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Hulme KD, Tong ZWM, Rowntree LC, van de Sandt CE, Ronacher K, Grant EJ, Dorey ES, Gallo LA, Gras S, Kedzierska K, Barrett HL, Short KR. Increasing HbA1c is associated with reduced CD8 + T cell functionality in response to influenza virus in a TCR-dependent manner in individuals with diabetes mellitus. Cell Mol Life Sci 2024; 81:35. [PMID: 38214784 PMCID: PMC10786977 DOI: 10.1007/s00018-023-05010-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Revised: 10/11/2023] [Accepted: 10/22/2023] [Indexed: 01/13/2024]
Abstract
Diabetes mellitus is on the rise globally and is a known susceptibility factor for severe influenza virus infections. However, the mechanisms by which diabetes increases the severity of an influenza virus infection are yet to be fully defined. Diabetes mellitus is hallmarked by high glucose concentrations in the blood. We hypothesized that these high glucose concentrations affect the functionality of CD8+ T cells, which play a key role eliminating virus-infected cells and have been shown to decrease influenza disease severity. To study the effect of hyperglycemia on CD8+ T cell function, we stimulated peripheral blood mononuclear cells (PBMCs) from donors with and without diabetes with influenza A virus, anti-CD3/anti-CD28-coated beads, PMA and ionomycin (PMA/I), or an influenza viral peptide pool. After stimulation, cells were assessed for functionality [as defined by expression of IFN-γ, TNF-α, macrophage inflammatory protein (MIP)-1β, and lysosomal-associated membrane protein-1 (CD107a)] using flow cytometry. Our results showed that increasing HbA1c correlated with a reduction in TNF-α production by CD8+ T cells in response to influenza stimulation in a TCR-specific manner. This was not associated with any changes to CD8+ T cell subsets. We conclude that hyperglycemia impairs CD8+ T cell function to influenza virus infection, which may be linked with the increased risk of severe influenza in patients with diabetes.
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Affiliation(s)
- Katina D Hulme
- School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, QLD, Australia
- Department of Medical Microbiology & Infection Prevention, Amsterdam University Medical Center, University of Amsterdam, Amsterdam, The Netherlands
| | - Zhen Wei Marcus Tong
- School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, QLD, Australia
| | - Louise C Rowntree
- Department of Microbiology and Immunology, University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Parkville, VIC, Australia
| | - Carolien E van de Sandt
- Department of Microbiology and Immunology, University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Parkville, VIC, Australia
- Department of Hematopoiesis, Sanquin Research and Landsteiner Laboratory, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
| | - Katharina Ronacher
- Mater Research Institute, Translational Research Institute, The University of Queensland, Brisbane, Australia
- Australian Infectious Diseases Research Centre, The University of Queensland, St Lucia, QLD, Australia
| | - Emma J Grant
- Department of Biochemistry and Chemistry, La Trobe Institute for Molecular Science, La Trobe University, Bundoora, VIC, Australia
- Department of Biochemistry and Molecular Biology and Infection and Immunity Program, Biomedicine Discovery Institute, Monash University, Clayton, VIC, Australia
| | - Emily S Dorey
- Mater Research Institute, Translational Research Institute, The University of Queensland, Brisbane, Australia
| | - Linda A Gallo
- School of Biomedical Sciences, The University of Queensland, St Lucia, QLD, Australia
- School of Health and Behavioural Sciences, University of the Sunshine Coast, Moreton Bay, QLD, Australia
| | - Stephanie Gras
- Department of Biochemistry and Chemistry, La Trobe Institute for Molecular Science, La Trobe University, Bundoora, VIC, Australia
- Department of Biochemistry and Molecular Biology and Infection and Immunity Program, Biomedicine Discovery Institute, Monash University, Clayton, VIC, Australia
| | - Katherine Kedzierska
- Department of Microbiology and Immunology, University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Parkville, VIC, Australia
| | - Helen L Barrett
- Mater Research Institute, Translational Research Institute, The University of Queensland, Brisbane, Australia
- Obstetric Medicine, The Royal Hospital for Women, Randwick, NSW, Australia
- School of Medicine, UNSW, Randwick, NSW, Australia
| | - Kirsty R Short
- School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, QLD, Australia.
- Australian Infectious Diseases Research Centre, The University of Queensland, St Lucia, QLD, Australia.
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2
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Binayke A, Zaheer A, Vishwakarma S, Singh S, Sharma P, Chandwaskar R, Gosain M, Raghavan S, Murugesan DR, Kshetrapal P, Thiruvengadam R, Bhatnagar S, Pandey AK, Garg PK, Awasthi A. A quest for universal anti-SARS-CoV-2 T cell assay: systematic review, meta-analysis, and experimental validation. NPJ Vaccines 2024; 9:3. [PMID: 38167915 PMCID: PMC10762233 DOI: 10.1038/s41541-023-00794-9] [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: 07/02/2023] [Accepted: 12/08/2023] [Indexed: 01/05/2024] Open
Abstract
Measuring SARS-CoV-2-specific T cell responses is crucial to understanding an individual's immunity to COVID-19. However, high inter- and intra-assay variability make it difficult to define T cells as a correlate of protection against COVID-19. To address this, we performed systematic review and meta-analysis of 495 datasets from 94 original articles evaluating SARS-CoV-2-specific T cell responses using three assays - Activation Induced Marker (AIM), Intracellular Cytokine Staining (ICS), and Enzyme-Linked Immunospot (ELISPOT), and defined each assay's quantitative range. We validated these ranges using samples from 193 SARS-CoV-2-exposed individuals. Although IFNγ ELISPOT was the preferred assay, our experimental validation suggested that it under-represented the SARS-CoV-2-specific T cell repertoire. Our data indicate that a combination of AIM and ICS or FluoroSpot assay would better represent the frequency, polyfunctionality, and compartmentalization of the antigen-specific T cell responses. Taken together, our results contribute to defining the ranges of antigen-specific T cell assays and propose a choice of assay that can be employed to better understand the cellular immune response against viral diseases.
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Affiliation(s)
- Akshay Binayke
- Immunology Core Laboratory, Translational Health Science and Technology Institute, Faridabad, India
- Centre for Immunobiology and Immunotherapy, Translational Health Science and Technology Institute, Faridabad, India
- Jawaharlal Nehru University, New Delhi, India
| | - Aymaan Zaheer
- Immunology Core Laboratory, Translational Health Science and Technology Institute, Faridabad, India
| | - Siddhesh Vishwakarma
- Immunology Core Laboratory, Translational Health Science and Technology Institute, Faridabad, India
| | - Savita Singh
- Translational Health Science and Technology Institute, Faridabad, India
| | - Priyanka Sharma
- Immunology Core Laboratory, Translational Health Science and Technology Institute, Faridabad, India
| | - Rucha Chandwaskar
- Department of Microbiology, AMITY University Rajasthan, Jaipur, India
| | - Mudita Gosain
- Translational Health Science and Technology Institute, Faridabad, India
| | | | | | | | - Ramachandran Thiruvengadam
- Translational Health Science and Technology Institute, Faridabad, India
- Pondicherry Institute of Medical Sciences, Puducherry, India
| | | | | | - Pramod Kumar Garg
- Translational Health Science and Technology Institute, Faridabad, India
- All India Institute of Medical Sciences, New Delhi, India
| | - Amit Awasthi
- Immunology Core Laboratory, Translational Health Science and Technology Institute, Faridabad, India.
- Centre for Immunobiology and Immunotherapy, Translational Health Science and Technology Institute, Faridabad, India.
