovery Institute, University of Nottingham Faculty of Medicine and Health Sciences, Nottingham, UK
| | - Peter Symonds
- Scancell Ltd, University of Nottingham Biodiscovery Institute, Nottingham, UK
| | - Katherine W Cook
- Scancell Ltd, University of Nottingham Biodiscovery Institute, Nottingham, UK
| | | | - Ruhul Choudhury
- Scancell Ltd, University of Nottingham Biodiscovery Institute, Nottingham, UK
| | - Poonam Vaghela
- Biodiscovery Institute, University of Nottingham Faculty of Medicine and Health Sciences, Nottingham, UK
| | - Mohamed Gijon
- Scancell Ltd, University of Nottingham Biodiscovery Institute, Nottingham, UK
| | | | | | - Cornelis J M Melief
- ISA Pharmaceuticals, Leiden, The Netherlands
- Department of Immunohematology and Blood Transfusion, Leiden University Medical Center, Leiden, Netherlands
| | - Lindy G Durrant
- Scancell Ltd, University of Nottingham Biodiscovery Institute, Nottingham, UK
- Biodiscovery Institute, University of Nottingham Faculty of Medicine and Health Sciences, Nottingham, UK
| |
Collapse
|
5
|
Zinsli LV, Stierlin N, Loessner MJ, Schmelcher M. Deimmunization of protein therapeutics - Recent advances in experimental and computational epitope prediction and deletion. Comput Struct Biotechnol J 2020; 19:315-329. [PMID: 33425259 PMCID: PMC7779837 DOI: 10.1016/j.csbj.2020.12.024] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2020] [Revised: 12/15/2020] [Accepted: 12/16/2020] [Indexed: 12/11/2022] Open
Abstract
Biotherapeutics, and antimicrobial proteins in particular, are of increasing interest for human medicine. An important challenge in the development of such therapeutics is their potential immunogenicity, which can induce production of anti-drug-antibodies, resulting in altered pharmacokinetics, reduced efficacy, and potentially severe anaphylactic or hypersensitivity reactions. For this reason, the development and application of effective deimmunization methods for protein drugs is of utmost importance. Deimmunization may be achieved by unspecific shielding approaches, which include PEGylation, fusion to polypeptides (e.g., XTEN or PAS), reductive methylation, glycosylation, and polysialylation. Alternatively, the identification of epitopes for T cells or B cells and their subsequent deletion through site-directed mutagenesis represent promising deimmunization strategies and can be accomplished through either experimental or computational approaches. This review highlights the most recent advances and current challenges in the deimmunization of protein therapeutics, with a special focus on computational epitope prediction and deletion tools.
Collapse
Key Words
- ABR, Antigen-binding region
- ADA, Anti-drug antibody
- ANN, Artificial neural network
- APC, Antigen-presenting cell
- Anti-drug-antibody
- B cell epitope
- BCR, B cell receptor
- Bab, Binding antibody
- CDR, Complementarity determining region
- CRISPR, Clustered regularly interspaced short palindromic repeats
- DC, Dendritic cell
- ELP, Elastin-like polypeptide
- EPO, Erythropoietin
- ER, Endoplasmatic reticulum
- GLK, Gelatin-like protein
- HAP, Homo-amino-acid polymer
- HLA, Human leukocyte antigen
- HMM, Hidden Markov model
- IL, Interleukin
- Ig, Immunoglobulin
- Immunogenicity
- LPS, Lipopolysaccharide
- MHC, Major histocompatibility complex
- NMR, Nuclear magnetic resonance
- Nab, Neutralizing antibody
- PAMP, Pathogen-associated molecular pattern
- PAS, Polypeptide composed of proline, alanine, and/or serine
- PBMC, Peripheral blood mononuclear cell
- PD, Pharmacodynamics
- PEG, Polyethylene glycol
- PK, Pharmacokinetics
- PRR, Pattern recognition receptor
- PSA, Sialic acid polymers
- Protein therapeutic
- RNN, Recurrent artificial neural network
- SVM, Support vector machine
- T cell epitope
- TAP, Transporter associated with antigen processing
- TCR, T cell receptor
- TLR, Toll-like receptor
- XTEN, “Xtended” recombinant polypeptide
Collapse
Affiliation(s)
- Léa V. Zinsli
- Institute of Food, Nutrition and Health, ETH Zurich, Zurich, Switzerland
| | - Noël Stierlin
- Institute of Food, Nutrition and Health, ETH Zurich, Zurich, Switzerland
| | - Martin J. Loessner
- Institute of Food, Nutrition and Health, ETH Zurich, Zurich, Switzerland
| | - Mathias Schmelcher
- Institute of Food, Nutrition and Health, ETH Zurich, Zurich, Switzerland
| |
Collapse
|
6
|
Peptides identified on monocyte-derived dendritic cells: a marker for clinical immunogenicity to FVIII products. Blood Adv 2020; 3:1429-1440. [PMID: 31053570 DOI: 10.1182/bloodadvances.2018030452] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2018] [Accepted: 03/18/2019] [Indexed: 12/14/2022] Open
Abstract
The immunogenicity of protein therapeutics is an important safety and efficacy concern during drug development and regulation. Strategies to identify individuals and subpopulations at risk for an undesirable immune response represent an important unmet need. The major histocompatibility complex (MHC)-associated peptide proteomics (MAPPs) assay directly identifies the presence of peptides derived from a specific protein therapeutic on a donor's MHC class II (MHC-II) proteins. We applied this technique to address several questions related to the use of factor VIII (FVIII) replacement therapy in the treatment of hemophilia A (HA). Although >12 FVIII therapeutics are marketed, most fall into 3 categories: (i) human plasma-derived FVIII (pdFVIII), (ii) full-length (FL)-recombinant FVIII (rFVIII; FL-rFVIII), and (iii) B-domain-deleted rFVIII. Here, we investigated whether there are differences between the FVIII peptides found on the MHC-II proteins of the same individual when incubated with these 3 classes. Based on several observational studies and a prospective, randomized, clinical trial showing that the originally approved rFVIII products may be more immunogenic than the pdFVIII products containing von Willebrand factor (VWF) in molar excess, it has been hypothesized that the pdFVIII molecules yield/present fewer peptides (ie, potential T-cell epitopes). We have experimentally tested this hypothesis and found that dendritic cells from HA patients and healthy donors present fewer FVIII peptides when administered pdFVIII vs FL-rFVIII, despite both containing the same molar VWF excess. Our results support the hypothesis that synthesis of pdFVIII under physiological conditions could result in reduced heterogeneity and/or subtle differences in structure/conformation which, in turn, may result in reduced FVIII proteolytic processing relative to FL-rFVIII.
Collapse
|
7
|
Brentville VA, Vankemmelbeke M, Metheringham RL, Durrant LG. Post-translational modifications such as citrullination are excellent targets for cancer therapy. Semin Immunol 2020; 47:101393. [PMID: 31932199 DOI: 10.1016/j.smim.2020.101393] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/01/2019] [Accepted: 01/01/2020] [Indexed: 11/28/2022]
Abstract
Under conditions of cellular stress, proteins can be post-translationally modified causing them to be recognized by the immune system. One such stress-induced post-translational modification (siPTM) is citrullination, the conversion of arginine residues to citrulline by peptidylarginine deiminase (PAD) enzymes. PAD enzymes are activated by millimolar concentrations of calcium which can occur during apoptosis, leading to precipitation of proteins, their subsequent uptake by B cells and stimulation of antibody responses. Detection of anti-citrullinated protein antibodies (ACPAs) is a diagnostic of rheumatoid arthritis (RA), where immune complexes stimulate inflammation around the joints. More recently, autophagy has been shown to play a role in the presentation of citrullinated peptides on MHC class II molecules to CD4+ helper T cells, suggesting that citrullination may be a way of alerting immune cells to cellular stress. Additionally, inflammation-induced IFNγ and concomitant MHC class II expression on target cells contributes to immune activation. Stressful conditions in the tumor microenvironment induce autophagy in cancer cells as a pro-survival mechanism. Cancer cells also over express PAD enzymes and in light of this the hypothesis that citrullinated peptides stimulate CD4+ T cell responses that would recognize these siPTM's produced during autophagy has been investigated. The induction of potent citrullinated peptide-specific CD4 responses has been shown in both humans and HLA transgenic mouse models. Responses in mouse models resulted in potent anti-tumour responses against tumours expressing either constitutive or IFNγ-inducible MHC class II. The anti-tumour effect relied upon direct recognition of tumours by specific CD4 T cells suggesting that citrullinated peptides are attractive targets for cancer vaccines.
