Présentation

Sujets de recherche

Protéomique fonctionnelle et structurale, Cellule, Dégénérescence cellulaire, Enzymes et protéines, Maladies neurodégénératives, Acides nucléiques.

Disciplines de recherche

Biochimie, Biologie cellulaire, Biologie moléculaire, Génétique.

Mots-clés

Annotation des génomes, Microscopie confocale, Mitochondries, Protéomique, Signalisation cellulaire, Synthèse protéique.

Intérêts de recherche

Les protéines sont souvent désignés comme les ouvrières de la cellule et déterminer l'ensemble des protéines exprimées à partir du génome humain est un défis contemporain important. Les protéines sont traduites à partir de séquences codantes dans les gènes, et une seule séquence codante est associé à chaque gène. Mon laboratoire a récemment découvert que les gènes contiennent non pas une mais plusieurs séquences codantes complètement différentes. Un grand nombre de protéines jusque-là négligées, et que nous avons surnommé «protéines alternatives", doivent donc être caractérisées. Nous étudions le rôle des protéines alternatives dans diverses maladies, comme les maladies neurodégénératives.

Centre de recherche

Centre de recherche du CHUS

Langues parlées et écrites

Anglais, Espagnol (castillan), Français

Prix et distinctions

• (2022) Canada Research Chair Tier1 in Functional Proteomics and Discovery of Novel Proteins. Instituts de recherche en santé du Canada. (Distinction).
• (2020) Prix de la recherche et de la création de l'Université de Sherbrooke. Université de Sherbrooke. (Distinction).
• (2019) OpenProt: a more comprehensive guide to explore eukaryotic coding potential and proteomes., Nucleic Acids Research, 2019 (doi: 10.1093/nar/gky936), has been recommended in F1000Prime as being of special significance in its field. F1000Prime. (Distinction).
• (2014) Prix Jean de Margerie pour la publication de l'année en sciences biomédicales. Université de Sherbrooke. (Distinction).
• (2014) Prix d'excellence, créativité et innovation du CHUS. Centre Hospitalier Univ. de Sherbrooke. (Distinction).
• (2014) Prix de la recherche et de la création de l'Université de Sherbrooke. Université de Sherbrooke. (Prix).
• (2014) Canadian researcher of the month, March 2014. Canadians for Health Research. (Distinction).
• (2014) Découverte de l'année par le magazine Québec Science (2013). Quebec Science Magazine. (Distinction).
• Dean's list for exceptional professoral performance (2016, 2017, 2018, 2019, 2020). Université de Sherbrooke. (Distinction).

Financement

Subvention. (En cours d’évaluation). Candidat principal. Challenging the dogmas of monocistronic genes and pseudogenes using proteogenomics and systems biology approaches to better define the human proteome in health and diseases. Instituts de Recherche en Santé du Canada (IRSC). Project grant. 1525000 $ (2021-2026).

Subvention. (Obtenu). Candidat principal. Challenging the dogmas of monocistronic genes and pseudogenes using proteogenomics and systems biology approaches to better define the human proteome in health and diseases. Instituts de Recherche en Santé du Canada (IRSC). Project. 1166625 $ (2021-2026).

Subvention. (Obtenu). Cocandidat. UbiquitinKEKS: function of a novel ubiquitin isoform encoded by UBBP4. Instituts de Recherche en Santé du Canada (IRSC). Project. 891226 $ (2018-2023).

Chaire de recherche. (Obtenu). Candidat principal. Canada Research Chair in Functional Proteomics and Discovery of Novel Proteins. Instituts de Recherche en Santé du Canada (IRSC). Canada Research Chair Tier1. 1400000 $ (2015-2022).

Subvention. (Obtenu). Cochercheur. Development of precision therapeutic vaccines against acute myeloid and lymphoid leukemias. Fonds de recherche du Québec - Santé (FRQS). Oncopole. 1500000 $ (2018-2021).

Subvention. (Obtenu). Candidat principal. Cracking the FUS code in ALS: From the dual-coding gene FUS, alt-FUS engages too in the pathology. Amyotrophic Lateral Sclerosis (ALS) Society of Canada. Operating. 125000 $ (2018-2021).

