Selected publications from CAPA (since 2014)

Quantitative proteomics

  • Kubiniok P., Finicle B.T., Piffaretti F., McCracken A.N., Perryman M., Hanessian S., Edinger A.L., Thibault P.
    Dynamic phosphoproteomics uncovers signaling pathways modulated by anti-oncogenic sphingolipid analogs
    Mol. Cell. Proteomics,18, 408 (2019).
  • McManus F.P., Bourdeau V. , Acevedo M., Lopes-Paciencia, S., Mignacca L., Lamoliatte F., Rojas Pino J.W., Ferbeyre G.*, Thibault P.
    Quantitative SUMO proteomics reveals the modulation of several PML nuclear body associated proteins and an anti-senescence function of UBC9
    Scientific Rep., 17, 7754 (2018).
  • P. Kubiniok, H. Lavoie, M. Therrien, P. Thibault
    Time-resolved phosphoproteome analysis of paradoxical RAF activation reveals novel targets of ERK
    Mol. Cell. Proteomics, 16, 663 (2017).
  • E. Kanshin, P. Kubiniok, Y. Thattikota, D. D'Amours, P. Thibault
    Phosphoproteome dynamics of Saccharomyces cerevisiae under heat shock and cold stress
    Mol Syst Biol. 2015 Jun 3;11(6):813.
  • M. Buscarlet, V. Krasteva, L. Ho, C. Simon, J. Hébert, B. Wilhelm, G.R. Crabtree, G. Sauvageau, P. Thibault, J.A. Lessard
    Essential role of BRG, the ATPase subunit of BAF chromatin remodeling complexes, in leukemia maintenance.
    Blood. 2014 Jan 29.

Cell biology

  • A.Sellam , J. Chaillot, J. Mallick, F.Tebbji, J.Richard Albert, MA. Cook, M.Tyers
    The p38/HOG stress-activated protein kinase network couples growth to division in Candida albicans
    PLoS Genet. 15(3):e1008052 (2019).
  • Kim SM, Nguyen TT, Ravi A, Kubiniok P, Finicle BT, Jayashankar V, Malacrida L, Hou J, Robertson J, Gao D, Chernoff J, Digman MA, Potma EO, Tromberg BJ, Thibault P, Edinger AL
    PTEN Deficiency and AMPK Activation Promote Nutrient Scavenging and Anabolism in Prostate Cancer Cells
    Cancer Discov. 8, 866 (2018).
  • J.A. Gross, C. Nagy, L. Lin, É. Bonneil, M. Maheu, P. Thibault, N. Mechawar, P. Jin, G. Turecki
    Global and Site-Specific Changes in 5-Methylcytosine and 5-Hydroxymethyl cytosine after Extended Post-mortem Interval
    Front in Genetics, 7, 120 (2016).
  • M. Dieude, C. Bell, J. Turgeon, D. Beillevaire, L Pomerleau, B. Yang, K. Hamelin, S. Qi, N. Pallet, C. Beland, J.F. Cailhier, M. Rousseau, C. Rondeau, D. Gingras, C. Perreault, M. Desjardins, E. Boilard, P. Thibault, M.J. Hebert
    The 20S proteasome core, active within apoptotic exosome-like vesicles, induces autoantibody production and accelerates rejection
    Science Translational Medicine, 7, 317ra200 (2015).
  • D.C. Jeffery, N. Kakusho, Z You, M. Gharib, B Wyse, E. Drury, M. Weinreich, P. Thibault, A. Verreault, H. Masai, K. Yankulov
    CDC28 phosphorylates Cac1p and regulates the association of chromatin assembly factor 1 with chromatin
    Cell Cycle, 14, 74-85 (2015).
  • N. Zaman, G. Paresa, S. Chowdhury, E. Bonneil, P. Thibault, E. Wang, M. Trifiro, M. Paliouras
    Proteomic-coupled-network analysis of T877A-androgen receptor interactomes can predict clinical prostate cancer outcomes between White (non-Hispanic) and African-American groups
    PLoS One. 2014 Nov 19;9(11):e113190.
  • G. Laflamme, T. Tremblay-Boudreault, MA Roy, P Andersen, E Bonneil, K Atchia, P. Thibault, D. D'Amours, BH Kwok
    Structural Maintenance of Chromosome (SMC) Proteins Link Microtubule Stability to Genome
    Integrity, J. Biol. Chem, 289, 27418-31 (2014)
  • ME. Bordeleau, R. Aucagne, J. Chagraoui, S. Girard, N. Mayotte, E. Bonneil , P. Thibault, C. Pabst, A. Bergeron, F. Barabé, J. Hébert, M. Sauvageau, C. Boutonnet, S. Meloche, G. Sauvageau
    UBAP2L is a novel BMI1-interacting protein essential for hematopoietic stem cell activity
    Blood., 124, 2362-9 (2014)
  • N. Desgolshaie, X Tang, E.D. Kanshin, E.C. Williams, A.D. Rudner, P. Thibault, M. Tyers, A. Verreault
    Regulation of the histone deacetylase Hst3 by cyclin-dependent kinases and the ubiquitin ligase SCFCdc4
    J. Biol. Chem., 289, 43-49 (2014).