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3
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Schnatbaum K, Holenya P, Pfeil S, Drosch M, Eckey M, Reimer U, Wenschuh H, Kern F. An Overview of Peptides and Peptide Pools for Antigen-Specific Stimulation in T-Cell Assays. Methods Mol Biol 2024; 2768:29-50. [PMID: 38502386 DOI: 10.1007/978-1-0716-3690-9_3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/21/2024]
Abstract
The analysis of antigen-specific T-cell responses has become routine in many laboratories. Functional T-cell assays like enzyme-linked-immuno-spot (ELISPOT), which depend on antigen-specific stimulation, increasingly use peptides to represent the antigen of interest. Besides single peptides, mixtures of peptides (peptide pools) are very frequently applied. Such peptide pools may, for example, represent entire proteins (with overlapping peptides covering a protein sequence) or include noncontiguous peptides such as a collection of T-cell-stimulating peptides. The optimum specification of single peptides or peptide pools for T-cell stimulation assays will depend on the purpose of the test, the target T-cell population, the availability of sample, requirements regarding reproducibility, and, last but not least, the available budget, to mention only the most important factors. Because of the way peptides are produced, they will always contain certain amounts of impurities such as peptides with deletions or truncated peptides, and there may be additional by-products of peptide synthesis. Optimized synthesis protocols as well as purification help reduce impurities that might otherwise cause false-positive assay results. However, specific requirements with respect to purity will vary depending on the purpose of an assay. Finally, storage conditions significantly affect the shelf life of peptides, which is relevant especially for longitudinal studies. The present book chapter addresses all of these aspects in detail. It should provide the researcher with all necessary background knowledge for making the right decisions when it comes to choosing, using, and storing peptides for ELISPOT and other T-cell stimulation assays.
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Affiliation(s)
| | | | | | | | | | - Ulf Reimer
- JPT Peptide Technologies, Berlin, Germany
| | | | - Florian Kern
- JPT Peptide Technologies, Berlin, Germany.
- Brighton and Sussex Medical School, Brighton, UK.
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4
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Lehmann AA, Roen DR, Megyesi Z, Lehmann PV. Reagent Tracker ™ Platform Verifies and Provides Audit Trails for the Error-Free Implementation of T-Cell ImmunoSpot ® Assays. Methods Mol Biol 2024; 2768:105-115. [PMID: 38502390 DOI: 10.1007/978-1-0716-3690-9_7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/21/2024]
Abstract
ELISPOT and FluoroSpot assays, collectively called ImmunoSpot assays, permit to reliable detection of rare antigen-specific T cells in freshly isolated cell material, such as peripheral blood mononuclear cells (PBMC). Establishing their frequency within all PBMC permits to assess the magnitude of antigen-specific T-cell immunity; the simultaneous measurement of their cytokine signatures reveals these T-cells' lineage and effector functions, that is, the quality of T-cell-mediated immunity. Because of their unparalleled sensitivity, ease of implementation, robustness, and frugality in PBMC utilization, T-cell ImmunoSpot assays are increasingly becoming part of the standard immune monitoring repertoire. For regulated workflows, stringent audit trails of the data generated are a requirement. While this has been fully accomplished for the analysis of T-cell ImmunoSpot assay results, such are missing for the wet laboratory implementation of the actual test performed. Here we introduce a solution for enhancing and verifying the error-free implementation of T-cell ImmunoSpot assays.
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Affiliation(s)
- Alexander A Lehmann
- Department of Research & Development, Cellular Technology Limited, Shaker Heights, OH, USA.
| | - Diana R Roen
- Department of Research & Development, Cellular Technology Limited, Shaker Heights, OH, USA
| | - Zoltán Megyesi
- Department of Research & Development, Cellular Technology Limited, Shaker Heights, OH, USA
| | - Paul V Lehmann
- Department of Research & Development, Cellular Technology Limited, Shaker Heights, OH, USA
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5
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Zhao X, Wang X, Yuan M, Zhang X, Yang X, Guan X, Li S, Ma J, Qiu HJ, Li Y. Identification of two novel T cell epitopes on the E2 protein of classical swine fever virus C-strain. Vet Microbiol 2023; 284:109814. [PMID: 37356277 DOI: 10.1016/j.vetmic.2023.109814] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Revised: 06/11/2023] [Accepted: 06/14/2023] [Indexed: 06/27/2023]
Abstract
C-strain, also known as the HCLV strain, is a well-known live attenuated vaccine against classical swine fever (CSF), a devastating disease caused by classical swine fever virus (CSFV). Vaccination with C-strain induces a rapid onset of protection, which is associated with virus-specific gamma interferon (IFN-γ)-secreting CD8+ T cell responses. The E2 protein of CSFV is a major protective antigen. However, the T cell epitopes on the E2 protein remain largely unknown. In this study, eight overlapping nonapeptides of the E2 protein were predicted and synthesized to screen for potential T cell epitopes on the CSFV C-strain E2 protein. Molecular docking was performed on the candidate epitopes with the swine leukocyte antigen-1*0401. The analysis obtained two highly conserved T cell epitopes, 90STEEMGDDF98 and 331ATDRHSDYF339, which were further identified by enzyme-linked immunospot assay. Interestingly, the mutants deleting or substituting the epitopes are nonviable. Further analysis demonstrated that 90STEEMGDDF98 is crucial for the E2 homodimerization, while CSFV infection is significantly inhibited by the 331ATDRHSDYF339 peptide treatment. The two novel T cell epitopes can be used to design new vaccines that are able to provide rapid-onset protection.
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Affiliation(s)
- Xiaotian Zhao
- State Key Laboratory for Animal Disease Control and Prevention, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, China; Tianjin Key Laboratory of Agricultural Animal Breeding and Healthy Husbandry, College of Animal Science and Veterinary Medicine, Tianjin Agricultural University, Tianjin, China
| | - Xiao Wang
- Department of Pathogenic Biology, School of Basic Medical Sciences, Binzhou Medical University, Yantai, China
| | - Mengqi Yuan
- State Key Laboratory for Animal Disease Control and Prevention, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, China
| | - Xin Zhang
- State Key Laboratory for Animal Disease Control and Prevention, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, China
| | - Xiaoke Yang
- State Key Laboratory for Animal Disease Control and Prevention, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, China
| | - Xiangyu Guan
- State Key Laboratory for Animal Disease Control and Prevention, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, China
| | - Shuwen Li
- State Key Laboratory for Animal Disease Control and Prevention, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, China
| | - Jifei Ma
- Tianjin Key Laboratory of Agricultural Animal Breeding and Healthy Husbandry, College of Animal Science and Veterinary Medicine, Tianjin Agricultural University, Tianjin, China.
| | - Hua-Ji Qiu
- State Key Laboratory for Animal Disease Control and Prevention, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, China.
| | - Yongfeng Li
- State Key Laboratory for Animal Disease Control and Prevention, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, China.