Collapse
Affiliation(s)
- V A Brentville
- Scancell Ltd, University of Nottingham Biodiscovery Institute, Science Road, University Park, Nottingham, NG7 2RD, UK.
| | - M Vankemmelbeke
- Scancell Ltd, University of Nottingham Biodiscovery Institute, Science Road, University Park, Nottingham, NG7 2RD, UK.
| | - R L Metheringham
- Scancell Ltd, University of Nottingham Biodiscovery Institute, Science Road, University Park, Nottingham, NG7 2RD, UK.
| | - L G Durrant
- Scancell Ltd, University of Nottingham Biodiscovery Institute, Science Road, University Park, Nottingham, NG7 2RD, UK; Division of Cancer and Stem Cells, School of Medicine, University of Nottingham Biodiscovery Institute, Science Road, University Park, Nottingham, NG7 2RD, UK.
| |
Collapse
|
8
|
Current In Vitro Assays for Prediction of T Cell Mediated Immunogenicity of Biotherapeutics and Manufacturing Impurities. J Pharm Innov 2019. [DOI: 10.1007/s12247-019-09412-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
|
9
|
Zutshi S, Kumar S, Chauhan P, Bansode Y, Nair A, Roy S, Sarkar A, Saha B. Anti-Leishmanial Vaccines: Assumptions, Approaches, and Annulments. Vaccines (Basel) 2019; 7:vaccines7040156. [PMID: 31635276 PMCID: PMC6963565 DOI: 10.3390/vaccines7040156] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2019] [Revised: 09/24/2019] [Accepted: 10/08/2019] [Indexed: 12/17/2022] Open
Abstract
Leishmaniasis is a neglected protozoan parasitic disease that occurs in 88 countries but a vaccine is unavailable. Vaccination with live, killed, attenuated (physically or genetically) Leishmania have met with limited success, while peptide-, protein-, or DNA-based vaccines showed promise only in animal models. Here, we critically assess several technical issues in vaccination and expectation of a host-protective immune response. Several studies showed that antigen presentation during priming and triggering of the same cells in infected condition are not comparable. Altered proteolytic processing, antigen presentation, protease-susceptible sites, and intracellular expression of pathogenic proteins during Leishmania infection may vary dominant epitope selection, MHC-II/peptide affinity, and may deter the reactivation of desired antigen-specific T cells generated during priming. The robustness of the memory T cells and their functions remains a concern. Presentation of the antigens by Leishmania-infected macrophages to antigen-specific memory T cells may lead to change in the T cells' functional phenotype or anergy or apoptosis. Although cells may be activated, the peptides generated during infection may be different and cross-reactive to the priming peptides. Such altered peptide ligands may lead to suppression of otherwise active antigen-specific T cells. We critically assess these different immunological issues that led to the non-availability of a vaccine for human use.
Collapse
Affiliation(s)
| | - Sunil Kumar
- National Centre for Cell Science, Ganeshkhind, Pune 411007, India.
| | - Prashant Chauhan
- National Centre for Cell Science, Ganeshkhind, Pune 411007, India.
| | - Yashwant Bansode
- National Centre for Cell Science, Ganeshkhind, Pune 411007, India.
| | - Arathi Nair
- National Centre for Cell Science, Ganeshkhind, Pune 411007, India.
| | - Somenath Roy
- Department of Human Physiology with Community Health, Vidyasagar University, Midnapore 721102, India.
| | - Arup Sarkar
- Department of Biotechnology, Trident Academy of Creative Technology, Bhubaneswar 751024, India.
| | - Bhaskar Saha
- National Centre for Cell Science, Ganeshkhind, Pune 411007, India.
- Department of Biotechnology, Trident Academy of Creative Technology, Bhubaneswar 751024, India.
| |
Collapse
|
10
|
Protein Vaccination Directs the CD4 + T Cell Response toward Shared Protective Epitopes That Can Be Recalled after Influenza Virus Infection. J Virol 2019; 93:JVI.00947-19. [PMID: 31341045 DOI: 10.1128/jvi.00947-19] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2019] [Accepted: 07/16/2019] [Indexed: 12/20/2022] Open
Abstract
Vaccination is widely used to generate protective immunity against influenza virus. CD4+ T cells contribute in diverse ways to protective immunity, most notably, in the provision of help for the production of neutralizing antibodies. Several recent reports have suggested that influenza virus infection elicits CD4+ T cells whose specificity only partially overlaps that of T cells elicited by vaccination. This finding has raised serious concerns regarding the utility of currently licensed inactivated influenza virus vaccines and novel protein-based vaccines. Here, using controlled animal models that allowed a broad sampling of the CD4+ T cell repertoire, we evaluated protein vaccine- versus infection-generated CD4+ T cell epitopes. Our studies revealed that all the infection-elicited CD4+ T cell epitope specificities are also elicited by protein vaccination, although the immunodominance hierarchies can differ. Finally, using a reverse-engineered influenza virus and a heterologous protein vaccination and infection challenge strategy, we show that protein vaccine-elicited CD4+ memory T cells are recalled and boosted after infection and provide early help to accelerate hemagglutinin (HA)-specific antibody responses. The early CD4+ T cell response and HA-specific antibody production are associated with lowered viral titers during the infection challenge. Our data lend confidence to the ability of current protein-based vaccines to elicit influenza virus-specific CD4+ T cells that can potentiate protective immunity upon influenza virus infection.IMPORTANCE Most current and new influenza vaccine candidates consist of a single influenza virus protein or combinations of influenza virus proteins. For these vaccines to elicit CD4+ T cells that can be recalled after infection, the peptide epitopes should be shared between the two modes of confrontation. Recently, questions regarding the relatedness of epitope selection by influenza virus infection and protein vaccination have been raised. However, the studies reported here show that the specificity of CD4+ T cells elicited by protein-based vaccines overlaps that of T cells elicited by infection and that CD4+ T cells primed by protein vaccines are recalled and contribute to protection of the host from a future infection.
Collapse
|
11
|
Sant AJ, DiPiazza AT, Nayak JL, Rattan A, Richards KA. CD4 T cells in protection from influenza virus: Viral antigen specificity and functional potential. Immunol Rev 2019; 284:91-105. [PMID: 29944766 DOI: 10.1111/imr.12662] [Citation(s) in RCA: 56] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
CD4 T cells convey a number of discrete functions to protective immunity to influenza, a complexity that distinguishes this arm of adaptive immunity from B cells and CD8 T cells. Although the most well recognized function of CD4 T cells is provision of help for antibody production, CD4 T cells are important in many aspects of protective immunity. Our studies have revealed that viral antigen specificity is a key determinant of CD4 T cell function, as illustrated both by mouse models of infection and human vaccine responses, a factor whose importance is due at least in part to events in viral antigen handling. We discuss research that has provided insight into the diverse viral epitope specificity of CD4 T cells elicited after infection, how this primary response is modified as CD4 T cells home to the lung, establish memory, and after challenge with a secondary and distinct influenza virus strain. Our studies in human subjects point out the challenges facing vaccine efforts to facilitate responses to novel and avian strains of influenza, as well as strategies that enhance the ability of CD4 T cells to promote protective antibody responses to both seasonal and potentially pandemic strains of influenza.
Collapse
Affiliation(s)
- Andrea J Sant
- David H. Smith Center for Vaccine Biology and Immunology, Department of Microbiology and Immunology, University of Rochester Medical Center, Rochester, NY, USA
| | - Anthony T DiPiazza
- David H. Smith Center for Vaccine Biology and Immunology, Department of Microbiology and Immunology, University of Rochester Medical Center, Rochester, NY, USA
| | - Jennifer L Nayak
- David H. Smith Center for Vaccine Biology and Immunology, Department of Microbiology and Immunology, University of Rochester Medical Center, Rochester, NY, USA.,Division of Infectious Diseases, Department of Pediatrics, University of Rochester Medical Center, Rochester, NY, USA
| | - Ajitanuj Rattan
- David H. Smith Center for Vaccine Biology and Immunology, Department of Microbiology and Immunology, University of Rochester Medical Center, Rochester, NY, USA
| | - Katherine A Richards
- David H. Smith Center for Vaccine Biology and Immunology, Department of Microbiology and Immunology, University of Rochester Medical Center, Rochester, NY, USA
| |
Collapse
|
12
|
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.