Subvention. (Obtenu). Candidat principal. OpenProt 2.0. Calcul Canada. Resource Allocation Competition. 35573 $ (2020-2021).

Subvention. (Terminé). Candidat principal. OpenProt. Calcul Canada. Fast Track. 116621 $ (2019-2020).

Subvention. (Terminé). Chercheur principal. Function of alternative proteins in Neurodegenerative Diseases. (2014-2019).

Subvention. (Terminé). Candidat principal. OpenProt. Calcul Canada. Fast Track (1138 CPU). 179983 $ (2018-2019).

Subvention. (Terminé). Cocandidat. Precision medicine: a mass spectrometer for the discovery of new protein biomarkers. Fondation Canadienne pour l'Innovation (FCI). John R. Evans Leaders Fund. 1583499 $ (2018-2019).

Subvention. (Terminé). Candidat principal. OpenProt. Calcul Canada. Resources for Research Groups (1224 CPU). 231140 $ (2017-2018).

Subvention. (Terminé). Candidat principal. OpenProt. Calcul Canada. Resources for Research Groups (1181 CPU). 195260 $ (2016-2017).

Subvention. (Terminé). Cocandidat. 600 MHz Solution-State NMR Upgrade for Structural Biology. Fondation Canadienne pour l'Innovation (FCI). John R. Evans Leaders Fund. 891938 $ (2016).