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Eickhoff CS, Meza KA, Terry FE, Colbert CG, Blazevic A, Gutiérrez AH, Stone ET, Brien JD, Pinto AK, El Sahly HM, Mulligan MJ, Rouphael N, Alcaide ML, Tomashek KM, Focht C, Martin WD, Moise L, De Groot AS, Hoft DF. Identification of immunodominant T cell epitopes induced by natural Zika virus infection. Front Immunol 2023; 14:1247876. [PMID: 37705976 PMCID: PMC10497216 DOI: 10.3389/fimmu.2023.1247876] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2023] [Accepted: 08/07/2023] [Indexed: 09/15/2023] Open
Abstract
Zika virus (ZIKV) is a flavivirus primarily transmitted by Aedes species mosquitoes, first discovered in Africa in 1947, that disseminated through Southeast Asia and the Pacific Islands in the 2000s. The first ZIKV infections in the Americas were identified in 2014, and infections exploded through populations in Brazil and other countries in 2015/16. ZIKV infection during pregnancy can cause severe brain and eye defects in offspring, and infection in adults has been associated with higher risks of Guillain-Barré syndrome. We initiated a study to describe the natural history of Zika (the disease) and the immune response to infection, for which some results have been reported. In this paper, we identify ZIKV-specific CD4+ and CD8+ T cell epitopes that induce responses during infection. Two screening approaches were utilized: an untargeted approach with overlapping peptide arrays spanning the entire viral genome, and a targeted approach utilizing peptides predicted to bind human MHC molecules. Immunoinformatic tools were used to identify conserved MHC class I supertype binders and promiscuous class II binding peptide clusters predicted to bind 9 common class II alleles. T cell responses were evaluated in overnight IFN-γ ELISPOT assays. We found that MHC supertype binding predictions outperformed the bulk overlapping peptide approach. Diverse CD4+ T cell responses were observed in most ZIKV-infected participants, while responses to CD8+ T cell epitopes were more limited. Most individuals developed a robust T cell response against epitopes restricted to a single MHC class I supertype and only a single or few CD8+ T cell epitopes overall, suggesting a strong immunodominance phenomenon. Noteworthy is that many epitopes were commonly immunodominant across persons expressing the same class I supertype. Nearly all of the identified epitopes are unique to ZIKV and are not present in Dengue viruses. Collectively, we identified 31 immunogenic peptides restricted by the 6 major class I supertypes and 27 promiscuous class II epitopes. These sequences are highly relevant for design of T cell-targeted ZIKV vaccines and monitoring T cell responses to Zika virus infection and vaccination.
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Affiliation(s)
- Christopher S. Eickhoff
- Department of Internal Medicine, Saint Louis University, Division of Infectious Diseases, Allergy, and Immunology, Saint Louis, MO, United States
| | - Krystal A. Meza
- Department of Internal Medicine, Saint Louis University, Division of Infectious Diseases, Allergy, and Immunology, Saint Louis, MO, United States
| | | | - Chase G. Colbert
- Department of Internal Medicine, Saint Louis University, Division of Infectious Diseases, Allergy, and Immunology, Saint Louis, MO, United States
| | - Azra Blazevic
- Department of Internal Medicine, Saint Louis University, Division of Infectious Diseases, Allergy, and Immunology, Saint Louis, MO, United States
| | | | - E. Taylor Stone
- Department of Molecular Microbiology and Immunology, Saint Louis University, Saint Louis, MO, United States
| | - James D. Brien
- Department of Molecular Microbiology and Immunology, Saint Louis University, Saint Louis, MO, United States
| | - Amelia K. Pinto
- Department of Molecular Microbiology and Immunology, Saint Louis University, Saint Louis, MO, United States
| | - Hana M. El Sahly
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, United States
| | - Mark J. Mulligan
- New York University Grossman School of Medicine, Division of Infectious Diseases and Immunology, New York, NY, United States
| | - Nadine Rouphael
- Emory University School of Medicine, Division of Infectious Diseases, Department of Internal Medicine, Atlanta, GA, United States
| | - Maria L. Alcaide
- University of Miami, Division of Infectious Diseases, Miller School of Medicine, Miami, FL, United States
| | - Kay M. Tomashek
- Division of Microbiology, Immunology and Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health (NIH), Bethesda, MD, United States
| | - Chris Focht
- The Emmes Company, LLC., Rockville, MD, United States
| | | | | | - Anne S. De Groot
- EpiVax, Inc., Providence, RI, United States
- University of Georgia Center for Vaccines and Immunology, Athens, GA, United States
| | - Daniel F. Hoft
- Department of Internal Medicine, Saint Louis University, Division of Infectious Diseases, Allergy, and Immunology, Saint Louis, MO, United States
- Department of Molecular Microbiology and Immunology, Saint Louis University, Saint Louis, MO, United States
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7
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Mørk SK, Kongsted P, Westergaard MCW, Albieri B, Granhøj JS, Donia M, Martinenaite E, Holmström MO, Madsen K, Kverneland AH, Kjeldsen JW, Holmstroem RB, Lorentzen CL, Nørgaard N, Andreasen LV, Wood GK, Christensen D, Klausen MS, Hadrup SR, thor Straten P, Andersen MH, Svane IM. First in man study: Bcl-Xl_42-CAF®09b vaccines in patients with locally advanced prostate cancer. Front Immunol 2023; 14:1122977. [PMID: 36999039 PMCID: PMC10043415 DOI: 10.3389/fimmu.2023.1122977] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Accepted: 02/23/2023] [Indexed: 03/15/2023] Open
Abstract
BackgroundThe B-cell lymphoma-extra-large (Bcl-XL) protein plays an important role in cancer cells’ resistance to apoptosis. Pre-clinical studies have shown that vaccination with Bcl-XL-derived peptides can induce tumor-specific T cell responses that may lead to the elimination of cancer cells. Furthermore, pre-clinical studies of the novel adjuvant CAF®09b have shown that intraperitoneal (IP) injections of this adjuvant can improve the activation of the immune system. In this study, patients with hormone-sensitive prostate cancer (PC) received a vaccine consisting of Bcl-XL-peptide with CAF®09b as an adjuvant. The primary aim was to evaluate the tolerability and safety of IP and intramuscular (IM) administration, determine the optimal route of administration, and characterize vaccine immunogenicity.Patients and methodsTwenty patients were included. A total of six vaccinations were scheduled: in Group A (IM to IP injections), ten patients received three vaccines IM biweekly; after a three-week pause, patients then received three vaccines IP biweekly. In Group B (IP to IM injections), ten patients received IP vaccines first, followed by IM under a similar vaccination schedule. Safety was assessed by logging and evaluating adverse events (AE) according to Common Terminology Criteria for Adverse Events (CTCAE v. 4.0). Vaccines-induced immune responses were analyzed by Enzyme-Linked Immunospot and flow cytometry.ResultsNo serious AEs were reported. Although an increase in T cell response against the Bcl-XL-peptide was found in all patients, a larger proportion of patients in group B demonstrated earlier and stronger immune responses to the vaccine compared to patients in group A. Further, we demonstrated vaccine-induced immunity towards patient-specific CD4, and CD8 T cell epitopes embedded in Bcl-XL-peptide and an increase in CD4 and CD8 T cell activation markers CD107a and CD137 following vaccination. At a median follow-up of 21 months, no patients had experienced clinically significant disease progression.ConclusionThe Bcl-XL-peptide-CAF®09b vaccination was feasible and safe in patients with l hormone-sensitive PC. In addition, the vaccine was immunogenic and able to elicit CD4 and CD8 T cell responses with initial IP administration eliciting early and high levels of vaccine-specific responses in a higher number og patients.Clinical trial registrationhttps://clinicaltrials.gov, identifier NCT03412786.