Collapse
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
| |
Collapse
|
13
|
Du L, Tai W, Yang Y, Zhao G, Zhu Q, Sun S, Liu C, Tao X, Tseng CTK, Perlman S, Jiang S, Zhou Y, Li F. Introduction of neutralizing immunogenicity index to the rational design of MERS coronavirus subunit vaccines. Nat Commun 2016; 7:13473. [PMID: 27874853 PMCID: PMC5121417 DOI: 10.1038/ncomms13473] [Citation(s) in RCA: 93] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2015] [Accepted: 10/06/2016] [Indexed: 12/13/2022] Open
Abstract
Viral subunit vaccines often contain immunodominant non-neutralizing epitopes that divert host immune responses. These epitopes should be eliminated in vaccine design, but there is no reliable method for evaluating an epitope's capacity to elicit neutralizing immune responses. Here we introduce a new concept 'neutralizing immunogenicity index' (NII) to evaluate an epitope's neutralizing immunogenicity. To determine the NII, we mask the epitope with a glycan probe and then assess the epitope's contribution to the vaccine's overall neutralizing immunogenicity. As proof-of-concept, we measure the NII for different epitopes on an immunogen comprised of the receptor-binding domain from MERS coronavirus (MERS-CoV). Further, we design a variant form of this vaccine by masking an epitope that has a negative NII score. This engineered vaccine demonstrates significantly enhanced efficacy in protecting transgenic mice from lethal MERS-CoV challenge. Our study may guide the rational design of highly effective subunit vaccines to combat MERS-CoV and other life-threatening viruses.
Collapse
Affiliation(s)
- Lanying Du
- Laboratory of Viral Immunology, Lindsley F. Kimball Research Institute, New York Blood Center, New York, New York 10065, USA
| | - Wanbo Tai
- Laboratory of Viral Immunology, Lindsley F. Kimball Research Institute, New York Blood Center, New York, New York 10065, USA
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing 100071, China
| | - Yang Yang
- Department of Pharmacology, University of Minnesota Medical School, Minneapolis, Minnesota 55455, USA
| | - Guangyu Zhao
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing 100071, China
| | - Qing Zhu
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing 100071, China
| | - Shihui Sun
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing 100071, China
| | - Chang Liu
- Department of Pharmacology, University of Minnesota Medical School, Minneapolis, Minnesota 55455, USA
| | - Xinrong Tao
- Department of Microbiology and Immunology and Center for Biodefense and Emerging Disease, University of Texas Medical Branch, Galveston, Texas 77555, USA
| | - Chien-Te K. Tseng
- Department of Microbiology and Immunology and Center for Biodefense and Emerging Disease, University of Texas Medical Branch, Galveston, Texas 77555, USA
| | - Stanley Perlman
- Department of Microbiology, University of Iowa, Iowa City, Iowa 52242, USA
| | - Shibo Jiang
- Laboratory of Viral Immunology, Lindsley F. Kimball Research Institute, New York Blood Center, New York, New York 10065, USA
- Key Laboratory of Medical Molecular Virology of Ministries of Education and Health, Shanghai Medical College and Institute of Medical Microbiology, Fudan University, Shanghai 200032, China
| | - Yusen Zhou
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing 100071, China
| | - Fang Li
- Department of Pharmacology, University of Minnesota Medical School, Minneapolis, Minnesota 55455, USA
| |
Collapse
|
14
|
Farrell D, Jones G, Pirson C, Malone K, Rue-Albrecht K, Chubb AJ, Vordermeier M, Gordon SV. Integrated computational prediction and experimental validation identifies promiscuous T cell epitopes in the proteome of Mycobacterium bovis. Microb Genom 2016; 2:e000071. [PMID: 28348866 PMCID: PMC5320590 DOI: 10.1099/mgen.0.000071] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2016] [Accepted: 05/26/2016] [Indexed: 11/18/2022] Open
Abstract
The discovery of novel antigens is an essential requirement in devising new diagnostics or vaccines for use in control programmes against human tuberculosis (TB) and bovine tuberculosis (bTB). Identification of potential epitopes recognised by CD4+ T cells requires prediction of peptide binding to MHC class-II, an obligatory prerequisite for T cell recognition. To comprehensively prioritise potential MHC-II-binding epitopes from Mycobacterium bovis, the agent of bTB and zoonotic TB in humans, we integrated three binding prediction methods with the M. bovisproteome using a subset of human HLA alleles to approximate the binding of epitope-containing peptides to the bovine MHC class II molecule BoLA-DRB3. Two parallel strategies were then applied to filter the resulting set of binders: identification of the top-scoring binders or clusters of binders. Our approach was tested experimentally by assessing the capacity of predicted promiscuous peptides to drive interferon-γ secretion from T cells of M. bovis infected cattle. Thus, 376 20-mer peptides, were synthesised (270 predicted epitopes, 94 random peptides with low predictive scores and 12 positive controls of known epitopes). The results of this validation demonstrated significant enrichment (>24 %) of promiscuously recognised peptides predicted in our selection strategies, compared with randomly selected peptides with low prediction scores. Our strategy offers a general approach to the identification of promiscuous epitopes tailored to target populations where there is limited knowledge of MHC allelic diversity.
Collapse
Affiliation(s)
- Damien Farrell
- 1School of Veterinary Medicine, University College Dublin, Dublin D4, Ireland
| | - Gareth Jones
- 2Department of Bacteriology, Animal and Plant Health Agency, New Haw, Surrey KT15 3NB, UK
| | - Christopher Pirson
- 2Department of Bacteriology, Animal and Plant Health Agency, New Haw, Surrey KT15 3NB, UK
| | - Kerri Malone
- 1School of Veterinary Medicine, University College Dublin, Dublin D4, Ireland
| | - Kevin Rue-Albrecht
- 1School of Veterinary Medicine, University College Dublin, Dublin D4, Ireland.,3School of Agriculture and Food Science, University College Dublin, Dublin 4, Ireland
| | - Anthony J Chubb
- 4School of Medicine, University College Dublin, Dublin D4, Ireland
| | - Martin Vordermeier
- 2Department of Bacteriology, Animal and Plant Health Agency, New Haw, Surrey KT15 3NB, UK
| | - Stephen V Gordon
- 6School of Biomolecular and Biomedical Science, University College Dublin, Dublin 4, Ireland.,5Conway Institute of Biomolecular and Biomedical Science, University College Dublin, Dublin D4, Ireland.,1School of Veterinary Medicine, University College Dublin, Dublin D4, Ireland.,4School of Medicine, University College Dublin, Dublin D4, Ireland
| |
Collapse
|
15
|
CD4 T cell epitope specificity determines follicular versus non-follicular helper differentiation in the polyclonal response to influenza infection or vaccination. Sci Rep 2016; 6:28287. [PMID: 27329272 PMCID: PMC4916409 DOI: 10.1038/srep28287] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2016] [Accepted: 06/01/2016] [Indexed: 02/06/2023] Open
Abstract
Follicular helper T cells (Tfh) are essential for B cell production of high-affinity, class-switched antibodies. Much interest in Tfh development focuses on the priming environment of CD4 T cells. Here we explored the role that peptide specificity plays in the partitioning of the polyclonal CD4 T cell repertoire between Tfh and NonTfh lineages during the response to influenza. Surprisingly, we found that CD4 T cells specific for different epitopes exhibited distinct tendencies to segregate into Tfh or NonTfh. To alter the microenvironment and abundance, viral antigens were introduced as purified recombinant proteins in adjuvant as native proteins. Also, the most prototypical epitopes were expressed in a completely foreign protein. In many cases, the epitope-specific response patterns of Tfh vs. NonTfh persisted. The functional TcR avidity of only a subset of epitope-specific cells correlated with the tendency to drive a Tfh response. Thus, we conclude that in a polyclonal CD4 T cell repertoire, features of TcR-peptide:MHC class II complex have a strong deterministic influence on the ability of CD4 T cells to become a Tfh or a NonTfh. Our data is most consistent with at least 2 checkpoints of Tfh selection that include both TcR affinity and B cell presentation.
