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 ResearchMeSH KeywordsCD8-Positive T-LymphocytesCOVID-19COVID-19 VaccinesEpitopes, T-LymphocyteHumansMachine LearningProteomicsSARS-CoV-2Spike Glycoprotein, CoronavirusConceptsT 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
2021
The mutational landscape of SARS-CoV-2 variants diversifies T cell targets in an HLA-supertype-dependent manner
Hamelin D, Fournelle D, Grenier J, Schockaert J, Kovalchik K, Kubiniok P, Mostefai F, Duquette J, Saab F, Sirois I, Smith M, Pattijn S, Soudeyns H, Decaluwe H, Hussin J, Caron E. The mutational landscape of SARS-CoV-2 variants diversifies T cell targets in an HLA-supertype-dependent manner. Cell Systems 2021, 13: 143-157.e3. PMID: 34637888, PMCID: PMC8492600, DOI: 10.1016/j.cels.2021.09.013.Peer-Reviewed Original ResearchConceptsSARS-CoV-2SARS-CoV-2 TSARS-CoV-2 variantsHLA-B allelesMutational landscapeFirst yearCell immunityCell immunosurveillanceCell epitopesMass vaccinationDelta variantCell targetsRNA levelsImmunodominant onesMutation typeEpitopesPrevalent mutantsPopulation levelCD8PandemicImmunosurveillanceVaccinationHLAYearsImmunity
2017
Deciphering the MHC-associated peptidome: a review of naturally processed ligand data
Vaughan K, Xu X, Caron E, Peters B, Sette A. Deciphering the MHC-associated peptidome: a review of naturally processed ligand data. Expert Review Of Proteomics 2017, 14: 729-736. PMID: 28756714, DOI: 10.1080/14789450.2017.1361825.Peer-Reviewed Original Research
2006
Asynchronous Differentiation of CD8 T Cells That Recognize Dominant and Cryptic Antigens
Baron C, Meunier M, Caron É, Côté C, Cameron M, Kelvin D, LeBlanc R, Rineau V, Perreault C. Asynchronous Differentiation of CD8 T Cells That Recognize Dominant and Cryptic Antigens. The Journal Of Immunology 2006, 177: 8466-8475. PMID: 17142744, DOI: 10.4049/jimmunol.177.12.8466.Peer-Reviewed Original ResearchConceptsCD8 T cellsT cell responsesT cellsDay 10Cell responsesEffector CD8 T cellsEffector T cellsT cell differentiation markersT cell repertoireT cell differentiation programMouse AgCryptic antigensEffector potentialCell differentiation markersImmune responseCell repertoireEffector functionsAg specificityDay 15Differentiation programSelective expansionDifferentiation markersCell differentiation programLongitudinal analysisContraction phase