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Affiliation(s)
- Sofie Kirial Mørk
- Department of Oncology, National Center for Cancer Immune Therapy (CCIT-DK), Copenhagen University Hospital, Herlev, Denmark
| | - Per Kongsted
- Department of Oncology, National Center for Cancer Immune Therapy (CCIT-DK), Copenhagen University Hospital, Herlev, Denmark
| | | | - Benedetta Albieri
- Department of Oncology, National Center for Cancer Immune Therapy (CCIT-DK), Copenhagen University Hospital, Herlev, Denmark
| | - Joachim Stoltenborg Granhøj
- Department of Oncology, National Center for Cancer Immune Therapy (CCIT-DK), Copenhagen University Hospital, Herlev, Denmark
| | - Marco Donia
- Department of Oncology, National Center for Cancer Immune Therapy (CCIT-DK), Copenhagen University Hospital, Herlev, Denmark
| | - Evelina Martinenaite
- Department of Oncology, National Center for Cancer Immune Therapy (CCIT-DK), Copenhagen University Hospital, Herlev, Denmark
- IO Biotech Aps, Copenhagen, Denmark
| | - Morten Orebo Holmström
- Department of Oncology, National Center for Cancer Immune Therapy (CCIT-DK), Copenhagen University Hospital, Herlev, Denmark
- Department of Immunology and Microbiology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Kasper Madsen
- Department of Oncology, National Center for Cancer Immune Therapy (CCIT-DK), Copenhagen University Hospital, Herlev, Denmark
| | - Anders H. Kverneland
- Department of Oncology, National Center for Cancer Immune Therapy (CCIT-DK), Copenhagen University Hospital, Herlev, Denmark
| | - Julie Westerlin Kjeldsen
- Department of Oncology, National Center for Cancer Immune Therapy (CCIT-DK), Copenhagen University Hospital, Herlev, Denmark
| | - Rikke Boedker Holmstroem
- Department of Oncology, National Center for Cancer Immune Therapy (CCIT-DK), Copenhagen University Hospital, Herlev, Denmark
| | - Cathrine Lund Lorentzen
- Department of Oncology, National Center for Cancer Immune Therapy (CCIT-DK), Copenhagen University Hospital, Herlev, Denmark
| | - Nis Nørgaard
- Department of Urology, Copenhagen University Hospital, Herlev, Denmark
| | | | - Grith Krøyer Wood
- Statens Serum Institut, Center for Vaccine Research, Copenhagen, Denmark
| | - Dennis Christensen
- Statens Serum Institut, Center for Vaccine Research, Copenhagen, Denmark
| | | | - Sine Reker Hadrup
- Department of Health Technology, Technical University of Denmark (DTU), HEALTH TECH, Kongens Lyngby, Denmark
| | - Per thor Straten
- Department of Oncology, National Center for Cancer Immune Therapy (CCIT-DK), Copenhagen University Hospital, Herlev, Denmark
- Department of Immunology and Microbiology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Mads Hald Andersen
- Department of Oncology, National Center for Cancer Immune Therapy (CCIT-DK), Copenhagen University Hospital, Herlev, Denmark
- Department of Immunology and Microbiology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Inge Marie Svane
- Department of Oncology, National Center for Cancer Immune Therapy (CCIT-DK), Copenhagen University Hospital, Herlev, Denmark
- *Correspondence: Inge Marie Svane,
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8
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Lehmann PV, Roen DR, Lehmann AA. Unbiased, High-Throughput Identification of T Cell Epitopes by ELISPOT. Methods Mol Biol 2023; 2673:69-88. [PMID: 37258907 DOI: 10.1007/978-1-0716-3239-0_5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
Recent systematic immune monitoring efforts suggest that, in humans, epitope recognition by T cells is far more complex than has been assumed based on minimalistic murine models. The increased complexity is due to the higher number of HLA loci in humans, the typical heterozygosity for these loci in the outbred population, and the high number of peptides that each HLA restriction element can bind with an affinity that suffices for antigen presentation. The sizable array of potential epitopes on any given antigen is due to each individual's unique HLA allele makeup. Of this individualized potential epitope space, chance events occurring in the course of the T cell response determine which epitopes induce dominant T cell expansions. Establishing the actually-engaged T cell repertoire in each human subject, including the individualized peptides targeted, therefore requires the systematic testing of all peptides that constitute the potential epitope space in that person. The goal of comprehensive, high-throughput epitope mapping can be readily established by the methods described in this chapter.
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Affiliation(s)
- Paul V Lehmann
- Research & Development Department, Cellular Technology Limited, Shaker Heights, OH, USA.
| | - Diana R Roen
- Research & Development Department, Cellular Technology Limited, Shaker Heights, OH, USA
| | - Alexander A Lehmann
- Research & Development Department, Cellular Technology Limited, Shaker Heights, OH, USA
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9
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Immel JR, Chilamari M, Bloom S. Combining flavin photocatalysis with parallel synthesis: a general platform to optimize peptides with non-proteinogenic amino acids. Chem Sci 2021; 12:10083-10091. [PMID: 34377401 PMCID: PMC8317666 DOI: 10.1039/d1sc02562g] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2021] [Accepted: 06/28/2021] [Indexed: 02/06/2023] Open
Abstract
Most peptide drugs contain non-proteinogenic amino acids (NPAAs), born out through extensive structure-activity relationship (SAR) studies using solid-phase peptide synthesis (SPPS). Synthetically laborious and expensive to manufacture, NPAAs also can have poor coupling efficiencies allowing only a small fraction to be sampled by conventional SPPS. To gain general access to NPAA-containing peptides, we developed a first-generation platform that merges contemporary flavin photocatalysis with parallel synthesis to simultaneously make, purify, quantify, and even test up to 96 single-NPAA peptide variants via the unique combination of boronic acids and a dehydroalanine residue in a peptide. We showcase the power of our newly minted platform to introduce NPAAs of diverse chemotypes-aliphatic, aromatic, heteroaromatic-directly into peptides, including 15 entirely new residues, and to evolve a simple proteinogenic peptide into an unnatural inhibitor of thrombin by non-classical peptide SAR.
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Affiliation(s)
- Jacob R Immel
- Department of Medicinal Chemistry, The University of Kansas Integrated Science Building Lawrence KS 66045 USA
| | - Maheshwerreddy Chilamari
- Department of Medicinal Chemistry, The University of Kansas Integrated Science Building Lawrence KS 66045 USA
| | - Steven Bloom
- Department of Medicinal Chemistry, The University of Kansas Integrated Science Building Lawrence KS 66045 USA
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10
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Stephens AJ, Burgess-Brown NA, Jiang S. Beyond Just Peptide Antigens: The Complex World of Peptide-Based Cancer Vaccines. Front Immunol 2021; 12:696791. [PMID: 34276688 PMCID: PMC8279810 DOI: 10.3389/fimmu.2021.696791] [Citation(s) in RCA: 53] [Impact Index Per Article: 17.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2021] [Accepted: 06/17/2021] [Indexed: 12/14/2022] Open
Abstract
Peptide-based cancer vaccines rely upon the strong activation of the adaptive immune response to elicit its effector function. They have shown to be highly specific and safe, but have yet to prove themselves as an efficacious treatment for cancer in the clinic. This is for a variety of reasons, including tumour heterogeneity, self-tolerance, and immune suppression. Importance has been placed on the overall design of peptide-based cancer vaccines, which have evolved from simple peptide derivatives of a cancer antigen, to complex drugs; incorporating overlapping regions, conjugates, and delivery systems to target and stimulate different components of antigen presenting cells, and to bolster antigen cross-presentation. Peptide-based cancer vaccines are increasingly becoming more personalised to an individual's tumour antigen repertoire and are often combined with existing cancer treatments. This strategy ultimately aids in combating the shortcomings of a more generalised vaccine strategy and provides a comprehensive treatment, taking into consideration cancer cell variability and its ability to avoid immune interrogation.
