1
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Muraleedharan A, Vanderperre B. The endo-lysosomal system in Parkinson's disease: expanding the horizon. J Mol Biol 2023:168140. [PMID: 37148997 DOI: 10.1016/j.jmb.2023.168140] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2023] [Revised: 04/22/2023] [Accepted: 04/27/2023] [Indexed: 05/08/2023]
Abstract
Parkinson's disease (PD) is the second most common neurodegenerative disorder after Alzheimer's disease, and its prevalence is increasing with age. A wealth of genetic evidence indicates that the endo-lysosomal system is a major pathway driving PD pathogenesis with a growing number of genes encoding endo-lysosomal proteins identified as risk factors for PD, making it a promising target for therapeutic intervention. However, detailed knowledge and understanding of the molecular mechanisms linking these genes to the disease are available for only a handful of them (e.g. LRRK2, GBA1, VPS35). Taking on the challenge of studying poorly characterized genes and proteins can be daunting, due to the limited availability of tools and knowledge from previous literature. This review aims at providing a valuable source of molecular and cellular insights into the biology of lesser-studied PD-linked endo-lysosomal genes, to help and encourage researchers in filling the knowledge gap around these less popular genetic players. Specific endo-lysosomal pathways discussed range from endocytosis, sorting, and vesicular trafficking to the regulation of membrane lipids of these membrane-bound organelles and the specific enzymatic activities they contain. We also provide perspectives on future challenges that the community needs to tackle and propose approaches to move forward in our understanding of these poorly studied endo-lysosomal genes. This will help harness their potential in designing innovative and efficient treatments to ultimately re-establish neuronal homeostasis in PD but also other diseases involving endo-lysosomal dysfunction.
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Affiliation(s)
- Amitha Muraleedharan
- Centre d'Excellence en Recherche sur les Maladies Orphelines - Fondation Courtois and Biological Sciences Department, Université du Québec à Montréal
| | - Benoît Vanderperre
- Centre d'Excellence en Recherche sur les Maladies Orphelines - Fondation Courtois and Biological Sciences Department, Université du Québec à Montréal
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2
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Senkevich K, Zorca CE, Dworkind A, Rudakou U, Somerville E, Yu E, Ermolaev A, Nikanorova D, Ahmad J, Ruskey JA, Asayesh F, Spiegelman D, Fahn S, Waters C, Monchi O, Dauvilliers Y, Dupré N, Greenbaum L, Hassin-Baer S, Grenn FP, Chiang MSR, Sardi SP, Vanderperre B, Blauwendraat C, Trempe JF, Fon EA, Durcan TM, Alcalay RN, Gan-Or Z. GALC variants affect galactosylceramidase enzymatic activity and risk of Parkinson’s disease. Brain 2022; 146:1859-1872. [PMID: 36370000 PMCID: PMC10151180 DOI: 10.1093/brain/awac413] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Revised: 10/05/2022] [Accepted: 10/16/2022] [Indexed: 11/13/2022] Open
Abstract
Abstract
The association between glucocerebrosidase (GCase), encoded by GBA, and Parkinson’s disease highlights the role of the lysosome in Parkinson’s disease pathogenesis. Genome-wide association studies (GWAS) in Parkinson’s disease have revealed multiple associated loci, including the GALC locus on chromosome 14. GALC encodes the lysosomal enzyme galactosylceramidase (GalCase), which plays a pivotal role in the glycosphingolipid metabolism pathway. It is still unclear whether GALC is the gene driving the association in the chromosome 14 locus, and if so, by which mechanism.
We first aimed to examine whether variants in the GALC locus and across the genome are associated with GalCase activity. We performed a GWAS in two independent cohorts from a)Columbia University and b)the Parkinson’s Progression Markers Initiative study, followed by a meta-analysis with a total of 976 Parkinson’s disease patients and 478 controls with available data on GalCase activity. We further analyzed the effects of common GALC variants on expression and GalCase activity using genomic colocalization methods. Mendelian randomization was used to study whether GalCase activity may be causal in Parkinson’s disease. To study the role of rare GALC variants we analyzed sequencing data from 5,028 Parkinson’s disease patients and 5,422 controls. Additionally, we studied the functional impact of GALC knock-out on alpha-synuclein accumulation and on GCase activity in neuronal cell models and performed in silico structural analysis of common GALC variants associated with altered GalCase activity.
The top hit in Parkinson's disease GWAS in the GALC locus, rs979812, is associated with increased GalCase activity (b = 1.2; se = 0.06; p = 5.10E-95). No other variants outside the GALC locus were associated with GalCase activity. Colocalization analysis demonstrated that rs979812 was also associated with increased GalCase expression. Mendelian randomization suggested that increased GalCase activity may be causally associated with Parkinson’s disease (b = 0.025, se = 0.007, p = 0.0008). We did not find an association between rare GALC variants and Parkinson’s disease. GALC knockout using CRISPR-Cas9 did not lead to alpha-synuclein accumulation, further supporting that increased rather than reduced GalCase levels may be associated with Parkinson’s disease. The structural analysis demonstrated that the common variant p.I562T may lead to improper maturation of GalCase affecting its activity.
Our results nominate GALC as the gene associated with Parkinson’s disease in this locus and suggest that the association of variants in the GALC locus may be driven by their effect of increasing GalCase expression and activity. Whether altering GalCase activity could be considered as a therapeutic target should be further studied.