Publications

Articles de revue

• Brunet, M*; Lucier, JF; Levesque, M; Leblanc, S*; Jacques, JF; Al-Saedi, H*; Guilloy, N*; Grenier, F; Avino, M; Fournier, I; Salzet, M; Ouangraoua, A; Scott, M; Boisvert, FM; Roucou, X. (2021). OpenProt 2021: deeper functional annotation of the coding potential of eukaryotic genomes. Nucleic Acids Research, N/A, N/A. (Révision demandée).
• Brunet MA*, Jacques JF, Nassari S, Tyzack GE, McGoldrick P, Zinman L, Jean S, Robertson J, Patani R, Roucou X. (2020). FUS gene is dual-coding with both proteins united in FUS-mediated toxicity. EMBO Reports, N/A, N/A. (Article accepté).
• Brunet M*, Lekehal A*, Roucou X. (2020). How to Illuminate the Dark Proteome Using the Multi-omic OpenProt Resource. Current Protocols in Bioinformatics, 71(1), e103. (Article publié).
• Cardon T,Hervé F, Delcourt V*, Roucou X, Salzet M, Franck J, Fournier I. (2020). Optimized Sample Preparation Workflow for Improved Identification of Ghost Proteins. Analytical Chemistry, 92(1), 1122-1129. (Article publié).
• Brunet MA*, Leblanc S*, Roucou X. (2020). Reconsidering proteomic diversity with functional investigation of alternative ORFs and small ORFs. Experimental Cell Research. Hidden SmORFs (Special), 393(1), 112057. (Article publié).
• Dubois ML*, Samandi S*, Brunelle M, Frion J*, Toupin A*, Brunet MA*, Beaudoin M*, Jacques JF, Lévesque D, Scott M, Lavigne P, Roucou X co-corresponding, Boisvert M co-corresponding. (2020). UBB Pseudogene 4 encodes novel ubiquitin variants. Nature Communications, 11(1), 1306. (Article publié).
• Brunet MA*, Roucou X. (2019). Mass Spectrometry-Based Proteomics Analyses Using the OpenProt Database to Unveil Novel Proteins Translated from Non-Canonical Open Reading Frames. Journal of Visual Experiments, 146, Not Applicable. (Article publié).
• Brunet MA*, Brunelle M, Lucier JF, Delcourt V*, Levesque M, Grenier F, Samandi S*, Leblanc S*, Aguilar JD, Dufour P, Jacques JF*, Fournier I, Ouangraoua A, Scott MS, Boisvert FM, Roucou X. (2019). OpenProt: a more comprehensive guideto explore eukaryotic coding potential and proteomes. Nucleic Acids Research, 47(D1), D403-D410. DOI. (Article publié).
• Brunet MA*, Levesque SA, Hunting DJ, Cohen AA, Roucou X. (2018). Recognition of the polycistronic nature of human genes is critical to understanding the genotype-phenotype relationship. Genome Research, 28(5), 609-624. DOI. (Article publié).
• Delcourt V*, Staskevicius A*, Salzet M, Fournier I, Roucou X. (2018). Small proteins encoded by unannotated ORFs are rising stars of the proteome, confirming shortcomings in genome annotations and current vision of an mRNA. Proteomics, 18(10), e1700058. (Article publié).
• Delcourt V*, Franck J, Quanico J, Gimeno JP, Wisztorski M, Raffo-Romero A, Kobeissy F, Roucou X, Salzet M, Fournier I. (2018). Spatially-Resolved Top-down Proteomics Bridged to MALDI MS Imaging Reveals the Molecular Physiome of Brain Regions. Molecular and Cellular Proteomics, 17(2), 357-372. (Article publié).
• Delcourt V*, Brunelle M, Roy AV*, Jacques JF, Salzet M, Fournier I, Roucou X. (2018). The protein coded by a short open reading frame, not by the annotated coding sequence is the main gene product of the dual-coding gene MIEF1. Molecular and Cellular Proteomics, 17(12), 2402-2411. DOI. (Article publié).