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Affiliation(s)
- Alexander J Stephens
- Department of Oncology, Medical Sciences Division, University of Oxford, Oxford, United Kingdom.,Centre for Medicines Discovery, Nuffield Department of Medicine, Medical Sciences Division, University of Oxford, Oxford, United Kingdom
| | - Nicola A Burgess-Brown
- Centre for Medicines Discovery, Nuffield Department of Medicine, Medical Sciences Division, University of Oxford, Oxford, United Kingdom
| | - Shisong Jiang
- Department of Oncology, Medical Sciences Division, University of Oxford, Oxford, United Kingdom
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11
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Lehmann AA, Kirchenbaum GA, Zhang T, Reche PA, Lehmann PV. Deconvoluting the T Cell Response to SARS-CoV-2: Specificity Versus Chance and Cognate Cross-Reactivity. Front Immunol 2021; 12:635942. [PMID: 34127926 PMCID: PMC8196231 DOI: 10.3389/fimmu.2021.635942] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Accepted: 03/11/2021] [Indexed: 01/08/2023] Open
Abstract
SARS-CoV-2 infection takes a mild or clinically inapparent course in the majority of humans who contract this virus. After such individuals have cleared the virus, only the detection of SARS-CoV-2-specific immunological memory can reveal the exposure, and hopefully the establishment of immune protection. With most viral infections, the presence of specific serum antibodies has provided a reliable biomarker for the exposure to the virus of interest. SARS-CoV-2 infection, however, does not reliably induce a durable antibody response, especially in sub-clinically infected individuals. Consequently, it is plausible for a recently infected individual to yield a false negative result within only a few months after exposure. Immunodiagnostic attention has therefore shifted to studies of specific T cell memory to SARS-CoV-2. Most reports published so far agree that a T cell response is engaged during SARS-CoV-2 infection, but they also state that in 20-81% of SARS-CoV-2-unexposed individuals, T cells respond to SARS-CoV-2 antigens (mega peptide pools), allegedly due to T cell cross-reactivity with Common Cold coronaviruses (CCC), or other antigens. Here we show that, by introducing irrelevant mega peptide pools as negative controls to account for chance cross-reactivity, and by establishing the antigen dose-response characteristic of the T cells, one can clearly discern between cognate T cell memory induced by SARS-CoV-2 infection vs. cross-reactive T cell responses in individuals who have not been infected with SARS-CoV-2.
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Affiliation(s)
- Alexander A Lehmann
- Research and Development, Cellular Technology Ltd., Shaker Heights, OH, United States
| | - Greg A Kirchenbaum
- Research and Development, Cellular Technology Ltd., Shaker Heights, OH, United States
| | - Ting Zhang
- Research and Development, Cellular Technology Ltd., Shaker Heights, OH, United States
| | - Pedro A Reche
- Laboratorio de Inmunomedicina & Inmunoinformatica, Departamento de Immunologia & O2, Facultad de Medicina, Universidad Complutense de Madrid, Madrid, Spain
| | - Paul V Lehmann
- Research and Development, Cellular Technology Ltd., Shaker Heights, OH, United States
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12
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Hwang W, Lei W, Katritsis NM, MacMahon M, Chapman K, Han N. Current and prospective computational approaches and challenges for developing COVID-19 vaccines. Adv Drug Deliv Rev 2021; 172:249-274. [PMID: 33561453 PMCID: PMC7871111 DOI: 10.1016/j.addr.2021.02.004] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2020] [Revised: 02/01/2021] [Accepted: 02/03/2021] [Indexed: 12/23/2022]
Abstract
SARS-CoV-2, which causes COVID-19, was first identified in humans in late 2019 and is a coronavirus which is zoonotic in origin. As it spread around the world there has been an unprecedented effort in developing effective vaccines. Computational methods can be used to speed up the long and costly process of vaccine development. Antigen selection, epitope prediction, and toxicity and allergenicity prediction are areas in which computational tools have already been applied as part of reverse vaccinology for SARS-CoV-2 vaccine development. However, there is potential for computational methods to assist further. We review approaches which have been used and highlight additional bioinformatic approaches and PK modelling as in silico methods which may be useful for SARS-CoV-2 vaccine design but remain currently unexplored. As more novel viruses with pandemic potential are expected to arise in future, these techniques are not limited to application to SARS-CoV-2 but also useful to rapidly respond to novel emerging viruses.
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Affiliation(s)
- Woochang Hwang
- Milner Therapeutics Institute, University of Cambridge, Cambridge, UK
| | - Winnie Lei
- Milner Therapeutics Institute, University of Cambridge, Cambridge, UK; Department of Surgery, University of Cambridge, Cambridge, UK
| | - Nicholas M Katritsis
- Milner Therapeutics Institute, University of Cambridge, Cambridge, UK; Department of Chemical Engineering and Biotechnology, University of Cambridge, Cambridge, UK
| | - Méabh MacMahon
- Milner Therapeutics Institute, University of Cambridge, Cambridge, UK; Centre for Therapeutics Discovery, LifeArc, Stevenage, UK
| | - Kathryn Chapman
- Milner Therapeutics Institute, University of Cambridge, Cambridge, UK
| | - Namshik Han
- Milner Therapeutics Institute, University of Cambridge, Cambridge, UK.
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13
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Sangewar N, Waghela SD, Yao J, Sang H, Bray J, Mwangi W. Novel Potent IFN-γ-Inducing CD8 + T Cell Epitopes Conserved among Diverse Bovine Viral Diarrhea Virus Strains. THE JOURNAL OF IMMUNOLOGY 2021; 206:1709-1718. [PMID: 33762324 DOI: 10.4049/jimmunol.2001424] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/16/2020] [Accepted: 02/12/2021] [Indexed: 11/19/2022]
Abstract
Studies of immune responses elicited by bovine viral diarrhea virus (BVDV) vaccines have primarily focused on the characterization of neutralizing B cell and CD4+ T cell epitopes. Despite the availability of commercial vaccines for decades, BVDV prevalence in cattle has remained largely unaffected. There is limited knowledge regarding the role of BVDV-specific CD8+ T cells in immune protection, and indirect evidence suggests that they play a crucial role during BVDV infection. In this study, the presence of BVDV-specific CD8+ T cells that are highly cross-reactive in cattle was demonstrated. Most importantly, novel potent IFN-γ-inducing CD8+ T cell epitopes were identified from different regions of BVDV polyprotein. Eight CD8+ T cell epitopes were identified from the following structural BVDV Ags: Erns, E1, and E2 glycoproteins. In addition, from nonstructural BVDV Ags Npro, NS2-3, NS4A-B, and NS5A-B, 20 CD8+ T cell epitopes were identified. The majority of these IFN-γ-inducing CD8+ T cell epitopes were found to be highly conserved among more than 200 strains from BVDV-1 and -2 genotypes. These conserved epitopes were also validated as cross-reactive because they induced high recall IFN-γ+CD8+ T cell responses ex vivo in purified bovine CD8+ T cells isolated from BVDV-1- and -2-immunized cattle. Altogether, 28 bovine MHC class I-binding epitopes were identified from key BVDV Ags that can elicit broadly reactive CD8+ T cells against diverse BVDV strains. The data presented in this study will lay the groundwork for the development of a contemporary CD8+ T cell-based BVDV vaccine capable of addressing BVDV heterogeneity more effectively than current vaccines.
