2024
Machine learning-enhanced immunopeptidomics applied to T-cell epitope discovery for COVID-19 vaccines
Kovalchik K, Hamelin D, Kubiniok P, Bourdin B, Mostefai F, Poujol R, Paré B, Simpson S, Sidney J, Bonneil É, Courcelles M, Saini S, Shahbazy M, Kapoor S, Rajesh V, Weitzen M, Grenier J, Gharsallaoui B, Maréchal L, Wu Z, Savoie C, Sette A, Thibault P, Sirois I, Smith M, Decaluwe H, Hussin J, Lavallée-Adam M, Caron E. Machine learning-enhanced immunopeptidomics applied to T-cell epitope discovery for COVID-19 vaccines. Nature Communications 2024, 15: 10316. PMID: 39609459, PMCID: PMC11604954, DOI: 10.1038/s41467-024-54734-9.Peer-Reviewed Original ResearchConceptsT cell epitopesT cellsCD8+ T cell epitopesT cell immunityT cell epitope discoverySARS-CoV-2T-cell-directed vaccinationDesigning effective vaccinesB7 supertypePatient's proteomesSARS-CoV-2 variantsVaccine epitopesViral antigensSpike antigenVaccine developmentEffective vaccineEpitope discoveryCOVID-19 vaccineVaccineEpitopesAntigenic featuresOmicron variantAntigenCOVID-19CD8
2023
Integrated Immunopeptidomics and Proteomics Study of SARS-CoV-2–Infected Calu-3 Cells Reveals Dynamic Changes in Allele-specific HLA Abundance and Antigen Presentation
Chen R, Fulton K, Tran A, Duque D, Kovalchik K, Caron E, Twine S, Li J. Integrated Immunopeptidomics and Proteomics Study of SARS-CoV-2–Infected Calu-3 Cells Reveals Dynamic Changes in Allele-specific HLA Abundance and Antigen Presentation. Molecular & Cellular Proteomics 2023, 22: 100645. PMID: 37709257, PMCID: PMC10580047, DOI: 10.1016/j.mcpro.2023.100645.Peer-Reviewed Original ResearchSARS-CoV-2 infectionHuman leukocyte antigenAdaptive immune systemHLA allelesAntigen presentationAcute respiratory syndrome coronavirus 2 infectionSevere acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infectionImmune systemSyndrome coronavirus 2 infectionCoronavirus disease 2019 (COVID-19) casesHost proteome changesCoronavirus 2 infectionCertain HLA allelesToll-like receptorsDifferent HLA allelesCoronavirus disease 2019Calu-3 cellsHost cellsLeukocyte antigenViral antigensDisease 2019Viral infectionDevelopment of therapeuticsInfectionClass I