• Delcourt V*, Franck J, Leblanc E, Narducci F, Robin YM, Gimeno JP, Quanico J, Wisztorski M, Kobeissy F, Jacques JF, Roucou X, Salzet M, Fournier I. (2017). Combined Mass SpectrometryImaging and Top-down Microproteomics Reveals Evidence of a Hidden Proteome inOvarian Cancer. EBioMedicine, 21, 55-64. DOI. (Article publié).
• Samandi S*, Roy AV*, Delcourt V*, Lucier JF, Gagnon J, Beaudoin MC*, Vanderperre B*, Breton MA*, Motard J, Jacques JF, Brunelle M, Gagnon-Arsenault I, Fournier I, Ouangraoua A, Hunting DJ, Cohen AA, Landry CR, Scott MS, Roucou X. (2017). Deep transcriptome annotation enables the discovery and functional characterizationof cryptic small proteins. eLife, 6:e27860, 1-32. DOI. (Article publié).
• Mouilleron H*, Delcourt V*, Roucou X. (2016). Death of a dogma: eukaryotic mRNAs can code for more than one protein. Nucleic Acids Research, 44(1), 14-23. (Article publié).
• Landry CR, Zhonga X*, Nielly-Thibault L*, Roucou X*. (2015). Found in translation: Function and evolution of a recently discovered proteome. Current Opinion in Structural Biology, 32, 74-81. (Article publié).
• Béland M*, Bédard M*, Tremblay G, Lavigne P, Roucou X. (2014). A? induces its ownprion protein N-terminal fragment (PrPN1)-mediated neutralization in amorphousaggregates. Neurobiol Aging, 35(7), 1537-1548. (Article publié).
• Roucou X. (2014). Regulation of PrP(C) signaling and processing by dimerization. Front Cell Dev Biol, 2(57), 1-6. (Article publié).
• Béland M*, Roucou X. (2014). Taking advantage of physiological proteolytic processing of the prion protein for a therapeutic perspective in prion and Alzheimer diseases. Prion, 8(1), 106-110. (Article publié).
• Bergeron D*, Lapointe C*, Bissonnette C*, Tremblay G, Motard J, Roucou X. (2013). An out-of-frame overlapping reading frame in the ataxin-1 coding sequence encodes a novel ataxin-1 interacting protein. J Biol Chem, 288(30), 21824-21835. (Article publié).
• Vanderperre B*, Lucier JF, Bissonnette C*, Motard J, Tremblay G, Vanderperre S*, Wisztorski M, Salzet M, Boisvert FM, Roucou X. (2013). Direct detection of alternative open reading framestranslation products in human significantly expands the proteome. PLoS One, 8(8), e70698. (Article publié).
• Béland M*, Roucou X. (2013). Homodimerization as a molecular switch between low and high efficiency PrP (C) cell surface delivery and neuroprotective activity. Prion, 7(2), 170-174. (Article publié).
• Forget KJ*, Tremblay G, Roucou X. (2013). p53Aggregates penetrate cells and induce the co-aggregation of intracellular p53. PLoS One, 8(7), e69242. (Article publié).
• Béland M*, Roucou X. (2012). The prion protein unstructured N-terminal region is a broad-spectrum molecular sensor with diverse and contrasting potential functions. Journal of neurochemistry, 120(6), 853-868. (Article publié).
• Roostaee A (student I supervised), Roostaee M, Roucou X. (2010). An Update on Prion Biology and Proteomics. Current Proteomics, 7(1), 36-48. (Article publié).