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Affiliation(s)
- Neha Sangewar
- Department of Diagnostic Medicine/Pathobiology, Kansas State University, Manhattan, KS 66506; and
| | - Suryakant D Waghela
- Department of Veterinary Pathobiology, Texas A&M University, College Station, TX 77843
| | - Jianxiu Yao
- Department of Diagnostic Medicine/Pathobiology, Kansas State University, Manhattan, KS 66506; and
| | - Huldah Sang
- Department of Diagnostic Medicine/Pathobiology, Kansas State University, Manhattan, KS 66506; and
| | - Jocelyn Bray
- Department of Veterinary Pathobiology, Texas A&M University, College Station, TX 77843
| | - Waithaka Mwangi
- Department of Diagnostic Medicine/Pathobiology, Kansas State University, Manhattan, KS 66506; and
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14
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Lehmann AA, Zhang T, Reche PA, Lehmann PV. Discordance Between the Predicted Versus the Actually Recognized CD8+ T Cell Epitopes of HCMV pp65 Antigen and Aleatory Epitope Dominance. Front Immunol 2021; 11:618428. [PMID: 33633736 PMCID: PMC7900545 DOI: 10.3389/fimmu.2020.618428] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2020] [Accepted: 12/22/2020] [Indexed: 12/13/2022] Open
Abstract
CD8+ T cell immune monitoring aims at measuring the size and functions of antigen-specific CD8+ T cell populations, thereby providing insights into cell-mediated immunity operational in a test subject. The selection of peptides for ex vivo CD8+ T cell detection is critical because within a complex antigen exists a multitude of potential epitopes that can be presented by HLA class I molecules. Further complicating this task, there is HLA class I polygenism and polymorphism which predisposes CD8+ T cell responses towards individualized epitope recognition profiles. In this study, we compare the actual CD8+ T cell recognition of a well-characterized model antigen, human cytomegalovirus (HCMV) pp65 protein, with its anticipated epitope coverage. Due to the abundance of experimentally defined HLA-A*02:01-restricted pp65 epitopes, and because in silico epitope predictions are most advanced for HLA-A*02:01, we elected to focus on subjects expressing this allele. In each test subject, every possible CD8+ T cell epitope was systematically covered testing 553 individual peptides that walk the sequence of pp65 in steps of single amino acids. Highly individualized CD8+ T cell response profiles with aleatory epitope recognition patterns were observed. No correlation was found between epitopes' ranking on the prediction scale and their actual immune dominance. Collectively, these data suggest that accurate CD8+ T cell immune monitoring may necessitate reliance on agnostic mega peptide pools, or brute force mapping, rather than electing individual peptides as representative epitopes for tetramer and other multimer labeling of surface antigen receptors.
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Affiliation(s)
- Alexander A. Lehmann
- Research and Development, Cellular Technology Ltd., Shaker Heights, OH, United States
| | - Ting Zhang
- Research and Development, Cellular Technology Ltd., Shaker Heights, OH, United States
| | - Pedro A. Reche
- Laboratorio de Inmunomedicina & Inmunoinformatica, Departamento de Immunologia & O2, Facultad de Medicina, Universidad Complutense de Madrid, Madrid, Spain
| | - Paul V. Lehmann
- Research and Development, Cellular Technology Ltd., Shaker Heights, OH, United States
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15
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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 DOI: 10.1016/j.jim.2021.112970] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [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.
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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.
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16
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CERI, CEFX, and CPI: Largely Improved Positive Controls for Testing Antigen-Specific T Cell Function in PBMC Compared to CEF. Cells 2021; 10:cells10020248. [PMID: 33514016 PMCID: PMC7911306 DOI: 10.3390/cells10020248] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2020] [Revised: 12/21/2020] [Accepted: 01/14/2021] [Indexed: 01/17/2023] Open
Abstract
Monitoring antigen-specific T cell immunity relies on functional tests that require T cells and antigen presenting cells to be uncompromised. Drawing of blood, its storage and shipment from the clinical site to the test laboratory, and the subsequent isolation, cryopreservation and thawing of peripheral blood mononuclear cells (PBMCs) before the actual test is performed can introduce numerous variables that may jeopardize the results. Therefore, no T cell test is valid without assessing the functional fitness of the PBMC being utilized. This can only be accomplished through the inclusion of positive controls that actually evaluate the performance of the antigen-specific T cell and antigen presenting cell (APC) compartments. For Caucasians, CEF peptides have been commonly used to this extent. Moreover, CEF peptides only measure CD8 cell functionality. We introduce here universal CD8+ T cell positive controls without any racial bias, as well as positive controls for the CD4+ T cell and APC compartments. In summary, we offer new tools and strategies for the assessment of PBMC functional fitness required for reliable T cell immune monitoring.
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17
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Przybyla A, Lehmann AA, Zhang T, Mackiewicz J, Galus Ł, Kirchenbaum GA, Mackiewicz A, Lehmann PV. Functional T Cell Reactivity to Melanocyte Antigens Is Lost during the Progression of Malignant Melanoma, but Is Restored by Immunization. Cancers (Basel) 2021; 13:cancers13020223. [PMID: 33435427 PMCID: PMC7827050 DOI: 10.3390/cancers13020223] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Revised: 01/04/2021] [Accepted: 01/07/2021] [Indexed: 02/07/2023] Open
Abstract
Simple Summary Healthy humans develop spontaneous CD8+ T cell responses to melanoma associated antigens (MA) expressed by normal melanocytes. This natural autoimmunity directed against melanocytes might confer protection against the development of malignant melanoma (MM), where MA are overexpressed tumor-associated antigens. We report that functional T cell reactivity to MA is diminished in untreated MM patients. Three lines of evidence suggest that the MA-reactive T cells present in healthy subjects undergo exhaustion once MM establishes itself. First, only the MA-specific T cell reactivity was affected in the MM patients. Second, in these patients, the residual MA-specific T cells were functionally impaired, showing a diminished per cell IFN-γ productivity. Third, immunizations with allogeneic melanoma cells restored natural CD8+ T cell autoimmunity to MA. Abstract Healthy human subjects develop spontaneous CD8+ T cell responses to melanoma associated antigens (MA) expressed by normal melanocytes, such as Tyrosinase, MAGE-A3, Melan/Mart-1, gp100, and NY-ESO-1. This natural autoimmunity directed against melanocytes might confer protection against the development of malignant melanoma (MM), where MA are present as overexpressed tumor-associated antigens. Consistent with this notion we report here that functional T cell reactivity to MA was found to be significantly diminished to MAGE-A3, Melan-A/Mart-1, and gp100 in untreated MM patients. Three lines of evidence suggest that the MA-reactive T cells present in healthy subjects undergo exhaustion once MM establishes itself. First, only the MA-specific T cell reactivity was affected in the MM patients; that to third party recall antigens was not. Second, in these patients, the residual MA-specific T cells, unlike third party antigen reactive T cells, were functionally impaired, showing a diminished per cell IFN-γ productivity. Third, we show that immunization with MA restored natural CD8+ T cell autoimmunity to MA in 85% of the MM patients. The role of natural T cell autoimmunity to tumor-associated MA is discussed based on discrete levels of T cell activation thresholds.
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Affiliation(s)
- Anna Przybyla
- Research and Development Department, Cellular Technology Limited (CTL), Shaker Heights, OH 44122, USA; (A.P.); (A.A.L.); (T.Z.); (G.A.K.)
- Department of Cancer Immunology, Medical Biotechnology, Poznan University of Medical Sciences, 61-866 Poznan, Poland;
| | - Alexander A. Lehmann
- Research and Development Department, Cellular Technology Limited (CTL), Shaker Heights, OH 44122, USA; (A.P.); (A.A.L.); (T.Z.); (G.A.K.)
| | - Ting Zhang
- Research and Development Department, Cellular Technology Limited (CTL), Shaker Heights, OH 44122, USA; (A.P.); (A.A.L.); (T.Z.); (G.A.K.)
| | - Jacek Mackiewicz
- Department of Medical and Experimental Oncology, University of Medical Sciences, 60-355 Poznan, Poland; (J.M.); (Ł.G.)