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Affiliation(s)
- Konstantin Senkevich
- The Neuro (Montreal Neurological Institute-Hospital), McGill University , Montreal, Quebec, H3A 2B4 , Canada
- Department of Neurology and neurosurgery, McGill University , Montréal, QC, H3A 2B4 , Canada
| | - Cornelia E Zorca
- Department of Neurology and neurosurgery, McGill University , Montréal, QC, H3A 2B4 , Canada
- Early Drug Discovery Unit (EDDU), Department of Neurology and Neurosurgery, Montreal Neurological Institute-Hospital, McGill University , Montreal, Quebec H3A 2B4 , Canada
| | - Aliza Dworkind
- Department of Physiology, McGill University , Montréal, QC, H3A 1A1 , Canada
| | - Uladzislau Rudakou
- The Neuro (Montreal Neurological Institute-Hospital), McGill University , Montreal, Quebec, H3A 2B4 , Canada
- Department of Neurology and neurosurgery, McGill University , Montréal, QC, H3A 2B4 , Canada
- Department of Human Genetics, McGill University , Montréal, QC, H3A 1A1 , Canada
| | - Emma Somerville
- The Neuro (Montreal Neurological Institute-Hospital), McGill University , Montreal, Quebec, H3A 2B4 , Canada
- Department of Human Genetics, McGill University , Montréal, QC, H3A 1A1 , Canada
| | - Eric Yu
- The Neuro (Montreal Neurological Institute-Hospital), McGill University , Montreal, Quebec, H3A 2B4 , Canada
- Department of Human Genetics, McGill University , Montréal, QC, H3A 1A1 , Canada
| | - Alexey Ermolaev
- Center of Molecular Biotechnology, Russian State Agrarian University-Moscow Timiryazev Agricultural Academy , Moscow, 127550 , Russia
- Bioinformatics Institute , Saint-Petersburg, 194100 , Russia
| | | | - Jamil Ahmad
- The Neuro (Montreal Neurological Institute-Hospital), McGill University , Montreal, Quebec, H3A 2B4 , Canada
- Department of Neurology and neurosurgery, McGill University , Montréal, QC, H3A 2B4 , Canada
| | - Jennifer A Ruskey
- The Neuro (Montreal Neurological Institute-Hospital), McGill University , Montreal, Quebec, H3A 2B4 , Canada
- Department of Neurology and neurosurgery, McGill University , Montréal, QC, H3A 2B4 , Canada
| | - Farnaz Asayesh
- The Neuro (Montreal Neurological Institute-Hospital), McGill University , Montreal, Quebec, H3A 2B4 , Canada
- Department of Human Genetics, McGill University , Montréal, QC, H3A 1A1 , Canada
| | - Dan Spiegelman
- The Neuro (Montreal Neurological Institute-Hospital), McGill University , Montreal, Quebec, H3A 2B4 , Canada
| | - Stanley Fahn
- Department of Neurology, College of Physicians and Surgeons, Columbia University Medical Center , 710 West 168th Street, New York, NY, 10032-3784 USA
| | - Cheryl Waters
- Department of Neurology, College of Physicians and Surgeons, Columbia University Medical Center , 710 West 168th Street, New York, NY, 10032-3784 USA
| | - Oury Monchi
- Department of Neurology and neurosurgery, McGill University , Montréal, QC, H3A 2B4 , Canada
- Department of Clinical Neurosciences and Department of Radiology, University of Calgary, 2500 University Drive NW Calgary , Alberta, T2N 1N4 , Canada
- Hotchkiss Brain Institute, Cumming School of Medicine, Calgary, 3330 Hospital Drive NW Calgary , Alberta, T2N 4N1 Canada
| | - Yves Dauvilliers
- National Reference Center for Narcolepsy, Sleep Unit, Department of Neurology, Gui-de-Chauliac Hospital, CHU Montpellier, University of Montpellier , Inserm U1061, Montpellier , France
| | - Nicolas Dupré
- Neuroscience Axis, CHU de Québec – Université Laval , Quebec City, G1V 4G2 , Canada
- Department of Medicine, Faculty of Medicine, Université Laval , Québec, QC, G1V 0A6 , Canada
| | - Lior Greenbaum
- The Danek Gertner Institute of Human Genetics, Sheba Medical Center , Tel Hashomer, 5265601 , Israel
- The Joseph Sagol Neuroscience Center, Sheba Medical Center , Tel Hashomer, 52621 , Israel
- Sackler Faculty of Medicine, Tel Aviv University , Tel Aviv, 69978 , Israel
| | - Sharon Hassin-Baer
- Sackler Faculty of Medicine, Tel Aviv University , Tel Aviv, 69978 , Israel
- The Movement Disorders Institute, Department of Neurology, Sheba Medical Center , Tel Hashomer, 52621 , Israel
| | - Francis P Grenn
- Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health , Bethesda, MD 20814 , USA
| | - Ming Sum Ruby Chiang
- Rare and Neurologic Diseases Therapeutic Area , Sanofi, Framingham, MA 01701 USA
| | - S Pablo Sardi
- Rare and Neurologic Diseases Therapeutic Area , Sanofi, Framingham, MA 01701 USA
| | - Benoît Vanderperre
- Département des sciences biologiques, Université du Québec à Montréal , Montréal, Québec, H2X 1Y4 , Canada
| | - Cornelis Blauwendraat
- Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health , Bethesda, MD 20814 , USA
| | - Jean-François Trempe
- Department of Pharmacology and Therapeutics and Centre de Recherche en Biologie Structurale, McGill University , Montreal, Quebec, H3A 1A3 , Canada
| | - Edward A Fon
- Department of Neurology and neurosurgery, McGill University , Montréal, QC, H3A 2B4 , Canada
- Early Drug Discovery Unit (EDDU), Department of Neurology and Neurosurgery, Montreal Neurological Institute-Hospital, McGill University , Montreal, Quebec H3A 2B4 , Canada
| | - Thomas M Durcan
- Early Drug Discovery Unit (EDDU), Department of Neurology and Neurosurgery, Montreal Neurological Institute-Hospital, McGill University , Montreal, Quebec H3A 2B4 , Canada
| | - Roy N Alcalay
- Department of Neurology, College of Physicians and Surgeons, Columbia University Medical Center , 710 West 168th Street, New York, NY, 10032-3784 USA
- Taub Institute for Research on Alzheimer’s Disease and the Aging Brain, Columbia University Medical Center , New York, NY 10032 , USA
| | - Ziv Gan-Or
- The Neuro (Montreal Neurological Institute-Hospital), McGill University , Montreal, Quebec, H3A 2B4 , Canada
- Department of Neurology and neurosurgery, McGill University , Montréal, QC, H3A 2B4 , Canada
- Department of Human Genetics, McGill University , Montréal, QC, H3A 1A1 , Canada
