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-19CD8Hypoxia is linked to acquired resistance to immune checkpoint inhibitors in lung cancer
Robles-Oteíza C, Hastings K, Choi J, Sirois I, Ravi A, Expósito F, de Miguel F, Knight J, López-Giráldez F, Choi H, Socci N, Merghoub T, Awad M, Getz G, Gainor J, Hellmann M, Caron É, Kaech S, Politi K. Hypoxia is linked to acquired resistance to immune checkpoint inhibitors in lung cancer. Journal Of Experimental Medicine 2024, 222: e20231106. PMID: 39585348, DOI: 10.1084/jem.20231106.Peer-Reviewed Original ResearchConceptsImmune checkpoint inhibitorsNon-small cell lung cancerAcquired resistanceCheckpoint inhibitorsResistant tumorsPatients treated with anti-PD-1/PD-L1 therapyAnti-PD-1/PD-L1 therapyLung cancerResistance to immune checkpoint inhibitorsAssociated with decreased progression-free survivalHypoxia activated pro-drugsTargeting hypoxic tumor regionsTreat non-small cell lung cancerAnti-CTLA-4Anti-PD-1Immune checkpoint inhibitionTumor metabolic featuresProgression-free survivalCell lung cancerResistant cancer cellsHypoxic tumor regionsMHC-II levelsRegions of hypoxiaKnock-outCheckpoint inhibition
2023
Scaling up robust immunopeptidomics technologies for a global T cell surveillance digital network
Kapoor S, Maréchal L, Sirois I, Caron É. Scaling up robust immunopeptidomics technologies for a global T cell surveillance digital network. Journal Of Experimental Medicine 2023, 221: e20231739. PMID: 38032361, PMCID: PMC10689202, DOI: 10.1084/jem.20231739.Peer-Reviewed Original ResearchThe SysteMHC Atlas v2.0, an updated resource for mass spectrometry-based immunopeptidomics
Huang X, Gan Z, Cui H, Lan T, Liu Y, Caron E, Shao W. The SysteMHC Atlas v2.0, an updated resource for mass spectrometry-based immunopeptidomics. Nucleic Acids Research 2023, 52: d1062-d1071. PMID: 38000392, PMCID: PMC10767952, DOI: 10.1093/nar/gkad1068.Peer-Reviewed Original ResearchUnlocking the potential of microfluidics in mass spectrometry-based immunopeptidomics for tumor antigen discovery
Stutzmann C, Peng J, Wu Z, Savoie C, Sirois I, Thibault P, Wheeler A, Caron E. Unlocking the potential of microfluidics in mass spectrometry-based immunopeptidomics for tumor antigen discovery. Cell Reports Methods 2023, 3: 100511. PMID: 37426761, PMCID: PMC10326451, DOI: 10.1016/j.crmeth.2023.100511.Peer-Reviewed Original ResearchConceptsSingle-cell proteomicsMicrofluidic technologyPotential of microfluidicsMass spectrometrySample preparationDroplet microfluidicsDigital microfluidicsMicrofluidic methodPhysical moleculesMicrofluidicsHigh sensitivityReproducible mannerPillar arraysRecent advancesSpectrometryMoleculesImmunopeptidomicsPowerful toolProteomicsPreparationMSPeptidesSolutionIntroduction to the Special Issue: The Immunopeptidome
Caron É, Perreault C. Introduction to the Special Issue: The Immunopeptidome. Seminars In Immunology 2023, 69: 101798. PMID: 37348326, DOI: 10.1016/j.smim.2023.101798.Peer-Reviewed Original Research
2022
Cellular senescence is immunogenic and promotes anti-tumor immunity
