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Immunopeptidomics-based design of mRNA vaccine formulations against Listeria monocytogenes. Nat Commun 2022; 13:6075. [PMID: 36241641 PMCID: PMC9562072 DOI: 10.1038/s41467-022-33721-y] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2022] [Accepted: 09/29/2022] [Indexed: 12/24/2022] Open
Abstract
Listeria monocytogenes is a foodborne intracellular bacterial pathogen leading to human listeriosis. Despite a high mortality rate and increasing antibiotic resistance no clinically approved vaccine against Listeria is available. Attenuated Listeria strains offer protection and are tested as antitumor vaccine vectors, but would benefit from a better knowledge on immunodominant vector antigens. To identify novel antigens, we screen for Listeria peptides presented on the surface of infected human cell lines by mass spectrometry-based immunopeptidomics. In between more than 15,000 human self-peptides, we detect 68 Listeria immunopeptides from 42 different bacterial proteins, including several known antigens. Peptides presented on different cell lines are often derived from the same bacterial surface proteins, classifying these antigens as potential vaccine candidates. Encoding these highly presented antigens in lipid nanoparticle mRNA vaccine formulations results in specific CD8+ T-cell responses and induces protection in vaccination challenge experiments in mice. Our results can serve as a starting point for the development of a clinical mRNA vaccine against Listeria and aid to improve attenuated Listeria vaccines and vectors, demonstrating the power of immunopeptidomics for next-generation bacterial vaccine development.
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Martínez L, Malaina I, Salcines-Cuevas D, Terán-Navarro H, Zeoli A, Alonso S, M De la Fuente I, Gonzalez-Lopez E, Ocejo-Vinyals JG, Gozalo-Margüello M, Calvo-Montes J, Alvarez-Dominguez C. First computational design using lambda-superstrings and in vivo validation of SARS-CoV-2 vaccine. Sci Rep 2022; 12:6410. [PMID: 35440789 PMCID: PMC9016385 DOI: 10.1038/s41598-022-09615-w] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2021] [Accepted: 03/07/2022] [Indexed: 12/23/2022] Open
Abstract
Coronavirus disease 2019 (COVID-19) is the greatest threat to global health at the present time, and considerable public and private effort is being devoted to fighting this recently emerged disease. Despite the undoubted advances in the development of vaccines against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the causative agent of COVID-19, uncertainty remains about their future efficacy and the duration of the immunity induced. It is therefore prudent to continue designing and testing vaccines against this pathogen. In this article we computationally designed two candidate vaccines, one monopeptide and one multipeptide, using a technique involving optimizing lambda-superstrings, which was introduced and developed by our research group. We tested the monopeptide vaccine, thus establishing a proof of concept for the validity of the technique. We synthesized a peptide of 22 amino acids in length, corresponding to one of the candidate vaccines, and prepared a dendritic cell (DC) vaccine vector loaded with the 22 amino acids SARS-CoV-2 peptide (positions 50-71) contained in the NTD domain (DC-CoVPSA) of the Spike protein. Next, we tested the immunogenicity, the type of immune response elicited, and the cytokine profile induced by the vaccine, using a non-related bacterial peptide as negative control. Our results indicated that the CoVPSA peptide of the Spike protein elicits noticeable immunogenicity in vivo using a DC vaccine vector and remarkable cellular and humoral immune responses. This DC vaccine vector loaded with the NTD peptide of the Spike protein elicited a predominant Th1-Th17 cytokine profile, indicative of an effective anti-viral response. Finally, we performed a proof of concept experiment in humans that included the following groups: asymptomatic non-active COVID-19 patients, vaccinated volunteers, and control donors that tested negative for SARS-CoV-2. The positive control was the current receptor binding domain epitope of COVID-19 RNA-vaccines. We successfully developed a vaccine candidate technique involving optimizing lambda-superstrings and provided proof of concept in human subjects. We conclude that it is a valid method to decipher the best epitopes of the Spike protein of SARS-CoV-2 to prepare peptide-based vaccines for different vector platforms, including DC vaccines.
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Affiliation(s)
- Luis Martínez
- Department of Mathematics, Faculty of Science and Technology, University of the Basque Country, UPV/EHU, 48940, Leioa, Spain. .,BCAM, Basque Center for Applied Mathematics, 48009, Bilbao, Spain.
| | - Iker Malaina
- Department of Mathematics, Faculty of Science and Technology, University of the Basque Country, UPV/EHU, 48940, Leioa, Spain.,BioCruces Health Research Institute, Cruces University Hospital, 48903, Barakaldo, Spain
| | | | - Héctor Terán-Navarro
- Instituto de Investigación Marqués de Valdecilla (IDIVAL), 39011, Santander, Spain
| | - Andrea Zeoli
- Instituto de Investigación Marqués de Valdecilla (IDIVAL), 39011, Santander, 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.,María Goyri Building. Animal Biotechnology Center, University of the Basque Country, UPV/EHU, 48940, Leioa, Spain
| | - Ildefonso M De la Fuente
- Department of Mathematics, Faculty of Science and Technology, University of the Basque Country, UPV/EHU, 48940, Leioa, Spain.,Department of Nutrition, CEBAS-CSIC Institute, Espinardo University Campus, 30100, Murcia, Spain
| | - Elena Gonzalez-Lopez
- Servicio de Inmunología, Hospital Universitario Marqués de Valdecilla, 39008, Santander, Spain
| | - J Gonzalo Ocejo-Vinyals
- Servicio de Inmunología, Hospital Universitario Marqués de Valdecilla, 39008, Santander, Spain
| | - Mónica Gozalo-Margüello
- Servicio de Microbiología, Hospital Universitario Marqués de Valdecilla, 39008, Santander, Spain
| | - Jorge Calvo-Montes
- Instituto de Investigación Marqués de Valdecilla (IDIVAL), 39011, Santander, Spain.,Servicio de Microbiología, Hospital Universitario Marqués de Valdecilla, 39008, Santander, Spain.,CIBER Enfermedades Infecciosas, ISCIII, Madrid, Spain
| | - Carmen Alvarez-Dominguez
- Instituto de Investigación Marqués de Valdecilla (IDIVAL), 39011, Santander, Spain. .,Universidad Internacional de La Rioja, 26006, Logroño, Spain.
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