2023
Unlocking 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 ResearchMeSH KeywordsAntigens, NeoplasmHistocompatibility Antigens Class IHLA AntigensHumansMass SpectrometryMicrofluidicsNeoplasmsConceptsSingle-cell proteomicsMicrofluidic technologyPotential of microfluidicsMass spectrometrySample preparationDroplet microfluidicsDigital microfluidicsMicrofluidic methodPhysical moleculesMicrofluidicsHigh sensitivityReproducible mannerPillar arraysRecent advancesSpectrometryMoleculesImmunopeptidomicsPowerful toolProteomicsPreparationMSPeptidesSolution
2021
MhcVizPipe: A Quality Control Software for Rapid Assessment of Small- to Large-Scale Immunopeptidome Datasets
Kovalchik K, Ma Q, Wessling L, Saab F, Duquette J, Kubiniok P, Hamelin D, Faridi P, Li C, Purcell A, Jang A, Paramithiotis E, Tognetti M, Reiter L, Bruderer R, Lanoix J, Bonneil É, Courcelles M, Thibault P, Caron E, Sirois I. MhcVizPipe: A Quality Control Software for Rapid Assessment of Small- to Large-Scale Immunopeptidome Datasets. Molecular & Cellular Proteomics 2021, 21: 100178. PMID: 34798331, PMCID: PMC8717601, DOI: 10.1016/j.mcpro.2021.100178.Peer-Reviewed Original ResearchConceptsModern web browsersLarge-scale datasetsQuality control softwareWeb browserHTML formatControl softwareSoftware toolsProteomics core facilitiesConsolidated viewDatasetImmunopeptidomic datasetsHigh-throughput technologiesDecision-making processData interpretationBrowserInstrument operatorsComputerAssurance systemAlgorithmQuality controlSoftwareCore facilitiesFormatServicesTechnologyImmunopeptidomics: 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 ResearchMeSH KeywordsHistocompatibility Antigens Class IHistocompatibility Antigens Class IIHLA AntigensHumansMass SpectrometryPeptidesReproducibility of ResultsConceptsImmunopeptidomics workflowsComposition of peptidesSample preparation procedureQuality control samplesMass spectrometry analysisPreparation procedureElution efficiencySample preparationSpectrometry analysisPeptidesImmunoaffinity purificationReagentsMoleculesComplexesPreparationPurificationStepMHC-peptide complexesControl samplesImmunopeptidomicsNew protocolReproducibilityEfficiencyBeadsTechnology platform
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 ResearchMeSH KeywordsAllelesAutoimmune DiseasesCohort StudiesHistocompatibility Antigens Class IHistocompatibility Antigens Class IIHLA AntigensHumansImmunotherapyInfectionsMass SpectrometryNeoplasmsPeptidesPrecision MedicinePrognosis
2018
A tissue-based draft map of the murine MHC class I immunopeptidome
Schuster H, Shao W, Weiss T, Pedrioli P, Roth P, Weller M, Campbell D, Deutsch E, Moritz R, Planz O, Rammensee H, Aebersold R, Caron E. A tissue-based draft map of the murine MHC class I immunopeptidome. Scientific Data 2018, 5: 180157. PMID: 30084848, PMCID: PMC6080492, DOI: 10.1038/sdata.2018.157.Peer-Reviewed Original ResearchMeSH KeywordsAnimalsHistocompatibility Antigens Class IMass SpectrometryMiceMice, Inbred C57BLOrgan SpecificityPeptidesConceptsMHC class IClass IMurine MHC class IPotential tumor-associated antigenMajor histocompatibility complex class IHistocompatibility complex class ITumor-associated antigensComplex class IC57BL/6 miceT cellsTranslational immunologyCancer modelImmune systemNormal tissuesMS injectionMost tissuesTissueInitial qualitative dataTotal numberPeptidesCD8AtlasAntigenMiceMinimal 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 ResearchComputational BiologyDatabases, ProteinHistocompatibility Antigens Class IHistocompatibility Antigens Class IIHumansPeptide FragmentsProteomicsSoftwareSpecimen Handling
2011
The MHC I immunopeptidome conveys to the cell surface an integrative view of cellular regulation