Protein modifications

  • Cheng X., Jobin-Robitaille O., Billon P., Buisson R., Niu H., Lacoste N., Abshiru N., Côté V., Thibault P., Krone S. J., Sung P., Brand C. J., Masson J.-Y., Côté J.
    Phospho-dependent recruitment of the yeast NuA4 acetyltransferase complex by MRX at DNA breaks regulates RPA dynamics during resection
    PNAS 115,10028 (2018).
  • S Daou, H Barbour, O Ahmed, L Masclef, C Baril, N Sen Nkwe, D Tchelougou, M Uriarte, E Bonneil, D Ceccarelli, N Mashtalir, M Tanji, JY Masson, P Thibault, F Sicheri, H Yang, M Carbone, M Therrien, AB Affar
    Monoubiquitination of ASXLs controls the deubiquitinase activity of the tumor suppressor BAP1
    Nature Commun. 9(1):4385 (2018).
  • Kanshin E, Pascariu M, Tyers M, D'Amours D, Thibault P.
    Combined enrichment/enzymatic approach to study tightly clustered multi-site phosphorylation on Ser-rich domains
    J. Prot. Res., 17, 3050 (2018).
  • Maroui M.A., Maarifi G., McManus F.P., Lamoliatte F., Thibault P., Chelbi-Alix M.K.
    PML requirement for interferon-induced global cellular SUMOylation
    Mol. Cell. Proteomics, 17, 1196 (2018).
  • McManus, F. Lamoliatte, F., Thibault P.
    Identification of crosstalk between SUMOylation and ubiquitylation using a sequential peptide immunopurification approach
    Nature Protocols, 12, 2342 (2017).
  • E. Kanshin, S. Giguere, J. Cheng, M.D. Tyers, P. Thibault
    Machine learning of global phosphoproteomic profiles enables discrimination of direct versus indirect kinase substrates
    Mol. Cell. Proteomics, 16, 786 (2017).
  • P. Kubiniok, H. Lavoie, M. Therrien, P. Thibault
    Time-resolved phosphoproteome analysis of paradoxical RAF activation reveals novel targets of ERK
    Mol. Cell. Proteomics, 16, 663 (2017).
  • F. Lamoliatte, F.M. McManus, G. Maarifi, M.K. Chelbi-Alix, P. Thibault
    Uncovering the SUMOylation and Ubiquitylation Crosstalk in Human Cells Using Sequential Peptide Immunopurification
    Nature Commun., 8:14109 (2017).
  • V. Bachmann, J.E. Mayrhofer, R. Llouz, P. Tschaikner, P. Raffeiner, R. Rock, M. Courcelles, Apelt, T-W. Lu, P. Thibault, P. Aanstad, U. Stelzl, S.S. Taylor, E. Stefan
    GPR161 anchoring of PKA consolidates GPCR and cAMP signaling
    P.N.A.S, 113, 7786 (2016).
  • N. Abshiru, R. E. Rajan, A. Verreault, P. Thibault
    Unraveling site-specific and combinatorial histone modifications using high-resolution mass spectrometry in histone deacetylase mutants of fission yeast
    J. Prot. Res, 15, 2132 (2016).
  • V. Kota, G. Sommer, C. Durette, P. Thibault, E. A. van Niekerk, J. L. Twiss, T. Heise
    SUMO-modification of the La protein facilitates binding to mRNA in vitro and in cell
    PLoS One, 11(5), e0156365 (2016).
  • F. McManus, C. Desroches Altamirano, P. Thibault
    In vitro assay to determine SUMOylation sites on protein substrate
    Nature protocols, 11, 387, 2016.
  • N. Abshiru, O. Caron-Lizotte, R.E. Rajan, A. Jamai, C. Pomies, A. Verreault, P. Thibault
    Discovery of protein acetylation patterns by deconvolution of peptide isomer mass spectra
    Nature Commun., 6, 8648 (2015).
  • J. Gagnon, S. Daou, N. Zamorano, NV. Iannantuono, I. Hammond-Martel, N. Mashtalir, E. Bonneil, H. Wurtele, P. Thibault, B. Affar el
    Undetectable histone O-GlcNAcylation in mammalian cells.
    Epigenetics. 2015 Aug 3;10(8):677-91.
  • E. Kanshin, M. Tyers, P. Thibault
    Sample Collection Method Bias Effects in Quantitative Phosphoproteomics
    J Proteome Res. 2015 Jul 2;14(7):2998-3004.
  • A. Simoneau, N. Delgoshaie, I. Celic, J. Dai, N. Abshiru, S. Costantino, P. Thibault, JD. Boeke, A. Verreault, H. Wurtele
    Interplay between histone H3 lysine 56 deacetylation and chromatin modifiers in response to DNA damage
    Genetics. 2015 May;200(1):185-205.
  • E. Kanshin, LP. Bergeron-Sandoval, SS. Isik, P. Thibault, SW. Michnick
    A cell-signaling network temporally resolves specific versus promiscuous phosphorylation
    Cell Rep. 2015 Feb 24;10(7):1202-14.
  • F. Lamoliatte, D. Caron, C. Durette, L. Mahrouche, M. A. Maroui, O. Caron-Lizotte, E. Bonneil, M.K. Chelbi-Alix, P. Thibault
    Large-scale analysis of lysine SUMOylation by SUMO remnant immunoaffinity profiling
    Nature Commun. 5, 5409 (2014).
  • J.A. Galan, K.M. Geraghty, G. Lavoie, E. Kanshin, J. Tcherkezian, V. Calabrese, G.R. Jeschke, B.E. Turk, B.A. Balli, J. Blenis, P. Thibault, P.P. Roux
    Phosphoproteomic analysis identifies the tumor suppressor PDCD4 as a RSK substrate negatively regulated by 14-3-3
    PNAS, 111, E2918-27 (2014).