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3
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Sheta R, Teixeira M, Idi W, Pierre M, de Rus Jacquet A, Emond V, Zorca CE, Vanderperre B, Durcan TM, Fon EA, Calon F, Chahine M, Oueslati A. Combining NGN2 programming and dopaminergic patterning for a rapid and efficient generation of hiPSC-derived midbrain neurons. Sci Rep 2022; 12:17176. [PMID: 36229560 PMCID: PMC9562300 DOI: 10.1038/s41598-022-22158-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Accepted: 10/10/2022] [Indexed: 01/04/2023] Open
Abstract
The use of human derived induced pluripotent stem cells (hiPSCs) differentiated to dopaminergic (DA) neurons offers a valuable experimental model to decorticate the cellular and molecular mechanisms of Parkinson's disease (PD) pathogenesis. However, the existing approaches present with several limitations, notably the lengthy time course of the protocols and the high variability in the yield of DA neurons. Here we report on the development of an improved approach that combines neurogenin-2 programming with the use of commercially available midbrain differentiation kits for a rapid, efficient, and reproducible directed differentiation of hiPSCs to mature and functional induced DA (iDA) neurons, with minimum contamination by other brain cell types. Gene expression analysis, associated with functional characterization examining neurotransmitter release and electrical recordings, support the functional identity of the iDA neurons to A9 midbrain neurons. iDA neurons showed selective vulnerability when exposed to 6-hydroxydopamine, thus providing a viable in vitro approach for modeling PD and for the screening of small molecules with neuroprotective proprieties.
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Affiliation(s)
- Razan Sheta
- grid.411081.d0000 0000 9471 1794CHU de Québec Research Center, Axe Neurosciences, Quebec City, Canada ,grid.23856.3a0000 0004 1936 8390Department of Molecular Medicine, Faculty of Medicine, Université Laval, Quebec City, Canada
| | - Maxime Teixeira
- grid.411081.d0000 0000 9471 1794CHU de Québec Research Center, Axe Neurosciences, Quebec City, Canada ,grid.23856.3a0000 0004 1936 8390Department of Molecular Medicine, Faculty of Medicine, Université Laval, Quebec City, Canada
| | - Walid Idi
- grid.411081.d0000 0000 9471 1794CHU de Québec Research Center, Axe Neurosciences, Quebec City, Canada ,grid.23856.3a0000 0004 1936 8390Department of Molecular Medicine, Faculty of Medicine, Université Laval, Quebec City, Canada
| | - Marion Pierre
- grid.23856.3a0000 0004 1936 8390CERVO Brain Research Center, 2601, rue de La Canardière, Quebec City, Canada
| | - Aurelie de Rus Jacquet
- grid.411081.d0000 0000 9471 1794CHU de Québec Research Center, Axe Neurosciences, Quebec City, Canada ,grid.23856.3a0000 0004 1936 8390Department of Psychiatry and Neurosciences, Faculty of Medicine, Université Laval, Quebec City, Canada
| | - Vincent Emond
- grid.411081.d0000 0000 9471 1794CHU de Québec Research Center, Axe Neurosciences, Quebec City, Canada
| | - Cornelia E. Zorca
- grid.14709.3b0000 0004 1936 8649McGill Parkinson Program and Neurodegenerative Diseases Group, Montreal Neurological Institute, McGill University, Montreal, Canada ,grid.14709.3b0000 0004 1936 8649The Neuro’s Early Drug Discovery Unit (EDDU), Montreal Neurological Institute, McGill University, Montreal, Canada
| | - Benoît Vanderperre
- grid.38678.320000 0001 2181 0211Département des sciences biologiques, Université du Québec à Montréal, Montreal, QC Canada ,Centre d’Excellence en Recherche sur les Maladies Orphelines – Fondation Courtois (CERMO-FC), Montreal, Canada
| | - Thomas M. Durcan
- grid.14709.3b0000 0004 1936 8649McGill Parkinson Program and Neurodegenerative Diseases Group, Montreal Neurological Institute, McGill University, Montreal, Canada ,grid.14709.3b0000 0004 1936 8649The Neuro’s Early Drug Discovery Unit (EDDU), Montreal Neurological Institute, McGill University, Montreal, Canada
| | - Edward A. Fon
- grid.14709.3b0000 0004 1936 8649McGill Parkinson Program and Neurodegenerative Diseases Group, Montreal Neurological Institute, McGill University, Montreal, Canada ,grid.14709.3b0000 0004 1936 8649The Neuro’s Early Drug Discovery Unit (EDDU), Montreal Neurological Institute, McGill University, Montreal, Canada
| | - Frédéric Calon
- grid.411081.d0000 0000 9471 1794CHU de Québec Research Center, Axe Neurosciences, Quebec City, Canada ,grid.23856.3a0000 0004 1936 8390Faculty of Pharmacy, Université Laval, Quebec City, Canada
| | - Mohamed Chahine
- grid.23856.3a0000 0004 1936 8390CERVO Brain Research Center, 2601, rue de La Canardière, Quebec City, Canada ,grid.23856.3a0000 0004 1936 8390Department of Medicine, Faculty of Medicine, Université Laval, Quebec City, Canada
| | - Abid Oueslati
- grid.411081.d0000 0000 9471 1794CHU de Québec Research Center, Axe Neurosciences, Quebec City, Canada ,grid.23856.3a0000 0004 1936 8390Department of Molecular Medicine, Faculty of Medicine, Université Laval, Quebec City, Canada
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4
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Krohn L, Öztürk TN, Vanderperre B, Ouled Amar Bencheikh B, Ruskey JA, Laurent SB, Spiegelman D, Postuma RB, Arnulf I, Hu MTM, Dauvilliers Y, Högl B, Stefani A, Monaca CC, Plazzi G, Antelmi E, Ferini-Strambi L, Heidbreder A, Rudakou U, Cochen De Cock V, Young P, Wolf P, Oliva P, Zhang XK, Greenbaum L, Liong C, Gagnon JF, Desautels A, Hassin-Baer S, Montplaisir JY, Dupré N, Rouleau GA, Fon EA, Trempe JF, Lamoureux G, Alcalay RN, Gan-Or Z. Genetic, Structural, and Functional Evidence Link TMEM175 to Synucleinopathies. Ann Neurol 2019; 87:139-153. [PMID: 31658403 DOI: 10.1002/ana.25629] [Citation(s) in RCA: 47] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2018] [Revised: 10/21/2019] [Accepted: 10/21/2019] [Indexed: 02/01/2023]
Abstract
