1
|
de Araújo LP, de Melo Santos NC, Corsetti PP, de Almeida LA. Immunoinformatic Approach for Rational Identification of Immunogenic Peptides Against Host Entry and/or Exit Mpox Proteins and Potential Multiepitope Vaccine Construction. J Infect Dis 2024; 229:S285-S292. [PMID: 37804521 DOI: 10.1093/infdis/jiad443] [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: 07/27/2023] [Revised: 09/27/2023] [Accepted: 10/03/2023] [Indexed: 10/09/2023] Open
Abstract
COVID-19 has intensified humanity's concern about the emergence of new pandemics. Since 2018, epidemic outbreaks of the mpox virus have become worrisome. In June 2022, the World Health Organization declared the disease a global health emergency, with 14 500 cases reported by the Centers for Disease Control and Prevention in 60 countries. Therefore, the development of a vaccine based on the current virus genome is paramount in combating new cases. In view of this, we hypothesized the obtainment of rational immunogenic peptides predicted from proteins responsible for entry of the mpox virus into the host (A17L, A26L/A30L, A33R, H2R, L1R), exit (A27L, A35R, A36R, C19L), and both (B5R). To achieve this, we aligned the genome sequencing data of mpox virus isolated from an infected individual in the United States in June 2022 (ON674051.1) with the reference genome dated 2001 (NC_003310.1) for conservation analysis. The Immune Epitope Database server was used for the identification and characterization of the epitopes of each protein related to major histocompatibility complex I or II interaction and recognition by B-cell receptors, resulting in 138 epitopes for A17L, 233 for A28L, 48 for A33R, 77 for H2R, 77 for L1R, 270 for A27L, 72 for A35R, A36R, 148 for C19L, and 276 for B5R. These epitopes were tested in silico for antigenicity, physicochemical properties, and allergenicity, resulting in 51, 40, 10, 34, 38, 57, 25, 7, 47, and 53 epitopes, respectively. Additionally, to select an epitope with the highest promiscuity of binding to major histocompatibility complexes and B-cell receptor simultaneously, all epitopes of each protein were aligned, and the most repetitive and antigenic regions were identified. By classifying the results, we obtained 23 epitopes from the entry proteins, 16 from the exit proteins, and 7 from both. Subsequently, 1 epitope from each protein was selected, and all 3 were fused to construct a chimeric protein that has potential as a multiepitope vaccine. The constructed vaccine was then analyzed for its physicochemical, antigenic, and allergenic properties. Protein modeling, molecular dynamics, and molecular docking were performed on Toll-like receptors 2, 4, and 8, followed by in silico immune simulation of the vaccine. Finally, the results indicate an effective, stable, and safe vaccine that can be further tested, especially in vitro and in vivo, to validate the findings demonstrated in silico.
Collapse
Affiliation(s)
| | | | - Patrícia Paiva Corsetti
- Departamento de Microbiologia e Imunologia, Universidade Federal de Alfenas, Alfenas, Brazil
| | | |
Collapse
|
2
|
Srivastava PK. Cancer neoepitopes viewed through negative selection and peripheral tolerance: a new path to cancer vaccines. J Clin Invest 2024; 134:e176740. [PMID: 38426497 PMCID: PMC10904052 DOI: 10.1172/jci176740] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/02/2024] Open
Abstract
A proportion of somatic mutations in tumors create neoepitopes that can prime T cell responses that target the MHC I-neoepitope complexes on tumor cells, mediating tumor control or rejection. Despite the compelling centrality of neoepitopes to cancer immunity, we know remarkably little about what constitutes a neoepitope that can mediate tumor control in vivo and what distinguishes such a neoepitope from the vast majority of similar candidate neoepitopes that are inefficacious in vivo. Studies in mice as well as clinical trials have begun to reveal the unexpected paradoxes in this area. Because cancer neoepitopes straddle that ambiguous ground between self and non-self, some rules that are fundamental to immunology of frankly non-self antigens, such as viral or model antigens, do not appear to apply to neoepitopes. Because neoepitopes are so similar to self-epitopes, with only small changes that render them non-self, immune response to them is regulated at least partially the way immune response to self is regulated. Therefore, neoepitopes are viewed and understood here through the clarifying lens of negative thymic selection. Here, the emergent questions in the biology and clinical applications of neoepitopes are discussed critically and a mechanistic and testable framework that explains the complexity and translational potential of these wonderful antigens is proposed.
Collapse
|
3
|
Jamaleddine H, Rogers D, Perreault G, Postat J, Patel D, Mandl JN, Khadra A. Chronic infection control relies on T cells with lower foreign antigen binding strength generated by N-nucleotide diversity. PLoS Biol 2024; 22:e3002465. [PMID: 38300945 PMCID: PMC10833529 DOI: 10.1371/journal.pbio.3002465] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Accepted: 12/08/2023] [Indexed: 02/03/2024] Open
Abstract
The breadth of pathogens to which T cells can respond is determined by the T cell receptors (TCRs) present in an individual's repertoire. Although more than 90% of the sequence diversity among TCRs is generated by terminal deoxynucleotidyl transferase (TdT)-mediated N-nucleotide addition during V(D)J recombination, the benefit of TdT-altered TCRs remains unclear. Here, we computationally and experimentally investigated whether TCRs with higher N-nucleotide diversity via TdT make distinct contributions to acute or chronic pathogen control specifically through the inclusion of TCRs with lower antigen binding strengths (i.e., lower reactivity to peptide-major histocompatibility complex (pMHC)). When T cells with high pMHC reactivity have a greater propensity to become functionally exhausted than those of low pMHC reactivity, our computational model predicts a shift toward T cells with low pMHC reactivity over time during chronic, but not acute, infections. This TCR-affinity shift is critical, as the elimination of T cells with lower pMHC reactivity in silico substantially increased the time to clear a chronic infection, while acute infection control remained largely unchanged. Corroborating an affinity-centric benefit for TCR diversification via TdT, we found evidence that TdT-deficient TCR repertoires possess fewer T cells with weaker pMHC binding strengths in vivo and showed that TdT-deficient mice infected with a chronic, but not an acute, viral pathogen led to protracted viral clearance. In contrast, in the case of a chronic fungal pathogen where T cells fail to clear the infection, both our computational model and experimental data showed that TdT-diversified TCR repertoires conferred no additional protection to the hosts. Taken together, our in silico and in vivo data suggest that TdT-mediated TCR diversity is of particular benefit for the eventual resolution of prolonged pathogen replication through the inclusion of TCRs with lower foreign antigen binding strengths.
Collapse
Affiliation(s)
| | - Dakota Rogers
- Department of Physiology, McGill University, Montreal, Quebec, Canada
- McGill University Research Centre on Complex Traits, Montreal, Quebec, Canada
| | - Geneviève Perreault
- McGill University Research Centre on Complex Traits, Montreal, Quebec, Canada
| | - Jérémy Postat
- Department of Physiology, McGill University, Montreal, Quebec, Canada
- McGill University Research Centre on Complex Traits, Montreal, Quebec, Canada
| | - Dhanesh Patel
- Department of Physiology, McGill University, Montreal, Quebec, Canada
- McGill University Research Centre on Complex Traits, Montreal, Quebec, Canada
| | - Judith N. Mandl
- Department of Physiology, McGill University, Montreal, Quebec, Canada
- McGill University Research Centre on Complex Traits, Montreal, Quebec, Canada
- Department of Microbiology and Immunology, McGill University, Montreal, Quebec, Canada
| | - Anmar Khadra
- Department of Physiology, McGill University, Montreal, Quebec, Canada
| |
Collapse
|
4
|
Ahmadi N, Aghasadeghi M, Hamidi-Fard M, Motevalli F, Bahramali G. Reverse Vaccinology and Immunoinformatic Approach for Designing a Bivalent Vaccine Candidate Against Hepatitis A and Hepatitis B Viruses. Mol Biotechnol 2023:10.1007/s12033-023-00867-z. [PMID: 37715882 DOI: 10.1007/s12033-023-00867-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2023] [Accepted: 08/21/2023] [Indexed: 09/18/2023]
Abstract
Hepatitis A and B are two crucial viral infections that still dramatically affect public health worldwide. Hepatitis A Virus (HAV) is the main cause of acute hepatitis, whereas Hepatitis B Virus (HBV) leads to the chronic form of the disease, possibly cirrhosis or liver failure. Therefore, vaccination has always been considered the most effective preventive method against pathogens. At this moment, we aimed at the immunoinformatic analysis of HAV-Viral Protein 1 (VP1) as the major capsid protein to come up with the most conserved immunogenic truncated protein to be fused by HBV surface antigen (HBs Ag) to achieve a bivalent vaccine against HAV and HBV using an AAY linker. Various computational approaches were employed to predict highly conserved regions and the most immunogenic B-cell and T-cell epitopes of HAV-VP1 capsid protein in both humans and BALB/c. Moreover, the predicted fusion protein was analyzed regarding primary and secondary structures and also homology validation. Afterward, the three-dimensional structure of vaccine constructs docked with various toll-like receptors (TLR) 2, 4 and 7. According to the bioinformatics tools, the region of 99-259 amino acids of VP1 was selected with high immunogenicity and conserved epitopes. T-cell epitope prediction showed that this region contains 32 antigenic peptides for Human leukocyte antigen (HLA) class I and 20 antigenic peptides in terms of HLA class II which are almost fully conserved in the Iranian population. The vaccine design includes 5 linear and 4 conformational B-cell lymphocyte (BCL) epitopes to induce humoral immune responses. The designed VP1-AAY-HBsAg fusion protein has the potency to be constructed and expressed to achieve a bivalent vaccine candidate, especially in the Iranian population. These findings led us to claim that the designed vaccine candidate provides potential pathways for creating an exploratory vaccine against Hepatitis A and Hepatitis B Viruses with high confidence for the identified strains.
Collapse
Affiliation(s)
- Neda Ahmadi
- Department of Microbiology, Faculty of Biological Sciences, North Tehran Branch, Islamic Azad University, Tehran, Iran
| | - Mohammadreza Aghasadeghi
- Department of Hepatitis and AIDS and Blood Borne Diseases, Pasteur Institute of Iran, No: 69, Pasteur Ave, Tehran, 13165, Iran
- Viral Vaccine Research Center, Pasteur Institute of Iran, Tehran, Iran
| | - Mojtaba Hamidi-Fard
- Department of Hepatitis and AIDS and Blood Borne Diseases, Pasteur Institute of Iran, No: 69, Pasteur Ave, Tehran, 13165, Iran
- Viral Vaccine Research Center, Pasteur Institute of Iran, Tehran, Iran
| | - Fatemeh Motevalli
- Department of Hepatitis and AIDS and Blood Borne Diseases, Pasteur Institute of Iran, No: 69, Pasteur Ave, Tehran, 13165, Iran
| | - Golnaz Bahramali
- Department of Hepatitis and AIDS and Blood Borne Diseases, Pasteur Institute of Iran, No: 69, Pasteur Ave, Tehran, 13165, Iran.
- Viral Vaccine Research Center, Pasteur Institute of Iran, Tehran, Iran.
| |
Collapse
|
5
|
Malaina I, Gonzalez-Melero L, Martínez L, Salvador A, Sanchez-Diez A, Asumendi A, Margareto J, Carrasco-Pujante J, Legarreta L, García MA, Pérez-Pinilla MB, Izu R, Martínez de la Fuente I, Igartua M, Alonso S, Hernandez RM, Boyano MD. Computational and Experimental Evaluation of the Immune Response of Neoantigens for Personalized Vaccine Design. Int J Mol Sci 2023; 24:ijms24109024. [PMID: 37240369 DOI: 10.3390/ijms24109024] [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: 04/04/2023] [Revised: 05/16/2023] [Accepted: 05/17/2023] [Indexed: 05/28/2023] Open
Abstract
In the last few years, the importance of neoantigens in the development of personalized antitumor vaccines has increased remarkably. In order to study whether bioinformatic tools are effective in detecting neoantigens that generate an immune response, DNA samples from patients with cutaneous melanoma in different stages were obtained, resulting in a total of 6048 potential neoantigens gathered. Thereafter, the immunological responses generated by some of those neoantigens ex vivo were tested, using a vaccine designed by a new optimization approach and encapsulated in nanoparticles. Our bioinformatic analysis indicated that no differences were found between the number of neoantigens and that of non-mutated sequences detected as potential binders by IEDB tools. However, those tools were able to highlight neoantigens over non-mutated peptides in HLA-II recognition (p-value 0.03). However, neither HLA-I binding affinity (p-value 0.08) nor Class I immunogenicity values (p-value 0.96) indicated significant differences for the latter parameters. Subsequently, the new vaccine, using aggregative functions and combinatorial optimization, was designed. The six best neoantigens were selected and formulated into two nanoparticles, with which the immune response ex vivo was evaluated, demonstrating a specific activation of the immune response. This study reinforces the use of bioinformatic tools in vaccine development, as their usefulness is proven both in silico and ex vivo.
Collapse
Affiliation(s)
- Iker Malaina
- Department of Mathematics, Faculty of Science and Technology, University of the Basque Country (UPV/EHU), 48940 Leioa, Spain
| | - Lorena Gonzalez-Melero
- NanoBioCel Research Group, Laboratory of Pharmaceutics, School of Pharmacy, University of the Basque Country (UPV/EHU), 01006 Vitoria-Gasteiz, Spain
- Bioaraba, NanoBioCel Research Group, 01009 Vitoria-Gasteiz, Spain
| | - Luis Martínez
- Department of Mathematics, Faculty of Science and Technology, University of the Basque Country (UPV/EHU), 48940 Leioa, Spain
- Luis Martínez, Basque Center for Applied Mathematics BCAM, 48009 Bilbao, Spain
| | - Aiala Salvador
- NanoBioCel Research Group, Laboratory of Pharmaceutics, School of Pharmacy, University of the Basque Country (UPV/EHU), 01006 Vitoria-Gasteiz, Spain
- Bioaraba, NanoBioCel Research Group, 01009 Vitoria-Gasteiz, Spain
- Biomedical Research Networking Centre in Bioengineering, Biomaterials and Nanomedicine (CIBER-BBN). Institute of Health Carlos III, 28029 Madrid, Spain
| | - Ana Sanchez-Diez
- Department of Dermatology, Basurto University Hospital, 48013 Bilbao, Spain
- Biocruces Bizkaia Health Research Institute, 48903 Barakaldo, Spain
| | - Aintzane Asumendi
- Biocruces Bizkaia Health Research Institute, 48903 Barakaldo, Spain
- Department of Cell Biology and Histology, Faculty of Medicine and Nursing, University of the Basque Country (UPV/EHU), 48940 Leioa, Spain
| | - Javier Margareto
- Technological Services Division, Health and Quality of Life, TECNALIA, 01510 Miñano, Spain
| | - Jose Carrasco-Pujante
- Department of Mathematics, Faculty of Science and Technology, University of the Basque Country (UPV/EHU), 48940 Leioa, Spain
- Luis Martínez, Basque Center for Applied Mathematics BCAM, 48009 Bilbao, Spain
| | - Leire Legarreta
- Department of Mathematics, Faculty of Science and Technology, University of the Basque Country (UPV/EHU), 48940 Leioa, Spain
- Luis Martínez, Basque Center for Applied Mathematics BCAM, 48009 Bilbao, Spain
| | - María Asunción García
- Department of Mathematics, Faculty of Science and Technology, University of the Basque Country (UPV/EHU), 48940 Leioa, Spain
- Luis Martínez, Basque Center for Applied Mathematics BCAM, 48009 Bilbao, Spain
| | - Martín Blas Pérez-Pinilla
- Department of Mathematics, Faculty of Science and Technology, University of the Basque Country (UPV/EHU), 48940 Leioa, Spain
- Luis Martínez, Basque Center for Applied Mathematics BCAM, 48009 Bilbao, Spain
| | - Rosa Izu
- Department of Dermatology, Basurto University Hospital, 48013 Bilbao, Spain
- Biocruces Bizkaia Health Research Institute, 48903 Barakaldo, Spain
| | - Ildefonso Martínez de la Fuente
- Department of Mathematics, Faculty of Science and Technology, University of the Basque Country (UPV/EHU), 48940 Leioa, Spain
- Luis Martínez, Basque Center for Applied Mathematics BCAM, 48009 Bilbao, Spain
- CEBAS-CSIC Institute, Department of Nutrition, 30100 Murcia, Spain
| | - Manoli Igartua
- NanoBioCel Research Group, Laboratory of Pharmaceutics, School of Pharmacy, University of the Basque Country (UPV/EHU), 01006 Vitoria-Gasteiz, Spain
- Bioaraba, NanoBioCel Research Group, 01009 Vitoria-Gasteiz, Spain
- Biomedical Research Networking Centre in Bioengineering, Biomaterials and Nanomedicine (CIBER-BBN). Institute of Health Carlos III, 28029 Madrid, Spain
| | - Santos Alonso
- Department of Genetics, Physical Anthropology and Animal Physiology, Faculty of Science and Technology, University of the Basque Country (UPV/EHU), 48940 Leioa, Spain
| | - Rosa Maria Hernandez
- NanoBioCel Research Group, Laboratory of Pharmaceutics, School of Pharmacy, University of the Basque Country (UPV/EHU), 01006 Vitoria-Gasteiz, Spain
- Bioaraba, NanoBioCel Research Group, 01009 Vitoria-Gasteiz, Spain
- Biomedical Research Networking Centre in Bioengineering, Biomaterials and Nanomedicine (CIBER-BBN). Institute of Health Carlos III, 28029 Madrid, Spain
| | - María Dolores Boyano
- Biocruces Bizkaia Health Research Institute, 48903 Barakaldo, Spain
- Department of Cell Biology and Histology, Faculty of Medicine and Nursing, University of the Basque Country (UPV/EHU), 48940 Leioa, Spain
| |
Collapse
|
6
|
Lu J, Meng M, Zhou X, Ding S, Feng K, Zeng Z, Huang T, Cai YD. Identification of COVID-19 severity biomarkers based on feature selection on single-cell RNA-Seq data of CD8 + T cells. Front Genet 2022; 13:1053772. [PMID: 36437952 PMCID: PMC9682094 DOI: 10.3389/fgene.2022.1053772] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Accepted: 10/27/2022] [Indexed: 07/30/2023] Open
Abstract
The global outbreak of the COVID-19 epidemic has become a major public health problem. COVID-19 virus infection triggers a complex immune response. CD8+ T cells, in particular, play an essential role in controlling the severity of the disease. However, the mechanism of the regulatory role of CD8+ T cells on COVID-19 remains poorly investigated. In this study, single-cell gene expression profiles from three CD8+ T cell subtypes (effector, memory, and naive T cells) were downloaded. Each cell subtype included three disease states, namely, acute COVID-19, convalescent COVID-19, and unexposed individuals. The profiles on each cell subtype were individually analyzed in the same way. Irrelevant features in the profiles were first excluded by the Boruta method. The remaining features for each CD8+ T cells subtype were further analyzed by Max-Relevance and Min-Redundancy, Monte Carlo feature selection, and light gradient boosting machine methods to obtain three feature lists. These lists were then brought into the incremental feature selection method to determine the optimal features for each cell subtype. Their corresponding genes may be latent biomarkers to determine COVID-19 severity. Genes, such as ZFP36, DUSP1, TCR, and IL7R, can be confirmed to play an immune regulatory role in COVID-19 infection and recovery. The results of functional enrichment analysis revealed that these important genes may be associated with immune functions, such as response to cAMP, response to virus, T cell receptor complex, T cell activation, and T cell differentiation. This study further set up different gene expression pattens, represented by classification rules, on three states of COVID-19 and constructed several efficient classifiers to distinguish COVID-19 severity. The findings of this study provided new insights into the biological processes of CD8+ T cells in regulating the immune response.