Caron E, Vincent K, Fortier M, Laverdure J, Bramoullé A, Hardy M, Voisin G, Roux P, Lemieux S, Thibault P, Perreault C. The MHC I immunopeptidome conveys to the cell surface an integrative view of cellular regulation. Molecular Systems Biology 2011, 7: msb201168. PMID: 21952136, PMCID: PMC3202804, DOI: 10.1038/msb.2011.68.Peer-Reviewed Original ResearchMeSH KeywordsAnimalsCD8-Positive T-LymphocytesCell Line, TumorCell MembraneGene Expression ProfilingHigh-Throughput Screening AssaysHistocompatibility Antigens Class IImmunityMajor Histocompatibility ComplexMass SpectrometryMetabolic Networks and PathwaysMiceOligonucleotide Array Sequence AnalysisPeptidesProteomicsSignal TransductionSirolimusSystems BiologyTandem Mass SpectrometryTOR Serine-Threonine KinasesConceptsCell surfaceMass spectrometry-based approachSystems-level evidenceSelf/non-self discriminationCellular regulationPredictive biologyCellular metabolic activityCellular metabolismNon-self discriminationRapamycin resultsMammalian targetMHC IBiochemical networksCD8 T lymphocytesSystems immunologyMajor histocompatibility complex (MHC) class I moleculesMetabolic eventsExtrinsic factorsMetabolic activityIntegrative viewClass I moleculesImmunotherapeutic interventionsT lymphocytesEssence of selfSystem-level perspective
2010
Deletion of Immunoproteasome Subunits Imprints on the Transcriptome and Has a Broad Impact on Peptides Presented by Major Histocompatibility Complex I molecules*
de Verteuil D, Muratore-Schroeder T, Granados D, Fortier M, Hardy M, Bramoullé A, Caron É, Vincent K, Mader S, Lemieux S, Thibault P, Perreault C. Deletion of Immunoproteasome Subunits Imprints on the Transcriptome and Has a Broad Impact on Peptides Presented by Major Histocompatibility Complex I molecules*. Molecular & Cellular Proteomics 2010, 9: 2034-2047. PMID: 20484733, PMCID: PMC2938112, DOI: 10.1074/mcp.m900566-mcp200.Peer-Reviewed Original ResearchConceptsMIP repertoireLabel-free quantitative proteomics approachComplex ICell type-specific signaturesBasic cellular processesUnstructured protein regionsProteasome-mediated proteolysisQuantitative proteomics approachSet of genesPrimary mouse dendritic cellsJawed vertebratesRegulated genesCellular processesProteomic approachMass spectrometry analysisGene transcriptionBioinformatics analysisChromosome 4Protein regionsPrimary cellsGenesCleavage preferenceSpectrometry analysisCell functionPeptidomics studies
2008
The MHC class I peptide repertoire is molded by the transcriptome
Fortier M, Caron E, Hardy M, Voisin G, Lemieux S, Perreault C, Thibault P. The MHC class I peptide repertoire is molded by the transcriptome. Journal Of Experimental Medicine 2008, 205: 595-610. PMID: 18299400, PMCID: PMC2275383, DOI: 10.1084/jem.20071985.Peer-Reviewed Original ResearchMeSH KeywordsAllelesAmino Acid SequenceAnimalsCell LineCell Line, TumorComputational BiologyGene Expression ProfilingGenes, MHC Class IHistocompatibility Antigens Class IMiceMultiprotein ComplexesOligonucleotide Array Sequence AnalysisPeptidesProtein BindingRNA, MessengerTandem Mass SpectrometryT-LymphocytesTransfectionConceptsMIP repertoireCyclin/cyclin-dependent kinasePrimary mouse thymocytesCyclin-dependent kinasesMass spectrometry approachMouse thymocytesAbundant transcriptsGlobal profilingHigh-throughput analysisPosttranscriptional mechanismsNeoplastic thymocytesRelative abundanceTranscriptomeMHC class INeoplastic transformationCancer cellsMHC IMolecular compositionPeptidomics dataRepertoirePeptidesClass IMajor histocompatibility complex I moleculesThymocytesHelicases
2005
The structure and location of SIMP/STT3B account for its prominent imprint on the MHC I immunopeptidome
Caron É, Charbonneau R, Huppé G, Brochu S, Perreault C. The structure and location of SIMP/STT3B account for its prominent imprint on the MHC I immunopeptidome. International Immunology 2005, 17: 1583-1596. PMID: 16263756, DOI: 10.1093/intimm/dxh336.Peer-Reviewed Original Research