Collapse
|
16
|
Ascough S, Ingram RJ, Chu KKY, Musson JA, Moore SJ, Gallagher T, Baillie L, Williamson ED, Robinson JH, Maillere B, Boyton RJ, Altmann DM. CD4+ T Cells Targeting Dominant and Cryptic Epitopes from Bacillus anthracis Lethal Factor. Front Microbiol 2016; 6:1506. [PMID: 26779161 PMCID: PMC4700811 DOI: 10.3389/fmicb.2015.01506] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2015] [Accepted: 12/14/2015] [Indexed: 12/31/2022] Open
Abstract
Anthrax is an endemic infection in many countries, particularly in the developing world. The causative agent, Bacillus anthracis, mediates disease through the secretion of binary exotoxins. Until recently, research into adaptive immunity targeting this bacterial pathogen has largely focused on the humoral response to these toxins. There is, however, growing recognition that cellular immune responses involving IFNγ producing CD4+ T cells also contribute significantly to a protective memory response. An established concept in adaptive immunity to infection is that during infection of host cells, new microbial epitopes may be revealed, leading to immune recognition of so called ‘cryptic’ or ‘subdominant’ epitopes. We analyzed the response to both cryptic and immunodominant T cell epitopes derived from the toxin component lethal factor and presented by a range of HLA-DR alleles. Using IFNγ-ELISpot assays we characterized epitopes that elicited a response following immunization with synthetic peptide and the whole protein and tested their capacities to bind purified HLA-DR molecules in vitro. We found that DR1 transgenics demonstrated T cell responses to a greater number of domain III cryptic epitopes than other HLA-DR transgenics, and that this pattern was repeated with the immunodominant epitopes, as a greater proportion of these epitopes induced a T cell response when presented within the context of the whole protein. Immunodominant epitopes LF457-476 and LF467-487 were found to induce a T cell response to the peptide, as well as to the whole native LF protein in DR1 and DR15, but not in DR4 transgenics. The analysis of Domain I revealed the presence of several unique cryptic epitopes all of which showed a strong to moderate relative binding affinity to HLA-DR4 molecules. However, none of the cryptic epitopes from either domain III or I displayed notably high binding affinities across all HLA-DR alleles assayed. These responses were influenced by the specific HLA alleles presenting the peptide, and imply that construction of future epitope string vaccines which are immunogenic across a wide range of HLA alleles could benefit from a combination of both cryptic and immunodominant anthrax epitopes.
Collapse
Affiliation(s)
| | - Rebecca J Ingram
- Centre for Infection and Immunity, Queen's University Belfast Belfast UK
| | - Karen K Y Chu
- Section of Infectious Diseases and Immunity, Department of Medicine, Imperial College London London, UK
| | - Julie A Musson
- Institute of Cellular Medicine, Newcastle University Newcastle upon Tyne, UK
| | - Stephen J Moore
- Center for Biomedical Engineering and Technology, University of Maryland School of Medicine Baltimore, MD, USA
| | - Theresa Gallagher
- Center for Biomedical Engineering and Technology, University of Maryland School of Medicine Baltimore, MD, USA
| | - Les Baillie
- School of Pharmacy and Pharmaceutical Sciences, Cardiff University Cardiff, UK
| | | | - John H Robinson
- Institute of Cellular Medicine, Newcastle University Newcastle upon Tyne, UK
| | - Bernard Maillere
- Service d'Ingénierie Moléculaire des Protéines, Insititut de Biologie et de Technologies de Saclay, Commiseriat à l'Energie Atomique, Gif Sur Yvette France
| | - Rosemary J Boyton
- Section of Infectious Diseases and Immunity, Department of Medicine, Imperial College London London, UK
| | - Daniel M Altmann
- Section of Infectious Diseases and Immunity, Department of Medicine, Imperial College London London, UK
| |
Collapse
|
17
|
Oyarzun P, Kobe B. Computer-aided design of T-cell epitope-based vaccines: addressing population coverage. Int J Immunogenet 2015. [PMID: 26211755 DOI: 10.1111/iji.12214] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Epitope-based vaccines (EVs) make use of short antigen-derived peptides corresponding to immune epitopes, which are administered to trigger a protective humoral and/or cellular immune response. EVs potentially allow for precise control over the immune response activation by focusing on the most relevant - immunogenic and conserved - antigen regions. Experimental screening of large sets of peptides is time-consuming and costly; therefore, in silico methods that facilitate T-cell epitope mapping of protein antigens are paramount for EV development. The prediction of T-cell epitopes focuses on the peptide presentation process by proteins encoded by the major histocompatibility complex (MHC). Because different MHCs have different specificities and T-cell epitope repertoires, individuals are likely to respond to a different set of peptides from a given pathogen in genetically heterogeneous human populations. In addition, protective immune responses are only expected if T-cell epitopes are restricted by MHC proteins expressed at high frequencies in the target population. Therefore, without careful consideration of the specificity and prevalence of the MHC proteins, EVs could fail to adequately cover the target population. This article reviews state-of-the-art algorithms and computational tools to guide EV design through all the stages of the process: epitope prediction, epitope selection and vaccine assembly, while optimizing vaccine immunogenicity and coping with genetic variation in humans and pathogens.
Collapse
Affiliation(s)
- P Oyarzun
- Biotechnology Centre, Facultad de Ingeniería y Tecnología, Universidad San Sebastián, Concepción, Chile
| | - B Kobe
- School of Chemistry and Molecular Biosciences, Institute for Molecular Bioscience and Australian Infectious Diseases Research Centre, University of Queensland, Brisbane, QLD, Australia
| |
Collapse
|
18
|
Nayak K, Jing L, Russell RM, Davies DH, Hermanson G, Molina DM, Liang X, Sherman DR, Kwok WW, Yang J, Kenneth J, Ahamed SF, Chandele A, Murali-Krishna K, Koelle DM. Identification of novel Mycobacterium tuberculosis CD4 T-cell antigens via high throughput proteome screening. Tuberculosis (Edinb) 2015; 95:275-87. [PMID: 25857935 DOI: 10.1016/j.tube.2015.03.001] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2014] [Revised: 02/24/2015] [Accepted: 03/01/2015] [Indexed: 10/23/2022]
Abstract
Elicitation of CD4 IFN-gamma T cell responses to Mycobacterium tuberculosis (MTB) is a rational vaccine strategy to prevent clinical tuberculosis. Diagnosis of MTB infection is based on T-cell immune memory to MTB antigens. The MTB proteome contains over four thousand open reading frames (ORFs). We conducted a pilot antigen identification study using 164 MTB proteins and MTB-specific T-cells expanded in vitro from 12 persons with latent MTB infection. Enrichment of MTB-reactive T-cells from PBMC used cell sorting or an alternate system compatible with limited resources. MTB proteins were used as single antigens or combinatorial matrices in proliferation and cytokine secretion readouts. Overall, our study found that 44 MTB proteins were antigenic, including 27 not previously characterized as CD4 T-cell antigens. Antigen truncation, peptide, NTM homology, and HLA class II tetramer studies confirmed malate synthase G (encoded by gene Rv1837) as a CD4 T-cell antigen. This simple, scalable system has potential utility for the identification of candidate MTB vaccine and biomarker antigens.