OBJECTIVE The TMEM175/GAK/DGKQ locus is the 3rd strongest risk locus in genome-wide association studies of Parkinson disease (PD). We aimed to identify the specific disease-associated variants in this locus, and their potential implications. METHODS Full sequencing of TMEM175/GAK/DGKQ followed by genotyping of specific associated variants was performed in PD (n = 1,575) and rapid eye movement sleep behavior disorder (RBD) patients (n = 533) and in controls (n = 1,583). Adjusted regression models and a meta-analysis were performed. Association between variants and glucocerebrosidase (GCase) activity was analyzed in 715 individuals with available data. Homology modeling, molecular dynamics simulations, and lysosomal localization experiments were performed on TMEM175 variants to determine their potential effects on structure and function. RESULTS Two coding variants, TMEM175 p.M393T (odds ratio [OR] = 1.37, p = 0.0003) and p.Q65P (OR = 0.72, p = 0.005), were associated with PD, and p.M393T was also associated with RBD (OR = 1.59, p = 0.001). TMEM175 p.M393T was associated with reduced GCase activity. Homology modeling and normal mode analysis demonstrated that TMEM175 p.M393T creates a polar side-chain in the hydrophobic core of the transmembrane, which could destabilize the domain and thus impair either its assembly, maturation, or trafficking. Molecular dynamics simulations demonstrated that the p.Q65P variant may increase stability and ion conductance of the transmembrane protein, and lysosomal localization was not affected by these variants. INTERPRETATION Coding variants in TMEM175 are likely to be responsible for the association in the TMEM175/GAK/DGKQ locus, which could be mediated by affecting GCase activity. ANN NEUROL 2020;87:139-153.
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Affiliation(s)
- Lynne Krohn
- Department of Human Genetics, McGill University, Montreal, Quebec, Canada.,Montreal Neurological Institute, McGill University, Montreal, Quebec, Canada
| | - Tuğba Nur Öztürk
- Department of Physics, Concordia University, Montreal, Quebec, Canada.,Centre for Research in Molecular Modeling (CERMM), Concordia University, Montreal, Quebec, Canada.,PROTEO, The Quebec Network for Research on Protein Function, Engineering and Applications, Quebec, Quebec, Canada
| | - Benoît Vanderperre
- Montreal Neurological Institute, McGill University, Montreal, Quebec, Canada.,Department of Neurology and Neurosurgery, McGill University, Montreal, Quebec, Canada
| | - Bouchra Ouled Amar Bencheikh
- Montreal Neurological Institute, McGill University, Montreal, Quebec, Canada.,Department of Neurology and Neurosurgery, McGill University, Montreal, Quebec, Canada
| | - Jennifer A Ruskey
- Montreal Neurological Institute, McGill University, Montreal, Quebec, Canada.,Department of Neurology and Neurosurgery, McGill University, Montreal, Quebec, Canada
| | - Sandra B Laurent
- Montreal Neurological Institute, McGill University, Montreal, Quebec, Canada.,Department of Neurology and Neurosurgery, McGill University, Montreal, Quebec, Canada
| | - Dan Spiegelman
- Montreal Neurological Institute, McGill University, Montreal, Quebec, Canada.,Department of Neurology and Neurosurgery, McGill University, Montreal, Quebec, Canada
| | - Ronald B Postuma
- Montreal Neurological Institute, McGill University, Montreal, Quebec, Canada.,Department of Neurology and Neurosurgery, McGill University, Montreal, Quebec, Canada
| | - Isabelle Arnulf
- Sleep Disorders Unit, Pitié Salpêtrière Hospital, Institute of Brain and Spinal Cord and Sorbonne University, Paris, France
| | - Michele T M Hu
- Oxford Parkinson's Disease Centre, University of Oxford, Oxford, United Kingdom.,Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, United Kingdom
| | - Yves Dauvilliers
- National Reference Center for Narcolepsy, Sleep Unit, Department of Neurology, Gui de Chauliac Hospital, University Hospital Center Montpellier, University of Montpellier, National Institute of Health and Medical Research U1061, Montpellier, France
| | - Birgit Högl
- Sleep Disorders Clinic, Department of Neurology, Medical University of Innsbruck, Innsbruck, Austria
| | - Ambra Stefani
- Sleep Disorders Clinic, Department of Neurology, Medical University of Innsbruck, Innsbruck, Austria
| | - Christelle Charley Monaca
- University of Lille Nord de France, Department of Clinical Neurophysiology and Sleep Center, University Hospital Center Lille, Lille, France
| | - Giuseppe Plazzi
- Department of Biomedical and Neuromotor Sciences, Alma Mater Studiorum, University of Bologna, Bologna, Italy.,Scientific Institute for Research and Health Care, Institute of Neurological Sciences of Bologna, Bologna, Italy
| | - Elena Antelmi
- Department of Biomedical and Neuromotor Sciences, Alma Mater Studiorum, University of Bologna, Bologna, Italy.,Scientific Institute for Research and Health Care, Institute of Neurological Sciences of Bologna, Bologna, Italy
| | - Luigi Ferini-Strambi
- Department of Neurological Sciences, Vita-Salute San Raffaele University, Milan, Italy
| | - Anna Heidbreder
- Institute of Sleep Medicine and Neuromuscular Disorders, University of Münster, Münster, Germany
| | - Uladzislau Rudakou
- Department of Human Genetics, McGill University, Montreal, Quebec, Canada.,Montreal Neurological Institute, McGill University, Montreal, Quebec, Canada
| | - Valérie Cochen De Cock
- Sleep and Neurology Unit, Beau Soleil Clinic, Montpellier, France.,EuroMov, University of Montpellier, Montpellier, France
| | - Peter Young
- Institute of Sleep Medicine and Neuromuscular Disorders, University of Münster, Münster, Germany
| | - Pavlina Wolf
- Biologics Structural and Functional Research, Biopharmaceutics Development, Genzyme, Framingham, MA
| | - Petra Oliva
- Biologics Structural and Functional Research, Biopharmaceutics Development, Genzyme, Framingham, MA
| | - Xiaokui Kate Zhang
- Biologics Structural and Functional Research, Biopharmaceutics Development, Genzyme, Framingham, MA