Collapse
Affiliation(s)
- Jian Lu
- Department of Mathematics, School of Sciences, Shanghai University, Shanghai, China
- CAS Key Laboratory of Computational Biology, Bio-Med Big Data Center, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Science, Shanghai, China
| | - Mei Meng
- State Key Laboratory of Oncogenes and Related Genes, Center for Single-Cell Omics, School of Public Health, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - XianChao Zhou
- State Key Laboratory of Oncogenes and Related Genes, Center for Single-Cell Omics, School of Public Health, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Shijian Ding
- School of Life Sciences, Shanghai University, Shanghai, China
| | - KaiYan Feng
- Department of Computer Science, Guangdong AIB Polytechnic College, Guangzhou, China
| | - Zhenbing Zeng
- Department of Mathematics, School of Sciences, Shanghai University, Shanghai, China
| | - Tao Huang
- CAS Key Laboratory of Computational Biology, Bio-Med Big Data Center, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Science, Shanghai, China
- CAS Key Laboratory of Tissue Microenvironment and Tumor, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Yu-Dong Cai
- School of Life Sciences, Shanghai University, Shanghai, China
| |
Collapse
|
7
|
LaVergne SM, Sakabe S, Momoh M, Kanneh L, Bond N, Garry RF, Grant DS, de la Torre JC, Oldstone MBA, Schieffelin JS, Sullivan BM. Expansion of CD8+ T cell population in Lassa virus survivors with low T cell precursor frequency reveals durable immune response in most survivors. PLoS Negl Trop Dis 2022; 16:e0010882. [PMID: 36441765 PMCID: PMC9731491 DOI: 10.1371/journal.pntd.0010882] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Revised: 12/08/2022] [Accepted: 10/11/2022] [Indexed: 11/29/2022] Open
Abstract
INTRODUCTION Lassa virus is a priority pathogen for vaccine research and development, however the duration of cellular immunity and protection in Lassa fever (LF) survivors remains unclear. METHODS We investigated Lassa virus specific CD8+ T cell responses in 93 LF survivors. Peripheral blood mononuclear cells from these individuals were infected with recombinant vesicular stomatitis virus encoding Lassa virus antigens and virus specific T cell responses were measured after 18-hour incubation. Participants who had undetectable CD8+ T cell response underwent further analysis using a 10-day T cell proliferation assays to evaluate for low T cell precursor frequency. RESULTS Forty-five of the 93 LF survivors did not have a Lassa virus specific CD8+ T cell response. Of those with responses and a known date of onset of LF (N = 11), 9 had LF within the last ten years. Most participants without a measurable CD8+ T cell response were more than 10 years removed from a clinical history of LF (N = 14/16). Fourteen of 21 patients (67%) with undetectable CD8+ T cell response had a measurable Lassa virus specific CD8+ T cell response with the 10-day assay. DISCUSSION Despite reports of strong CD8+ T cell responses during acute Lassa virus infection, circulating Lassa virus-specific CD8+ T cells declined to undetectable levels in most Lassa fever survivors after ten years when evaluated with an 18-hour T cell stimulation. However, when Lassa virus-specific T cells were expanded prior to restimulation, a Lassa virus-specific CD8+ T cell response could be detected in many if the samples that were negative in the 18-hour stimulation assay, suggesting that prolonged cellular immunity does exist in Lassa fever survivors at low frequencies.
Collapse
Affiliation(s)
- Stephanie M. LaVergne
- Viral-Immunobiology Laboratory, Department of Immunology and Microbiology, Scripps Research, San Diego, California, United States of America
- Division of Infectious Diseases, University of California, San Diego, California, United States of America
| | - Saori Sakabe
- Viral-Immunobiology Laboratory, Department of Immunology and Microbiology, Scripps Research, San Diego, California, United States of America
| | - Mambu Momoh
- Viral Hemorrhagic Fever Program, Kenema Government Hospital, Kenema, Sierra Leone
- Ministry of Health and Sanitation, Freetown, Sierra Leone
- Eastern Technical University of Sierra Leone, Kenema, Sierra Leone
| | - Lansana Kanneh
- Viral Hemorrhagic Fever Program, Kenema Government Hospital, Kenema, Sierra Leone
- Ministry of Health and Sanitation, Freetown, Sierra Leone
| | - Nell Bond
- Department of Immunology and Microbiology, Tulane University School of Medicine, New Orleans, Louisiana, United States of America
| | - Robert F. Garry
- Department of Immunology and Microbiology, Tulane University School of Medicine, New Orleans, Louisiana, United States of America
| | - Donald S. Grant
- Viral Hemorrhagic Fever Program, Kenema Government Hospital, Kenema, Sierra Leone
- Ministry of Health and Sanitation, Freetown, Sierra Leone
- College of Medicine and Allied Health Sciences, University of Sierra Leone, Freetown, Sierra Leone
| | - Juan Carlos de la Torre
- Viral-Immunobiology Laboratory, Department of Immunology and Microbiology, Scripps Research, San Diego, California, United States of America
| | - Michael B. A. Oldstone
- Viral-Immunobiology Laboratory, Department of Immunology and Microbiology, Scripps Research, San Diego, California, United States of America
| | - John S. Schieffelin
- Department of Pediatrics, Tulane University School of Medicine, New Orleans, Louisiana, United States of America
| | - Brian M. Sullivan
- Viral-Immunobiology Laboratory, Department of Immunology and Microbiology, Scripps Research, San Diego, California, United States of America
- La Jolla Institute for Immunology, San Diego, California, United States of America
| |
Collapse
|
8
|
Epitope-based minigene vaccine targeting fibroblast activation protein α induces specific immune responses and anti-tumor effects in 4 T1 murine breast cancer model. Int Immunopharmacol 2022; 112:109237. [PMID: 36152535 DOI: 10.1016/j.intimp.2022.109237] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Revised: 08/31/2022] [Accepted: 09/05/2022] [Indexed: 11/21/2022]
Abstract
Fibroblast activation protein (FAPα) is a tumor stromal antigen expressed by cancer-associated fibroblasts (CAFs) in more than 90 % of malignant epithelial carcinomas. FAPα-based immunotherapy has been reported and showed that FAPα-specific immune response can remold immune microenvironment and contribute to tumor regression. Many FAPα-based vaccines have been investigated in preclinical trials, which can elicit strong and durable cytolytic T lymphocytes (CTL) with good safety. However, epitope-based FAPα vaccines are rarely reported. To break tolerance against self-antigens, analogue epitopes with modified peptides at the anchor residues are typically used to improve epitope immunogenicity. To investigate the feasibility of a FAPα epitope-based vaccine for cancer immunotherapy in vivo, we conducted a preclinical study to identify a homologous CTL epitope of human and mouse FAPα and obtained its analogue epitope in BALB/c mice, and explored the anti-tumor activity of their minigene vaccines in 4 T1 tumor-bearing mice. By using in silico epitope prediction tools and immunogenicity assays, immunodominant epitope FAP.291 (YYFSWLTWV) and its analogue epitope FAP.291I9 (YYFSWLTWI) were identified. The FAP.291-based epitope minigene vaccine successfully stimulated CTLs targeting CAFs and exhibited anti-tumor activity in a 4 T1 murine breast cancer model. Furthermore, although the analogue epitope FAP.291I9 enhanced FAP.291-specific immune responses, improvement of anti-tumor immunity effects was not observed. Check of immunosuppressive factors revealed that the high levels of IL-10, IL-13, myeloid-derived suppressor cells and iNOS induced by FAP.291I9 increased, which considered the main cause of the failure of the analogue epitope-based vaccine. Thus, we demonstrated for the first time that the FAP.291 minigene vaccine could induce mouse CTLs and also function as a tumor regression antigen, providing the basis for future studies of FAPα epitope-based vaccines. This study may also be valuable for further improvement of the immunogenicity of analogue epitope vaccines.
Collapse
|
9
|
Araújo LPD, Dias MEC, Scodeler GC, Santos ADS, Soares LM, Corsetti PP, Padovan ACB, Silveira NJDF, de Almeida LA. Epitope identification of SARS-CoV-2 structural proteins using in silico approaches to obtain a conserved rational immunogenic peptide. IMMUNOINFORMATICS 2022; 7:100015. [PMID: 35721890 PMCID: PMC9188263 DOI: 10.1016/j.immuno.2022.100015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/23/2021] [Revised: 04/08/2022] [Accepted: 06/10/2022] [Indexed: 10/29/2022]
|
10
|
Bánki Z, Mateus J, Rössler A, Schäfer H, Bante D, Riepler L, Grifoni A, Sette A, Simon V, Falkensammer B, Ulmer H, Neurauter B, Borena W, Krammer F, von Laer D, Weiskopf D, Kimpel J. Heterologous ChAdOx1/BNT162b2 vaccination induces stronger immune response than homologous ChAdOx1 vaccination: The pragmatic, multi-center, three-arm, partially randomized HEVACC trial. EBioMedicine 2022; 80:104073. [PMID: 35617826 PMCID: PMC9126042 DOI: 10.1016/j.ebiom.2022.104073] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Revised: 04/27/2022] [Accepted: 05/06/2022] [Indexed: 12/30/2022] Open
Abstract
BACKGROUND Several COVID-19 vaccines have been approved. The mRNA vaccine from Pfizer/BioNTech (Comirnaty, BNT162b2; BNT) and the vector vaccine from AstraZeneca (Vaxzevria, ChAdOx1; AZ) have been widely used. mRNA vaccines induce high antibody and T cell responses, also to SARS-CoV-2 variants, but are costlier and less stable than the slightly less effective vector vaccines. For vector vaccines, heterologous vaccination schedules have generally proven more effective than homologous schedules. METHODS In the HEVACC three-arm, single-blinded, adaptive design study (ClinicalTrials.gov Identifier: NCT04907331), participants between 18 and 65 years with no prior history of SARS-CoV-2 infection and a first dose of AZ or BNT were included. The AZ/AZ and the AZ/BNT arms were randomized (in a 1:1 ratio stratified by sex and trial site) and single-blinded, the third arm (BNT/BNT) was observational. We compared the reactogenicity between the study arms and hypothesized that immunogenicity was higher for the heterologous AZ/BNT compared to the homologous AZ/AZ regimen using neutralizing antibody titers as primary endpoint. FINDINGS This interim analysis was conducted after 234 participants had been randomized and 254 immunized (N=109 AZ/AZ, N=115 AZ/BNZ, N=30 BNT/BNT). Heterologous AZ/BNT vaccination was well tolerated without study-related severe adverse events. Neutralizing antibody titers on day 30 were statistically significant higher in the AZ/BNT and the BNT/BNT groups than in the AZ/AZ group, for B.1.617.2 (Delta) AZ/AZ median reciprocal titer 75.9 (99.9% CI 58.0 - 132.5), AZ/BNT 571.5 (99.9% CI 396.6 - 733.1), and BNT/BNT 404.5 (99.9% CI 68.3 - 1024). Similarly, the frequency and multifunctionality of spike-specific T cell responses was comparable between the AZ/BNT and the BNT/BNT groups, but lower in the AZ/AZ vaccinees. INTERPRETATION This study clearly shows the immunogenicity and safety of heterologous AZ/BNT vaccination and encourages further studies on heterologous vaccination schedules. FUNDING This work was supported by the Medical University of Innsbruck, and partially funded by NIAID contracts No. 75N9301900065, 75N93021C00016, and 75N93019C00051.
Collapse
Affiliation(s)
- Zoltán Bánki
- Institute of Virology, Department of Hygiene, Microbiology and Public Health, Medical University of Innsbruck, Peter-Mayr-Str. 4b, 6020 Innsbruck, Austria
| | - Jose Mateus
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology (LJI), La Jolla, CA 92037, USA
| | - Annika Rössler
- Institute of Virology, Department of Hygiene, Microbiology and Public Health, Medical University of Innsbruck, Peter-Mayr-Str. 4b, 6020 Innsbruck, Austria
| | - Helena Schäfer
- Institute of Virology, Department of Hygiene, Microbiology and Public Health, Medical University of Innsbruck, Peter-Mayr-Str. 4b, 6020 Innsbruck, Austria
| | - David Bante
- Institute of Virology, Department of Hygiene, Microbiology and Public Health, Medical University of Innsbruck, Peter-Mayr-Str. 4b, 6020 Innsbruck, Austria
| | - Lydia Riepler
- Institute of Virology, Department of Hygiene, Microbiology and Public Health, Medical University of Innsbruck, Peter-Mayr-Str. 4b, 6020 Innsbruck, Austria
| | - Alba Grifoni
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology (LJI), La Jolla, CA 92037, USA
| | - Alessandro Sette
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology (LJI), La Jolla, CA 92037, USA; Department of Medicine, Division of Infectious Diseases and Global Public Health, University of California, San Diego (UCSD), La Jolla, CA 92037, USA
| | - Viviana Simon
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Pathology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Division of Infectious Diseases, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; The Global Health and Emerging Pathogen Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Barbara Falkensammer
- Institute of Virology, Department of Hygiene, Microbiology and Public Health, Medical University of Innsbruck, Peter-Mayr-Str. 4b, 6020 Innsbruck, Austria
| | - Hanno Ulmer
- Department of Medical Statistics, Informatics and Health Economics, Medical University of Innsbruck, Austria
| | - Bianca Neurauter
- Institute of Virology, Department of Hygiene, Microbiology and Public Health, Medical University of Innsbruck, Peter-Mayr-Str. 4b, 6020 Innsbruck, Austria
| | - Wegene Borena
- Institute of Virology, Department of Hygiene, Microbiology and Public Health, Medical University of Innsbruck, Peter-Mayr-Str. 4b, 6020 Innsbruck, Austria
| | - Florian Krammer
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Pathology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.
| | - Dorothee von Laer
- Institute of Virology, Department of Hygiene, Microbiology and Public Health, Medical University of Innsbruck, Peter-Mayr-Str. 4b, 6020 Innsbruck, Austria.
| | - Daniela Weiskopf
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology (LJI), La Jolla, CA 92037, USA.
| | - Janine Kimpel
- Institute of Virology, Department of Hygiene, Microbiology and Public Health, Medical University of Innsbruck, Peter-Mayr-Str. 4b, 6020 Innsbruck, Austria.
| |
Collapse
|
11
|
Sana M, Javed A, Babar Jamal S, Junaid M, Faheem M. Development of multivalent vaccine targeting M segment of Crimean Congo Hemorrhagic Fever Virus (CCHFV) using immunoinformatic approaches. Saudi J Biol Sci 2022; 29:2372-2388. [PMID: 35531180 PMCID: PMC9072894 DOI: 10.1016/j.sjbs.2021.12.004] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Revised: 11/25/2021] [Accepted: 12/04/2021] [Indexed: 01/23/2023] Open
Abstract
Crimean-Congo Hemorrhagic Fever (CCHF) is a tick-borne viral infection with no licensed vaccine or therapeutics available for its treatment. In the present study we have developed the first multi-epitope subunit vaccine effective against all the seven genotypes of CCHF virus (CCHFV). The vaccine contains five B-cell, two MHC-II (HTL), and three MHC-I (CTL) epitopes screened from two structural glycoproteins (Gc and Gn in M segment) of CCHFV with an N-terminus human β-defensin as an adjuvant, as well as an N-terminus EAAAK sequence. The epitopes were rigorously investigated for their antigenicity, allergenicity, IFN gamma induction, anti-inflammatory responses, stability, and toxicity. The three-dimensional structure of the vaccine was predicted and docked with TLR-3, TLR-8, and TLR-9 receptors to find the strength of the binding complexes via molecular dynamics simulation. After codon adaptation, the subunit vaccine construct was developed in a pDual-GC plasmid and has population coverage of 98.47% of the world's population (HLA-I & II combined). The immune simulation studies were carried out on the C-ImmSim in-silico interface showing a marked increase in the production of cellular and humoral response (B-cell and T-cell) as well as TGFβ, IL-2, IL-10, and IL-12 indicating that the proposed vaccine would be able to sufficiently provoke both humoral and cell-mediated immune responses. Thus, making it a new and promising vaccine candidate against CCHFV.
Collapse
Affiliation(s)
- Maaza Sana
- Atta-ur-Rahman School of Applied Biosciences, National University of Science and Technology, Sector H-12, Islamabad, Pakistan
| | - Aneela Javed
- Atta-ur-Rahman School of Applied Biosciences, National University of Science and Technology, Sector H-12, Islamabad, Pakistan
| | - Syed Babar Jamal
- Deparment of Biological Sciences, National University of Medical Sciences, Abid Majeed Rd, Rawalpindi, Punjab 46000, Pakistan
| | - Muhammad Junaid
- Precision Medicine Laboratory, Rehman Medical Institute, Hayatabad, Peshawar, KPK, 25000, Pakistan
| | - Muhammad Faheem
- Deparment of Biological Sciences, National University of Medical Sciences, Abid Majeed Rd, Rawalpindi, Punjab 46000, Pakistan
| |
Collapse
|
12
|
Moore MJ, Zhong M, Hansen J, Gartner H, Grant C, Huang M, Harris FM, Tu N, Bowerman NA, Edelmann KH, Barry T, Herbin O, Tay CS, DiLillo DJ, Decker CE, Levenkova N, Shevchuk J, Dhanik A, Meagher KA, Karr A, Roos J, Lee WY, Suh D, Eckersdorff M, Meagher TC, Koss M, Esau L, Sleeman MA, Babb R, Chen G, Kyratsous CA, Poueymirou WT, McWhirter JR, Voronina VA, Guo C, Gurer C, Yancopoulos GD, Murphy AJ, Macdonald LE. Humanization of T cell-mediated immunity in mice. Sci Immunol 2021; 6:eabj4026. [PMID: 34919442 DOI: 10.1126/sciimmunol.abj4026] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
[Figure: see text].