Marin I, Boix O, Garcia-Garijo A, Sirois I, Caballe A, Zarzuela E, Ruano I, Attolini C, Prats N, López-Domínguez J, Kovatcheva M, Garralda E, Muñoz J, Caron E, Abad M, Gros A, Pietrocola F, Serrano M. Cellular senescence is immunogenic and promotes anti-tumor immunity. Cancer Discovery 2022, 13: 410-431. PMID: 36302218, PMCID: PMC7614152, DOI: 10.1158/2159-8290.cd-22-0523.Peer-Reviewed Original ResearchConceptsCD8 T cellsAntitumor immune responseImmunogenic cell deathDendritic cellsSenescent cancer cellsT cellsCancer cellsImmune responseAntigen-specific CD8 T cellsSenescent cellsRelease of alarminsAnti-tumor immunityInnate immune cellsHuman primary cancer cellsActivation of IFNCellular senescencePrimary cancer cellsAdaptive immune systemCell deathCD8 lymphocytesAntitumor protectionImmune cellsImmune systemContext of cancerInduction of senescence
2021
Generation of HLA Allele-Specific Spectral Libraries to Identify and Quantify Immunopeptidomes by SWATH/DIA-MS
Kovalchik K, Hamelin D, Caron E. Generation of HLA Allele-Specific Spectral Libraries to Identify and Quantify Immunopeptidomes by SWATH/DIA-MS. Methods In Molecular Biology 2021, 2420: 137-147. PMID: 34905171, DOI: 10.1007/978-1-0716-1936-0_11.Peer-Reviewed Original ResearchRHybridFinder: An R package to process immunopeptidomic data for putative hybrid peptide discovery
Saab F, Hamelin D, Ma Q, Kovalchik K, Sirois I, Faridi P, Li C, Purcell A, Kubiniok P, Caron E. RHybridFinder: An R package to process immunopeptidomic data for putative hybrid peptide discovery. STAR Protocols 2021, 2: 100875. PMID: 34746858, PMCID: PMC8551247, DOI: 10.1016/j.xpro.2021.100875.Peer-Reviewed Original ResearchImmunopeptidomics: Isolation of Mouse and Human MHC Class I- and II-Associated Peptides for Mass Spectrometry Analysis.
Sirois I, Isabelle M, Duquette J, Saab F, Caron E. Immunopeptidomics: Isolation of Mouse and Human MHC Class I- and II-Associated Peptides for Mass Spectrometry Analysis. Journal Of Visualized Experiments 2021 PMID: 34723952, DOI: 10.3791/63052.Peer-Reviewed Original ResearchConceptsImmunopeptidomics workflowsComposition of peptidesSample preparation procedureQuality control samplesMass spectrometry analysisPreparation procedureElution efficiencySample preparationSpectrometry analysisPeptidesImmunoaffinity purificationReagentsMoleculesComplexesPreparationPurificationStepMHC-peptide complexesControl samplesImmunopeptidomicsNew protocolReproducibilityEfficiencyBeadsTechnology platformThe 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
2020
The SysteMHC Atlas: a Computational Pipeline, a Website, and a Data Repository for Immunopeptidomic Analyses
Shao W, Caron E, Pedrioli P, Aebersold R. The SysteMHC Atlas: a Computational Pipeline, a Website, and a Data Repository for Immunopeptidomic Analyses. Methods In Molecular Biology 2020, 2120: 173-181. PMID: 32124319, DOI: 10.1007/978-1-0716-0327-7_12.Peer-Reviewed Original Research
2019
The Human Immunopeptidome Project: A Roadmap to Predict and Treat Immune Diseases*
Vizcaíno J, Kubiniok P, Kovalchik K, Ma Q, Duquette J, Mongrain I, Deutsch E, Peters B, Sette A, Sirois I, Caron E. The Human Immunopeptidome Project: A Roadmap to Predict and Treat Immune Diseases*. Molecular & Cellular Proteomics 2019, 19: 31-49. PMID: 31744855, PMCID: PMC6944237, DOI: 10.1074/mcp.r119.001743.Peer-Reviewed Original Research
2018
Minimal Information About an Immuno‐Peptidomics Experiment (MIAIPE)
Lill J, van Veelen P, Tenzer S, Admon A, Caron E, Elias J, Heck A, Marcilla M, Marino F, Müller M, Peters B, Purcell A, Sette A, Sturm T, Ternette N, Vizcaíno J, Bassani‐Sternberg M. Minimal Information About an Immuno‐Peptidomics Experiment (MIAIPE). Proteomics 2018, 18: 1800110. PMID: 29791771, PMCID: PMC6033177, DOI: 10.1002/pmic.201800110.Peer-Reviewed Original Research