Chapitres de livre

• Maxime Béland, Xavier Roucou. (2014). Utiliser la protéine prion contre les espèces toxiques du peptide amyloïde Abeta dans la maladie d'Alzheimer. Jean-Paul Tillement, Jean-Jacques Hauw, Vassilios Papadopoulos Vieillissement et démences Un défis médical, scientifique et socio-économique (133-137). France : Lavoisier Médecine Sciences. (Article publié).

Articles de journaux

• Vanderperre B, Staskevicius AB, Tremblay G, McCoy M, O'Neill MA, Cashman NR, Roucou X. (2011). An overlapping reading frame in the PRNP gene encodes a novel polypeptide distinct from the prion protein. FASEB J. 2373-2386.

Ressources en ligne

• (2019). OpenProt : deeper functional annotation of the coding potential of eukaryotic genomes. Site Web.

Articles de conférence

• Brunet MA*, Jacques JF, Nassari S, Jean S, Roucou X. (2018). Large-scale proteomic analysis of alternative open reading frames reveals novel pivotal proteins in neurodegenerative diseases such as ALS. HUman Proteome Organization, Orlando, USA, September 30-October 3. (Article accepté).
• Marie Brunet*, Vivian Delcourt*, Jean-Francois Jacques, Xavier Roucou. (2017). ALS-linked FUS gene encodes for a second small protein, altFUS, that regulates FUS localization andmacro-autophagy. Gordon Research Conference: Amyotrophic Lateral Sclerosis and related neurodegenerative disorders. (Article publié).
• Marie Brunet*, Vivian Delcourt*, Jean-Francois Jacques, Xavier Roucou. (2017). FUSDiscovery of a novel protein encoded in an alternative open reading frame (ORF) of gene and its importance in Amyotrophic Lateral Sclerosis (ALS). Keystone Symposia: Omics Strategies to Study the Proteome. (Article publié).
• Marie Brunet*, Vivian Delcourt*, Jean-Francois Jacques, Xavier Roucou. (2017). Large-scale proteomicanalysis of alternative open reading frames reveals a new player in ALS, altFUSencoded within FUS gene. Canadian National Proteomic Network 2017 Annual Meeting. (Article publié).
• Maxime Béland*, Xavier Roucou. (2014). Using the prion protein against toxic species of Aß amyloid peptide in Alzheimer's disease. Aging and dementia: a medical, scientific and socio-economic challenge (Paris, France), (Article publié).
• Béland M*, Tremblay G, Roucou X. (2013). A? induces its own prion protein N-terminal fragment (PrPN1)-mediated neutralization in amorphous aggregates. Prion 2013 (Banff, Canada), (Article publié).
• Beaudoin S*, Tremblay G, Roucou X. (2012). Genetic mutants of prion protein inhibit the assembly of stress granules and P-Bodies, two RNA granules implicated in mRNA decay. Prion 2012 (Amsterdam, The Netherlands), (Article publié).
• Vanderperre B*, Tremblay G, Motard J, Boisvert, FM, Roucou X. (2012). Large-scale identification of alternative open reading frames translation products expands the human proteome. Human Protein Organization 2012 (Boston, USA), (Article publié).
• Vanderperre B (supervised student), Staskevicius AB, Tremblay G, McCoy M, O’Neill MA, Cashman NR, Roucou X. (2011). An overlapping reading frame in the PRNP gene encodes a novel polypeptide distinct from the prion protein. Prion 2011 (Montreal, Canada), (Article publié).
• Shott R, Appanah C, Grenier C, Tremblay G, Roucou X, Schang L. (2011). Cytoplasmic PrP Dysregulates Signaling Pathways that Control Protein Synthesis and Aggresome Formation. Prion 2011 (Montreal, Canada), (Article publié).
• Béland M (supervised student), Roucou X. (2011). Dimerization of PrP Induces a Signalling Cascade Responsible for the Cleavage, Secretion, and Accumulation of the Unstructured N-terminal Domain in Insoluble Extracellular Deposits. Prion 2011 (Montreal, Canada), (Article publié).
• Roostaee A (supervised student), Roucou X. (2011). Prion-Like Propagation and Neurotoxicity of Recombinant ?-Synuclein Aggregates Initiated by Dimerization. Prion 2011 (Montreal, Canada), (Article publié).
• Vanderperre B (supervised student), Staskevicius A (supervised student), Tremblay G, Roucou X. (2010). AltPrP : a novel, stress regulated peptide encoded by Prnp. Prionet Canada (Ottawa, Canada). (Article publié).
• Vanderperre B (supervised student), Staskevicius A (supervised student), Tremblay G, Roucou X. (2010). AltPrP: a novel cryptic out-of-frame polypeptide encoded by Prnp. Prion 2010 (Salzburg, Austria). (Article publié).
• Béland M (supervised student), Roucou X. (2010). Dimerization of PrP induces a TACE-mediated proteolytic cleavage and release of its N-terminal domain in the extracellular space. Prionet Canada 2010 (Vancouver, Canada), (Article publié).
• Beaudoin S (supervised student). (2010). Genetic prion mutants inhibit two RNA granules, P-Bodies and stress granules. Prionet Canada (Ottawa, Canada). (Article publié).
• Roostaee A (supervised student), Roucou X. (2010). In vitro propagation and neurotoxicity of dimerization-induced prion aggregates. PROTEO (Montreal, Canada). (Article publié).
• Vanderperre B (supervised student), Staskevicius A (supervised student), Tremblay G, Roucou X. (2010). PrP's mRNA encodes two proteins : PrP and a novel cryptic out-of-frame polypeptide termed AltPrP. Prionet Canada (Vancouver, Canada). (Article publié).