Collapse
Affiliation(s)
- Michael J Moore
- Regeneron Pharmaceuticals, 777 Old Saw Mill River Rd, Tarrytown, NY 10591, USA
| | - Maggie Zhong
- Regeneron Pharmaceuticals, 777 Old Saw Mill River Rd, Tarrytown, NY 10591, USA
| | - Johanna Hansen
- Regeneron Pharmaceuticals, 777 Old Saw Mill River Rd, Tarrytown, NY 10591, USA
| | - Hans Gartner
- Regeneron Pharmaceuticals, 777 Old Saw Mill River Rd, Tarrytown, NY 10591, USA
| | - Craig Grant
- Regeneron Pharmaceuticals, 777 Old Saw Mill River Rd, Tarrytown, NY 10591, USA
| | - Mei Huang
- Regeneron Pharmaceuticals, 777 Old Saw Mill River Rd, Tarrytown, NY 10591, USA
| | - Faith M Harris
- Regeneron Pharmaceuticals, 777 Old Saw Mill River Rd, Tarrytown, NY 10591, USA
| | - Naxin Tu
- Regeneron Pharmaceuticals, 777 Old Saw Mill River Rd, Tarrytown, NY 10591, USA
| | - Natalie A Bowerman
- Regeneron Pharmaceuticals, 777 Old Saw Mill River Rd, Tarrytown, NY 10591, USA
| | - Kurt H Edelmann
- Regeneron Pharmaceuticals, 777 Old Saw Mill River Rd, Tarrytown, NY 10591, USA
| | - Thomas Barry
- Regeneron Pharmaceuticals, 777 Old Saw Mill River Rd, Tarrytown, NY 10591, USA
| | - Olivier Herbin
- Regeneron Pharmaceuticals, 777 Old Saw Mill River Rd, Tarrytown, NY 10591, USA
| | - Chin-Siean Tay
- Regeneron Pharmaceuticals, 777 Old Saw Mill River Rd, Tarrytown, NY 10591, USA
| | - David J DiLillo
- Regeneron Pharmaceuticals, 777 Old Saw Mill River Rd, Tarrytown, NY 10591, USA
| | - Corinne E Decker
- Regeneron Pharmaceuticals, 777 Old Saw Mill River Rd, Tarrytown, NY 10591, USA
| | - Natasha Levenkova
- Regeneron Pharmaceuticals, 777 Old Saw Mill River Rd, Tarrytown, NY 10591, USA
| | - James Shevchuk
- Regeneron Pharmaceuticals, 777 Old Saw Mill River Rd, Tarrytown, NY 10591, USA
| | - Ankur Dhanik
- Regeneron Pharmaceuticals, 777 Old Saw Mill River Rd, Tarrytown, NY 10591, USA
| | - Karoline A Meagher
- Regeneron Pharmaceuticals, 777 Old Saw Mill River Rd, Tarrytown, NY 10591, USA
| | - Amanda Karr
- Regeneron Pharmaceuticals, 777 Old Saw Mill River Rd, Tarrytown, NY 10591, USA
| | - Jan Roos
- Regeneron Pharmaceuticals, 777 Old Saw Mill River Rd, Tarrytown, NY 10591, USA
| | - Wen-Yi Lee
- Regeneron Pharmaceuticals, 777 Old Saw Mill River Rd, Tarrytown, NY 10591, USA
| | - David Suh
- Regeneron Pharmaceuticals, 777 Old Saw Mill River Rd, Tarrytown, NY 10591, USA
| | - Mark Eckersdorff
- Regeneron Pharmaceuticals, 777 Old Saw Mill River Rd, Tarrytown, NY 10591, USA
| | - T Craig Meagher
- Regeneron Pharmaceuticals, 777 Old Saw Mill River Rd, Tarrytown, NY 10591, USA
| | - Matthew Koss
- Regeneron Pharmaceuticals, 777 Old Saw Mill River Rd, Tarrytown, NY 10591, USA
| | - Lakeisha Esau
- Regeneron Pharmaceuticals, 777 Old Saw Mill River Rd, Tarrytown, NY 10591, USA
| | - Matthew A Sleeman
- Regeneron Pharmaceuticals, 777 Old Saw Mill River Rd, Tarrytown, NY 10591, USA
| | - Robert Babb
- Regeneron Pharmaceuticals, 777 Old Saw Mill River Rd, Tarrytown, NY 10591, USA
| | - Gang Chen
- Regeneron Pharmaceuticals, 777 Old Saw Mill River Rd, Tarrytown, NY 10591, USA
| | | | | | - John R McWhirter
- Regeneron Pharmaceuticals, 777 Old Saw Mill River Rd, Tarrytown, NY 10591, USA
| | - Vera A Voronina
- Regeneron Pharmaceuticals, 777 Old Saw Mill River Rd, Tarrytown, NY 10591, USA
| | - Chunguang Guo
- Regeneron Pharmaceuticals, 777 Old Saw Mill River Rd, Tarrytown, NY 10591, USA
| | - Cagan Gurer
- Regeneron Pharmaceuticals, 777 Old Saw Mill River Rd, Tarrytown, NY 10591, USA
| | | | - Andrew J Murphy
- Regeneron Pharmaceuticals, 777 Old Saw Mill River Rd, Tarrytown, NY 10591, USA
| | - Lynn E Macdonald
- Regeneron Pharmaceuticals, 777 Old Saw Mill River Rd, Tarrytown, NY 10591, USA
| |
Collapse
|
13
|
Novel Antigenic Targets of HPV Therapeutic Vaccines. Vaccines (Basel) 2021; 9:vaccines9111262. [PMID: 34835193 PMCID: PMC8621534 DOI: 10.3390/vaccines9111262] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2021] [Revised: 10/25/2021] [Accepted: 10/29/2021] [Indexed: 01/01/2023] Open
Abstract
Human papillomavirus (HPV) infection is the cause of the majority of cervical cancers and head and neck cancers worldwide. Although prophylactic vaccines and cervical cancer screening programs have shown efficacy in preventing HPV-associated cervical cancer, cervical cancer is still a major cause of morbidity and mortality, especially in third world countries. Furthermore, head and neck cancer cases caused by HPV infection and associated mortality are increasing. The need for better therapy is clear, and therapeutic vaccination generating cytotoxic T cells against HPV proteins is a promising strategy. This review covers the current scene of HPV therapeutic vaccines in clinical development and discusses relevant considerations for the design of future HPV therapeutic vaccines and clinical trials, such as HPV protein expression patterns, immunogenicity, and exhaustion in relation to the different stages and types of HPV-associated lesions and cancers. Ultimately, while the majority of the HPV therapeutic vaccines currently in clinical testing target the two HPV oncoproteins E6 and E7, we suggest that there is a need to include more HPV antigens in future HPV therapeutic vaccines to increase efficacy and find that especially E1 and E2 could be promising novel targets.
Collapse
|
14
|
Mateus J, Dan JM, Zhang Z, Rydyznski Moderbacher C, Lammers M, Goodwin B, Sette A, Crotty S, Weiskopf D. Low-dose mRNA-1273 COVID-19 vaccine generates durable memory enhanced by cross-reactive T cells. Science 2021; 374:eabj9853. [PMID: 34519540 PMCID: PMC8542617 DOI: 10.1126/science.abj9853] [Citation(s) in RCA: 204] [Impact Index Per Article: 68.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2021] [Accepted: 09/07/2021] [Indexed: 12/12/2022]
Abstract
Vaccine-specific CD4+ T cell, CD8+ T cell, binding antibody, and neutralizing antibody responses to the 25-μg Moderna messenger RNA (mRNA)–1273 vaccine were examined over the course of 7 months after immunization, including in multiple age groups, with a particular interest in assessing whether preexisting cross-reactive T cell memory affects vaccine-generated immunity. Vaccine-generated spike-specific memory CD4+ T cells 6 months after the second dose of the vaccine were comparable in quantity and quality to COVID-19 cases, including the presence of T follicular helper cells and interferon-γ–expressing cells. Spike-specific CD8+ T cells were generated in 88% of subjects, with equivalent memory at 6 months post-boost compared with COVID-19 cases. Lastly, subjects with preexisting cross-reactive CD4+ T cell memory exhibited stronger CD4+ T cell and antibody responses to the vaccine, demonstrating the biological relevance of severe acute respiratory syndrome coronavirus 2–cross-reactive CD4+ T cells.
Collapse
Affiliation(s)
- Jose Mateus
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology (LJI), La Jolla, CA 92037, USA
| | - Jennifer M. Dan
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology (LJI), La Jolla, CA 92037, USA
- Department of Medicine, Division of Infectious Diseases and Global Public Health, University of California, San Diego (UCSD), La Jolla, CA 92037, USA
| | - Zeli Zhang
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology (LJI), La Jolla, CA 92037, USA
| | - Carolyn Rydyznski Moderbacher
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology (LJI), La Jolla, CA 92037, USA
| | - Marshall Lammers
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology (LJI), La Jolla, CA 92037, USA
| | - Benjamin Goodwin
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology (LJI), La Jolla, CA 92037, USA
| | - Alessandro Sette
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology (LJI), La Jolla, CA 92037, USA
- Department of Medicine, Division of Infectious Diseases and Global Public Health, University of California, San Diego (UCSD), La Jolla, CA 92037, USA
| | - Shane Crotty
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology (LJI), La Jolla, CA 92037, USA
- Department of Medicine, Division of Infectious Diseases and Global Public Health, University of California, San Diego (UCSD), La Jolla, CA 92037, USA
| | - Daniela Weiskopf
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology (LJI), La Jolla, CA 92037, USA
| |
Collapse
|
15
|
Wellington D, Yin Z, Kessler BM, Dong T. Immunodominance complexity: lessons yet to be learned from dominant T cell responses to SARS-COV-2. Curr Opin Virol 2021; 50:183-191. [PMID: 34534732 PMCID: PMC8424056 DOI: 10.1016/j.coviro.2021.08.009] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Revised: 08/27/2021] [Accepted: 08/31/2021] [Indexed: 11/14/2022]
Abstract
Immunodominance is a complex and highly debated topic of T cell biology. The current SARS-CoV-2 pandemic has provided the opportunity to profile adaptive immune responses and determine molecular factors contributing to emerging responses towards immunodominant viral epitopes. Here, we discuss parameters that alter the dynamics of CD8 viral epitope processing, generation and T-cell responses, and how immunodominance counteracts viral immune escape mechanisms that develop in the context of emerging SARS-CoV-2 variants.
Collapse
Affiliation(s)
- Dannielle Wellington
- MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, Oxford University, Oxford, OX3 9DS, UK; Chinese Academy of Medical Sciences (CAMS) Oxford Institute, Nuffield Department of Medicine, Oxford University, Oxford, OX3 7BN, UK.
| | - Zixi Yin
- MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, Oxford University, Oxford, OX3 9DS, UK; Chinese Academy of Medical Sciences (CAMS) Oxford Institute, Nuffield Department of Medicine, Oxford University, Oxford, OX3 7BN, UK
| | - Benedikt M Kessler
- MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, Oxford University, Oxford, OX3 9DS, UK; Target Discovery Institute, Nuffield Department of Medicine, Oxford University, Oxford, OX3 7BN, UK
| | - Tao Dong
- MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, Oxford University, Oxford, OX3 9DS, UK; Chinese Academy of Medical Sciences (CAMS) Oxford Institute, Nuffield Department of Medicine, Oxford University, Oxford, OX3 7BN, UK.
| |
Collapse
|
16
|
Teahan B, Ong E, Yang Z. Identification of Mycobacterium tuberculosis Antigens with Vaccine Potential Using a Machine Learning-Based Reverse Vaccinology Approach. Vaccines (Basel) 2021; 9:vaccines9101098. [PMID: 34696207 PMCID: PMC8538456 DOI: 10.3390/vaccines9101098] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2021] [Revised: 09/20/2021] [Accepted: 09/22/2021] [Indexed: 11/16/2022] Open
Abstract
Tuberculosis (TB) is the leading cause of death of any single infectious agent, having led to 1.4 million deaths in 2019 alone. Moreover, an estimated one-quarter of the global population is latently infected with Mycobacterium tuberculosis (MTB), presenting a huge pool of potential future disease. Nonetheless, the only currently licensed TB vaccine fails to prevent the activation of latent TB infections (LTBI). These facts together illustrate the desperate need for a more effective TB vaccine strategy that can prevent both primary infection and the activation of LTBI. In this study, we employed a machine learning-based reverse vaccinology approach to predict the likelihood that each protein within the proteome of MTB laboratory reference strain H37Rv would be a protective antigen (PAg). The proteins predicted most likely to be a PAg were assessed for their belonging to a protein family of previously established PAgs, the relevance of their biological processes to MTB virulence and latency, and finally the immunogenic potential that they may provide in terms of the number of promiscuous epitopes within each. This study led to the identification of 16 proteins with the greatest vaccine potential for further in vitro and in vivo studies. It also demonstrates the value of computational methods in vaccine development.
Collapse
Affiliation(s)
- Blaine Teahan
- Epidemiology Department, School of Public Health, University of Michigan, Ann Arbor, MI 48109, USA;
| | - Edison Ong
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA;
| | - Zhenhua Yang
- Epidemiology Department, School of Public Health, University of Michigan, Ann Arbor, MI 48109, USA;
- Correspondence:
| |
Collapse
|
17
|
Grifoni A, Sidney J, Vita R, Peters B, Crotty S, Weiskopf D, Sette A. SARS-CoV-2 human T cell epitopes: Adaptive immune response against COVID-19. Cell Host Microbe 2021; 29:1076-1092. [PMID: 34237248 PMCID: PMC8139264 DOI: 10.1016/j.chom.2021.05.010] [Citation(s) in RCA: 192] [Impact Index Per Article: 64.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2021] [Revised: 04/23/2021] [Accepted: 05/18/2021] [Indexed: 02/07/2023]
Abstract
Over the past year, numerous studies in the peer reviewed and preprint literature have reported on the virological, epidemiological and clinical characteristics of the coronavirus, SARS-CoV-2. To date, 25 studies have investigated and identified SARS-CoV-2-derived T cell epitopes in humans. Here, we review these recent studies, how they were performed, and their findings. We review how epitopes identified throughout the SARS-CoV2 proteome reveal significant correlation between number of epitopes defined and size of the antigen provenance. We also report additional analysis of SARS-CoV-2 human CD4 and CD8 T cell epitope data compiled from these studies, identifying 1,400 different reported SARS-CoV-2 epitopes and revealing discrete immunodominant regions of the virus and epitopes that are more prevalently recognized. This remarkable breadth of epitope repertoire has implications for vaccine design, cross-reactivity, and immune escape by SARS-CoV-2 variants.
Collapse
Affiliation(s)
- Alba Grifoni
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology (LJI), La Jolla, CA 92037, USA
| | - John Sidney
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology (LJI), La Jolla, CA 92037, USA
| | - Randi Vita
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology (LJI), La Jolla, CA 92037, USA
| | - Bjoern Peters
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology (LJI), La Jolla, CA 92037, USA; Department of Medicine, Division of Infectious Diseases and Global Public Health, University of California, San Diego (UCSD), La Jolla, CA 92037, USA
| | - Shane Crotty
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology (LJI), La Jolla, CA 92037, USA; Department of Medicine, Division of Infectious Diseases and Global Public Health, University of California, San Diego (UCSD), La Jolla, CA 92037, USA
| | - Daniela Weiskopf
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology (LJI), La Jolla, CA 92037, USA
| | - Alessandro Sette
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology (LJI), La Jolla, CA 92037, USA; Department of Medicine, Division of Infectious Diseases and Global Public Health, University of California, San Diego (UCSD), La Jolla, CA 92037, USA.
| |
Collapse
|
18
|
Smyth M, Khamina K, Popa A, Gudipati V, Agerer B, Lercher A, Kosack L, Endler L, Baazim H, Viczenczova C, Huppa JB, Bergthaler A. Characterization of CD8 T Cell-Mediated Mutations in the Immunodominant Epitope GP33-41 of Lymphocytic Choriomeningitis Virus. Front Immunol 2021; 12:638485. [PMID: 34194424 PMCID: PMC8236698 DOI: 10.3389/fimmu.2021.638485] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2020] [Accepted: 05/25/2021] [Indexed: 11/13/2022] Open
Abstract
Cytotoxic T lymphocytes (CTLs) represent key immune effectors of the host response against chronic viruses, due to their cytotoxic response to virus-infected cells. In response to this selection pressure, viruses may accumulate escape mutations that evade CTL-mediated control. To study the emergence of CTL escape mutations, we employed the murine chronic infection model of lymphocytic choriomeningitis virus (LCMV). We developed an amplicon-based next-generation sequencing pipeline to detect low frequency mutations in the viral genome and identified non-synonymous mutations in the immunodominant LCMV CTL epitope, GP33-41, in infected wildtype mice. Infected Rag2-deficient mice lacking CTLs did not contain such viral mutations. By using transgenic mice with T cell receptors specific to GP33-41, we characterized the emergence of viral mutations in this epitope under varying selection pressure. We investigated the two most abundant viral mutations by employing reverse genetically engineered viral mutants encoding the respective mutations. These experiments provided evidence that these mutations prevent activation and expansion of epitope-specific CD8 T cells. Our findings on the mutational dynamics of CTL escape mutations in a widely-studied viral infection model contributes to our understanding of how chronic viruses interact with their host and evade the immune response. This may guide the development of future treatments and vaccines against chronic infections.
