Etienne Caron, PhD
Research & Publications
Biography
Locations
Research Summary
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 to influence disease susceptibility, progression, or resistance. Nevertheless, very little is known about it from a systems-level and population-scale 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. In collaboration with researchers and clinical investivators, immediate applications of their work focus on improving vaccine design and targeted immunotherapies against cancer, infectious diseases as well as autoimmune disorders.
To achieve this goal, the Caron Lab prioritizes the development and application of innovative experimental and computational approaches to create and analyze high-resolution digital maps of immunopeptidomes at population-scale from any cell type. Such technologies include microfluidics and antibody-independent techniques for rapid, efficient and specific isolation of HLA-bound peptides, single-molecule peptide sequencing technologies, methods for population-scale HLA typing, Liquid Chromatography coupled to tandem Mass Spectrometry (LC-MS/MS) techniques, and deep learning algorithms for quantitative immunopeptidomics.
In longer term, the Caron Lab also aims to apply their technologies and knowledge to unravel how the immune system operates in outer space, positioning humanity to thrive both on Earth and venture into uncharted territories beyond our planet.
Coauthors
Research Interests
Autoimmune Diseases; HLA Antigens; Immunotherapy; Major Histocompatibility Complex; Mass Spectrometry; Antigen Presentation; Computational Biology; Cancer Vaccines; Neurodegenerative Diseases; Proteomics; Microfluidics; Systems Biology; Infectious Disease Medicine; Single-Cell Analysis; Spatial Analysis; Space Research
Public Health Interests
Bioinformatics; Biomarkers; Cancer; Chronic Diseases; Immunology; Infectious Diseases; Vaccines; Child/Adolescent Health
Research Image
Moving from genomics to immunopeptidomics surveillance
(A) World map illustrating the ambition of profiling immunopeptidomes across human populations using advanced immunopeptidomics technologies. A microfluidic device for automated sample preparation and a mass spectrometer for data acquisition are shown as representative examples of technologies that will be further developed. (B) Schematic of the workflow to identify immunopeptidomic signatures of disease susceptibility/resistance to stratify patients and help personalize mitigation strategies in future pandemics. SARS-CoV-2 is used for illustrating the concept. In this example, viral peptides are isolated at population-scale from plasma samples (patient cohorts). Fictive bar plot of HLA-I-allele-specific self peptides in different organs (patient #1) and population-scale quantitative digital maps of soluble HLA-associated SARS-CoV-2 peptides from plasma samples are illustrated.
Selected Publications
- Scaling up robust immunopeptidomics technologies for a global T cell surveillance digital networkKapoor 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.
- The SysteMHC Atlas v2.0, an updated resource for mass spectrometry-based immunopeptidomicsHuang 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.
- Integrated Immunopeptidomics and Proteomics Study of SARS-CoV-2–Infected Calu-3 Cells Reveals Dynamic Changes in Allele-specific HLA Abundance and Antigen PresentationChen 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.
- Unlocking the potential of microfluidics in mass spectrometry-based immunopeptidomics for tumor antigen discoveryStutzmann 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.
- Introduction to the Special Issue: The ImmunopeptidomeCaron 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.
- Cellular senescence is immunogenic and promotes anti-tumor immunityMarin 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.
- Understanding the constitutive presentation of MHC class I immunopeptidomes in primary tissuesKubiniok P, Marcu A, Bichmann L, Kuchenbecker L, Schuster H, Hamelin D, Duquette J, Kovalchik K, Wessling L, Kohlbacher O, Rammensee H, Neidert M, Sirois I, Caron E. Understanding the constitutive presentation of MHC class I immunopeptidomes in primary tissues. IScience 2022, 25: 103768. PMID: 35141507, PMCID: PMC8810409, DOI: 10.1016/j.isci.2022.103768.
- Generation of HLA Allele-Specific Spectral Libraries to Identify and Quantify Immunopeptidomes by SWATH/DIA-MSKovalchik K, Hamelin D, Caron E. Generation of HLA Allele-Specific Spectral Libraries to Identify and Quantify Immunopeptidomes by SWATH/DIA-MS. 2021, 2420: 137-147. PMID: 34905171, DOI: 10.1007/978-1-0716-1936-0_11.
- MhcVizPipe: A Quality Control Software for Rapid Assessment of Small- to Large-Scale Immunopeptidome DatasetsKovalchik 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.
- RHybridFinder: An R package to process immunopeptidomic data for putative hybrid peptide discoverySaab 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.
- Immunopeptidomics: 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.
- The mutational landscape of SARS-CoV-2 variants diversifies T cell targets in an HLA-supertype-dependent mannerHamelin 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.
- The SysteMHC Atlas: a Computational Pipeline, a Website, and a Data Repository for Immunopeptidomic AnalysesShao W, Caron E, Pedrioli P, Aebersold R. The SysteMHC Atlas: a Computational Pipeline, a Website, and a Data Repository for Immunopeptidomic Analyses. 2020, 2120: 173-181. PMID: 32124319, DOI: 10.1007/978-1-0716-0327-7_12.
- 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.
- A tissue-based draft map of the murine MHC class I immunopeptidomeSchuster 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.
