Etienne Caron, PhD
Assistant ProfessorCards
About
Research
Overview
In the post-GWAS era, the HLA has been established as the region of the genome that is associated with the greatest number of human diseases, ranging from cancer and infectious diseases to autoimmune and neurodegenerative disorders.
HLA proteins present an extremely large and complex array of peptide fragments, which include both self and nonself peptides, collectively referred to as the human immunopeptidome.
CD8+ and CD4+ T cells interact with the human immunopeptidome through constant TCR recognition of both agonist and antagonist peptides, together shaping disease susceptibility, progression, or resistance. Nevertheless, very little is known about it from a systems-level and mechanistic perspective.
In this context, the overarching goal of the Caron Lab is to develop and apply mass spectrometry-based methods and systems immunology approaches to understand the generation, composition and dynamics of both the self and nonself immunopeptidome, as well as its interaction with CD8+ and CD4+ T cells, with the ultimate goal of innovating treatments and preventive strategies for a broad range of immune-related diseases.
To achieve this goal, the Caron Lab prioritizes the development of next-generation immunopeptidomics technologies, develops a systems immunopeptidomics framework to challenge the current T-cell activation paradigm, and collaborates with clinical investigators and researchers in the fields of autoimmunity, infectious diseases, and cancer to make an impact in vaccine design and T-cell-based immunotherapy.
Medical Research Interests
Antigen Presentation; Autoimmune Diseases; Cancer Vaccines; Computational Biology; HLA Antigens; Immunotherapy; Infectious Disease Medicine; Major Histocompatibility Complex; Mass Spectrometry; Microfluidics; Neurodegenerative Diseases; Proteomics; Single-Cell Analysis; Space Research; Spatial Analysis; Systems Biology
Public Health Interests
Bioinformatics; Biomarkers; Cancer; Child/Adolescent Health; Chronic Diseases; Infectious Diseases; Immunology; Vaccines
Publications
2025
MBPeace treaty: How myelin self-peptides broker CNS tolerance.
Leo I, Caron E. MBPeace treaty: How myelin self-peptides broker CNS tolerance. Sci Immunol 2025, 10: eadx0208. PMID: 40053606, DOI: 10.1126/sciimmunol.adx0208.Commentaries, Editorials and Letters
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, PMCID: PMC11602551, 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 inhibitionDeciphering the HLA-E immunopeptidome with mass spectrometry: an opportunity for universal mRNA vaccines and T-cell-directed immunotherapies
Weitzen M, Shahbazy M, Kapoor S, Caron E. Deciphering the HLA-E immunopeptidome with mass spectrometry: an opportunity for universal mRNA vaccines and T-cell-directed immunotherapies. Frontiers In Immunology 2024, 15: 1442783. PMID: 39301027, PMCID: PMC11410602, DOI: 10.3389/fimmu.2024.1442783.Peer-Reviewed Reviews, Practice Guidelines, Standards, and Consensus StatementsMass spectrometryHLA-EHLA moleculesT-cell-directed immunotherapyCD8+ T cellsNovel cell surface antigensNon-classical HLA-EHLA-E moleculesCell surface antigensPeptides to CD8T cellsMRNA vaccinesTherapeutic efficacySurface antigensImmunotherapyMoleculesSpectrometryTherapeutic targetImmunopeptidomePathogen-derivedCD8Peptide repertoirePeptide fragmentsHLAMinimal polymorphism
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.Commentaries, Editorials and LettersThe 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 ResearchIntegrated 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 IUnlocking 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.Commentaries, Editorials and LettersConceptsSingle-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.Commentaries, Editorials and Letters
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
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Caron Lab
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300 George Street, Fl 3rd, Rm 353G
New Haven, CT 06511