Collapse
Affiliation(s)
- Mark Smyth
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Kseniya Khamina
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Alexandra Popa
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Venugopal Gudipati
- Center for Pathophysiology, Infectiology and Immunology, Institute for Hygiene and Applied Immunology, Medical University of Vienna, Vienna, Austria
| | - Benedikt Agerer
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Alexander Lercher
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Lindsay Kosack
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Lukas Endler
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Hatoon Baazim
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Csilla Viczenczova
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Johannes B Huppa
- Center for Pathophysiology, Infectiology and Immunology, Institute for Hygiene and Applied Immunology, Medical University of Vienna, Vienna, Austria
| | - Andreas Bergthaler
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| |
Collapse
|
19
|
Gilfillan CB, Hebeisen M, Rufer N, Speiser DE. Constant regulation for stable CD8 T-cell functional avidity and its possible implications for cancer immunotherapy. Eur J Immunol 2021; 51:1348-1360. [PMID: 33704770 PMCID: PMC8252569 DOI: 10.1002/eji.202049016] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2020] [Revised: 12/16/2020] [Accepted: 03/05/2021] [Indexed: 12/30/2022]
Abstract
The functional avidity (FA) of cytotoxic CD8 T cells impacts strongly on their functional capabilities and correlates with protection from infection and cancer. FA depends on TCR affinity, downstream signaling strength, and TCR affinity-independent parameters of the immune synapse, such as costimulatory and inhibitory receptors. The functional impact of coreceptors on FA remains to be fully elucidated. Despite its importance, FA is infrequently assessed and incompletely understood. There is currently no consensus as to whether FA can be enhanced by optimized vaccine dose or boosting schedule. Recent findings suggest that FA is remarkably stable in vivo, possibly due to continued signaling modulation of critical receptors in the immune synapse. In this review, we provide an overview of the current knowledge and hypothesize that in vivo, codominant T cells constantly "equalize" their FA for similar function. We present a new model of constant FA regulation, and discuss practical implications for T-cell-based cancer immunotherapy.
Collapse
Affiliation(s)
- Connie B. Gilfillan
- Department of OncologyUniversity Hospital and University of LausanneLausanneSwitzerland
| | - Michael Hebeisen
- Department of OncologyUniversity Hospital and University of LausanneLausanneSwitzerland
| | - Nathalie Rufer
- Department of OncologyUniversity Hospital and University of LausanneLausanneSwitzerland
| | - Daniel E. Speiser
- Department of OncologyUniversity Hospital and University of LausanneLausanneSwitzerland
| |
Collapse
|
20
|
Michelo CM, Dalel JA, Hayes P, Fernandez N, Fiore-Gartland A, Kilembe W, Tang J, Streatfield C, Gilmour J, Hunter E. Comprehensive epitope mapping using polyclonally expanded human CD8 T cells and a two-step ELISpot assay for testing large peptide libraries. J Immunol Methods 2021; 491:112970. [PMID: 33529681 PMCID: PMC8008507 DOI: 10.1016/j.jim.2021.112970] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2020] [Revised: 11/30/2020] [Accepted: 01/18/2021] [Indexed: 02/01/2023]
Abstract
The genetic diversity of circulating HIV-1 strains poses a major barrier to the design, development and evaluation of HIV-1 vaccines. The assessment of both vaccine- and natural infection-elicited T cell responses is commonly done with multivalent peptides that are designed to maximally capture the diversity of potential T cell epitopes (PTEs) observed in natural circulating sequences. However, depending on the sequence diversity of viral subtypes and number of the HIV immunogens under investigation, PTE estimates, including HLA-guided computational methods, can easily generate enormous peptide libraries. Evaluation of T cell epitope specificity using such extensive peptide libraries is usually limited by sample availability, even for high-throughput and robust epitope mapping techniques like ELISpot assays. Here we describe a novel, two-step protocol for in-vitro polyclonal expansion of CD8 T cells from a single vial of frozen PBMC, which facilitated the screening 441 HIV-1 Gag peptides for immune responses among 32 HIV-1 positive subjects and 40 HIV-1 negative subjects for peptide qualification. Using a pooled-peptide mapping strategy, epitopes were mapped in two sequential ELISpot assays; the first ELISpot screened 33 large peptide pools using CD8 T cells expanded for 7 days, while the second step tested pool-matrix peptides to identify individual peptides using CD8 T cells expanded for 10 days. This comprehensive epitope screening established the breadth and magnitude of HIV-1 Gag-specific CD8 T cells and further revealed the extent of immune responses to variable/polymorphic epitopes.
Collapse
Affiliation(s)
- Clive M Michelo
- Zambia Emory HIV Research Project, B22/737 Mwembelelo, Emmasdale, Lusaka, Zambia
| | - Jama A Dalel
- Human Immunology Laboratory, International AIDS Vaccine Initiative, Imperial College London, London, United Kingdom
| | - Peter Hayes
- Human Immunology Laboratory, International AIDS Vaccine Initiative, Imperial College London, London, United Kingdom
| | - Natalia Fernandez
- Human Immunology Laboratory, International AIDS Vaccine Initiative, Imperial College London, London, United Kingdom
| | - Andrew Fiore-Gartland
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109, USA
| | - William Kilembe
- Zambia Emory HIV Research Project, B22/737 Mwembelelo, Emmasdale, Lusaka, Zambia
| | - Jianming Tang
- Department of Medicine, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Claire Streatfield
- Human Immunology Laboratory, International AIDS Vaccine Initiative, Imperial College London, London, United Kingdom
| | - Jill Gilmour
- Human Immunology Laboratory, International AIDS Vaccine Initiative, Imperial College London, London, United Kingdom
| | - Eric Hunter
- Zambia Emory HIV Research Project, B22/737 Mwembelelo, Emmasdale, Lusaka, Zambia; Emory Vaccine Center, Yerkes National Primate Research Center, 954 Gatewood Road NE, Atlanta, GA 30329, USA.
| |
Collapse
|
21
|
Dan JM, Mateus J, Kato Y, Hastie KM, Yu ED, Faliti CE, Grifoni A, Ramirez SI, Haupt S, Frazier A, Nakao C, Rayaprolu V, Rawlings SA, Peters B, Krammer F, Simon V, Saphire EO, Smith DM, Weiskopf D, Sette A, Crotty S. Immunological memory to SARS-CoV-2 assessed for up to 8 months after infection. Science 2021; 371:eabf4063. [PMID: 33408181 PMCID: PMC7919858 DOI: 10.1126/science.abf4063] [Citation(s) in RCA: 1816] [Impact Index Per Article: 605.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2020] [Accepted: 12/23/2020] [Indexed: 12/11/2022]
Abstract
Understanding immune memory to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is critical for improving diagnostics and vaccines and for assessing the likely future course of the COVID-19 pandemic. We analyzed multiple compartments of circulating immune memory to SARS-CoV-2 in 254 samples from 188 COVID-19 cases, including 43 samples at ≥6 months after infection. Immunoglobulin G (IgG) to the spike protein was relatively stable over 6+ months. Spike-specific memory B cells were more abundant at 6 months than at 1 month after symptom onset. SARS-CoV-2-specific CD4+ T cells and CD8+ T cells declined with a half-life of 3 to 5 months. By studying antibody, memory B cell, CD4+ T cell, and CD8+ T cell memory to SARS-CoV-2 in an integrated manner, we observed that each component of SARS-CoV-2 immune memory exhibited distinct kinetics.
Collapse
Affiliation(s)
- Jennifer M Dan
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology (LJI), La Jolla, CA 92037, USA
- Department of Medicine, Division of Infectious Diseases and Global Public Health, University of California, San Diego (UCSD), La Jolla, CA 92037, USA
| | - Jose Mateus
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology (LJI), La Jolla, CA 92037, USA
| | - Yu Kato
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology (LJI), La Jolla, CA 92037, USA
| | - Kathryn M Hastie
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology (LJI), La Jolla, CA 92037, USA
| | - Esther Dawen Yu
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology (LJI), La Jolla, CA 92037, USA
| | - Caterina E Faliti
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology (LJI), La Jolla, CA 92037, USA
| | - Alba Grifoni
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology (LJI), La Jolla, CA 92037, USA
| | - Sydney I Ramirez
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology (LJI), La Jolla, CA 92037, USA
- Department of Medicine, Division of Infectious Diseases and Global Public Health, University of California, San Diego (UCSD), La Jolla, CA 92037, USA
| | - Sonya Haupt
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology (LJI), La Jolla, CA 92037, USA
| | - April Frazier
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology (LJI), La Jolla, CA 92037, USA
| | - Catherine Nakao
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology (LJI), La Jolla, CA 92037, USA
| | - Vamseedhar Rayaprolu
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology (LJI), La Jolla, CA 92037, USA
| | - Stephen A Rawlings
- Department of Medicine, Division of Infectious Diseases and Global Public Health, University of California, San Diego (UCSD), La Jolla, CA 92037, USA
| | - Bjoern Peters
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology (LJI), La Jolla, CA 92037, USA
- Department of Medicine, University of California, San Diego (UCSD), La Jolla, CA 92037, USA
| | - Florian Krammer
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Viviana Simon
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Division of Infectious Diseases, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- The Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Erica Ollmann Saphire
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology (LJI), La Jolla, CA 92037, USA
- Department of Medicine, Division of Infectious Diseases and Global Public Health, University of California, San Diego (UCSD), La Jolla, CA 92037, USA
| | - Davey M Smith
- Department of Medicine, Division of Infectious Diseases and Global Public Health, University of California, San Diego (UCSD), La Jolla, CA 92037, USA
| | - Daniela Weiskopf
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology (LJI), La Jolla, CA 92037, USA.
| | - Alessandro Sette
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology (LJI), La Jolla, CA 92037, USA.
- Department of Medicine, Division of Infectious Diseases and Global Public Health, University of California, San Diego (UCSD), La Jolla, CA 92037, USA
| | - Shane Crotty
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology (LJI), La Jolla, CA 92037, USA.
- Department of Medicine, Division of Infectious Diseases and Global Public Health, University of California, San Diego (UCSD), La Jolla, CA 92037, USA
| |
Collapse
|
22
|
Ghaffari AD, Dalimi A, Ghaffarifar F, Pirestani M, Majidiani H. Immunoinformatic analysis of immunogenic B- and T-cell epitopes of MIC4 protein to designing a vaccine candidate against Toxoplasma gondii through an in-silico approach. Clin Exp Vaccine Res 2021; 10:59-77. [PMID: 33628756 PMCID: PMC7892946 DOI: 10.7774/cevr.2021.10.1.59] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2020] [Accepted: 01/25/2021] [Indexed: 12/21/2022] Open
Abstract
Purpose Toxoplasmosis, transmitted by Toxoplasma gondii, is a worldwide parasitic disease that affects approximately one-third of the world's inhabitants. Today, there are no appropriate drugs to deter tissue cysts from developing in infected hosts. So, developing an effective vaccine would be valuable to avoid from toxoplasmosis. Considering the role of microneme antigens such as microneme protein 4 (MIC4) in T. gondii pathogenesis, it can be used as potential candidates for vaccine against T. gondii. Materials and Methods In this study several bioinformatics methods were used to assess the different aspects of MIC4 protein such as secondary and tertiary structure, physicochemical characteristics, the transmembrane domains, subcellular localization, B-cell, helper-T lymphocyte, cytotoxic-T lymphocyte epitopes, and other notable characteristic of this protein design a suitable vaccine against T. gondii. Results The studies revealed that MIC4 protein includes 59 potential post-translational modification sites without any transmembrane domains. Moreover, several probable epitopes of B- and T-cells were detected for MIC4. The secondary structure comprised 55.69% random coil, 5.86% beta-turn, 19.31% extended strand, and 19.14% alpha helix. According to the Ramachandran plot results, 87.42% of the amino acid residues were located in the favored, 9.44% in allowed, and 3.14% in outlier regions. The protein allergenicity and antigenicity revealed that it was non-allergenic and antigenic. Conclusion This study gives vital basic on MIC4 protein for further research and also established an effective vaccine with different techniques against acute and chronic toxoplasmosis.
Collapse
Affiliation(s)
- Ali Dalir Ghaffari
- Department of Parasitology, Faculty of Medical Sciences, Tarbiat Modares University, Tehran, Iran
| | - Abdolhossein Dalimi
- Department of Parasitology, Faculty of Medical Sciences, Tarbiat Modares University, Tehran, Iran
| | - Fatemeh Ghaffarifar
- Department of Parasitology, Faculty of Medical Sciences, Tarbiat Modares University, Tehran, Iran
| | - Majid Pirestani
- Department of Parasitology, Faculty of Medical Sciences, Tarbiat Modares University, Tehran, Iran
| | - Hamidreza Majidiani
- Department of Parasitology, Faculty of Medical Sciences, Tarbiat Modares University, Tehran, Iran
| |
Collapse
|
23
|
Computational Analysis of African Swine Fever Virus Protein Space for the Design of an Epitope-Based Vaccine Ensemble. Pathogens 2020; 9:pathogens9121078. [PMID: 33371523 PMCID: PMC7767518 DOI: 10.3390/pathogens9121078] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2020] [Revised: 12/12/2020] [Accepted: 12/18/2020] [Indexed: 12/11/2022] Open
Abstract
African swine fever virus is the etiological agent of African swine fever, a transmissible severe hemorrhagic disease that affects pigs, causing massive economic losses. There is neither a treatment nor a vaccine available, and the only method to control its spread is by extensive culling of pigs. So far, classical vaccine development approaches have not yielded sufficiently good results in terms of concomitant safety and efficacy. Nowadays, thanks to advances in genomic and proteomic techniques, a reverse vaccinology strategy can be explored to design alternative vaccine formulations. In this study, ASFV protein sequences were analyzed using an in-house pipeline based on publicly available immunoinformatic tools to identify epitopes of interest for a prospective vaccine ensemble. These included experimentally validated sequences from the Immune Epitope Database, as well as de novo predicted sequences. Experimentally validated and predicted epitopes were prioritized following a series of criteria that included evolutionary conservation, presence in the virulent and currently circulating variant Georgia 2007/1, and lack of identity to either the pig proteome or putative proteins from pig gut microbiota. Following this strategy, 29 B-cell, 14 CD4+ T-cell and 6 CD8+ T-cell epitopes were selected, which represent a starting point to investigating the protective capacity of ASFV epitope-based vaccines.
Collapse
|
24
|
Dan JM, Mateus J, Kato Y, Hastie KM, Yu ED, Faliti CE, Grifoni A, Ramirez SI, Haupt S, Frazier A, Nakao C, Rayaprolu V, Rawlings SA, Peters B, Krammer F, Simon V, Saphire EO, Smith DM, Weiskopf D, Sette A, Crotty S. Immunological memory to SARS-CoV-2 assessed for up to eight months after infection. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2020:2020.11.15.383323. [PMID: 33442687 PMCID: PMC7805444 DOI: 10.1101/2020.11.15.383323] [Citation(s) in RCA: 59] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Understanding immune memory to SARS-CoV-2 is critical for improving diagnostics and vaccines, and for assessing the likely future course of the COVID-19 pandemic. We analyzed multiple compartments of circulating immune memory to SARS-CoV-2 in 254 samples from 188 COVID-19 cases, including 43 samples at ≥ 6 months post-infection. IgG to the Spike protein was relatively stable over 6+ months. Spike-specific memory B cells were more abundant at 6 months than at 1 month post symptom onset. SARS-CoV-2-specific CD4 + T cells and CD8 + T cells declined with a half-life of 3-5 months. By studying antibody, memory B cell, CD4 + T cell, and CD8 + T cell memory to SARS-CoV-2 in an integrated manner, we observed that each component of SARS-CoV-2 immune memory exhibited distinct kinetics.
Collapse
Affiliation(s)
- Jennifer M. Dan
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology (LJI), La Jolla, CA 92037, USA
- Department of Medicine, Division of Infectious Diseases and Global Public Health, University of California, San Diego (UCSD), La Jolla, CA 92037, USA
| | - Jose Mateus
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology (LJI), La Jolla, CA 92037, USA
| | - Yu Kato
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology (LJI), La Jolla, CA 92037, USA
| | - Kathryn M. Hastie
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology (LJI), La Jolla, CA 92037, USA
| | - Esther Dawen Yu
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology (LJI), La Jolla, CA 92037, USA
| | - Caterina E. Faliti
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology (LJI), La Jolla, CA 92037, USA
| | - Alba Grifoni
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology (LJI), La Jolla, CA 92037, USA
| | - Sydney I. Ramirez
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology (LJI), La Jolla, CA 92037, USA
- Department of Medicine, Division of Infectious Diseases and Global Public Health, University of California, San Diego (UCSD), La Jolla, CA 92037, USA
| | - Sonya Haupt
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology (LJI), La Jolla, CA 92037, USA
| | - April Frazier
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology (LJI), La Jolla, CA 92037, USA
| | - Catherine Nakao
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology (LJI), La Jolla, CA 92037, USA
| | - Vamseedhar Rayaprolu
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology (LJI), La Jolla, CA 92037, USA
| | - Stephen A. Rawlings
- Department of Medicine, Division of Infectious Diseases and Global Public Health, University of California, San Diego (UCSD), La Jolla, CA 92037, USA
| | - Bjoern Peters
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology (LJI), La Jolla, CA 92037, USA
- Department of Medicine, University of California, San Diego (UCSD), La Jolla, CA 92037, USA
| | - Florian Krammer
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Viviana Simon
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, New York
- Division of Infectious Diseases, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- The Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Erica Ollmann Saphire
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology (LJI), La Jolla, CA 92037, USA
- Department of Medicine, Division of Infectious Diseases and Global Public Health, University of California, San Diego (UCSD), La Jolla, CA 92037, USA
| | - Davey M. Smith
- Department of Medicine, Division of Infectious Diseases and Global Public Health, University of California, San Diego (UCSD), La Jolla, CA 92037, USA
| | - Daniela Weiskopf
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology (LJI), La Jolla, CA 92037, USA
| | - Alessandro Sette
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology (LJI), La Jolla, CA 92037, USA
- Department of Medicine, Division of Infectious Diseases and Global Public Health, University of California, San Diego (UCSD), La Jolla, CA 92037, USA
| | - Shane Crotty
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology (LJI), La Jolla, CA 92037, USA
- Department of Medicine, Division of Infectious Diseases and Global Public Health, University of California, San Diego (UCSD), La Jolla, CA 92037, USA
| |
Collapse
|
25
|
Sidney J, Peters B, Sette A. Epitope prediction and identification- adaptive T cell responses in humans. Semin Immunol 2020; 50:101418. [PMID: 33131981 DOI: 10.1016/j.smim.2020.101418] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/19/2020] [Revised: 09/24/2020] [Accepted: 10/22/2020] [Indexed: 12/16/2022]
Abstract
Epitopes, in the context of T cell recognition, are short peptides typically derived by antigen processing, and presented on the cell surface bound to MHC molecules (HLA molecules in humans) for TCR scrutiny. The identification of epitopes is a context-dependent process, with consideration given to, for example, the source pathogen and protein, the host organism, and state of the immune reaction (e.g., following natural infection, vaccination, etc.). In the following review, we consider the various approaches used to define T cell epitopes, including both bioinformatic and experimental approaches, and discuss the concepts of immunodominance and immunoprevalence. We also discuss HLA polymorphism and epitope restriction, and the resulting impact on the identification of, and potential population coverage afforded by, epitopes or epitope-based vaccines. Finally, some examples of the practical application of T cell epitope identification are provided, showing how epitopes have been valuable for deriving novel immunological insights in the context of the immune response to various pathogens and allergens.