- Department of Diagnostics and Cancer Immunology, Greater Poland Cancer Center, 61-866 Poznan, Poland
| | - Łukasz Galus
- Department of Medical and Experimental Oncology, University of Medical Sciences, 60-355 Poznan, Poland; (J.M.); (Ł.G.)
- Department of Diagnostics and Cancer Immunology, Greater Poland Cancer Center, 61-866 Poznan, Poland
- Chemotherapy Department, Greater Poland Cancer Center, 61-866 Poznan, Poland
| | - Greg A. Kirchenbaum
- Research and Development Department, Cellular Technology Limited (CTL), Shaker Heights, OH 44122, USA; (A.P.); (A.A.L.); (T.Z.); (G.A.K.)
| | - Andrzej Mackiewicz
- Department of Cancer Immunology, Medical Biotechnology, Poznan University of Medical Sciences, 61-866 Poznan, Poland;
- Department of Diagnostics and Cancer Immunology, Greater Poland Cancer Center, 61-866 Poznan, Poland
| | - Paul V. Lehmann
- Research and Development Department, Cellular Technology Limited (CTL), Shaker Heights, OH 44122, USA; (A.P.); (A.A.L.); (T.Z.); (G.A.K.)
- Correspondence: ; Tel.: +1-216-965-6311
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18
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Kennedy DA, Read AF. Monitor for COVID-19 vaccine resistance evolution during clinical trials. PLoS Biol 2020; 18:e3001000. [PMID: 33166303 PMCID: PMC7676675 DOI: 10.1371/journal.pbio.3001000] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Revised: 11/19/2020] [Indexed: 11/18/2022] Open
Abstract
Although less common than the evolution of antimicrobial drug resistance, vaccine resistance can and has evolved. How likely is it that COVID-19 vaccines currently in development will be undermined by viral evolution? We argue that this can be determined by repurposing samples that are already being collected as part of clinical trials. Such information would be useful for prioritizing investment among candidate vaccines and maximizing the potential long-term impact of COVID-19 vaccines.
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Affiliation(s)
- David A. Kennedy
- Center for Infectious Disease Dynamics, Department of Biology, The Pennsylvania State University, Pennsylvania, United States of America
- * E-mail:
| | - Andrew F. Read
- Center for Infectious Disease Dynamics, Department of Biology, The Pennsylvania State University, Pennsylvania, United States of America
- Department of Entomology, The Pennsylvania State University, Pennsylvania, United States of America
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19
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Powlson J, Wright D, Zeltina A, Giza M, Nielsen M, Rampling T, Venkatrakaman N, Bowden TA, Hill AVS, Ewer KJ. Characterization of Antigenic MHC-Class-I-Restricted T Cell Epitopes in the Glycoprotein of Ebolavirus. Cell Rep 2020; 29:2537-2545.e3. [PMID: 31775024 PMCID: PMC6899439 DOI: 10.1016/j.celrep.2019.10.105] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2019] [Revised: 07/20/2019] [Accepted: 10/25/2019] [Indexed: 11/05/2022] Open
Abstract
Ebolavirus causes highly lethal hemorrhagic fever in humans. The envelope-displayed viral glycoprotein (GP) is the primary target of humoral immunity induced by natural exposure and vaccination. No T cell epitopes in the GP have been characterized in humans. A phase I clinical trial of a heterologous prime-boost vaccination regime with viral vectors encoding filovirus antigens elicits humoral and T cell responses in vaccinees. The most frequently recognized peptide pools are deconvoluted to identify the minimal epitopes recognized by antigen-specific T cells. We characterize nine immunogenic epitopes on the Ebolavirus GP. Histocompatibility leukocyte antigen (HLA) typing with in silico epitope analysis determines the likely MHC class I restriction elements. Thirteen HLA-A and -B alleles are predicted to present the identified CD8+ T cell epitopes, suggesting promiscuous recognition and a broad immune response. Delivery of the Ebolavirus GP antigen by using a heterologous prime-boost approach is immunogenic in genetically diverse human populations, with responses against multiple epitopes. Vaccination induces high T cell responses to the Ebola virus glycoprotein in humans Eight CD8+ epitopes were defined, recognized through multiple MHC class I alleles Responses match those observed in Ebola survivors and could boost vaccine efficacy
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Affiliation(s)
- Jonathan Powlson
- The Jenner Institute, Old Road Campus Research Building, University of Oxford, Oxford OX3 7DQ, UK
| | - Daniel Wright
- The Jenner Institute, Old Road Campus Research Building, University of Oxford, Oxford OX3 7DQ, UK
| | - Antra Zeltina
- Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK
| | - Mark Giza
- The Jenner Institute, Old Road Campus Research Building, University of Oxford, Oxford OX3 7DQ, UK
| | - Morten Nielsen
- Department of Health Technology, The Technical University of Denmark, Anker Engelunds Vej 1 Bygning 101A, 2800 Kgs Lyngby, Denmark
| | - Tommy Rampling
- The Jenner Institute, Old Road Campus Research Building, University of Oxford, Oxford OX3 7DQ, UK
| | - Navin Venkatrakaman
- The Jenner Institute, Old Road Campus Research Building, University of Oxford, Oxford OX3 7DQ, UK
| | - Thomas A Bowden
- Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK
| | - Adrian V S Hill
- The Jenner Institute, Old Road Campus Research Building, University of Oxford, Oxford OX3 7DQ, UK
| | - Katie J Ewer
- The Jenner Institute, Old Road Campus Research Building, University of Oxford, Oxford OX3 7DQ, UK.
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20
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Körber N, Behrends U, Protzer U, Bauer T. Evaluation of T-activated proteins as recall antigens to monitor Epstein-Barr virus and human cytomegalovirus-specific T cells in a clinical trial setting. J Transl Med 2020; 18:242. [PMID: 32552697 PMCID: PMC7298696 DOI: 10.1186/s12967-020-02385-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2019] [Accepted: 05/21/2020] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND Pools of overlapping synthetic peptides are routinely used for ex vivo monitoring of antigen-specific T-cell responses. However, it is rather unlikely that these peptides match those resulting from naturally processed antigens. T-activated proteins have been described as immunogenic and more natural stimulants, since they have to pass through antigen processing and comprise activation of all clinically relevant effector cell populations. METHODS We performed comparative analysis of numbers and cytokine expression pattern of CD4 and CD8 T cells after stimulation with recombinant, urea-formulated T-activated EBV-BZLF1, -EBNA3A, and HCMV-IE1, and -pp65 proteins or corresponding overlapping peptide pools. Freshly isolated and cryopreserved PBMC of 30 EBV- and 19 HCMV-seropositive and seven EBV- and HCMV-seronegative subjects were stimulated ex vivo and analysed for IFN-γ, TNF and IL-2 production by flow cytometry-based intracellular cytokine staining. RESULTS T-activated proteins showed a high specificity of 100% (EBV-BZLF1, HCMV-IE1, and -pp65) and 86% (EBV-EBNA3A), and a high T-cell stimulatory capacity of 73-95% and 67-95% using freshly isolated and cryopreserved PBMC, respectively. The overall CD4 T-cell response rates in both cohorts were comparable after stimulation with either T-activated protein or peptide pools with the exception of lower numbers of CD8 T cells detected after stimulation with T-activated EBV-EBNA3A- (p = 0.038) and HCMV-pp65- (p = 0.0006). Overall, the number of detectable antigen-specific T cells varied strongly between individuals. Cytokine expression patterns in response to T-activated protein and peptide pool-based stimulation were similar for CD4, but significantly different for CD8 T-cell responses. CONCLUSION EBV and HCMV-derived T-activated proteins represent innovative, highly specific recall antigens suitable for use in immunological endpoint assays to evaluate success or failure in immunotherapy clinical trials (e.g. to assess the risk of EBV and/or HCMV reactivation after allogenic hematopoietic stem cell transplantation). T-activated proteins could be of particular importance, if an impaired antigen processing (e.g. in a post-transplant setting) must be taken into account.