Collapse
Affiliation(s)
- Kaustuv Nayak
- ICGEB-Emory Vaccine Center, International Center for Genetic Engineering and Biotechnology, Aruna Asaf Ali Marg, New Delhi 110067, India.
| | - Lichen Jing
- Department of Medicine, Division of Infectious Diseases, University of Washington, Box 358061, Seattle, WA 98195, USA.
| | - Ronnie M Russell
- Department of Medicine, Division of Infectious Diseases, University of Washington, Box 358061, Seattle, WA 98195, USA.
| | - D Huw Davies
- Department of Medicine, Division of Infectious Diseases, University of California, Room 376D Med-Surg II, Irvine, CA 92697-4068, USA; Antigen Discovery, Inc., 1 Technology Drive Suite E309, Irvine, CA 92618, USA.
| | - Gary Hermanson
- Antigen Discovery, Inc., 1 Technology Drive Suite E309, Irvine, CA 92618, USA.
| | - Douglas M Molina
- Antigen Discovery, Inc., 1 Technology Drive Suite E309, Irvine, CA 92618, USA.
| | - Xiaowu Liang
- Antigen Discovery, Inc., 1 Technology Drive Suite E309, Irvine, CA 92618, USA.
| | - David R Sherman
- Seattle Biomedical Research Institute, 307 Westlake Ave. North, No. 500, Seattle, WA 98109, USA; Department of Global Health, University of Washington, Box 359931, Seattle, WA 98195, USA.
| | - William W Kwok
- Benaroya Research Institute at Virginia Mason, 1201 9th Ave., Seattle, WA, 98101, USA.
| | - Junbao Yang
- Benaroya Research Institute at Virginia Mason, 1201 9th Ave., Seattle, WA, 98101, USA.
| | - John Kenneth
- Division of Infectious Diseases, St. John's Research Institute, St. John's National Academy of Health Sciences, Sarjapur Road, Koramangala 2 Block, Bangaluru, Karnataka 560034, India.
| | - Syed F Ahamed
- Division of Infectious Diseases, St. John's Research Institute, St. John's National Academy of Health Sciences, Sarjapur Road, Koramangala 2 Block, Bangaluru, Karnataka 560034, India.
| | - Anmol Chandele
- ICGEB-Emory Vaccine Center, International Center for Genetic Engineering and Biotechnology, Aruna Asaf Ali Marg, New Delhi 110067, India; Emory Vaccine Center, 1510 Clifton Road, Atlanta, GA 30329, USA.
| | - Kaja Murali-Krishna
- ICGEB-Emory Vaccine Center, International Center for Genetic Engineering and Biotechnology, Aruna Asaf Ali Marg, New Delhi 110067, India; Emory Vaccine Center, 1510 Clifton Road, Atlanta, GA 30329, USA; Department of Pediatrics, Emory University, 1760 Haygood Drive, Atlanta, GA 30322, USA.
| | - David M Koelle
- Department of Medicine, Division of Infectious Diseases, University of Washington, Box 358061, Seattle, WA 98195, USA; Department of Global Health, University of Washington, Box 359931, Seattle, WA 98195, USA; Benaroya Research Institute at Virginia Mason, 1201 9th Ave., Seattle, WA, 98101, USA; Department of Laboratory Medicine, University of Washington, Box 358070, Seattle, WA 98195, USA; Vaccine and Infectious Diseases Division, Fred Hutchinson Cancer Research Center, 1100 Eastlake Ave. East, Seattle, WA 98109, USA.
| |
Collapse
|
19
|
Oyarzun P, Ellis JJ, Gonzalez-Galarza FF, Jones AR, Middleton D, Boden M, Kobe B. A bioinformatics tool for epitope-based vaccine design that accounts for human ethnic diversity: application to emerging infectious diseases. Vaccine 2015; 33:1267-73. [PMID: 25629524 DOI: 10.1016/j.vaccine.2015.01.040] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2014] [Revised: 12/11/2014] [Accepted: 01/14/2015] [Indexed: 11/17/2022]
Abstract
BACKGROUND Peptide vaccination based on multiple T-cell epitopes can be used to target well-defined ethnic populations. Because the response to T-cell epitopes is restricted by HLA proteins, the HLA specificity of T-cell epitopes becomes a major consideration for epitope-based vaccine design. We have previously shown that CD4+ T-cell epitopes restricted by 95% of human MHC class II proteins can be predicted with high-specificity. METHODS We describe here the integration of epitope prediction with population coverage and epitope selection algorithms. The population coverage assessment makes use of the Allele Frequency Net Database. We present the computational platform Predivac-2.0 for HLA class II-restricted epitope-based vaccine design, which accounts comprehensively for human genetic diversity. RESULTS We validated the performance of the tool on the identification of promiscuous and immunodominant CD4+ T-cell epitopes from the human immunodeficiency virus (HIV) protein Gag. We further describe an application for epitope-based vaccine design in the context of emerging infectious diseases associated with Lassa, Nipah and Hendra viruses. Putative CD4+ T-cell epitopes were mapped on the surface glycoproteins of these pathogens and are good candidates to be experimentally tested, as they hold potential to provide cognate help in vaccination settings in their respective target populations. CONCLUSION Predivac-2.0 is a novel approach in epitope-based vaccine design, particularly suited to be applied to virus-related emerging infectious diseases, because the geographic distributions of the viruses are well defined and ethnic populations in need of vaccination can be determined ("ethnicity-oriented approach"). Predivac-2.0 is accessible through the website http://predivac.biosci.uq.edu.au/.
Collapse
Affiliation(s)
- Patricio Oyarzun
- School of Chemistry and Molecular Biosciences, Institute for Molecular Bioscience and Australian Infectious Diseases Research Centre, University of Queensland, Australia; Biotechnology Centre, Universidad San Sebastián, Concepción, Chile.
| | - Jonathan J Ellis
- School of Chemistry and Molecular Biosciences, Institute for Molecular Bioscience and Australian Infectious Diseases Research Centre, University of Queensland, Australia
| | | | - Andrew R Jones
- Institute of Integrative Biology, University of Liverpool, United Kingdom
| | - Derek Middleton
- Transplant Immunology Laboratory, Royal Liverpool University Hospital & School of Infection and Host Defence University of Liverpool, United Kingdom
| | - Mikael Boden
- School of Chemistry and Molecular Biosciences, Institute for Molecular Bioscience and Australian Infectious Diseases Research Centre, University of Queensland, Australia; School of Information Technology and Electrical Engineering, University of Queensland, Queensland 4072, Australia
| | - Bostjan Kobe
- School of Chemistry and Molecular Biosciences, Institute for Molecular Bioscience and Australian Infectious Diseases Research Centre, University of Queensland, Australia.
| |
Collapse
|
20
|
Pavlović MD, Jandrlić DR, Mitić NS. Epitope distribution in ordered and disordered protein regions. Part B — Ordered regions and disordered binding sites are targets of T- and B-cell immunity. J Immunol Methods 2014; 407:90-107. [DOI: 10.1016/j.jim.2014.03.027] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2013] [Revised: 03/31/2014] [Accepted: 03/31/2014] [Indexed: 01/04/2023]
|
21
|
Ascough S, Ingram RJ, Chu KK, Reynolds CJ, Musson JA, Doganay M, Metan G, Ozkul Y, Baillie L, Sriskandan S, Moore SJ, Gallagher TB, Dyson H, Williamson ED, Robinson JH, Maillere B, Boyton RJ, Altmann DM. Anthrax lethal factor as an immune target in humans and transgenic mice and the impact of HLA polymorphism on CD4+ T cell immunity. PLoS Pathog 2014; 10:e1004085. [PMID: 24788397 PMCID: PMC4006929 DOI: 10.1371/journal.ppat.1004085] [Citation(s) in RCA: 15] [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: 12/17/2013] [Accepted: 03/07/2014] [Indexed: 11/23/2022] Open
Abstract
Bacillus anthracis produces a binary toxin composed of protective antigen (PA) and one of two subunits, lethal factor (LF) or edema factor (EF). Most studies have concentrated on induction of toxin-specific antibodies as the correlate of protective immunity, in contrast to which understanding of cellular immunity to these toxins and its impact on infection is limited. We characterized CD4+ T cell immunity to LF in a panel of humanized HLA-DR and DQ transgenic mice and in naturally exposed patients. As the variation in antigen presentation governed by HLA polymorphism has a major impact on protective immunity to specific epitopes, we examined relative binding affinities of LF peptides to purified HLA class II molecules, identifying those regions likely to be of broad applicability to human immune studies through their ability to bind multiple alleles. Transgenics differing only in their expression of human HLA class II alleles showed a marked hierarchy of immunity to LF. Immunogenicity in HLA transgenics was primarily restricted to epitopes from domains II and IV of LF and promiscuous, dominant epitopes, common to all HLA types, were identified in domain II. The relevance of this model was further demonstrated by the fact that a number of the immunodominant epitopes identified in mice were recognized by T cells from humans previously infected with cutaneous anthrax and from vaccinated individuals. The ability of the identified epitopes to confer protective immunity was demonstrated by lethal anthrax challenge of HLA transgenic mice immunized with a peptide subunit vaccine comprising the immunodominant epitopes that we identified. Anthrax is of concern with respect to human exposure in endemic regions, concerns about bioterrorism and the considerable global burden of livestock infections. The immunology of this disease remains poorly understood. Vaccination has been based on B. anthracis filtrates or attenuated spore-based vaccines, with more recent trials of next-generation recombinant vaccines. Approaches generally require extensive vaccination regimens and there have been concerns about immunogenicity and adverse reactions. An ongoing need remains for rationally designed, effective and safe anthrax vaccines. The importance of T cell stimulating vaccines is inceasingly recognized. An essential step is an understanding of immunodominant epitopes and their relevance across the diverse HLA immune response genes of human populations. We characterized CD4 T cell immunity to anthrax Lethal Factor (LF), using HLA transgenic mice, as well as testing candidate peptide epitopes for binding to a wide range of HLA alleles. We identified anthrax epitopes, noteworthy in that they elicit exceptionally strong immunity with promiscuous binding across multiple HLA alleles and isotypes. T cell responses in humans exposed to LF through either natural anthrax infection or vaccination were also examined. Epitopes identified as candidates were used to protect HLA transgenic mice from anthrax challenge.