Collapse
Affiliation(s)
- John Sidney
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, 9420 Athena Circle, La Jolla, CA, 92037, USA
| | - Bjoern Peters
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, 9420 Athena Circle, La Jolla, CA, 92037, USA; Department of Medicine, Division of Infectious Diseases and Global Public Health, University of California, San Diego, La Jolla, CA, 92037, USA
| | - Alessandro Sette
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, 9420 Athena Circle, La Jolla, CA, 92037, USA; Department of Medicine, Division of Infectious Diseases and Global Public Health, University of California, San Diego, La Jolla, CA, 92037, USA.
| |
Collapse
|
26
|
Şahar EA, Can H, İz SG, Döşkaya AD, Kalantari-Dehaghi M, Deveci R, Gürüz AY, Döşkaya M. Development of a hexavalent recombinant protein vaccine adjuvanted with Montanide ISA 50 V and determination of its protective efficacy against acute toxoplasmosis. BMC Infect Dis 2020; 20:493. [PMID: 32650739 PMCID: PMC7348124 DOI: 10.1186/s12879-020-05220-2] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2019] [Accepted: 07/02/2020] [Indexed: 01/07/2023] Open
Abstract
Background Toxoplasma gondii is an obligate intracellular parasite that can infect almost all warm-blooded animals, avian species and humans. Toxoplasmosis is asymptomatic in healthy individuals, whereas it may lead to death in immune suppressed or deficient patients. A vaccine against T. gondii is required to prevent consequences of the infection. The aim of this study is to generate a multivalent recombinant protein vaccine against T. gondii. Methods 49 previously discovered antigenic proteins of T gondii were evaluated by their expression level in E. coli and by comprehensive bioinformatics analyses to determine antigenic epitopes. Based on these analyses, six vaccine candidate proteins were selected to generate a hexavalent recombinant protein vaccine adjuvanted with Montanide ISA 50 V. Humoral and cellular immune responses were determined by flow cytometry and ELISA. Vaccinated mice were challenged with T. gondii Ankara strain tachyzoites. Results In mice vaccinated with hexavalent vaccine, strong total IgG (P < 0.0001) and IgG2a (P < 0.001) responses were induced compared to controls, the ratio of CD4+ and CD8+ T lymphocytes secreting IFN-γ increased, and significantly higher extracellular IFN-γ secretion was achieved compared to the controls (P < 0.001). The survival time of the vaccinated mice increased to 8.38 ± 2.13 days which was significantly higher than controls (P < 0.01). Conclusions Altogether, these results show that the hexavalent vaccine which is developed for the first time against T. gondii induced strong and balanced Th1 and Th2 immune responses as well as conferred significant protection against challenge with lethal toxoplasmosis in murine model.
Collapse
Affiliation(s)
- Esra Atalay Şahar
- Present address: Department of Parasitology, Vaccine Research and Development Laboratory, Faculty of Medicine, Ege University, Bornova, 35100, İzmir, Turkey.,Department of Molecular Biology, Faculty of Science, Ege University, İzmir, 35100, Bornova, Turkey.,Department of Biotechnology, Ege University Faculty of Science, Bornova, 35100, İzmir, Turkey
| | - Hüseyin Can
- Department of Molecular Biology, Faculty of Science, Ege University, İzmir, 35100, Bornova, Turkey
| | - Sultan Gülçe İz
- Department of Bioengineering, Ege University Faculty of Engineering, Bornova, 35100, İzmir, Turkey
| | - Aysu Değirmenci Döşkaya
- Present address: Department of Parasitology, Vaccine Research and Development Laboratory, Faculty of Medicine, Ege University, Bornova, 35100, İzmir, Turkey
| | | | - Remziye Deveci
- Department of Molecular Biology, Faculty of Science, Ege University, İzmir, 35100, Bornova, Turkey
| | - Adnan Yüksel Gürüz
- Present address: Department of Parasitology, Vaccine Research and Development Laboratory, Faculty of Medicine, Ege University, Bornova, 35100, İzmir, Turkey
| | - Mert Döşkaya
- Present address: Department of Parasitology, Vaccine Research and Development Laboratory, Faculty of Medicine, Ege University, Bornova, 35100, İzmir, Turkey.
| |
Collapse
|
27
|
Ghaffari AD, Dalimi A, Ghaffarifar F, Pirestani M. Antigenic properties of dense granule antigen 12 protein using bioinformatics tools in order to improve vaccine design against Toxoplasma gondii. Clin Exp Vaccine Res 2020; 9:81-96. [PMID: 32864364 PMCID: PMC7445328 DOI: 10.7774/cevr.2020.9.2.81] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2019] [Revised: 02/23/2020] [Accepted: 07/28/2020] [Indexed: 12/24/2022] Open
Abstract
PURPOSE Toxoplasma gondii is an opportunistic parasite infecting all warm-blooded animals including humans. The dense granule antigens (GRAs) play an important role in parasite survival and virulence and in forming the parasitophorous vacuole. Identification of protein characteristics increases our knowledge about them and leads to develop the vaccine and diagnostic studies. MATERIALS AND METHODS This paper gave a comprehensive definition of the important aspects of GRA12 protein, including physico-chemical features, a transmembrane domain, subcellular position, secondary and tertiary structure, potential epitopes of B-cells and T-cells, and other important features of this protein using different and reliable bioinformatics methods to determine potential epitopes for designing of a high-efficient vaccine. RESULTS The findings showed that GRA12 protein had 53 potential post-translational modification sites. Also, only one transmembrane domain was recognized for this protein. The secondary structure of GRA12 protein comprises 35.55% alpha-helix, 19.50% extended strand, and 44.95% random coil. Moreover, several potential B- and T-cell epitopes were identified for GRA12. Based on the results of the Ramachandran plot, 79.26% of amino acid residues were located in favored, 11.85% in allowed and 8.89% in outlier regions. Furthermore, the results of the antigenicity and allergenicity assessment noted that GRA12 is immunogenic and non-allergenic. CONCLUSION This research provided important basic and conceptual data on GRA12 to develop an effective vaccine against acute and chronic toxoplasmosis for further in vivo investigations. More studies are required on vaccine development using the GRA12 alone or combined with other antigens in the future.
Collapse
Affiliation(s)
- Ali Dalir Ghaffari
- Department of Parasitology, Faculty of Medical Sciences, Tarbiat Modares University, Tehran, Iran
| | - Abdolhossein Dalimi
- Department of Parasitology, Faculty of Medical Sciences, Tarbiat Modares University, Tehran, Iran
| | - Fatemeh Ghaffarifar
- Department of Parasitology, Faculty of Medical Sciences, Tarbiat Modares University, Tehran, Iran
| | - Majid Pirestani
- Department of Parasitology, Faculty of Medical Sciences, Tarbiat Modares University, Tehran, Iran
| |
Collapse
|
28
|
Identification of Common CD8 + T Cell Epitopes from Lassa Fever Survivors in Nigeria and Sierra Leone. J Virol 2020; 94:JVI.00153-20. [PMID: 32269122 PMCID: PMC7307091 DOI: 10.1128/jvi.00153-20] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2020] [Accepted: 03/24/2020] [Indexed: 01/01/2023] Open
Abstract
The high morbidity and mortality associated with clinical cases of Lassa fever, together with the lack of licensed vaccines and limited and partially effective interventions, make Lassa virus (LASV) an important health concern in its regions of endemicity in West Africa. Previous infection with LASV protects from disease after subsequent exposure, providing a framework for designing vaccines to elicit similar protective immunity. Multiple major lineages of LASV circulate in West Africa, and therefore, ideal vaccine candidates should elicit immunity to all lineages. We therefore sought to identify common T cell epitopes between Lassa fever survivors from Sierra Leone and Nigeria, where distinct lineages circulate. We identified three such epitopes derived from highly conserved regions within LASV proteins. In this process, we also identified nine other T cell epitopes. These data should help in the design of an effective pan-LASV vaccine. Early and robust T cell responses have been associated with survival from Lassa fever (LF), but the Lassa virus-specific memory responses have not been well characterized. Regions within the virus surface glycoprotein (GPC) and nucleoprotein (NP) are the main targets of the Lassa virus-specific T cell responses, but, to date, only a few T cell epitopes within these proteins have been identified. We identified GPC and NP regions containing T cell epitopes and HLA haplotypes from LF survivors and used predictive HLA-binding algorithms to identify putative epitopes, which were then experimentally tested using autologous survivor samples. We identified 12 CD8-positive (CD8+) T cell epitopes, including epitopes common to both Nigerian and Sierra Leonean survivors. These data should be useful for the identification of dominant Lassa virus-specific T cell responses in Lassa fever survivors and vaccinated individuals as well as for designing vaccines that elicit cell-mediated immunity. IMPORTANCE The high morbidity and mortality associated with clinical cases of Lassa fever, together with the lack of licensed vaccines and limited and partially effective interventions, make Lassa virus (LASV) an important health concern in its regions of endemicity in West Africa. Previous infection with LASV protects from disease after subsequent exposure, providing a framework for designing vaccines to elicit similar protective immunity. Multiple major lineages of LASV circulate in West Africa, and therefore, ideal vaccine candidates should elicit immunity to all lineages. We therefore sought to identify common T cell epitopes between Lassa fever survivors from Sierra Leone and Nigeria, where distinct lineages circulate. We identified three such epitopes derived from highly conserved regions within LASV proteins. In this process, we also identified nine other T cell epitopes. These data should help in the design of an effective pan-LASV vaccine.
Collapse
|
29
|
Condotta SA, Downey J, Pardy RD, Valbon SF, Tarrab E, Lamarre A, Divangahi M, Richer MJ. Cyclophilin D Regulates Antiviral CD8 + T Cell Survival in a Cell-Extrinsic Manner. Immunohorizons 2020; 4:217-230. [PMID: 32332052 DOI: 10.4049/immunohorizons.2000016] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2020] [Accepted: 04/07/2020] [Indexed: 11/19/2022] Open
Abstract
CD8+ T cell-mediated immunity is critical for host defense against viruses and requires mitochondria-mediated type I IFN (IFN-I) signaling for optimal protection. Cyclophilin D (CypD) is a mitochondrial matrix protein that modulates the mitochondrial permeability transition pore, but its role in IFN-I signaling and CD8+ T cell responses to viral infection has not been previously explored. In this study, we demonstrate that CypD plays a critical extrinsic role in the survival of Ag-specific CD8+ T cell following acute viral infection with lymphocytic choriomeningitis virus in mice. CypD deficiency resulted in reduced IFN-I and increased CD8+ T cell death, resulting in a reduced antiviral CD8+ T cell response. In addition, CypD deficiency was associated with an increase in pathogen burden at an early time-point following infection. Furthermore, our data demonstrate that transfer of wild-type macrophages (expressing CypD) to CypD-deficient mice can partially restore CD8+ T cell responses. These results establish that CypD plays an extrinsic role in regulating optimal effector CD8+ T cell responses to viral infection. Furthermore, this suggests that, under certain circumstances, inhibition of CypD function may have a detrimental impact on the host's ability to respond to viral infection.
Collapse
Affiliation(s)
- Stephanie A Condotta
- Department of Microbiology and Immunology, McGill University, Montreal, Quebec H3G 1Y6, Canada
| | - Jeffrey Downey
- Department of Microbiology and Immunology, McGill University, Montreal, Quebec H3G 1Y6, Canada
- Meakins-Christie Laboratories, McGill University Health Centre, Montreal, Quebec H4A 3J1, Canada
- Department of Medicine, McGill University Health Centre, Montreal, Quebec H4A 3J1, Canada
- Department of Pathology, McGill University Health Centre, Montreal, Quebec H4A 3J1, Canada
- McGill International TB Centre, McGill University Health Centre, Montreal, Quebec H4A 3J1, Canada
| | - Ryan D Pardy
- Department of Microbiology and Immunology, McGill University, Montreal, Quebec H3G 1Y6, Canada
| | - Stefanie F Valbon
- Department of Microbiology and Immunology, McGill University, Montreal, Quebec H3G 1Y6, Canada
| | - Esther Tarrab
- Laboratoire d'Immunovirologie, Institut National de la Recherche Scientifique, Institut National de la Recherche Scientifique-Institut Armand-Frappier, Laval, Quebec H7V 1B7, Canada; and
| | - Alain Lamarre
- Laboratoire d'Immunovirologie, Institut National de la Recherche Scientifique, Institut National de la Recherche Scientifique-Institut Armand-Frappier, Laval, Quebec H7V 1B7, Canada; and
| | - Maziar Divangahi
- Department of Microbiology and Immunology, McGill University, Montreal, Quebec H3G 1Y6, Canada
- Meakins-Christie Laboratories, McGill University Health Centre, Montreal, Quebec H4A 3J1, Canada
- Department of Medicine, McGill University Health Centre, Montreal, Quebec H4A 3J1, Canada
- Department of Pathology, McGill University Health Centre, Montreal, Quebec H4A 3J1, Canada
- McGill International TB Centre, McGill University Health Centre, Montreal, Quebec H4A 3J1, Canada
| | - Martin J Richer
- Department of Microbiology and Immunology, McGill University, Montreal, Quebec H3G 1Y6, Canada;
- Rosalind and Morris Goodman Cancer Research Centre, McGill University, Montreal, Quebec H3G 1Y6, Canada
| |
Collapse
|
30
|
High crossreactivity of human T cell responses between Lassa virus lineages. PLoS Pathog 2020; 16:e1008352. [PMID: 32142546 PMCID: PMC7080273 DOI: 10.1371/journal.ppat.1008352] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2019] [Revised: 03/18/2020] [Accepted: 01/24/2020] [Indexed: 12/27/2022] Open
Abstract
Lassa virus infects hundreds of thousands of people each year across rural West Africa, resulting in a high number of cases of Lassa fever (LF), a febrile disease associated with high morbidity and significant mortality. The lack of approved treatments or interventions underscores the need for an effective vaccine. At least four viral lineages circulate in defined regions throughout West Africa with substantial interlineage nucleotide and amino acid diversity. An effective vaccine should be designed to elicit Lassa virus specific humoral and cell mediated immunity across all lineages. Most current vaccine candidates use only lineage IV antigens encoded by Lassa viruses circulating around Sierra Leone, Liberia, and Guinea but not Nigeria where lineages I-III are found. As previous infection is known to protect against disease from subsequent exposure, we sought to determine whether LF survivors from Nigeria and Sierra Leone harbor memory T cells that respond to lineage IV antigens. Our results indicate a high degree of cross-reactivity of CD8+ T cells from Nigerian LF survivors to lineage IV antigens. In addition, we identified regions within the Lassa virus glycoprotein complex and nucleoprotein that contributed to these responses while T cell epitopes were not widely conserved across our study group. These data are important for current efforts to design effective and efficient vaccine candidates that can elicit protective immunity across all Lassa virus lineages. Lassa virus (LASV), the causative agent of the hemorrhagic illness Lassa fever (LF), is found throughout West Africa. Humans are usually infected after contact with infected rodent excreta or aerosolized virus. The mortality rate among hospitalized LF cases is high and no effective treatments or vaccines exist. A vaccine effective against the four main lineages of LASV is needed to protect susceptible individuals across West Africa. To understand how this protection could occur, we examined the immune responses of LF survivors from two different regions of West Africa. As previous infection with Lassa virus protects from disease after subsequent exposure, the immune response of LF survivors provides a model of protective immunity that could be induced after vaccination. We found that LASV strains from lineages different from those that infected the LF survivors efficiently activated memory CD8+ T cell responses. We identified regions within LASV proteins that elicit memory responses in the majority of individuals. From these data, we propose that an effective vaccine that protects against lineages across West Africa should be designed to elicit memory CD8+ T cell responses in addition to antibody responses.
Collapse
|
31
|
Ong E, He Y, Yang Z. Epitope promiscuity and population coverage of Mycobacterium tuberculosis protein antigens in current subunit vaccines under development. INFECTION GENETICS AND EVOLUTION 2020; 80:104186. [PMID: 31923726 DOI: 10.1016/j.meegid.2020.104186] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/01/2019] [Revised: 01/05/2020] [Accepted: 01/07/2020] [Indexed: 02/06/2023]
Abstract
Tuberculosis (TB) is the leading infectious cause of death worldwide and claimed over 1.6 million lives in 2017. Furthermore, one-third of the world population is estimated to be latently infected with Mycobacterium tuberculosis (MTB). A safe and effective MTB vaccine that can prevent both the primary infection and the reactivation of latent tuberculosis infection (LTBI), and that can protect against all forms of TB in adults and adolescents is urgently needed. In this study, using computational approaches, we predicted the capacity of the epitopes to be presented by the HLA molecules for ten MTB protein antigens (Mtb39a, Mtb32a, Ag85B, ESAT-6, TB10.4, Rv2660, Rv2608, Rv3619, Rv3620, and Rv1813) constituting five MTB subunit vaccines (M72, H1, H4, H56, and ID93) that are currently in clinical trials. We also assessed the promiscuity of the predicted epitopes based on a reference set of alleles and supertype alleles, and estimated the population coverage of the ten antigens in three high TB burden countries (China, India, and South Africa). Among the ten antigens evaluated, Rv2608 was found to have the highest number of promiscuous epitopes predicted to bind the most MHC-I and MHC-II supertype alleles, highest predicted immunogenicity, and the broadest population coverage in three high burden countries. Between the two latency-related antigens (Rv1813 and Rv2660), Rv1813 was predicted to have a better epitope diversity and promiscuity, immunogenicity, and population coverage. As a result, the ID93 vaccine consisted of Rv2608, Rv1813, Rv3619, and Rv3620 was predicted to have the best potential for preventing both active and latent TB infection. Our results highlighted the importance and usefulness of a systematic and comprehensive assessment of protein antigens using computational approaches in MTB vaccine development.