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 ResearchA Case for a Human Immuno-Peptidome Project Consortium
Caron E, Aebersold R, Banaei-Esfahani A, Chong C, Bassani-Sternberg M. A Case for a Human Immuno-Peptidome Project Consortium. Immunity 2017, 47: 203-208. PMID: 28813649, DOI: 10.1016/j.immuni.2017.07.010.Peer-Reviewed Original Research
2016
Contribution of Mass Spectrometry-Based Proteomics to the Understanding of TNF‑α Signaling
Ciuffa R, Caron E, Leitner A, Uliana F, Gstaiger M, Aebersold R. Contribution of Mass Spectrometry-Based Proteomics to the Understanding of TNF‑α Signaling. Journal Of Proteome Research 2016, 16: 14-33. PMID: 27762135, DOI: 10.1021/acs.jproteome.6b00728.Peer-Reviewed Original ResearchConceptsTNF-α signalingProteomics researchDimeric transcription factorsComplex signaling cascadesSystems-level understandingProteome levelProteomic landscapeCellular processesTranscription factorsSignaling cascadesNF-κBSignalingLevel understandingMass spectrometryProteomeActivationProteomicsSpite of decadesCytokines IL-1βDifferentiationLimited knowledgePathwayCascadeFamilyTNF
2015
Epigenetics and Proteomics Join Transcriptomics in the Quest for Tuberculosis Biomarkers
Esterhuyse M, Weiner J, Caron E, Loxton A, Iannaccone M, Wagman C, Saikali P, Stanley K, Wolski W, Mollenkopf H, Schick M, Aebersold R, Linhart H, Walzl G, Kaufmann S. Epigenetics and Proteomics Join Transcriptomics in the Quest for Tuberculosis Biomarkers. MBio 2015, 6: 10.1128/mbio.01187-15. PMID: 26374119, PMCID: PMC4600108, DOI: 10.1128/mbio.01187-15.Peer-Reviewed Original ResearchConceptsTB patientsPilot studyActive tuberculosis diseaseLarge-scale studiesSpread of TBLTBI controlLTBI participantsTuberculosis infectionTuberculosis diseaseDisease progressionHealthy controlsPrognostic biomarkerImmune responseBiologic mechanismsHealthy individualsPatientsHost responseInfected individualsBetter careInfectious diseasesMycobacterium tuberculosisSmall sample sizeBiomarker developmentRegulation of functionDNA methylation
2014
A repository of assays to quantify 10,000 human proteins by SWATH-MS
Rosenberger G, Koh CC, Guo T, Röst HL, Kouvonen P, Collins BC, Heusel M, Liu Y, Caron E, Vichalkovski A, Faini M, Schubert OT, Faridi P, Ebhardt HA, Matondo M, Lam H, Bader SL, Campbell DS, Deutsch EW, Moritz RL, Tate S, Aebersold R. A repository of assays to quantify 10,000 human proteins by SWATH-MS. Scientific Data 2014, 1: 140031. PMID: 25977788, PMCID: PMC4322573, DOI: 10.1038/sdata.2014.31.Peer-Reviewed Original Research
2013
The stress model of chronic pain: evidence from basal cortisol and hippocampal structure and function in humans
Vachon-Presseau E, Roy M, Martel M, Caron E, Marin M, Chen J, Albouy G, Plante I, Sullivan M, Lupien S, Rainville P. The stress model of chronic pain: evidence from basal cortisol and hippocampal structure and function in humans. Brain 2013, 136: 815-827. PMID: 23436504, DOI: 10.1093/brain/aws371.Peer-Reviewed Original ResearchConceptsChronic back painChronic painHippocampal volumeBack painControl subjectsParahippocampal gyrusPain-evoked activityPersistent pain statesAnterior parahippocampal gyrusHealthy control subjectsSmaller hippocampal volumesChronic pain intensityEndocrine stress responsePain statesPain intensityPain responseBasal cortisolPainHippocampal structureCortisol levelsMaladaptive physiological responsesHigher cortisolHippocampal complexConsecutive daysPatients