Collapse
Affiliation(s)
- Stephanie Ascough
- Department of Medicine, Imperial College London, London, United Kingdom
| | - Rebecca J. Ingram
- Centre for Infection and Immunity, Queen's University Belfast, Belfast, United Kingdom
| | - Karen K. Chu
- Department of Medicine, Imperial College London, London, United Kingdom
| | | | - Julie A. Musson
- Institute for Cellular Medicine, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Mehmet Doganay
- Department of Infectious Disease, Erciyes University Hospital, Kayseri, Turkey
| | - Gökhan Metan
- Department of Infectious Disease, Erciyes University Hospital, Kayseri, Turkey
| | - Yusuf Ozkul
- Department of Medical Genetics, Erciyes University Hospital, Kayseri, Turkey
| | - Les Baillie
- School of Pharmacy and Pharmaceutical Sciences, Cardiff University, Cardiff, United Kingdom
| | | | - Stephen J. Moore
- BIOMET, University of Maryland School of Medicine, Baltimore, Maryland, United States of America
| | - Theresa B. Gallagher
- BIOMET, University of Maryland School of Medicine, Baltimore, Maryland, United States of America
| | - Hugh Dyson
- Defence Science Technology Laboratory, Porton Down, Salisbury, United Kingdom
| | - E. Diane Williamson
- Defence Science Technology Laboratory, Porton Down, Salisbury, United Kingdom
| | - John H. Robinson
- Institute for Cellular Medicine, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Bernard Maillere
- CEA, iBiTecS, Service d'Ingénierie Moléculaire des Protéines (SIMOPRO), Gif Sur Yvette, France
| | | | - Daniel M. Altmann
- Department of Medicine, Imperial College London, London, United Kingdom
- * E-mail:
| |
Collapse
|
22
|
Mitić NS, Pavlović MD, Jandrlić DR. Epitope distribution in ordered and disordered protein regions - part A. T-cell epitope frequency, affinity and hydropathy. J Immunol Methods 2014; 406:83-103. [PMID: 24614036 DOI: 10.1016/j.jim.2014.02.012] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2013] [Revised: 02/27/2014] [Accepted: 02/27/2014] [Indexed: 02/08/2023]
Abstract
Highly disordered protein regions are prevalently hydrophilic, extremely sensitive to proteolysis in vitro, and are expected to be under-represented as T-cell epitopes. The aim of this research was to find out whether disorder and hydropathy prediction methods could help in understanding epitope processing and presentation. According to the pan-specific T-cell epitope predictors NetMHCpan and NetMHCIIpan and 9 publicly available disorder predictors, frequency of epitopes presented by human leukocyte antigens (HLA) class-I or -II was found to be more than 2.5 times higher in ordered than in disordered protein regions (depending on the disorder predictor). Both HLA class-I and HLA class-II binding epitopes are prevalently hydrophilic in disordered and prevalently hydrophobic in ordered protein regions, whereas epitopes recognized by HLA class-II alleles are more hydrophobic than those recognized by HLA class-I. As regards both classes of HLA molecules, high-affinity binding epitopes display more hydrophobicity than low affinity-binding epitopes (in both ordered and disordered regions). Epitopes belonging to disordered protein regions were not predicted to have poor affinity to HLA class-II molecules, as expected from disorder intrinsic proteolytic instability. The relation of epitope hydrophobicity and order/disorder location was also valid if alleles were grouped according to the HLA class-I and HLA class-II supertypes, except for the class-I supertype A3 in which the main part of recognized epitopes was prevalently hydrophilic. Regarding specific supertypes, the affinity of epitopes belonging to ordered regions varies only slightly (depending on the disorder predictor) compared to the affinity of epitopes in corresponding disordered regions. The distribution of epitopes in ordered and disordered protein regions has revealed that the curves of order-epitope distribution were convex-like while the curves of disorder-epitope distribution were concave-like. The percentage of prevalently hydrophobic epitopes increases with the enhancement of epitope promiscuity level and moving from disordered to ordered regions. These data suggests that reverse vaccinology, oriented towards promiscuous and high-affinity epitopes, is also oriented towards prevalently hydrophobic, ordered regions. The analysis of predicted and experimentally evaluated epitopes of cancer-testis antigen MAGE-A3 has confirmed that the majority of T-cell epitopes, particularly those that are promiscuous or naturally processed, was located in ordered and disorder/order boundary protein regions overlapping hydrophobic regions.
Collapse
Affiliation(s)
- Nenad S Mitić
- University of Belgrade, Faculty of Mathematics, P.O.B. 550, Studentski trg 16, Belgrade, Serbia.
| | - Mirjana D Pavlović
- University of Belgrade, Institute of General and Physical Chemistry, Studentski trg 12/V, Belgrade, Serbia.
| | - Davorka R Jandrlić
- University of Belgrade, Faculty of Mechanical Engineering, Kraljice Marije 16, Belgrade, Serbia.
| |
Collapse
|
23
|
Sant AJ, Chaves FA, Leddon SA, Tung J. The control of the specificity of CD4 T cell responses: thresholds, breakpoints, and ceilings. Front Immunol 2013; 4:340. [PMID: 24167504 PMCID: PMC3805957 DOI: 10.3389/fimmu.2013.00340] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2013] [Accepted: 10/04/2013] [Indexed: 12/31/2022] Open
Abstract
It has been known for over 25 years that CD4 T cell responses are restricted to a finite number of peptide epitopes within pathogens or protein vaccines. These selected peptide epitopes are termed "immunodominant." Other peptides within the antigen that can bind to host MHC molecules and recruit CD4 T cells as single peptides are termed "cryptic" because they fail to induce responses when expressed in complex proteins or when in competition with other peptides during the immune response. In the last decade, our laboratory has evaluated the mechanisms that underlie the preferential specificity of CD4 T cells and have discovered that both intracellular events within antigen presenting cells, particular selective DM editing, and intercellular regulatory pathways, involving IFN-γ, indoleamine 2,3-dioxygenase, and regulatory T cells, play a role in selecting the final peptide specificity of CD4 T cells. In this review, we summarize our findings, discuss the implications of this work on responses to pathogens and vaccines and speculate on the logic of these regulatory events.
Collapse
Affiliation(s)
- Andrea J. Sant
- Department of Microbiology and Immunology, David H. Smith Center for Vaccine Biology and Immunology, University of Rochester Medical Center, Rochester, NY, USA
| | - Francisco A. Chaves
- Department of Microbiology and Immunology, David H. Smith Center for Vaccine Biology and Immunology, University of Rochester Medical Center, Rochester, NY, USA
| | - Scott A. Leddon
- Department of Microbiology and Immunology, David H. Smith Center for Vaccine Biology and Immunology, University of Rochester Medical Center, Rochester, NY, USA
| | - Jacqueline Tung
- Department of Microbiology and Immunology, David H. Smith Center for Vaccine Biology and Immunology, University of Rochester Medical Center, Rochester, NY, USA
| |
Collapse
|
24
|
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.