Collapse
Affiliation(s)
- Edison Ong
- Department of Computational Medicine and Bioinformatics, University of Michigan, 500 S State St, Ann Arbor, MI 48109, United States.
| | - Yongqun He
- Unit for Laboratory Animal Medicine, University of Michigan, 500 S State St, Ann Arbor, MI 48109, United States; Department of Microbiology and Immunology Department, University of Michigan, 500 S State St, Ann Arbor, MI 48109, United States; Center of Computational Medicine and Bioinformatics, University of Michigan, 500 S State St, Ann Arbor, MI 48109, United States.
| | - Zhenhua Yang
- Department of Epidemiology, School of Public Health, University of Michigan, 500 S State St, Ann Arbor, MI 48109, United States.
| |
Collapse
|
32
|
Colston JM, Hutchings C, Chinnakannan S, Highton A, Perez‐Shibayama C, Ludewig B, Klenerman P. Divergent memory responses driven by adenoviral vectors are impacted by epitope competition. Eur J Immunol 2019; 49:1356-1363. [PMID: 31106398 PMCID: PMC6772135 DOI: 10.1002/eji.201948143] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2019] [Revised: 03/29/2019] [Accepted: 05/16/2019] [Indexed: 11/11/2022]
Abstract
Adenoviral vectors induce robust epitope-specific CD8+ T cell responses. Within the repertoire of responses generated both conventional memory evolution and the phenomenon of memory inflation are seen. The rules governing which epitopes inflate are not fully known, but may include a role for both antigen processing and competition. To investigate this, we looked at memory generated from vectors targeting the Gp33-41 (KAVYNFATC/K9C) epitope from the gp of lymphocytic choriomeningitis virus (LCMV) in mice. This well-described epitope has both the Gp33-41 and Gp34-41 epitopes embedded within it. Vaccination with a full-length gp or a minigene Ad-Gp33/K9C vector-induced conventional memory responses against the immunodominant Gp33/K9C epitope but a strong inflationary response against the Gp34/A8C epitope. These responses showed sustained in vivo function, with complete protection against LCMV infectious challenge. Given the unexpected competition between epitopes seen in the minigene model, we further tested epitope competition using the full-length Ad-LacZ (β-galactosidase) model. Generation of an Ad-LacZ vector with a single amino acid disruption of the inflationary β-gal96-103 /D8V epitope transformed the β-gal497-504 /I8V epitope from conventional to inflationary memory. This work collectively demonstrates the importance of epitope competition within adenoviral vector inserts and is of relevance to future studies using adenoviral vectored immunogens.
Collapse
Affiliation(s)
- Julia M Colston
- Nuffield Department of MedicinePeter Medawar Building for Pathogen Research, University of OxfordOxfordUK
- Institute of ImmunobiologyKantonsspital St. GallenSt. GallenSwitzerland
| | - Claire Hutchings
- Nuffield Department of MedicinePeter Medawar Building for Pathogen Research, University of OxfordOxfordUK
| | - Senthil Chinnakannan
- Nuffield Department of MedicinePeter Medawar Building for Pathogen Research, University of OxfordOxfordUK
| | - Andrew Highton
- Nuffield Department of MedicinePeter Medawar Building for Pathogen Research, University of OxfordOxfordUK
| | | | - Burkhard Ludewig
- Institute of ImmunobiologyKantonsspital St. GallenSt. GallenSwitzerland
| | - Paul Klenerman
- Nuffield Department of MedicinePeter Medawar Building for Pathogen Research, University of OxfordOxfordUK
| |
Collapse
|
33
|
scFv6.C4 DNA vaccine with fragment C of Tetanus toxin increases protective immunity against CEA-expressing tumor. Gene Ther 2019; 26:441-454. [PMID: 30770895 DOI: 10.1038/s41434-019-0062-y] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2018] [Revised: 01/28/2019] [Accepted: 01/31/2019] [Indexed: 12/21/2022]
Abstract
The carcinoembryonic antigen (CEA) is the main tumor-associated antigen of colorectal cancers. Previously, we developed a DNA vaccine using scFv6.C4, a CEA surrogate, against CEA-expressing tumors; 40% of the vaccinated mice were tumor-free after tumor challenge. In order to enhance vaccine efficacy, fragment C of Tetanus Toxin (FrC) was tested as adjuvant. C57BL/6J-CEA2682 mice were electroporated intramuscularly 4 times with uP-PS/scFv6.C4-FrC or uP-PS/scFv6.C4, challenged by s.c. injection of 1 × 105 MC38-CEA cells, and tumor growth was monitored over 100 days. The humoral and cellular immune responses were assessed by ELISA, immunocytochemistry, in-vitro lymphocyte proliferation, and CTL cytotoxicity assays. Immunization with uP-PS/scFv6.C4-FrC or uP-PS/scFv6.C4 induced similar anti-CEA antibody titers. However, immunocytochemistry analysis showed stronger staining with uP-PS/scFv6.C4-FrC-immunized mice sera. When challenged with MC38-CEA cells, 63% of the FrC-vaccinated mice did not develop tumors, half of the rest had a significant tumor growth delay, and the probability of being free of tumors was on average 40% higher than that of scFv6.C4-immunized mice. Addition of the adjuvant led to higher CD4+ and CD8+ proliferative responses and strong CD8+ CTL response against MC38-CEA cells. DNA immunization with scFv6.C4 and FrC increased antitumor effect via induction of high and specific humoral and cellular immune responses to CEA.
Collapse
|
34
|
Forsyth KS, DeHaven B, Mendonca M, Paul S, Sette A, Eisenlohr LC. Poor Antigen Processing of Poxvirus Particles Limits CD4 + T Cell Recognition and Impacts Immunogenicity of the Inactivated Vaccine. THE JOURNAL OF IMMUNOLOGY 2019; 202:1340-1349. [PMID: 30700590 DOI: 10.4049/jimmunol.1801099] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/09/2018] [Accepted: 12/27/2018] [Indexed: 12/25/2022]
Abstract
CD4+ T cells play critical roles in defending against poxviruses, both by potentiating cellular and humoral responses and by directly killing infected cells. Despite this central role, the basis for pox-specific CD4+ T cell activation, specifically the origin of the poxvirus-derived peptides (epitopes) that activate CD4+ T cells, remains poorly understood. In addition, because the current licensed poxvirus vaccines can cause serious adverse events and even death, elucidating the requirements for MHC class II (MHC-II) processing and presentation of poxviral Ags could be of great use. To address these questions, we explored the CD4+ T cell immunogenicity of ectromelia, the causative agent of mousepox. Having identified a large panel of novel epitopes via a screen of algorithm-selected synthetic peptides, we observed that immunization of mice with inactivated poxvirus primes a virtually undetectable CD4+ T cell response, even when adjuvanted, and is unable to provide protection against disease after a secondary challenge. We postulated that an important contributor to this outcome is the poor processability of whole virions for MHC-II-restricted presentation. In line with this hypothesis, we observed that whole poxvirions are very inefficiently converted into MHC-II-binding peptides by the APC as compared with subviral material. Thus, stability of the virion structure is a critical consideration in the rational design of a safe alternative to the existing live smallpox vaccine.
Collapse
Affiliation(s)
- Katherine S Forsyth
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104
| | - Brian DeHaven
- Department of Biology, La Salle University, Philadelphia, PA 19141
| | - Mark Mendonca
- Department of Microbiology and Immunology, Thomas Jefferson University, Philadelphia, PA 19107
| | - Sinu Paul
- La Jolla Institute for Allergy and Immunology, La Jolla, CA 92037
| | - Alessandro Sette
- La Jolla Institute for Allergy and Immunology, La Jolla, CA 92037.,Department of Medicine, University of California, San Diego, La Jolla, CA, 92093; and
| | - Laurence C Eisenlohr
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104; .,Children's Hospital of Philadelphia, Philadelphia, PA 19104
| |
Collapse
|
35
|
Dhanda SK, Karosiene E, Edwards L, Grifoni A, Paul S, Andreatta M, Weiskopf D, Sidney J, Nielsen M, Peters B, Sette A. Predicting HLA CD4 Immunogenicity in Human Populations. Front Immunol 2018; 9:1369. [PMID: 29963059 PMCID: PMC6010533 DOI: 10.3389/fimmu.2018.01369] [Citation(s) in RCA: 76] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2018] [Accepted: 06/01/2018] [Indexed: 12/12/2022] Open
Abstract
Background Prediction of T cell immunogenicity is a topic of considerable interest, both in terms of basic understanding of the mechanisms of T cells responses and in terms of practical applications. HLA binding affinity is often used to predict T cell epitopes, since HLA binding affinity is a key requisite for human T cell immunogenicity. However, immunogenicity at the population it is complicated by the high level of variability of HLA molecules, potential other factors beyond HLA as well as the frequent lack of HLA typing data. To overcome those issues, we explored an alternative approach to identify the common characteristics able to distinguish immunogenic peptides from non-recognized peptides. Methods Sets of dominant epitopes derived from peer-reviewed published papers were used in conjunction with negative peptides from the same experiments/donors to train neural networks and generate an “immunogenicity score.” We also compared the performance of the immunogenicity score with previously described method for immunogenicity prediction based on HLA class II binding at the population level. Results The immunogenicity score was validated on a series of independent datasets derived from the published literature, representing 57 independent studies where immunogenicity in human populations was assessed by testing overlapping peptides spanning different antigens. Overall, these testing datasets corresponded to over 2,000 peptides and tested in over 1,600 different human donors. The 7-allele method prediction and the immunogenicity score were associated with similar performance [average area under the ROC curve (AUC) values of 0.703 and 0.702, respectively] while the combined methods reached an average AUC of 0.725. This increase in average AUC value is significant compared with the immunogenicity score (p = 0.0135) and a strong trend toward significance is observed when compared to the 7-allele method (p = 0.0938). The new immunogenicity score method is now freely available using CD4 T cell immunogenicity prediction tool on the Immune Epitope Database website (http://tools.iedb.org/CD4episcore). Conclusion The new immunogenicity score predicts CD4 T cell immunogenicity at the population level starting from protein sequences and with no need for HLA typing. Its efficacy has been validated in the context of different antigen sources, ethnicities, and disparate techniques for epitope identification.
Collapse
Affiliation(s)
- Sandeep Kumar Dhanda
- Division of Vaccine Discovery, La Jolla Institute for Allergy and Immunology, La Jolla, CA, United States
| | - Edita Karosiene
- Division of Vaccine Discovery, La Jolla Institute for Allergy and Immunology, La Jolla, CA, United States
| | - Lindy Edwards
- Division of Vaccine Discovery, La Jolla Institute for Allergy and Immunology, La Jolla, CA, United States
| | - Alba Grifoni
- Division of Vaccine Discovery, La Jolla Institute for Allergy and Immunology, La Jolla, CA, United States
| | - Sinu Paul
- Division of Vaccine Discovery, La Jolla Institute for Allergy and Immunology, La Jolla, CA, United States
| | - Massimo Andreatta
- Instituto de Investigaciones Biotecnológicas, Universidad Nacional de San Martín, Buenos Aires, Argentina
| | - Daniela Weiskopf
- Division of Vaccine Discovery, La Jolla Institute for Allergy and Immunology, La Jolla, CA, United States
| | - John Sidney
- Division of Vaccine Discovery, La Jolla Institute for Allergy and Immunology, La Jolla, CA, United States
| | - Morten Nielsen
- Instituto de Investigaciones Biotecnológicas, Universidad Nacional de San Martín, Buenos Aires, Argentina.,Department of Bio and Health Informatics, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Bjoern Peters
- Division of Vaccine Discovery, La Jolla Institute for Allergy and Immunology, La Jolla, CA, United States.,University of California San Diego, La Jolla, CA, United States
| | - Alessandro Sette
- Division of Vaccine Discovery, La Jolla Institute for Allergy and Immunology, La Jolla, CA, United States.,University of California San Diego, La Jolla, CA, United States
| |
Collapse
|
36
|
Khan A, Junaid M, Kaushik AC, Ali A, Ali SS, Mehmood A, Wei DQ. Computational identification, characterization and validation of potential antigenic peptide vaccines from hrHPVs E6 proteins using immunoinformatics and computational systems biology approaches. PLoS One 2018; 13:e0196484. [PMID: 29715318 PMCID: PMC5929558 DOI: 10.1371/journal.pone.0196484] [Citation(s) in RCA: 60] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2017] [Accepted: 04/13/2018] [Indexed: 01/01/2023] Open
Abstract
High-risk human papillomaviruses (hrHPVs) are the most prevalent viruses in human diseases including cervical cancers. Expression of E6 protein has already been reported in cervical cancer cases, excluding normal tissues. Continuous expression of E6 protein is making it ideal to develop therapeutic vaccines against hrHPVs infection and cervical cancer. Therefore, we carried out a meta-analysis of multiple hrHPVs to predict the most potential prophylactic peptide vaccines. In this study, immunoinformatics approach was employed to predict antigenic epitopes of hrHPVs E6 proteins restricted to 12 Human HLAs to aid the development of peptide vaccines against hrHPVs. Conformational B-cell and CTL epitopes were predicted for hrHPVs E6 proteins using ElliPro and NetCTL. The potential of the predicted peptides were tested and validated by using systems biology approach considering experimental concentration. We also investigated the binding interactions of the antigenic CTL epitopes by using docking. The stability of the resulting peptide-MHC I complexes was further studied by molecular dynamics simulations. The simulation results highlighted the regions from 46–62 and 65–76 that could be the first choice for the development of prophylactic peptide vaccines against hrHPVs. To overcome the worldwide distribution, the predicted epitopes restricted to different HLAs could cover most of the vaccination and would help to explore the possibility of these epitopes for adaptive immunotherapy against HPVs infections.
Collapse
Affiliation(s)
- Abbas Khan
- State Key Laboratory of Microbial Metabolism, and College of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Muhammad Junaid
- State Key Laboratory of Microbial Metabolism, and College of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Aman Chandra Kaushik
- State Key Laboratory of Microbial Metabolism, and College of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Arif Ali
- State Key Laboratory of Microbial Metabolism, and College of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Syed Shujait Ali
- Center for Biotechnology and Microbiology, University of Swat, Khyber Pakhtunkhwa, Pakistan
| | - Aamir Mehmood
- State Key Laboratory of Microbial Metabolism, and College of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Dong-Qing Wei
- State Key Laboratory of Microbial Metabolism, and College of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
- * E-mail:
| |
Collapse
|
37
|
Perez-Martinez AP, Ong E, Zhang L, Marrs CF, He Y, Yang Z. Conservation in gene encoding Mycobacterium tuberculosis antigen Rv2660 and a high predicted population coverage of H56 multistage vaccine in South Africa. INFECTION GENETICS AND EVOLUTION 2017; 55:244-250. [PMID: 28941991 DOI: 10.1016/j.meegid.2017.09.023] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/13/2017] [Revised: 09/11/2017] [Accepted: 09/19/2017] [Indexed: 01/26/2023]
Abstract
H56/AERAS-456+IC31 (H56), composed of two early secretion proteins, Ag85B and ESAT-6, and a latency associated protein, Rv2660, and the IC31 Intercell adjuvant, is a new fusion subunit vaccine candidate designed to induce immunity against both new infection and reactivation of latent tuberculosis infection. Efficacy of subunit vaccines may be affected by the diversity of vaccine antigens among clinical strains and the extent of recognition by the diverse HLA molecules in the recipient population. Although a previous study showed the conservative nature of Ag85B- and ESAT-6-encoding genes, genetic diversity of Rv2660c that encodes RV2660 is largely unknown. The population coverage of H56 as a whole yet remains to be assessed. The present study was conducted to address these important knowledge gaps. DNA sequence analysis of Rv2660c found no variation among 83 of the 84 investigated clinical strains belonging to four genetic lineages. H56 was predicted to have as high as 99.6% population coverage in the South Africa population using the Immune Epitope Database (IEDB) Population Coverage Tool. Further comparison of H56 population coverage between South African Blacks and Caucasians based on the phenotypic frequencies of binding MHC Class I and Class II supertype alleles found that all of the nine MHC-I and six of eight MHC-II human leukocyte antigen (HLA) supertype alleles analyzed were significantly differentially expressed between the two subpopulations. This finding suggests the presence of race-specific functional binding motifs of MHC-I and MHC-II HLA alleles, which, in turn, highlights the importance of including diverse populations in vaccine clinical evaluation. In conclusion, H56 vaccine is predicted to have a promising population coverage in South Africa; this study demonstrates the utility of integrating comparative genomics and bioinformatics in bridging animal and clinical studies of novel TB vaccines.
Collapse
Affiliation(s)
- Angy P Perez-Martinez
- Department of Epidemiology, School of Public Health, University of Michigan, 1415 Washington Heights, Ann Arbor, MI 48109-2029, United States.
| | - Edison Ong
- Department of Computational Medicine and Bioinformatics, University of Michigan, 1415 Washington Heights, Ann Arbor, MI 48109-2029, United States.
| | - Lixin Zhang
- Department of Epidemiology, School of Public Health, University of Michigan, 1415 Washington Heights, Ann Arbor, MI 48109-2029, United States.
| | - Carl F Marrs
- Department of Epidemiology, School of Public Health, University of Michigan, 1415 Washington Heights, Ann Arbor, MI 48109-2029, United States.
| | - Yongqun He
- Unit for Laboratory Animal Medicine, University of Michigan, 1415 Washington Heights, Ann Arbor, MI 48109-2029, United States; Department of Microbiology and Immunology Department, University of Michigan, 1415 Washington Heights, Ann Arbor, MI 48109-2029, United States; Center of Computational Medicine and Bioinformatics, University of Michigan, 1415 Washington Heights, Ann Arbor, MI 48109-2029, United States.
| | - Zhenhua Yang
- Department of Epidemiology, School of Public Health, University of Michigan, 1415 Washington Heights, Ann Arbor, MI 48109-2029, United States.
| |
Collapse
|
38
|
Jiménez-Sánchez A, Memon D, Pourpe S, Veeraraghavan H, Li Y, Vargas HA, Gill MB, Park KJ, Zivanovic O, Konner J, Ricca J, Zamarin D, Walther T, Aghajanian C, Wolchok JD, Sala E, Merghoub T, Snyder A, Miller ML. Heterogeneous Tumor-Immune Microenvironments among Differentially Growing Metastases in an Ovarian Cancer Patient. Cell 2017; 170:927-938.e20. [PMID: 28841418 PMCID: PMC5589211 DOI: 10.1016/j.cell.2017.07.025] [Citation(s) in RCA: 340] [Impact Index Per Article: 48.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2016] [Revised: 06/06/2017] [Accepted: 07/14/2017] [Indexed: 12/12/2022]
Abstract
We present an exceptional case of a patient with high-grade serous ovarian cancer, treated with multiple chemotherapy regimens, who exhibited regression of some metastatic lesions with concomitant progression of other lesions during a treatment-free period. Using immunogenomic approaches, we found that progressing metastases were characterized by immune cell exclusion, whereas regressing and stable metastases were infiltrated by CD8+ and CD4+ T cells and exhibited oligoclonal expansion of specific T cell subsets. We also detected CD8+ T cell reactivity against predicted neoepitopes after isolation of cells from a blood sample taken almost 3 years after the tumors were resected. These findings suggest that multiple distinct tumor immune microenvironments co-exist within a single individual and may explain in part the heterogeneous fates of metastatic lesions often observed in the clinic post-therapy. VIDEO ABSTRACT.