| | - Lior Greenbaum
- Danek Gertner Institute of Human Genetics, Sheba Medical Center, Tel Hashomer, Israel.,Joseph Sagol Neuroscience Center, Sheba Medical Center, Tel Hashomer, Israel.,Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Christopher Liong
- Department of Neurology, College of Physicians and Surgeons, Columbia University Medical Center, New York, NY
| | - Jean-François Gagnon
- Center for Advanced Research in Sleep Medicine, Sacred Heart Hospital of Montreal, Montreal, Quebec, Canada.,Department of Psychology, University of Quebec at Montreal, Montreal, Quebec, Canada
| | - Alex Desautels
- Center for Advanced Research in Sleep Medicine, Sacred Heart Hospital of Montreal, Montreal, Quebec, Canada.,Department of Neurosciences, University of Quebec at Montreal, Montreal, Quebec, Canada
| | - Sharon Hassin-Baer
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel.,Department of Neurology, College of Physicians and Surgeons, Columbia University Medical Center, New York, NY.,The Movement Disorders Institute, Department of Neurology, Sheba Medical Center, Tel Hashomer, Israel
| | - Jacques Y Montplaisir
- Center for Advanced Research in Sleep Medicine, Sacred Heart Hospital of Montreal, Montreal, Quebec, Canada.,Department of Psychiatry, University of Montreal, Montreal, Quebec, Canada
| | - Nicolas Dupré
- Division of Neurosciences, University Hospital Center of Quebec, Laval University, Quebec City, Quebec, Canada.,Department of Medicine, Faculty of Medicine, Laval University, Quebec City, Quebec, Canada
| | - Guy A Rouleau
- Department of Human Genetics, McGill University, Montreal, Quebec, Canada.,Montreal Neurological Institute, McGill University, Montreal, Quebec, Canada.,Department of Neurology and Neurosurgery, McGill University, Montreal, Quebec, Canada
| | - Edward A Fon
- Montreal Neurological Institute, McGill University, Montreal, Quebec, Canada.,Department of Neurology and Neurosurgery, McGill University, Montreal, Quebec, Canada
| | - Jean-François Trempe
- Department of Pharmacology and Therapeutics, McGill University, Montreal, Quebec, Canada
| | - Guillaume Lamoureux
- Department of Physics, Concordia University, Montreal, Quebec, Canada.,Centre for Research in Molecular Modeling (CERMM), Concordia University, Montreal, Quebec, Canada.,PROTEO, The Quebec Network for Research on Protein Function, Engineering and Applications, Quebec, Quebec, Canada.,Department of Chemistry, Rutgers University - Camden, Camden, NJ, USA.,Center for Computational and Integrative Biology (CCIB), Camden, NY, USA
| | - Roy N Alcalay
- Department of Neurology, College of Physicians and Surgeons, Columbia University Medical Center, New York, NY.,Taub Institute for Research on Alzheimer's Disease and the Aging Brain, College of Physicians and Surgeons, Columbia University Medical Center, New York, NY
| | - Ziv Gan-Or
- Department of Human Genetics, McGill University, Montreal, Quebec, Canada.,Montreal Neurological Institute, McGill University, Montreal, Quebec, Canada.,Department of Neurology and Neurosurgery, McGill University, Montreal, Quebec, Canada
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5
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Alcalay RN, Mallett V, Vanderperre B, Tavassoly O, Dauvilliers Y, Wu RY, Ruskey JA, Leblond CS, Ambalavanan A, Laurent SB, Spiegelman D, Dionne-Laporte A, Liong C, Levy OA, Fahn S, Waters C, Kuo SH, Chung WK, Ford B, Marder KS, Kang UJ, Hassin-Baer S, Greenbaum L, Trempe JF, Wolf P, Oliva P, Zhang XK, Clark LN, Langlois M, Dion PA, Fon EA, Dupre N, Rouleau GA, Gan-Or Z. SMPD1 mutations, activity, and α-synuclein accumulation in Parkinson's disease. Mov Disord 2019; 34:526-535. [PMID: 30788890 PMCID: PMC6469643 DOI: 10.1002/mds.27642] [Citation(s) in RCA: 62] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2018] [Revised: 11/21/2018] [Accepted: 01/10/2019] [Indexed: 11/11/2022] Open
Abstract
BACKGROUND SMPD1 (acid-sphingomyelinase) variants have been associated with Parkinson's disease in recent studies. The objective of this study was to further investigate the role of SMPD1 mutations in PD. METHODS SMPD1 was sequenced in 3 cohorts (Israel Ashkenazi Jewish cohort, Montreal/Montpellier, and New York), including 1592 PD patients and 975 controls. Additional data were available for 10,709 Ashkenazi Jewish controls. Acid-sphingomyelinase activity was measured by a mass spectrometry-based assay in the New York cohort. α-Synuclein levels were measured in vitro following CRISPR/Cas9-mediated knockout and siRNA knockdown of SMPD1 in HeLa and BE(2)-M17 cells. Lysosomal localization of acid-sphingomyelinase with different mutations was studied, and in silico analysis of their effect on acid-sphingomyelinase structure was performed. RESULTS SMPD1 mutations were associated with PD in the Ashkenazi Jewish cohort, as 1.4% of PD patients carried the p.L302P or p.fsP330 mutation, compared with 0.37% in 10,709 Ashkenazi Jewish controls (OR, 3.7; 95%CI, 1.6-8.2; P = 0.0025). In the Montreal/Montpellier cohort, the p.A487V variant was nominally associated with PD (1.5% versus 0.14%; P = 0.0065, not significant after correction for multiple comparisons). Among PD patients, reduced acid-sphingomyelinase activity was associated with a 3.5- to 5.8-year earlier onset of PD in the lowest quartile versus the highest quartile of acid-sphingomyelinase activity (P = 0.01-0.001). We further demonstrated that SMPD1 knockout and knockdown resulted in increased α-synuclein levels in HeLa and BE(2)-M17 dopaminergic cells and that the p.L302P and p.fsP330 mutations impair the traffic of acid-sphingomyelinase to the lysosome. CONCLUSIONS Our results support an association between SMPD1 variants, acid-sphingomyelinase activity, and PD. Furthermore, they suggest that reduced acid-sphingomyelinase activity may lead to α-synuclein accumulation. © 2019 International Parkinson and Movement Disorder Society.