Propriétés intellectuelles

Brevets

• (2011). OLIGOMER-SPECIFIC AMYLOID BETA EPITOPE AND ANTIBODIES. WO2011106885 A1. Canada. (Délivré).

Droits d'auteur enregistrés

• Alternative human proteins used as biomarkers and therapeutic targets. (Enregistré).

Autres contributions

Cours enseignés

• Biochimie des protéines-Pathologies associées. BCH711. (2013-01-16). Université de Sherbrooke. Canada. Niveau : Cycles supérieurs. (2CR).
• Maladies à prions. VIM6012. (2007-12-04 à 2012-12-07). INRS-Institut Armand Frappier. Canada. Niveau : Cycles supérieurs. (3CR).
• Prions et neuropathogenèse. MCB6045. (2007-11-08 à 2012-11-15). Institut de recherches cliniques de Montréal. Canada. Niveau : Cycles supérieurs. (3CR).
• Biotechnologies de la santé. BCM504. (2006-08-03). Université de Sherbrooke. Canada. Niveau : Premier cycle. (3CR).
• Structure et mécanismes des macromolécules biologiques. BCH720. (2005-09-07). Université de Sherbrooke. Canada. Niveau : Cycles supérieurs. (2CR).

Présentations

• Brunet MA*, Jacques JF, Lekehal AM*. (2020). Proteogenomic analysis reveals FUS gene as dual-coding with both proteins united in molecular hallmarks of amyotrophic lateral sclerosis. US HUman PrOteome (HUPO) 2020: From Genes to Function. États-Unis.
• (2019). OpenProt, a modern vision of the coding potential of transcripts to capture missing proteins. Canadian National Proteomic Network. Quebec, Canada.
• (2018). Back to reality: updating the coding potential of genomes and recognizing the polycistronic nature of eukaryotic genes. Recomb-CG 2018. Canada.
• (2018). Large-scale proteomic analysis of alternative open reading frames reveals novel pivotal proteins inneurodegenerative diseases such as ALS. HUman Proteome Organization. Orlando, États-Unis.
• (2018). OpenProt: a more comprehensive database to explore proteomes in neurodegenerative diseases. First symposium The seven centers of Excellence in Neurodegeneration. Montpellier, France.
• (2017). ALS-linked FUS gene encodes for a second small protein, altFUS, that regulates FUS localization and macro-autophagy. Gordon Research Conference: Amyotrophic Lateral Sclerosis and related motoneuron diseases. Stowe, États-Unis.
• (2017). Alternative protein in neurodegenerative diseases. Cross-disease analysis of pathways in amyloid-based neurodegenerative diseases symposium. Paris, France.
• (2017). Alternative proteins in ALS. ALS Research Forum. Toronto, Canada.
• (2017). Discovery of a novel protein encoded in an alternative open reading frame (ORF) of FUS gene and its importance in Amyotrophic Lateral Sclerosis (ALS). Keystone Symposia: Omics Strategies to Study the Proteome. États-Unis.
• (2017). Large-scale proteomic analysis of alternative open reading frames reveals a new player in ALS, altFUS encoded within FUS gene. Canadian National Proteomic Network. Toronto, Canada.
• (2016). MID51/Mief1 codes for two different proteins, both involved in mitochondrial fission. 2nd International Symposium "One mitochondrion, many diseases. Biological and molecular perspectives. Allemagne.
• (2015). A new proteome expessed from neglected coding sequences. Scientific conference at Vertex Pharmaceuticals (Canada) Inc. Montreal, Canada.
• (2015). Dual-coding genes in neurodegenerative disorders. Groupe de recherche universitaire sur le médicament and Groupe de recherche sur le système nerveux central. Montreal, Canada.
• (2015). Mitochondrial dynamics protein of 51 kDa (MID51) and its alternative protein. 1st International Symposium "One mitochondrion, many diseases. Biological and molecular perspectives. Canada.
• (2014). An unexplored parallel proteome expressed from "forgotten" coding sequences. Centre de recherche du CHU de Québec/Hôtel-Dieu. Québec, Canada.
• (2014). An unexplored parallel proteome expressed from "forgotten"coding sequences. Journée Phare 2014. Orford, Canada.
• (2014). An unexplored proteome in neurodegenerative disorders. Conférences scientifiques du centre de recherche de l'institut universitaire en santé mentale de Québec. Québec, Canada.
• (2014). Dual coding genes in neurodegenerative disorders. Neuroscience for mental health seminars, Douglas Mental Health University Institute. Montreal, Canada.
• (2013). Function of the alternative proteome in neurodegenerative diseases. Department of Biochemistry, University of Toronto. Toronto, Canada.
• (2013). Function of the alternative proteome in neurodegenerative diseases. Aging and dementia, a triple medical, scientific and socio-academic challenge. National medical academy, France. Paris, France.
• (2012). Large-scale identification of alternative open reading frames translation products expands the human proteome. Human Protein Organization 2012. Boston, États-Unis.
• (2012). Prnp, one gene, two proteins:PrP and Alt-PrP. PrioNet Canada. Vancouver, Canada.
• (2011). Prion protein mutants interfere with RNA silencing. Mechanisms of Neurodegeneration Rocky Mountain Laboratories. Hamilton, États-Unis.
• (2011). The alternative prion protein AltPrP. Department of Medical Microbiology University of Manitoba. Winnipeg, Canada.
• Vanderperre, B (supervised student); Staskevicius (supervised student); Tremblay, G. (2010). AltPrP: a novel cryptic out-of-frame polypeptide encoded by Prnp. Prion 2010. Salzburg, Autriche.
• (2010). A stress-induced alternative polypeptide encoded within the prion protein gene. Dept of Cell Biology University of Geneva. Geneva, Suisse.
• (2010). A stress-induced alternative polypeptide encoded within the prion protein gene. Prion Japan. Tokyo, Japon.
• Staskevicius, A (supervised student). (2010). Cryptic out-of-frame initiation of human PrP mRNA produces a novel 9 kDa polypeptide. Prion Canada. Ottawa, Canada.
• (2010). Prion protein mutants interfere with the assembly of RNA granules. Dept of Pathology and Cell Biology. Montreal, Canada.