Collapse
Affiliation(s)
- Alejandro Jiménez-Sánchez
- Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Robinson Way, Cambridge CB2 0RE, UK
| | - Danish Memon
- Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Robinson Way, Cambridge CB2 0RE, UK; European Molecular Biology Laboratory (EMBL), European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Stephane Pourpe
- Department of Medicine, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY 10065, USA
| | - Harini Veeraraghavan
- Department of Medical Physics, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY 10065, USA
| | - Yanyun Li
- Ludwig Collaborative/Swim Across America Laboratory, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY 10065, USA
| | - Hebert Alberto Vargas
- Department of Radiology, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY 10065, USA
| | - Michael B Gill
- Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Robinson Way, Cambridge CB2 0RE, UK
| | - Kay J Park
- Department of Pathology, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY 10065, USA
| | - Oliver Zivanovic
- Gynecology Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY 10065, USA
| | - Jason Konner
- Gynecologic Medical Oncology Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY 10065, USA
| | - Jacob Ricca
- Ludwig Collaborative/Swim Across America Laboratory, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY 10065, USA
| | - Dmitriy Zamarin
- Ludwig Collaborative/Swim Across America Laboratory, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY 10065, USA; Department of Medicine, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY 10065, USA
| | - Tyler Walther
- Department of Medicine, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY 10065, USA
| | - Carol Aghajanian
- Gynecologic Medical Oncology Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY 10065, USA
| | - Jedd D Wolchok
- Ludwig Collaborative/Swim Across America Laboratory, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY 10065, USA; Parker Institute for Cancer Immunotherapy, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY 10065, USA; Department of Medicine, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY 10065, USA; Department of Medicine, Weill Cornell Medical College, New York, NY, USA; Immunology and Microbial Pathogenesis Programs, Weill Cornell Graduate School of Medical Sciences, New York, NY 10065, USA
| | - Evis Sala
- Department of Radiology, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY 10065, USA
| | - Taha Merghoub
- Ludwig Collaborative/Swim Across America Laboratory, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY 10065, USA
| | - Alexandra Snyder
- Department of Medicine, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY 10065, USA; Department of Medicine, Weill Cornell Medical College, New York, NY, USA.
| | - Martin L Miller
- Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Robinson Way, Cambridge CB2 0RE, UK.
| |
Collapse
|
39
|
Heterologous Immunity and Persistent Murine Cytomegalovirus Infection. J Virol 2017; 91:JVI.01386-16. [PMID: 27807227 DOI: 10.1128/jvi.01386-16] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2016] [Accepted: 10/25/2016] [Indexed: 11/20/2022] Open
Abstract
One's history of infections can affect the immune response to unrelated pathogens and influence disease outcome through the process of heterologous immunity. This can occur after acute viral infections, such as infections with lymphocytic choriomeningitis virus (LCMV) and vaccinia virus, where the pathogens are cleared, but it becomes a more complex issue in the context of persistent infections. In this study, murine cytomegalovirus (MCMV) was used as a persistent infection model to study heterologous immunity with LCMV. If mice were previously immune to LCMV and then infected with MCMV (LCMV+MCMV), they had more severe immunopathology, enhanced viral burden in multiple organs, and suppression of MCMV-specific T cell memory inflation. MCMV infection initially reduced the numbers of LCMV-specific memory T cells, but continued MCMV persistence did not further erode memory T cells specific to LCMV. When MCMV infection was given first (MCMV+LCMV), the magnitude of the acute T cell response to LCMV declined with age though this age-dependent decline was not dependent on MCMV. However, some of these MCMV persistently infected mice with acute LCMV infection (7 of 36) developed a robust immunodominant CD8 T cell response apparently cross-reactive between a newly defined putative MCMV epitope sequence, M57727-734, and the normally subdominant LCMV epitope L2062-2069, indicating a profound private specificity effect in heterologous immunity between these two viruses. These results further illustrate how a history of an acute or a persistent virus infection can substantially influence the immune responses and immune pathology associated with acute or persistent infections with an unrelated virus. IMPORTANCE This study extends our understanding of heterologous immunity in the context of persistent viral infection. The phenomenon has been studied mostly with viruses such as LCMV that are cleared, but the situation can be more complex with a persistent virus such as MCMV. We found that the history of LCMV infection intensifies MCMV immunopathology, enhances MCMV burden in multiple organs, and suppresses MCMV-specific T cell memory inflation. In the reverse infection sequence, we show that some of the long-term MCMV-immune mice mount a robust CD8 T cell cross-reactive response between a newly defined putative MCMV epitope sequence and a normally subdominant LCMV epitope. These results further illustrate how a history of infection can substantially influence the immune responses and immune pathology associated with infections with an unrelated virus.
Collapse
|
40
|
Weiskopf D, Angelo MA, Grifoni A, O'Rourke PH, Sidney J, Paul S, De Silva AD, Phillips E, Mallal S, Premawansa S, Premawansa G, Wijewickrama A, Peters B, Sette A. HLA-DRB1 Alleles Are Associated With Different Magnitudes of Dengue Virus-Specific CD4+ T-Cell Responses. J Infect Dis 2016; 214:1117-24. [PMID: 27443615 DOI: 10.1093/infdis/jiw309] [Citation(s) in RCA: 65] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2016] [Accepted: 07/15/2016] [Indexed: 12/25/2022] Open
Abstract
BACKGROUND Each year dengue virus (DENV) infects 400 million human but causes symptomatic disease in only a subset of patients, suggesting that host genetic factors may play a role. HLA molecules that restrict T-cell responses are one of the most polymorphic host factors in humans. METHODS Here we map HLA DRB1-restricted DENV-specific epitopes in individuals previously exposed to DENV, to identify the breadth and specificity of CD4(+) T-cell responses. To investigate whether HLA-specific variations in the magnitude of response might predict associations between dengue outcomes and HLA-DRB1 alleles, we assembled samples from hospitalized patients with known severity of disease. RESULTS The capsid protein followed by nonstructural protein 3 (NS3), NS2A, and NS5 were the most targeted proteins. We further noticed a wide variation in magnitude of T-cell responses as a function of the restricting DRB1 allele and found several HLA alleles that showed trends toward a lower risk of hospitalized disease were associated with a higher magnitude of T-cell responses. CONCLUSIONS Comprehensive identification of unique CD4(+) T-cell epitopes across the 4 DENV serotypes allows the testing of T-cell responses by use of a simple, approachable technique and points to important implications for vaccine design.
Collapse
Affiliation(s)
- Daniela Weiskopf
- Division of Vaccine Discovery, La Jolla Institute for Allergy and Immunology, California
| | - Michael A Angelo
- Division of Vaccine Discovery, La Jolla Institute for Allergy and Immunology, California
| | - Alba Grifoni
- Division of Vaccine Discovery, La Jolla Institute for Allergy and Immunology, California
| | - Patrick H O'Rourke
- Division of Vaccine Discovery, La Jolla Institute for Allergy and Immunology, California
| | - John Sidney
- Division of Vaccine Discovery, La Jolla Institute for Allergy and Immunology, California
| | - Sinu Paul
- Division of Vaccine Discovery, La Jolla Institute for Allergy and Immunology, California
| | - Aruna D De Silva
- Division of Vaccine Discovery, La Jolla Institute for Allergy and Immunology, California Genetech Research Institute
| | - Elizabeth Phillips
- Department of Medicine, Vanderbilt University School of Medicine, Nashville, Tennessee Institute for Immunology and Infectious Diseases, Murdoch University, Perth, Australia
| | - Simon Mallal
- Department of Medicine, Vanderbilt University School of Medicine, Nashville, Tennessee Institute for Immunology and Infectious Diseases, Murdoch University, Perth, Australia
| | - Sunil Premawansa
- Department of Zoology and Environmental Science, Science Faculty, University of Colombo
| | | | | | - Bjoern Peters
- Division of Vaccine Discovery, La Jolla Institute for Allergy and Immunology, California
| | - Alessandro Sette
- Division of Vaccine Discovery, La Jolla Institute for Allergy and Immunology, California
| |
Collapse
|
41
|
Immunodominant Dengue Virus-Specific CD8+ T Cell Responses Are Associated with a Memory PD-1+ Phenotype. J Virol 2016; 90:4771-4779. [PMID: 26912627 DOI: 10.1128/jvi.02892-15] [Citation(s) in RCA: 59] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2015] [Accepted: 02/20/2016] [Indexed: 11/20/2022] Open
Abstract
UNLABELLED Dengue disease is a large public health problem that mainly afflicts tropical and subtropical regions. Understanding of the correlates of protection against dengue virus (DENV) is poor and hinders the development of a successful human vaccine. The present study aims to define DENV-specific CD8(+)T cell responses in general and those of HLA alleles associated with dominant responses in particular. In human blood donors in Nicaragua, we observed a striking dominance of HLA B-restricted responses in general and of the allele B*35:01 in particular. Comparing these patterns to those in the general population of Sri Lanka, we found a strong correlation between restriction of the HLA allele and the breadth and magnitude of CD8(+)T cell responses, suggesting that HLA genes profoundly influence the nature of responses. The majority of gamma interferon (IFN-γ) responses were associated with effector memory phenotypes, which were also detected in non-B*35:01-expressing T cells. However, only the B*35:01 DENV-specific T cells were associated with marked expression of the programmed death 1 protein (PD-1). These cells did not coexpress other inhibitory receptors and were able to proliferate in response to DENV-specific stimulation. Thus, the expression of particular HLA class I alleles is a defining characteristic influencing the magnitude and breadth of CD8 responses, and a distinct, highly differentiated phenotype is specifically associated with dominant CD8(+)T cells. These results are of relevance for both vaccine design and the identification of robust correlates of protection in natural immunity. IMPORTANCE Dengue is an increasingly significant public health problem as its mosquito vectors spread over greater areas; no vaccines against the virus have yet been approved. An important step toward vaccine development is defining protective immune responses; toward that end, we here characterize the phenotype of the immunodominant T cell responses. These DENV-reactive T cells express high levels of the receptor programmed death 1 protein (PD-1), while those from disease-susceptible alleles do not. Not only does this represent a possible correlate of immunodominance, but it raises the hypothesis that PD-1 might be a regulator that prevents excessive damage while preserving antiviral function. Further, as this study employs distinct populations (Nicaraguan and Sri Lankan donors), we also confirmed that this pattern holds despite geographic and ethnic differences. This finding indicates that HLA type is the major determinant in shaping T cell responses.
Collapse
|
42
|
Trolle T, McMurtrey CP, Sidney J, Bardet W, Osborn SC, Kaever T, Sette A, Hildebrand WH, Nielsen M, Peters B. The Length Distribution of Class I-Restricted T Cell Epitopes Is Determined by Both Peptide Supply and MHC Allele-Specific Binding Preference. THE JOURNAL OF IMMUNOLOGY 2016; 196:1480-7. [PMID: 26783342 DOI: 10.4049/jimmunol.1501721] [Citation(s) in RCA: 130] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Received: 07/31/2015] [Accepted: 12/13/2015] [Indexed: 12/11/2022]
Abstract
HLA class I-binding predictions are widely used to identify candidate peptide targets of human CD8(+) T cell responses. Many such approaches focus exclusively on a limited range of peptide lengths, typically 9 aa and sometimes 9-10 aa, despite multiple examples of dominant epitopes of other lengths. In this study, we examined whether epitope predictions can be improved by incorporating the natural length distribution of HLA class I ligands. We found that, although different HLA alleles have diverse length-binding preferences, the length profiles of ligands that are naturally presented by these alleles are much more homogeneous. We hypothesized that this is due to a defined length profile of peptides available for HLA binding in the endoplasmic reticulum. Based on this, we created a model of HLA allele-specific ligand length profiles and demonstrate how this model, in combination with HLA-binding predictions, greatly improves comprehensive identification of CD8(+) T cell epitopes.
Collapse
Affiliation(s)
- Thomas Trolle
- Department of Systems Biology, Center for Biological Sequence Analysis, Technical University of Denmark, DK-2800 Kongens Lyngby, Denmark
| | - Curtis P McMurtrey
- Department of Microbiology and Immunology, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104
| | - John Sidney
- Division of Vaccine Discovery, La Jolla Institute for Allergy and Immunology, La Jolla, CA 92037; and
| | - Wilfried Bardet
- Department of Microbiology and Immunology, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104
| | - Sean C Osborn
- Department of Microbiology and Immunology, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104
| | - Thomas Kaever
- Division of Vaccine Discovery, La Jolla Institute for Allergy and Immunology, La Jolla, CA 92037; and
| | - Alessandro Sette
- Division of Vaccine Discovery, La Jolla Institute for Allergy and Immunology, La Jolla, CA 92037; and
| | - William H Hildebrand
- Department of Microbiology and Immunology, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104
| | - Morten Nielsen
- Department of Systems Biology, Center for Biological Sequence Analysis, Technical University of Denmark, DK-2800 Kongens Lyngby, Denmark; Instituto de Investigaciones Biotecnológicas, Universidad Nacional de San Martín, San Martín, B 1650 HMP Buenos Aires, Argentina
| | - Bjoern Peters
- Division of Vaccine Discovery, La Jolla Institute for Allergy and Immunology, La Jolla, CA 92037; and
| |
Collapse
|
43
|
Bailey A, Dalchau N, Carter R, Emmott S, Phillips A, Werner JM, Elliott T. Selector function of MHC I molecules is determined by protein plasticity. Sci Rep 2015; 5:14928. [PMID: 26482009 PMCID: PMC5224517 DOI: 10.1038/srep14928] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2015] [Accepted: 09/09/2015] [Indexed: 12/27/2022] Open
Abstract
The selection of peptides for presentation at the surface of most nucleated cells by major histocompatibility complex class I molecules (MHC I) is crucial to the immune response in vertebrates. However, the mechanisms of the rapid selection of high affinity peptides by MHC I from amongst thousands of mostly low affinity peptides are not well understood. We developed computational systems models encoding distinct mechanistic hypotheses for two molecules, HLA-B*44:02 (B*4402) and HLA-B*44:05 (B*4405), which differ by a single residue yet lie at opposite ends of the spectrum in their intrinsic ability to select high affinity peptides. We used in vivo biochemical data to infer that a conformational intermediate of MHC I is significant for peptide selection. We used molecular dynamics simulations to show that peptide selector function correlates with protein plasticity, and confirmed this experimentally by altering the plasticity of MHC I with a single point mutation, which altered in vivo selector function in a predictable way. Finally, we investigated the mechanisms by which the co-factor tapasin influences MHC I plasticity. We propose that tapasin modulates MHC I plasticity by dynamically coupling the peptide binding region and α3 domain of MHC I allosterically, resulting in enhanced peptide selector function.
Collapse
Affiliation(s)
- Alistair Bailey
- Institute for Life Sciences, Building 85, University of Southampton, SO17 1BJ, UK
- Cancer Sciences Unit, Faculty of Medicine, University of Southampton, Southampton, SO16 6YD, UK
- Centre for Biological Sciences, Faculty of Natural & Environmental Sciences, Building 85, University of Southampton, SO17 1BJ, UK
| | - Neil Dalchau
- Computational Science Laboratory, Microsoft Research, 21 Station Road, Cambridge, CB1 2FB, UK
| | - Rachel Carter
- Institute for Life Sciences, Building 85, University of Southampton, SO17 1BJ, UK
- Cancer Sciences Unit, Faculty of Medicine, University of Southampton, Southampton, SO16 6YD, UK
| | - Stephen Emmott
- Computational Science Laboratory, Microsoft Research, 21 Station Road, Cambridge, CB1 2FB, UK
| | - Andrew Phillips
- Computational Science Laboratory, Microsoft Research, 21 Station Road, Cambridge, CB1 2FB, UK
| | - Jörn M. Werner
- Institute for Life Sciences, Building 85, University of Southampton, SO17 1BJ, UK
- Centre for Biological Sciences, Faculty of Natural & Environmental Sciences, Building 85, University of Southampton, SO17 1BJ, UK
| | - Tim Elliott
- Institute for Life Sciences, Building 85, University of Southampton, SO17 1BJ, UK
- Cancer Sciences Unit, Faculty of Medicine, University of Southampton, Southampton, SO16 6YD, UK
| |
Collapse
|
44
|
Bergmann T, Moore C, Sidney J, Miller D, Tallmadge R, Harman RM, Oseroff C, Wriston A, Shabanowitz J, Hunt DF, Osterrieder N, Peters B, Antczak DF, Sette A. The common equine class I molecule Eqca-1*00101 (ELA-A3.1) is characterized by narrow peptide binding and T cell epitope repertoires. Immunogenetics 2015; 67:675-89. [PMID: 26399241 DOI: 10.1007/s00251-015-0872-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2015] [Accepted: 09/14/2015] [Indexed: 11/29/2022]
Abstract
Here we describe a detailed quantitative peptide-binding motif for the common equine leukocyte antigen (ELA) class I allele Eqca-1*00101, present in roughly 25 % of Thoroughbred horses. We determined a preliminary binding motif by sequencing endogenously bound ligands. Subsequently, a positional scanning combinatorial library (PSCL) was used to further characterize binding specificity and derive a quantitative motif involving aspartic acid in position 2 and hydrophobic residues at the C-terminus. Using this motif, we selected and tested 9- and 10-mer peptides derived from the equine herpesvirus type 1 (EHV-1) proteome for their capacity to bind Eqca-1*00101. PSCL predictions were very efficient, with an receiver operating characteristic (ROC) curve performance of 0.877, and 87 peptides derived from 40 different EHV-1 proteins were identified with affinities of 500 nM or higher. Quantitative analysis revealed that Eqca-1*00101 has a narrow peptide-binding repertoire, in comparison to those of most human, non-human primate, and mouse class I alleles. Peripheral blood mononuclear cells from six EHV-1-infected, or vaccinated but uninfected, Eqca-1*00101-positive horses were used in IFN-γ enzyme-linked immunospot (ELISPOT) assays. When we screened the 87 Eqca-1*00101-binding peptides for T cell reactivity, only one Eqca-1*00101 epitope, derived from the intermediate-early protein ICP4, was identified. Thus, despite its common occurrence in several horse breeds, Eqca-1*00101 is associated with a narrow binding repertoire and a similarly narrow T cell response to an important equine viral pathogen. Intriguingly, these features are shared with other human and macaque major histocompatibility complex (MHC) molecules with a similar specificity for D in position 2 or 3 in their main anchor motif.