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Affiliation(s)
- Roy N. Alcalay
- Department of Neurology, College of Physicians and Surgeons, Columbia University, New York, NY, USA
- Taub Institute for Research on Alzheimer's Disease and the Aging Brain, Columbia University, New York, NY, USA
| | - Victoria Mallett
- Montreal Neurological Institute, McGill University, Montréal, QC, Canada
| | - Benoît Vanderperre
- McGill Parkinson Program and Neurodegenerative Diseases Group, Montreal Neurological Institute, McGill University, Montréal, QC, Canada
| | - Omid Tavassoly
- McGill Parkinson Program and Neurodegenerative Diseases Group, Montreal Neurological Institute, McGill University, Montréal, QC, Canada
| | - Yves Dauvilliers
- Sleep Unit, National Reference Network for Narcolepsy, Department of Neurology Hôpital-Gui-de Chauliac, CHU Montpellier, INSERM U1061, France
| | - Richard Y.J. Wu
- Montreal Neurological Institute, McGill University, Montréal, QC, Canada
- Imperial College School of Medicine, Imperial College London, London, United Kingdom
| | - Jennifer A. Ruskey
- Montreal Neurological Institute, McGill University, Montréal, QC, Canada
- Department of Neurology and Neurosurgery, McGill University, Montréal, QC, Canada
| | - Claire S. Leblond
- Montreal Neurological Institute, McGill University, Montréal, QC, Canada
- Department of Human Genetics, McGill University, Montréal, QC, Canada
| | - Amirthagowri Ambalavanan
- Montreal Neurological Institute, McGill University, Montréal, QC, Canada
- Department of Human Genetics, McGill University, Montréal, QC, Canada
| | - Sandra B. Laurent
- Montreal Neurological Institute, McGill University, Montréal, QC, Canada
- Department of Neurology and Neurosurgery, McGill University, Montréal, QC, Canada
| | - Dan Spiegelman
- Montreal Neurological Institute, McGill University, Montréal, QC, Canada
- Department of Neurology and Neurosurgery, McGill University, Montréal, QC, Canada
| | - Alexandre Dionne-Laporte
- Montreal Neurological Institute, McGill University, Montréal, QC, Canada
- Department of Neurology and Neurosurgery, McGill University, Montréal, QC, Canada
| | - Christopher Liong
- Department of Neurology, College of Physicians and Surgeons, Columbia University, New York, NY, USA
| | - Oren A. Levy
- Department of Neurology, College of Physicians and Surgeons, Columbia University, New York, NY, USA
| | - Stanley Fahn
- Department of Neurology, College of Physicians and Surgeons, Columbia University, New York, NY, USA
| | - Cheryl Waters
- Department of Neurology, College of Physicians and Surgeons, Columbia University, New York, NY, USA
| | - Sheng-Han Kuo
- Department of Neurology, College of Physicians and Surgeons, Columbia University, New York, NY, USA
| | - Wendy K. Chung
- Department of Medicine, College of Physicians and Surgeons, Columbia University, New York, NY, USA
- Department of Pediatrics, College of Physicians and Surgeons, Columbia University, New York, NY, USA
| | - Blair Ford
- Department of Neurology, College of Physicians and Surgeons, Columbia University, New York, NY, USA
| | - Karen S. Marder
- Department of Neurology, College of Physicians and Surgeons, Columbia University, New York, NY, USA
| | - Un Jung Kang
- Department of Neurology, College of Physicians and Surgeons, Columbia University, New York, NY, USA
| | - Sharon Hassin-Baer
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
- Department of Neurology, Sheba Medical Center, Tel Hashomer, Israel
- Movement Disorders Institute, Sheba Medical Center, Tel Hashomerf, Israel
| | - Lior Greenbaum
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
- The Danek Gertner Institute of Human Genetics, Sheba Medical Center, Tel Hashomer, Israel
- The Joseph Sagol Neuroscience Center, Sheba Medical Center, Tel Hashomer, Israel
| | - Jean-Francois Trempe
- Department of Pharmacology & Therapeutics, McGill University, Montréal, Québec, Canada
| | - Pavlina Wolf
- Translational Science, Sanofi, Framingham, MA, USA
| | - Petra Oliva
- Translational Science, Sanofi, Framingham, MA, USA
| | | | - Lorraine N. Clark
- Taub Institute for Research on Alzheimer's Disease and the Aging Brain, Columbia University, New York, NY, USA
- Laboratory of Personalized Genomic Medicine, Department of Pathology and Cell Biology, Columbia University, New York, NY, USA
- Department of Pathology and Cell Biology, Columbia University, New York, NY, USA
| | - Melanie Langlois
- Axe neurosciences du CHU de Québec - Université Laval, Québec, QC, Canada
- Faculty of Medicine, Department of Medicine, Laval University, Québec, QC, Canada
| | - Patrick A. Dion
- Montreal Neurological Institute, McGill University, Montréal, QC, Canada