Collapse
|
25
|
Ghosh M, Solanki AK, Roy K, Dhoke RR, Ashish, Roy S. Carrier protein influences immunodominance of a known epitope: implication in peptide vaccine design. Vaccine 2013; 31:4682-8. [PMID: 23928464 DOI: 10.1016/j.vaccine.2013.06.110] [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: 04/16/2013] [Revised: 06/10/2013] [Accepted: 06/14/2013] [Indexed: 11/29/2022]
Abstract
We investigated how the processing of a given antigen by antigen presenting cells (APC) is dictated by the conformation of the antigen and how this governs the immunodominance hierarchy. To address the question, a known immunodominant sequence of bacteriophage lambda repressor N-terminal sequence 12-26 [λR(12-26)] was engineered at the N and C termini of a heterologous leishmanial protein, Kinetoplastid membrane protein-11 (KMP-11); the resulting proteins were defined as N-KMP-11 and C-KMP-11 respectively. The presence of λR(12-26) in N-KMP-11 and C-KMP-11 was established by western blot analysis with antibody to λR(12-26) peptide. N-KMP-11 but not C-KMP-11 could stimulate the anti λR(12-26) T-cell clonal population very efficiently in the presence of APCs. Priming of BALB/c mice with N-KMP-11 or C-KMP-11 generated similar levels of anti-KMP-11 IgG, but anti-λR(12-26) specific IgG was observed only upon priming with N-KMP-11. Interestingly, uptake of both N-KMP-11 and C-KMP-11 by APCs was similar but catabolism of N-KMP-11 but not C-KMP-11 was biphasic and fast at the initial time point. Kratky plots of small angle X-ray scattering showed that while N-KMP-11 adopts flexible Gaussian type of topology, C-KMP-11 prefers Globular nature. To show that KMP-11 is not unique as a carrier protein, an epitope (SPITBTNLBTMBK) of Plasmodium yoelii (PY) apical membrane protein 1[AMA-1 (136-148)], is placed at the C and N terminals of a dominant T-cell epitope of ovalbumin protein OVA(323-339) and the resulting peptides are defined as PY-OVA and OVA-PY respectively. Interestingly, only OVA-PY could stimulate anti-OVA T-cells and produce IgG response upon priming of BALB/c mice with it. Thus for rational design of peptide vaccine it is important to place the dominant epitope appropriately in the context of the carrier protein.
Collapse
Affiliation(s)
- Moumita Ghosh
- Division of Infectious diseases and Immunology, CSIR-Indian Institute of Chemical Biology, 4 Raja S.C. Mullick Road, Kolkata 700032, India
| | | | | | | | | | | |
Collapse
|
26
|
Oyarzún P, Ellis JJ, Bodén M, Kobe B. PREDIVAC: CD4+ T-cell epitope prediction for vaccine design that covers 95% of HLA class II DR protein diversity. BMC Bioinformatics 2013; 14:52. [PMID: 23409948 PMCID: PMC3598884 DOI: 10.1186/1471-2105-14-52] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2012] [Accepted: 01/31/2013] [Indexed: 12/18/2022] Open
Abstract
Background CD4+ T-cell epitopes play a crucial role in eliciting vigorous protective immune responses during peptide (epitope)-based vaccination. The prediction of these epitopes focuses on the peptide binding process by MHC class II proteins. The ability to account for MHC class II polymorphism is critical for epitope-based vaccine design tools, as different allelic variants can have different peptide repertoires. In addition, the specificity of CD4+ T-cells is often directed to a very limited set of immunodominant peptides in pathogen proteins. The ability to predict what epitopes are most likely to dominate an immune response remains a challenge. Results We developed the computational tool Predivac to predict CD4+ T-cell epitopes. Predivac can make predictions for 95% of all MHC class II protein variants (allotypes), a substantial advance over other available methods. Predivac bases its prediction on the concept of specificity-determining residues. The performance of the method was assessed both for high-affinity HLA class II peptide binding and CD4+ T-cell epitope prediction. In terms of epitope prediction, Predivac outperformed three available pan-specific approaches (delivering the highest specificity). A central finding was the high accuracy delivered by the method in the identification of immunodominant and promiscuous CD4+ T-cell epitopes, which play an essential role in epitope-based vaccine design. Conclusions The comprehensive HLA class II allele coverage along with the high specificity in identifying immunodominant CD4+ T-cell epitopes makes Predivac a valuable tool to aid epitope-based vaccine design in the context of a genetically heterogeneous human population.The tool is available at: http://predivac.biosci.uq.edu.au/.
Collapse
Affiliation(s)
- Patricio Oyarzún
- School of Chemistry and Molecular Biosciences, Institute for Molecular Bioscience and Australian Infectious Diseases Research Centre, University of Queensland, Brisbane, QLD 4072, Australia.
| | | | | | | |
Collapse
|
27
|
Roy BM, Zhukov DV, Maynard JA. Flanking residues are central to DO11.10 T cell hybridoma stimulation by ovalbumin 323-339. PLoS One 2012; 7:e47585. [PMID: 23110081 PMCID: PMC3479146 DOI: 10.1371/journal.pone.0047585] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2012] [Accepted: 09/18/2012] [Indexed: 11/30/2022] Open
Abstract
T cell activation requires formation of a tri-molecular interaction between a major histocompatibility complex (MHC), peptide, and T cell receptor. In a common model system, the ovalbumin epitope 323–339 binds the murine class II MHC, I-Ad, in at least three distinct registers. The DO11.10 T cell recognizes the least stable of these, as determined by peptide-MHC dissociation rates. Using exogenous peptides and peptide insertions into a carrier protein in combination with IL-2 secretion assays, we show that the alternate registers do not competitively inhibit display of the active register four. In contrast, this weakly binding register is stabilized by the presence of n-terminal flanking residues active in MHC binding. The DO11.10 hybridoma is sensitive to the presence of specific wild-type residues extending to at least the P-3 peptide position. Transfer of the P-4 to P-2 flanking residues to a hen egg lysozyme epitope also presented by I-Ad increases the activity of that epitope substantially. These results illustrate the inherent complexity in delineating the interaction of multiple registers based on traditional thermodynamic measurements and demonstrate the potential of flanking residue modification for increasing the activity of weakly bound epitopes. The latter technique represents an alternative to substitution of anchor residues within a weakly bound register, which we show can significantly decrease the activity of the epitope to a responding T cell.
Collapse
Affiliation(s)
- Benjamin M. Roy
- Department of Chemical Engineering, University of Minnesota, Minneapolis, Minnesota, United States of America
- Department of Chemical Engineering, University of Texas at Austin, Austin Texas, United States of America
| | - Dmitriy V. Zhukov
- Department of Chemical Engineering, University of Texas at Austin, Austin Texas, United States of America
| | - Jennifer A. Maynard
- Department of Chemical Engineering, University of Texas at Austin, Austin Texas, United States of America
- * E-mail:
| |
Collapse
|
28
|
Kroeger DR, Rudulier CD, Peters NC, Bretscher PA. Direct demonstration of CD4 T cell cooperation in the primary in vivo generation of CD4 effector T cells. Int Immunol 2012; 24:519-27. [PMID: 22527289 DOI: 10.1093/intimm/dxs055] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Many observations bear upon the cellular and molecular requirements for CD4 T cell activation. The interaction of CD4 T cells with dendritic cells (DC), central to the induction of most immune responses, is the most studied. However, leukocytes other than DC can dramatically affect the induction and differentiation of CD4 T cells into effector cells. We recently provided indirect evidence that in vivo CD4 T cooperation facilitates the activation of CD4 T cells. Here, we demonstrate that the activation of CD4 T cells, specific for the hen egg lysozyme (HEL)(105) (-120) peptide, is optimally achieved when BALB/c mice are immunized with additional MHC class II-binding HEL peptides in incomplete Freund's adjuvant. This cooperation cannot be mimicked by the coadministration of LPS or of an agonistic antibody to CD40, at the time of immunization. In contrast, OX40-OX40L interactions are necessary for CD4 T cell cooperation in that an OX40 agonistic antibody can replace, and an OX40L-blocking antibody can abrogate, CD4 T cell cooperation in situations where such cooperation would otherwise enhance the activation of CD4 T cells.