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Affiliation(s)
- Nina Körber
- Institute of Virology, Helmholtz Zentrum München/Technical University of Munich, School of Medicine, Schneckenburgerstr. 8, 81675, Munich, Germany.
| | - Uta Behrends
- Children's Hospital, School of Medicine, Technical University of Munich, Munich, Germany.,Research Unit Gene Vectors, Helmholtz Zentrum München, Munich, Germany.,German Center for Infection Research (DZIF), Partner Site, Munich, Germany
| | - Ulrike Protzer
- Institute of Virology, Helmholtz Zentrum München/Technical University of Munich, School of Medicine, Schneckenburgerstr. 8, 81675, Munich, Germany.,German Center for Infection Research (DZIF), Partner Site, Munich, Germany
| | - Tanja Bauer
- Institute of Virology, Helmholtz Zentrum München/Technical University of Munich, School of Medicine, Schneckenburgerstr. 8, 81675, Munich, Germany.,German Center for Infection Research (DZIF), Partner Site, Munich, Germany
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Grau-Vorster M, López-Montañés M, Cantó E, Vives J, Oliver-Vila I, Barba P, Querol S, Rudilla F. Characterization of a Cytomegalovirus-Specific T Lymphocyte Product Obtained Through a Rapid and Scalable Production Process for Use in Adoptive Immunotherapy. Front Immunol 2020; 11:271. [PMID: 32161589 PMCID: PMC7052482 DOI: 10.3389/fimmu.2020.00271] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2019] [Accepted: 02/03/2020] [Indexed: 12/19/2022] Open
Abstract
Immunosuppressed patients are susceptible to virus reactivation or de novo infection. Adoptive immunotherapy, based on virus-specific T lymphocytes (VST), can prevent or treat viral diseases. However, donor availability, HLA-compatibility restrictions, high costs, and time required for the production of personalized medicines constitute considerable limitations to this treatment. Ex vivo rapid and large-scale expansion of VST, compliant with current good manufacturing practice (cGMP) standards, with an associated cell donor registry would overcome these limitations. This study aimed to characterize a VST product obtained through an expansion protocol transferable to cGMP standards. Antigenic stimulus consisted of cytomegalovirus (CMV) pp65 peptide pool-pulsed autologous dendritic cells (DCs) derived from monocytes. G-Rex technology, cytokines IL-2, IL-7, and IL-15, and anti-CD3 and anti-CD28 antibodies were used for culture. At day 14 of cell culture, the final product was characterized regarding T cell subsets, specificity, and functionality. The final product, comprised mainly CD4+ and CD8+ T lymphocytes (49.2 ± 24.7 and 42.3 ± 25.2, respectively). The culture conditions made it possible to achieve at least a 98.89-fold increase in pp65-specific CD3+ IFN-γ+ cells. These cells were specific, as pp65-specific cytotoxicity was demonstrated. Additionally, in complete HLA mismatch and without the presence of pp65, alloreactivity resulted in <5% cell lysis. In conclusion, a cGMP scalable process for the generation of a large number of doses of CMV-specific cytotoxic T cells was successfully performed.
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Affiliation(s)
- Marta Grau-Vorster
- Cell Therapy Service, Banc de Sang i Teixits, Barcelona, Spain.,Transfusion Medicine Group, Vall d'Hebron Research Institute, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - María López-Montañés
- Cell Therapy Service, Banc de Sang i Teixits, Barcelona, Spain.,Transfusion Medicine Group, Vall d'Hebron Research Institute, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Ester Cantó
- Cell Therapy Service, Banc de Sang i Teixits, Barcelona, Spain.,Transfusion Medicine Group, Vall d'Hebron Research Institute, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Joaquim Vives
- Cell Therapy Service, Banc de Sang i Teixits, Barcelona, Spain.,Musculoskeletal Tissue Engineering Group, Vall d'Hebron Research Institute (VHIR), Universitat Autònoma de Barcelona, Barcelona, Spain.,Medicine Department, Universitat Autònoma de Barcelona, Barcelona, Spain
| | | | - Pere Barba
- Hematology Department, Hospital Universitari Vall d'Hebron, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Sergi Querol
- Cell Therapy Service, Banc de Sang i Teixits, Barcelona, Spain
| | - Francesc Rudilla
- Cell Therapy Service, Banc de Sang i Teixits, Barcelona, Spain.,Transfusion Medicine Group, Vall d'Hebron Research Institute, Universitat Autònoma de Barcelona, Barcelona, Spain
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Quinzo MJ, Lafuente EM, Zuluaga P, Flower DR, Reche PA. Computational assembly of a human Cytomegalovirus vaccine upon experimental epitope legacy. BMC Bioinformatics 2019; 20:476. [PMID: 31823715 PMCID: PMC6905002 DOI: 10.1186/s12859-019-3052-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2019] [Accepted: 08/23/2019] [Indexed: 01/05/2023] Open
Abstract
Background Human Cytomegalovirus (HCMV) is a ubiquitous herpesvirus affecting approximately 90% of the world population. HCMV causes disease in immunologically naive and immunosuppressed patients. The prevention, diagnosis and therapy of HCMV infection are thus crucial to public health. The availability of effective prophylactic and therapeutic treatments remain a significant challenge and no vaccine is currently available. Here, we sought to define an epitope-based vaccine against HCMV, eliciting B and T cell responses, from experimentally defined HCMV-specific epitopes. Results We selected 398 and 790 experimentally validated HCMV-specific B and T cell epitopes, respectively, from available epitope resources and apply a knowledge-based approach in combination with immunoinformatic predictions to ensemble a universal vaccine against HCMV. The T cell component consists of 6 CD8 and 6 CD4 T cell epitopes that are conserved among HCMV strains. All CD8 T cell epitopes were reported to induce cytotoxic activity, are derived from early expressed genes and are predicted to provide population protection coverage over 97%. The CD4 T cell epitopes are derived from HCMV structural proteins and provide a population protection coverage over 92%. The B cell component consists of just 3 B cell epitopes from the ectodomain of glycoproteins L and H that are highly flexible and exposed to the solvent. Conclusions We have defined a multiantigenic epitope vaccine ensemble against the HCMV that should elicit T and B cell responses in the entire population. Importantly, although we arrived to this epitope ensemble with the help of computational predictions, the actual epitopes are not predicted but are known to be immunogenic.
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Affiliation(s)
- Monica J Quinzo
- Faculty of Medicine, University Complutense of Madrid, Pza Ramon y Cajal, s/n, 28040, Madrid, Spain
| | - Esther M Lafuente
- Faculty of Medicine, University Complutense of Madrid, Pza Ramon y Cajal, s/n, 28040, Madrid, Spain
| | - Pilar Zuluaga
- Faculty of Medicine, University Complutense of Madrid, Pza Ramon y Cajal, s/n, 28040, Madrid, Spain
| | - Darren R Flower
- School of Life and Health Sciences, Aston University, Aston Triangle, Birmingham, B4 7ET, UK
| | - Pedro A Reche
- Faculty of Medicine, University Complutense of Madrid, Pza Ramon y Cajal, s/n, 28040, Madrid, Spain.
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