- Department of Neurology and Neurosurgery, McGill University, Montréal, QC, Canada
| | - Edward A. Fon
- McGill Parkinson Program and Neurodegenerative Diseases Group, Montreal Neurological Institute, McGill University, Montréal, QC, Canada
| | - Nicolas Dupre
- Axe neurosciences du CHU de Québec - Université Laval, Québec, QC, Canada
- Faculty of Medicine, Department of Medicine, Laval University, Québec, QC, Canada
| | - Guy A. Rouleau
- Montreal Neurological Institute, McGill University, Montréal, QC, Canada
- Department of Neurology and Neurosurgery, McGill University, Montréal, QC, Canada
- Department of Human Genetics, McGill University, Montréal, QC, Canada
| | - Ziv Gan-Or
- Montreal Neurological Institute, McGill University, Montréal, QC, Canada
- Department of Neurology and Neurosurgery, McGill University, Montréal, QC, Canada
- Department of Human Genetics, McGill University, Montréal, QC, Canada
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6
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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. Deep transcriptome annotation enables the discovery and functional characterization of cryptic small proteins. eLife 2017; 6:27860. [PMID: 29083303 PMCID: PMC5703645 DOI: 10.7554/elife.27860] [Citation(s) in RCA: 78] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2017] [Accepted: 10/29/2017] [Indexed: 01/10/2023] Open
Abstract
Recent functional, proteomic and ribosome profiling studies in eukaryotes have concurrently demonstrated the translation of alternative open-reading frames (altORFs) in addition to annotated protein coding sequences (CDSs). We show that a large number of small proteins could in fact be coded by these altORFs. The putative alternative proteins translated from altORFs have orthologs in many species and contain functional domains. Evolutionary analyses indicate that altORFs often show more extreme conservation patterns than their CDSs. Thousands of alternative proteins are detected in proteomic datasets by reanalysis using a database containing predicted alternative proteins. This is illustrated with specific examples, including altMiD51, a 70 amino acid mitochondrial fission-promoting protein encoded in MiD51/Mief1/SMCR7L, a gene encoding an annotated protein promoting mitochondrial fission. Our results suggest that many genes are multicoding genes and code for a large protein and one or several small proteins. Proteins are often referred to as the workhorses of the cell, and these molecules affect all aspects of human health and disease. Thus, deciphering the entire set of proteins made by an organism is often an important challenge for biologists. Genes contain the instructions to make a protein, but first they must be copied into a molecule called an mRNA. The part of the mRNA that actually codes for the protein is referred to as an open reading frame (or ORF for short). For many years, most scientists assumed that, except for in bacteria, each mature mRNA in an organism has just a single functional ORF, and that this was generally the longest possible ORF within the mRNA. Many also assumed that RNAs copied from genes that had been labelled as “non-coding” or as “pseudogenes” did not contain functional ORFs. Yet, new ORFs encoding small proteins were recently discovered in RNAs (or parts of RNA) that had previously been annotated as non-coding. Working out what these small proteins actually do will require scientists being able to find more of these overlooked ORFs. The RNAs produced by many organisms – from humans and mice to fruit flies and yeast – have been catalogued and the data stored in publicly accessible databases. Samandi, Roy et al. have now taken a fresh look at the data for nine different organisms, and identified several thousand examples of possibly overlooked ORFs, which they refer to as “alternative ORFs”. This included more than 180,000 from humans. Further analysis of other datasets that captured details of the proteins actually produced in human cells uncovered thousands of small proteins encoded by the predicted alternative ORFs. Many of the so-called alternative proteins also resembled parts of other proteins that have a known activity or function. Lastly, Samandi, Roy et al. focused on two alternative proteins and showed that they both might affect the activity of the proteins coded within the main ORF in their respective genes. These findings reveal new details about the different proteins encoded within the genes of humans and other organisms, including that many mRNAs encode more that one protein. The implications and applications of this research could be far-reaching, and may help scientists to better understand how genes work in both health and disease.