Immunology and MHC I peptides

  • Laumont CM, Vincent K, Hesnard L, Audemard É, Bonneil É, Laverdure JP, Gendron P, Courcelles M, Hardy MP, Côté C, Durette C, St-Pierre C, Benhammadi M, Lanoix J, Vobecky S, Haddad E, Lemieux S, Thibault P, Perreault C
    Noncoding regions are the main source of targetable tumor-specific antigens
    Science Transl. Med., 10, 470 (2018).
  • Lanoix J., Durette C., Courcelles M., Cossette, E., Comtois-Marotte S., Hardy M.-P., Côté C., Perreault C., Thibault P.
    Comparison of the MHC I immunopeptidome repertoire of B-cell lymphoblasts using two isolation methods
    Proteomics, 18, e1700251 (2018).
  • H. Pearson, T .Daouda, D.P. Granados, C. Durette, E. Bonneil, M. Courcelles, A. Rodenbrock, J.P. Laverdure, C. Côté, S. Mader, S. Lemieux, P. Thibault, C.Perreault
    MHC class I-associated peptides derive from selective regions of the human genome
    J. Clin. Invest., 126, 4690 (2016)
  • N.A. Nagarajan, D.A. deVerteuil, D. Sriranganadane, W. Yahyaoui, P. Thibault, C. Perreault, N. Shastri
    ERAAP Shapes the Peptidome Associated with Classical and Nonclassical MHC Class I Molecules
    J. Immunol., 197, 1035 (2016).
  • D. Granados, A. Rodenbrock, J.-P. Laverdure, C. Côté, O. Caron-Lizotte, C. Carli, H. Pearson, V. Janelle, C. Durette, É. Bonneil, D.-C. Roy, J.-S. Delisle, S. Lemieux, P. Thibault, C. Perreault
    Proteogenomic-based discovery of minor histocompatibility antigens with suitable features for immunotherapy of hematologic cancers
    Leukemia, 30, 1344-1354 (2016)
  • C.M. Laumont, T. Douada, J.-P. Laverdure, E. Bonneil, O. Caron-Lizotte, M.P. Hardy, D.P. Granados, C. Durette, S. Lemieux, P. Thibault, C. Perreault
    Global proteogenomic analysis of human MHC class I-associated peptides derived from non-canonical reading frames
    Nature Commun., 7;10238 (2016)
  • D. Paola Granados, C. Laumont, P. Thibault, C. Perreault
    The nature of self for T cells - A systems-level perspective
    Curr Opin Immunol. 2015 Jun;34:1-8.
  • D. Paola Granados, D. Sriranganadane, T. Daouda, A. Zieger, C. M. Laumont, O. Caron-Lizotte, G. Boucher, M.-P. Hardy, P. Gendron, C. Côté, S. Lemieux, P. Thibault, C. Perreault
    Impact of Genomic Polymorphisms on the Repertoire of Human MHC Class I-Associated Peptides
    Nature Commun. 2014 Apr 9;5:3600. doi: 10.1038