- The SysteMHC Atlas project.Shao W, Pedrioli PGA, Wolski W, Scurtescu C, Schmid E, Vizcaíno JA, Courcelles M, Schuster H, Kowalewski D, Marino F, Arlehamn CSL, Vaughan K, Peters B, Sette A, Ottenhoff THM, Meijgaarden KE, Nieuwenhuizen N, Kaufmann SHE, Schlapbach R, Castle JC, Nesvizhskii AI, Nielsen M, Deutsch EW, Campbell DS, Moritz RL, Zubarev RA, Ytterberg AJ, Purcell AW, Marcilla M, Paradela A, Wang Q, Costello CE, Ternette N, van Veelen PA, van Els CACM, Heck AJR, de Souza GA, Sollid LM, Admon A, Stevanovic S, Rammensee HG, Thibault P, Perreault C, Bassani-Sternberg M, Aebersold R, Caron E. The SysteMHC Atlas project. Nucleic Acids Res 2018, 46: D1237-D1247. PMID: 28985418, DOI: 10.1093/nar/gkx664.
- A Case for a Human Immuno-Peptidome Project ConsortiumCaron 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.
- Precise Temporal Profiling of Signaling Complexes in Primary Cells Using SWATH Mass SpectrometryCaron E, Roncagalli R, Hase T, Wolski W, Choi M, Menoita M, Durand S, García-Blesa A, Fierro-Monti I, Sajic T, Heusel M, Weiss T, Malissen M, Schlapbach R, Collins B, Ghosh S, Kitano H, Aebersold R, Malissen B, Gstaiger M. Precise Temporal Profiling of Signaling Complexes in Primary Cells Using SWATH Mass Spectrometry. Cell Reports 2017, 18: 3219-3226. PMID: 28355572, PMCID: PMC5382234, DOI: 10.1016/j.celrep.2017.03.019.
- Analysis of Major Histocompatibility Complex (MHC) Immunopeptidomes Using Mass SpectrometryCaron E, Kowalewski D, Chiek Koh C, Sturm T, Schuster H, Aebersold R. Analysis of Major Histocompatibility Complex (MHC) Immunopeptidomes Using Mass Spectrometry. Molecular & Cellular Proteomics 2015, 14: 3105-3117. DOI: 10.1074/mcp.m115.052431.
- Epigenetics and Proteomics Join Transcriptomics in the Quest for Tuberculosis BiomarkersEsterhuyse 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: e01187-15. PMID: 26374119, PMCID: PMC4600108, DOI: 10.1128/mbio.01187-15.
- An open-source computational and data resource to analyze digital maps of immunopeptidomesCaron E, Espona L, Kowalewski D, Schuster H, Ternette N, Alpízar A, Schittenhelm R, Ramarathinam S, Arlehamn C, Koh C, Gillet L, Rabsteyn A, Navarro P, Kim S, Lam H, Sturm T, Marcilla M, Sette A, Campbell D, Deutsch E, Moritz R, Purcell A, Rammensee H, Stevanovic S, Aebersold R. An open-source computational and data resource to analyze digital maps of immunopeptidomes. ELife 2015, 4: e07661. PMID: 26154972, PMCID: PMC4507788, DOI: 10.7554/elife.07661.
- Checkpoint blockade cancer immunotherapy targets tumour-specific mutant antigensGubin MM, Zhang X, Schuster H, Caron E, Ward JP, Noguchi T, Ivanova Y, Hundal J, Arthur CD, Krebber WJ, Mulder GE, Toebes M, Vesely MD, Lam SS, Korman AJ, Allison JP, Freeman GJ, Sharpe AH, Pearce EL, Schumacher TN, Aebersold R, Rammensee HG, Melief CJ, Mardis ER, Gillanders WE, Artyomov MN, Schreiber RD. Checkpoint blockade cancer immunotherapy targets tumour-specific mutant antigens. Nature 2014, 515: 577-581. PMID: 25428507, PMCID: PMC4279952, DOI: 10.1038/nature13988.
- A repository of assays to quantify 10,000 human proteins by SWATH-MSRosenberger 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.
- The MHC I immunopeptidome conveys to the cell surface an integrative view of cellular regulationCaron 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: 533-533. PMID: 21952136, PMCID: PMC3202804, DOI: 10.1038/msb.2011.68.
- 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.
- A comprehensive map of the mTOR signaling networkCaron E, Ghosh S, Matsuoka Y, Ashton-Beaucage D, Therrien M, Lemieux S, Perreault C, Roux P, Kitano H. A comprehensive map of the mTOR signaling network. Molecular Systems Biology 2010, 6: 453-453. PMID: 21179025, PMCID: PMC3018167, DOI: 10.1038/msb.2010.108.
- ER stress affects processing of MHC class I-associated peptidesGranados D, Tanguay P, Hardy M, Caron É, de Verteuil D, Meloche S, Perreault C. ER stress affects processing of MHC class I-associated peptides. BMC Immunology 2009, 10: 10. PMID: 19220912, PMCID: PMC2657905, DOI: 10.1186/1471-2172-10-10.
- The MHC class I peptide repertoire is molded by the transcriptomeFortier 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.