Collapse
Affiliation(s)
- David R Kroeger
- Department of Microbiology and Immunology, University of Saskatchewan, Saskatoon, Saskatchewan S7N 5E5, Canada
| | | | | | | |
Collapse
|
29
|
Chaves FA, Lee AH, Nayak JL, Richards KA, Sant AJ. The utility and limitations of current Web-available algorithms to predict peptides recognized by CD4 T cells in response to pathogen infection. THE JOURNAL OF IMMUNOLOGY 2012; 188:4235-48. [PMID: 22467652 DOI: 10.4049/jimmunol.1103640] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
The ability to track CD4 T cells elicited in response to pathogen infection or vaccination is critical because of the role these cells play in protective immunity. Coupled with advances in genome sequencing of pathogenic organisms, there is considerable appeal for implementation of computer-based algorithms to predict peptides that bind to the class II molecules, forming the complex recognized by CD4 T cells. Despite recent progress in this area, there is a paucity of data regarding the success of these algorithms in identifying actual pathogen-derived epitopes. In this study, we sought to rigorously evaluate the performance of multiple Web-available algorithms by comparing their predictions with our results--obtained by purely empirical methods for epitope discovery in influenza that used overlapping peptides and cytokine ELISPOTs--for three independent class II molecules. We analyzed the data in different ways, trying to anticipate how an investigator might use these computational tools for epitope discovery. We come to the conclusion that currently available algorithms can indeed facilitate epitope discovery, but all shared a high degree of false-positive and false-negative predictions. Therefore, efficiencies were low. We also found dramatic disparities among algorithms and between predicted IC(50) values and true dissociation rates of peptide-MHC class II complexes. We suggest that improved success of predictive algorithms will depend less on changes in computational methods or increased data sets and more on changes in parameters used to "train" the algorithms that factor in elements of T cell repertoire and peptide acquisition by class II molecules.
Collapse
Affiliation(s)
- Francisco A Chaves
- Department of Microbiology and Immunology, University of Rochester Medical Center, Rochester, NY 14642, USA
| | | | | | | | | |
Collapse
|
30
|
Reiser M, Wieland A, Plachter B, Mertens T, Greiner J, Schirmbeck R. The Immunodominant CD8 T Cell Response to the Human Cytomegalovirus Tegument Phosphoprotein pp65495–503Epitope Critically Depends on CD4 T Cell Help in Vaccinated HLA-A*0201 Transgenic Mice. THE JOURNAL OF IMMUNOLOGY 2011; 187:2172-80. [DOI: 10.4049/jimmunol.1002512] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
|
31
|
Richards KA, Chaves FA, Sant AJ. The memory phase of the CD4 T-cell response to influenza virus infection maintains its diverse antigen specificity. Immunology 2011; 133:246-56. [PMID: 21517839 DOI: 10.1111/j.1365-2567.2011.03435.x] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
A major gap in our understanding of the immune response to pathogens and vaccines is how closely the antigen specificity in the memory phase mimics repertoire that is rapidly expanded upon priming. Understanding the diversity of the CD4 T-cell memory compartment after a primary response to pathogens is hampered by the technical challenges of epitope discovery and suitable models to study primary immune responses. Recently, we have used overlapping synthetic peptides to empirically map most of the specificities present in the primary response to live influenza infection. We found that the CD4 T-cell response can be exceptionally diverse, depending on the allele(s) of MHC class II molecules expressed. In the current study, using a mouse model of primary influenza infection and peptide-specific cytokine EliSpots, we have asked how this broad CD4 T-cell immunodominance hierarchy changes as the immune response contracts and memory is established. Our studies revealed that, for the most part, diversity is maintained, and most specificities, including those for relatively minor epitopes, are preserved in the memory CD4 T-cell compartment. A modest, but reproducible shift in specificity toward haemagglutinin-derived epitopes was observed, raising the possibility that protein or peptide persistence might play a role in the evolution of the memory phase of the CD4 T-cell response.
Collapse
Affiliation(s)
- Katherine A Richards
- Department of Microbiology and Immunology, David H. Smith Center for Vaccine Biology and Immunology, AaB Institute of Biomedical Sciences, University of Rochester, Rochester, NY 14642, USA
| | | | | |
Collapse
|
32
|
Léonetti M, Gadzinski A, Moine G. Cell surface heparan sulfate proteoglycans influence MHC class II-restricted antigen presentation. THE JOURNAL OF IMMUNOLOGY 2010; 185:3847-56. [PMID: 20826758 DOI: 10.4049/jimmunol.0902724] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Heparan sulfate proteoglycans (HSPGs) are glycoproteins ubiquitously distributed on the cell surface and in the extracellular matrix. Their heparan sulfate moieties often represent alternative attachment points for extracellular proteins that target specific receptors. Thus, HSPGs modulate ligand-receptor encounters and participate in numerous biological processes. In this study, we examined whether HSPGs can also influence MHC class II-restricted Ag presentation. We selected a heparan sulfate ligand derived from the HIV-1 Tat protein and coupled it to a model protein Ag. We showed that coupling of the Tat fragment makes the Ag capable of binding cells, including APCs, and increases its ability to stimulate specific T cells up to 180-fold. The boosting effect depends on Ag processing; it vanished in the presence of an excess of heparin or free Tat fragment, indicating that HSPGs can behave as receptors involved in MHC class II processing and presentation. Furthermore, with FcγRII-bearing APCs, immune complexes containing the coupled Ag stimulated T cells up to 700-fold more efficiently than Ag-containing immune complexes. This effect vanished in the presence of heparin and is not found with FcγRII(-) APCs, indicating that HSPGs can also behave as coreceptors during FcγRIIR-mediated Ag presentation. These results indicate that ubiquitous receptors, such as HSPGs, can influence MHC class II-restricted Ag presentation and suggest that proteins will be supported more efficiently by the immune system if they have the inherent capacity to bind heparan sulfate.
Collapse
Affiliation(s)
- Michel Léonetti
- Institut de Biologie et Technologies de Saclay, Service de Pharmacologie et d' Immunoanalyse, and Laboratoire d'Ingénierie des Anticorps pour la Santé, Commissariat à l'Energie Atomique et aux Energies Alternatives, Gif-sur-Yvette, France.
| | | | | |
Collapse
|
33
|
Abortive activation of CD4 T cell responses during competitive priming in vivo. Proc Natl Acad Sci U S A 2009; 106:8647-52. [PMID: 19423666 DOI: 10.1073/pnas.0811584106] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Immunodominance refers to the highly selective peptide reactivity of T cells during an immune response. In this study, we tested the hypothesis that persistence of peptide:class II complexes is one key parameter that selects the final specificity of CD4 T cells. We found that low-stability peptide:class II complexes support the initial priming and expansion of CD4 T cells, but the expansion becomes strikingly aborted in the presence of competitive T cell responses to unrelated peptides. Our experiments revealed that for inhibition to occur, the competitive responses must be initiated by the same antigen presenting cell, and it is not because of competition for MHC binding. These studies not only provide an insight into the events that regulate competitive CD4 T cell priming in vivo, but also provide a previously undescribed conceptual framework to understand the parameters that select the final specificity of the T cell repertoire during pathogen or vaccine-induced immune responses.
Collapse
|
34
|
Weaver JM, Sant AJ. Understanding the focused CD4 T cell response to antigen and pathogenic organisms. Immunol Res 2009; 45:123-43. [PMID: 19198764 DOI: 10.1007/s12026-009-8095-8] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Immunodominance is a term that reflects the final, very limited peptide specificity of T cells that are elicited during an immune response. Recent experiments in our laboratory compel us to propose a new paradigm for the control of immunodominance in CD4 T cell responses, stating that immunodominance is peptide-intrinsic and is dictated by the off-rate of peptides from MHC class II molecules. Our studies have revealed that persistence of peptide:class II complexes both predicts and controls CD4 T cell immunodominance and that this parameter can be rationally manipulated to either promote or eliminate immune responses. Mechanistically, we have determined that DM editing in APC is a key event that is influenced by the kinetic stability of class II:peptide complexes and that differential persistence of complexes also impacts the expansion phase of the immune response. These studies have important implications for rational vaccine design and for understanding the immunological mechanisms that limit the specificity of CD4 T cell responses.
Collapse
Affiliation(s)
- Jason M Weaver
- David H. Smith Center for Vaccine Biology and Immunology, AaB Institute of Biomedical Sciences, Department of Microbiology and Immunology, University of Rochester, NY 14642, USA
| | | |
Collapse
|