  • M.A. Germain, L. Chatel-Chaix, B. Gagné, E. Bonneil, P. Thibault, F. Pradezynski, B. de Chassey, L. Meyniel-Schicklin, V. Lotteau, M. Baril, D. Lamarre
    Elucidating novel hepatitis C virus-host interactions using combined mass spectrometry and functional genomics approaches
    Mol. Cell. Proteomics, 13, 184-203 (2014).
  • K. Vincent, M._P. Hardy, A. Trofimov, C.M. Laumont, D. Sriranganadane, S. Hadj-Mimoune, I. Salem Fourati, H. Soudeyns, P. Thibault, C. Perreault
    Rejection of mouse leukemic cells requires antigen-specific T cells with high functional avidity
    Biology of Blood and Marrow Transplantation, 20, 37-45 (2014).

Technology development

  • Pfammatter S., Bonneil E., McManus F.P., Thibault P.
    Accurate quantitative proteomic analyses using metabolic labeling and High Field Asymmetric Waveform Ion Mobility Spectrometry (FAIMS)
    J. Proteome Res., in press (2019).
  • Pfammatter S, Bonneil E, McManus FP, Prasad S, Bailey DJ, Belford M, Dunyach JJ, Thibault P.
    A novel differential ion mobility device expands the depth of proteome coverage and the sensitivity of multiplex proteomic measurements
    Mol. Cell. Proteomics, 17, 2051 (2018).
  • Pfammatter, S., Bonneil, E., McManus, F., Thibault, P.
    Gas-phase enrichment of multiply-charged peptide ions by differential ion mobility extend the comprehensiveness of SUMO proteome analyses
    J. Am. Soc. Mass Spectrom., 29, 1111 (2018) .
  • Courcelles, J. Coulombe-Huntington, É. Cossette, A.C. Gingras, P. Thibault, M. Tyers
    CLMSVault: A Software Suite for Protein Cross-Linking Mass-Spectrometry Data Analysis and Visualization
    J. Proteome Res., 16, 2645 (2017.
  • J. Koszela, NT. Pham, D. Evans, S. Mann, I.Perez-Pi, S. Shave, DFJ. Ceccarelli, F. Sicheri, M. Tyers, M. Auer
    Real-time tracking of complex ubiquitination cascades using a fluorescent confocal on-bead assay.
    BMC Biol. 16(1):88, (2018)
  • S. Pfammatter, E. Bonneil, P. Thibault
    Improvement of quantitative measurements in multiplex proteomics using high-field asymmetric waveform ion mobility spectrometry
    J. Proteome Res., 15, 4653 (2016).
  • E. Bonneil, S. Pfammatter, P. Thibault
    Enhancement of mass spectrometry performance for proteomic analyses using High-Field asymmetric waveform ion mobility spectrometry (FAIMS)
    Invited review in J. Mass Spectrom. 50, 1181-1195 (2015).