Collapse
Affiliation(s)
- Tobias Bergmann
- Institut für Virologie, Freie Universtiät Berlin, 14163, Berlin, Germany
| | - Carrie Moore
- Department of Vaccine Discovery, La Jolla Institute for Allergy and Immunology, La Jolla, CA, 92037, USA
| | - John Sidney
- Department of Vaccine Discovery, La Jolla Institute for Allergy and Immunology, La Jolla, CA, 92037, USA
| | - Donald Miller
- Baker Institute for Animal Health, College of Veterinary Medicine, Cornell University, Ithaca, NY, 14853, USA
| | - Rebecca Tallmadge
- Department of Clinical Sciences, College of Veterinary Medicine, Cornell University, Ithaca, NY, 14853, USA
| | - Rebecca M Harman
- Baker Institute for Animal Health, College of Veterinary Medicine, Cornell University, Ithaca, NY, 14853, USA
| | - Carla Oseroff
- Department of Vaccine Discovery, La Jolla Institute for Allergy and Immunology, La Jolla, CA, 92037, USA
| | - Amanda Wriston
- Department of Chemistry, University of Virginia, Charlottesville, VA, 22904, USA
| | - Jeffrey Shabanowitz
- Department of Chemistry, University of Virginia, Charlottesville, VA, 22904, USA
| | - Donald F Hunt
- Department of Chemistry, University of Virginia, Charlottesville, VA, 22904, USA.,Department of Pathology, University of Virginia, Charlottesville, VA, 22904, USA
| | | | - Bjoern Peters
- Department of Vaccine Discovery, La Jolla Institute for Allergy and Immunology, La Jolla, CA, 92037, USA
| | - Douglas F Antczak
- Baker Institute for Animal Health, College of Veterinary Medicine, Cornell University, Ithaca, NY, 14853, USA
| | - Alessandro Sette
- Department of Vaccine Discovery, La Jolla Institute for Allergy and Immunology, La Jolla, CA, 92037, USA.
| |
Collapse
|
45
|
Leblanc P, Moise L, Luza C, Chantaralawan K, Lezeau L, Yuan J, Field M, Richer D, Boyle C, Martin WD, Fishman JB, Berg EA, Baker D, Zeigler B, Mais DE, Taylor W, Coleman R, Warren HS, Gelfand JA, De Groot AS, Brauns T, Poznansky MC. VaxCelerate II: rapid development of a self-assembling vaccine for Lassa fever. Hum Vaccin Immunother 2015; 10:3022-38. [PMID: 25483693 DOI: 10.4161/hv.34413] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Development of effective vaccines against emerging infectious diseases (EID) can take as much or more than a decade to progress from pathogen isolation/identification to clinical approval. As a result, conventional approaches fail to produce field-ready vaccines before the EID has spread extensively. Lassa is a prototypical emerging infectious disease endemic to West Africa for which no successful vaccine is available. We established the VaxCelerate Consortium to address the need for more rapid vaccine development by creating a platform capable of generating and pre-clinically testing a new vaccine against specific pathogen targets in less than 120 d A self-assembling vaccine is at the core of the approach. It consists of a fusion protein composed of the immunostimulatory Mycobacterium tuberculosis heat shock protein 70 (MtbHSP70) and the biotin binding protein, avidin. Mixing the resulting protein (MAV) with biotinylated pathogen-specific immunogenic peptides yields a self-assembled vaccine (SAV). To meet the time constraint imposed on this project, we used a distributed R&D model involving experts in the fields of protein engineering and production, bioinformatics, peptide synthesis/design and GMP/GLP manufacturing and testing standards. SAV immunogenicity was first tested using H1N1 influenza specific peptides and the entire VaxCelerate process was then tested in a mock live-fire exercise targeting Lassa fever virus. We demonstrated that the Lassa fever vaccine induced significantly increased class II peptide specific interferon-γ CD4(+) T cell responses in HLA-DR3 transgenic mice compared to peptide or MAV alone controls. We thereby demonstrated that our SAV in combination with a distributed development model may facilitate accelerated regulatory review by using an identical design for each vaccine and by applying safety and efficacy assessment tools that are more relevant to human vaccine responses than current animal models.
Collapse
Key Words
- 6MDP, 6-muramyl dipeptide
- CGE, Capillary Gel Electrophoresis
- CLO97, TLR7 ligand
- CTL, Cytotoxic T-lymphocyte
- CpG1826, Synthetic Oligodeoxynucleotide containing unmethylated dinucleotide sequences (Toll-like receptor 9 agonist)
- DARPA, Defense Advanced Research Projects Agency
- EIDs, Emerging Infectious Diseases
- Flu vaccine
- GLP, Good Laboratory Practice
- GMP, Good Manufacturing Practice
- GP1, Glycoprotein-1
- GP2, Glycoprotein-2
- HLA, Human Leukocyte Antigen
- HRP, Horseradish Peroxidase
- LV, Lassa Fever Virus
- Lassa fever virus
- MAV, Mycobacterium tuberculosis Heat Shock Protein 70 – Avidin
- MtbHSP70, Mycobacterium tuberculosis Heat Shock Protein 70
- NHP, Non-human Primates
- OVA, Ovalbumin
- PAGE, Polyacrylamide Gel Electrophoresis
- PBMC, Peripheral Blood Mononuclear Cell
- PEG, Polyethyleneglycol
- RVKR, Furin Cleavage Site (Arginine, Valine, Lysine, Arginine)
- SAV, Self-assembled vaccine
- SAVL; Self-assembled vaccine formulated for Lassa Fever Virus
- VaxCelerate
- arenavirus
- emerging infectious diseases
- mycobacterium tuberculosis heat shock protein 70
- peptide design
- self-assembled vaccine
- vaccine
Collapse
Affiliation(s)
- Pierre Leblanc
- a Vaccine and Immunotherapy Center; Massachusetts General Hospital ; Charlestown , MA USA
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
46
|
The Nucleoprotein Is Required for Lymphocytic Choriomeningitis Virus-Based Vaccine Vector Immunogenicity. J Virol 2015; 89:11734-8. [PMID: 26355095 DOI: 10.1128/jvi.01613-15] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2015] [Accepted: 09/06/2015] [Indexed: 12/14/2022] Open
Abstract
Recombinant glycoprotein-deficient lymphocytic choriomeningitis virus-based vaccine vectors (rLCMV/ΔGP) are potent CD8(+) T cell inducers. To investigate the underlying molecular requirements, we generated a nucleoprotein-deficient vector counterpart (rLCMV/ΔNP). NP but not GP is a minimal trans-acting factor for viral transcription and genome replication. We found that, unlike rLCMV/ΔGP, rLCMV/ΔNP failed to elicit detectable CD8(+) T cell responses unless NP was trans complemented in a transgenic host. Hence, NP-dependent intracellular gene expression is essential for LCMV vector immunogenicity.
Collapse
|
47
|
CD169+ macrophages are sufficient for priming of CTLs with specificities left out by cross-priming dendritic cells. Proc Natl Acad Sci U S A 2015; 112:5461-6. [PMID: 25922518 DOI: 10.1073/pnas.1423356112] [Citation(s) in RCA: 90] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Dendritic cells (DCs) are considered the most potent antigen-presenting cells (APCs), which directly prime or cross-prime MHC I-restricted cytotoxic T cells (CTLs). However, recent evidence suggests the existence of other, as-yet unidentified APCs also able to prime T cells. To identify those APCs, we used adenoviral (rAd) vectors, which do not infect DCs but selectively accumulate in CD169(+) macrophages (MPs). In mice that lack DCs, infection of CD169(+) MPs was sufficient to prime CTLs specific for all epitopes tested. In contrast, CTL responses relying exclusively on cross-presenting DCs were biased to selected strong MHC I-binding peptides only. When both DCs and MPs were absent, no CTL responses could be elicited. Therefore, CD169(+) MPs can be considered APCs that significantly contribute to CTL responses.
Collapse
|
48
|
Evaluation of non-reciprocal heterologous immunity between unrelated viruses. Virology 2015; 482:89-97. [PMID: 25838115 DOI: 10.1016/j.virol.2015.03.002] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2014] [Revised: 12/17/2014] [Accepted: 03/03/2015] [Indexed: 11/22/2022]
Abstract
Heterologous immunity refers to the phenomenon whereby a history of an immune response against one pathogen can provide a level of immunity to a second unrelated pathogen. Previous investigations have shown that heterologous immunity is not necessarily reciprocal, such as in the case of vaccinia virus (VACV). Replication of VACV is reduced in mice immune to a variety of pathogens, while VACV fails to induce immunity to several of the same pathogens, including lymphocytic choriomeningitis virus (LCMV). Here we examine the lack of reciprocity of heterologous immunity between VACV and LCMV and find that they induce qualitatively different memory CD8 T cells. However, depending on the repertoire of an individual host, VACV can provide protection against LCMV simply by experimentally amplifying the quantity of T cells cross-reactive with the two viruses. Thus, one cause for lack of reciprocity is differences in the frequencies of cross-reactive T cells in immune hosts.
Collapse
|
49
|
Cheloha RW, Sullivan J, Wang T, Sand JM, Sidney J, Sette A, Cook ME, Suresh M, Gellman SH. Consequences of periodic α-to-β(3) residue replacement for immunological recognition of peptide epitopes. ACS Chem Biol 2015; 10:844-54. [PMID: 25559929 PMCID: PMC4372116 DOI: 10.1021/cb500888q] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2014] [Accepted: 12/08/2014] [Indexed: 01/27/2023]
Abstract
Oligomers that contain both α- and β-amino acid residues, or "α/β-peptides", have emerged as promising mimics of signal-bearing polypeptides that can inhibit or augment natural protein-protein interactions. α/β-Peptides that contain a sufficient proportion of β residues evenly distributed along the sequence can be highly resistant to enzymatic degradation, which is favorable with regard to in vivo applications. Little is known, however, about recognition of α/β-peptides by the immune system. Prior studies have focused almost entirely on examples that contain a single β residue; such α/β-peptides frequently retain the immunological profile of the analogous α-peptide. We have conducted α-peptide vs α/β-peptide comparisons involving higher β residue content, focusing on molecules with αααβ and ααβαααβ backbone repeat patterns. Among analogues of an 18-mer derived from the Bim BH3 domain and an 8-mer derived from secreted phospholipase-2 (sPLA2), we find that recognition by antibodies raised against the prototype α-peptide is suppressed by periodic α → β replacements. Complementary studies reveal that antibodies raised against Bim BH3- or sPLA2-derived α/β-peptides fail to recognize prototype α-peptides displaying identical side chain repertoires. Because polypeptides containing d-α-amino acid residues are of growing interest for biomedical applications, we included the enantiomer of the sPLA2-derived α-peptide in these studies; this d-peptide is fully competent as a hapten, but the resulting antibodies do not cross react with the enantiomeric peptide. Among analogues of the 9-mer CD8(+) T-cell viral epitope GP33, we observe that periodic α → β replacements suppress participation in the MHC I + peptide + T-cell receptor ternary complexes that activate cytotoxic T-lymphocytes, due in part to disruption of MHC binding.
Collapse
MESH Headings
- Amino Acid Sequence
- Animals
- Antibodies/chemistry
- Antibodies/immunology
- Antibodies/isolation & purification
- Antibody Specificity
- Antigens, Viral/chemistry
- Antigens, Viral/immunology
- Apoptosis Regulatory Proteins/chemistry
- Apoptosis Regulatory Proteins/immunology
- Bcl-2-Like Protein 11
- Binding Sites
- Chickens
- Enzyme-Linked Immunosorbent Assay
- Epitopes/chemistry
- Epitopes/immunology
- Humans
- Kinetics
- Membrane Proteins/chemistry
- Membrane Proteins/immunology
- Models, Molecular
- Molecular Sequence Data
- Oligopeptides/chemical synthesis
- Oligopeptides/chemistry
- Oligopeptides/immunology
- Phospholipases A2/chemistry
- Phospholipases A2/immunology
- Protein Binding
- Protein Structure, Secondary
- Protein Structure, Tertiary
- Proto-Oncogene Proteins/chemistry
- Proto-Oncogene Proteins/immunology
- Receptors, Antigen, T-Cell/chemistry
- Receptors, Antigen, T-Cell/immunology
- Stereoisomerism
- T-Lymphocytes, Cytotoxic/cytology
- T-Lymphocytes, Cytotoxic/immunology
Collapse
Affiliation(s)
- Ross W. Cheloha
- Department of Chemistry, Department of Surgery, Department of Pathobiological Sciences, Department of Animal
Sciences, University of Wisconsin, Madison, Wisconsin 53706, United States
| | - Jeremy
A. Sullivan
- Department of Chemistry, Department of Surgery, Department of Pathobiological Sciences, Department of Animal
Sciences, University of Wisconsin, Madison, Wisconsin 53706, United States
| | - Tong Wang
- Department of Chemistry, Department of Surgery, Department of Pathobiological Sciences, Department of Animal
Sciences, University of Wisconsin, Madison, Wisconsin 53706, United States
| | - Jordan M. Sand
- Department of Chemistry, Department of Surgery, Department of Pathobiological Sciences, Department of Animal
Sciences, University of Wisconsin, Madison, Wisconsin 53706, United States
| | - John Sidney
- La
Jolla Institute for Allergy and Immunology, La Jolla, California United States
| | - Alessandro Sette
- La
Jolla Institute for Allergy and Immunology, La Jolla, California United States
| | - Mark E. Cook
- Department of Chemistry, Department of Surgery, Department of Pathobiological Sciences, Department of Animal
Sciences, University of Wisconsin, Madison, Wisconsin 53706, United States
| | - M. Suresh
- Department of Chemistry, Department of Surgery, Department of Pathobiological Sciences, Department of Animal
Sciences, University of Wisconsin, Madison, Wisconsin 53706, United States
| | - Samuel H. Gellman
- Department of Chemistry, Department of Surgery, Department of Pathobiological Sciences, Department of Animal
Sciences, University of Wisconsin, Madison, Wisconsin 53706, United States
| |
Collapse
|
50
|
Johnson S, Bergthaler A, Graw F, Flatz L, Bonilla WV, Siegrist CA, Lambert PH, Regoes RR, Pinschewer DD. Protective efficacy of individual CD8+ T cell specificities in chronic viral infection. THE JOURNAL OF IMMUNOLOGY 2015; 194:1755-62. [PMID: 25567678 DOI: 10.4049/jimmunol.1401771] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Specific CD8(+) T cells (CTLs) play an important role in resolving protracted infection with hepatitis B and C virus in humans and lymphocytic choriomeningitis virus (LCMV) in mice. The contribution of individual CTL specificities to chronic virus control, as well as epitope-specific patterns in timing and persistence of antiviral selection pressure, remain, however, incompletely defined. To monitor and characterize the antiviral efficacy of individual CTL specificities throughout the course of chronic infection, we coinoculated mice with a mixture of wild-type LCMV and genetically engineered CTL epitope-deficient mutant virus. A quantitative longitudinal assessment of viral competition revealed that mice continuously exerted CTL selection pressure on the persisting virus population. The timing of selection pressure characterized individual epitope specificities, and its magnitude varied considerably between individual mice. This longitudinal assessment of "antiviral efficacy" provides a novel parameter to characterize CTL responses in chronic viral infection. It demonstrates remarkable perseverance of all antiviral CTL specificities studied, thus raising hope for therapeutic vaccination in the treatment of persistent viral diseases.
Collapse
Affiliation(s)
- Susan Johnson
- Department of Pathology and Immunology, University of Geneva, 1211 Geneva 4, Switzerland; World Health Organization Collaborating Centre for Vaccine Immunology, University of Geneva, 1211 Geneva 4, Switzerland
| | - Andreas Bergthaler
- Department of Pathology and Immunology, University of Geneva, 1211 Geneva 4, Switzerland; CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090 Vienna, Austria
| | - Frederik Graw
- Center for Modeling and Simulation in the Biosciences, BioQuant-Center, Heidelberg University, 69120 Heidelberg, Germany; Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, NM 87544; Institute of Integrative Biology, ETH Zurich, 8092 Zurich, Switzerland
| | - Lukas Flatz
- Department of Pathology and Immunology, University of Geneva, 1211 Geneva 4, Switzerland; Department of Dermatology, University Hospital of Lausanne, 1011 Lausanne, Switzerland; and
| | - Weldy V Bonilla
- Department of Pathology and Immunology, University of Geneva, 1211 Geneva 4, Switzerland; World Health Organization Collaborating Centre for Vaccine Immunology, University of Geneva, 1211 Geneva 4, Switzerland; Division of Experimental Virology, Department of Biomedicine, University of Basel, 4009 Basel, Switzerland
| | - Claire-Anne Siegrist
- Department of Pathology and Immunology, University of Geneva, 1211 Geneva 4, Switzerland; World Health Organization Collaborating Centre for Vaccine Immunology, University of Geneva, 1211 Geneva 4, Switzerland
| | - Paul-Henri Lambert
- Department of Pathology and Immunology, University of Geneva, 1211 Geneva 4, Switzerland; World Health Organization Collaborating Centre for Vaccine Immunology, University of Geneva, 1211 Geneva 4, Switzerland
| | - Roland R Regoes
- Institute of Integrative Biology, ETH Zurich, 8092 Zurich, Switzerland
| | - Daniel D Pinschewer
- Department of Pathology and Immunology, University of Geneva, 1211 Geneva 4, Switzerland; World Health Organization Collaborating Centre for Vaccine Immunology, University of Geneva, 1211 Geneva 4, Switzerland; Division of Experimental Virology, Department of Biomedicine, University of Basel, 4009 Basel, Switzerland
| |
Collapse
|