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Affiliation(s)
- Sondos Samandi
- Department of Biochemistry, Université de Sherbrooke, Sherbrooke, Canada.,PROTEO, Québec Network for Research on Protein Function, Structure and Engineering, Québec, Canada
| | - Annie V Roy
- Department of Biochemistry, Université de Sherbrooke, Sherbrooke, Canada.,PROTEO, Québec Network for Research on Protein Function, Structure and Engineering, Québec, Canada
| | - Vivian Delcourt
- Department of Biochemistry, Université de Sherbrooke, Sherbrooke, Canada.,PROTEO, Québec Network for Research on Protein Function, Structure and Engineering, Québec, Canada.,INSERM U1192, Laboratoire Protéomique, Réponse Inflammatoire & Spectrométrie de Masse (PRISM) F-59000 Lille, Université de Lille, Lille, France
| | - Jean-François Lucier
- Department of Biology, Université de Sherbrooke, Québec, Canada.,Center for Scientific computing, Information Technologies Services,, Université de Sherbrooke, Québec, Canada
| | - Jules Gagnon
- Department of Biology, Université de Sherbrooke, Québec, Canada.,Center for Scientific computing, Information Technologies Services,, Université de Sherbrooke, Québec, Canada
| | - Maxime C Beaudoin
- Department of Biochemistry, Université de Sherbrooke, Sherbrooke, Canada.,PROTEO, Québec Network for Research on Protein Function, Structure and Engineering, Québec, Canada
| | - Benoît Vanderperre
- Department of Biochemistry, Université de Sherbrooke, Sherbrooke, Canada
| | - Marc-André Breton
- Department of Biochemistry, Université de Sherbrooke, Sherbrooke, Canada
| | - Julie Motard
- Department of Biochemistry, Université de Sherbrooke, Sherbrooke, Canada.,PROTEO, Québec Network for Research on Protein Function, Structure and Engineering, Québec, Canada
| | - Jean-François Jacques
- Department of Biochemistry, Université de Sherbrooke, Sherbrooke, Canada.,PROTEO, Québec Network for Research on Protein Function, Structure and Engineering, Québec, Canada
| | - Mylène Brunelle
- Department of Biochemistry, Université de Sherbrooke, Sherbrooke, Canada.,PROTEO, Québec Network for Research on Protein Function, Structure and Engineering, Québec, Canada
| | - Isabelle Gagnon-Arsenault
- PROTEO, Québec Network for Research on Protein Function, Structure and Engineering, Québec, Canada.,Département de biochimie, microbiologie et bioinformatique, Université Laval, Québec, Canada.,IBIS, Université Laval, Québec, Canada
| | - Isabelle Fournier
- INSERM U1192, Laboratoire Protéomique, Réponse Inflammatoire & Spectrométrie de Masse (PRISM) F-59000 Lille, Université de Lille, Lille, France
| | - Aida Ouangraoua
- Department of Computer Science, Université de Sherbrooke, Québec, Canada
| | - Darel J Hunting
- Department of Nuclear Medicine and Radiobiology, Université de Sherbrooke, Québec, Canada
| | - Alan A Cohen
- Department of Family Medicine, Université de Sherbrooke, Québec, Canada
| | - Christian R Landry
- PROTEO, Québec Network for Research on Protein Function, Structure and Engineering, Québec, Canada.,Département de biochimie, microbiologie et bioinformatique, Université Laval, Québec, Canada.,IBIS, Université Laval, Québec, Canada
| | - Michelle S Scott
- Department of Biochemistry, Université de Sherbrooke, Sherbrooke, Canada
| | - Xavier Roucou
- Department of Biochemistry, Université de Sherbrooke, Sherbrooke, Canada.,PROTEO, Québec Network for Research on Protein Function, Structure and Engineering, Québec, Canada
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Manecka DL, Vanderperre B, Fon EA, Durcan TM. The Neuroprotective Role of Protein Quality Control in Halting the Development of Alpha-Synuclein Pathology. Front Mol Neurosci 2017; 10:311. [PMID: 29021741 PMCID: PMC5623686 DOI: 10.3389/fnmol.2017.00311] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2017] [Accepted: 09/14/2017] [Indexed: 12/21/2022] Open
Abstract
Synucleinopathies are a family of neurodegenerative disorders that comprises Parkinson's disease, dementia with Lewy bodies, and multiple system atrophy. Each of these disorders is characterized by devastating motor, cognitive, and autonomic consequences. Current treatments for synucleinopathies are not curative and are limited to improvement of quality of life for affected individuals. Although the underlying causes of these diseases are unknown, a shared pathological hallmark is the presence of proteinaceous inclusions containing the α-synuclein (α-syn) protein in brain tissue. In the past few years, it has been proposed that these inclusions arise from the self-templated, prion-like spreading of misfolded and aggregated forms of α-syn throughout the brain, leading to neuronal dysfunction and death. In this review, we describe how impaired protein homeostasis is a prominent factor in the α-syn aggregation cascade, with alterations in protein quality control (PQC) pathways observed in the brains of patients. We discuss how PQC modulates α-syn accumulation, misfolding and aggregation primarily through chaperoning activity, proteasomal degradation, and lysosome-mediated degradation. Finally, we provide an overview of experimental data indicating that targeting PQC pathways is a promising avenue to explore in the design of novel neuroprotective approaches that could impede the spreading of α-syn pathology and thus provide a curative treatment for synucleinopathies.
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Affiliation(s)
| | | | | | - Thomas M. Durcan
- Neurodegenerative Diseases Group and iPSC-CRISPR Core Facility, Montreal Neurological Institute, McGill University, Montreal, QC, Canada
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8
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Vanderperre B, Cermakova K, Escoffier J, Kaba M, Bender T, Nef S, Martinou JC. MPC1-like Is a Placental Mammal-specific Mitochondrial Pyruvate Carrier Subunit Expressed in Postmeiotic Male Germ Cells. J Biol Chem 2016; 291:16448-61. [PMID: 27317664 DOI: 10.1074/jbc.m116.733840] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2016] [Indexed: 12/13/2022] Open
Abstract
Selective transport of pyruvate across the inner mitochondrial membrane by the mitochondrial pyruvate carrier (MPC) is a fundamental step that couples cytosolic and mitochondrial metabolism. The recent molecular identification of the MPC complex has revealed two interacting subunits, MPC1 and MPC2. Although in yeast, an additional subunit, MPC3, can functionally replace MPC2, no alternative MPC subunits have been described in higher eukaryotes. Here, we report for the first time the existence of a novel MPC subunit termed MPC1-like (MPC1L), which is present uniquely in placental mammals. MPC1L shares high sequence, structural, and topological homology with MPC1. In addition, we provide several lines of evidence to show that MPC1L is functionally equivalent to MPC1: 1) when co-expressed with MPC2, it rescues pyruvate import in a MPC-deleted yeast strain; 2) in mammalian cells, it can associate with MPC2 to form a functional carrier as assessed by bioluminescence resonance energy transfer; 3) in MPC1 depleted mouse embryonic fibroblasts, MPC1L rescues the loss of pyruvate-driven respiration and stabilizes MPC2 expression; and 4) MPC1- and MPC1L-mediated pyruvate imports show similar efficiency. However, we show that MPC1L has a highly specific expression pattern and is localized almost exclusively in testis and more specifically in postmeiotic spermatids and sperm cells. This is in marked contrast to MPC1/MPC2, which are ubiquitously expressed throughout the organism. To date, the biological importance of this alternative MPC complex during spermatogenesis in placental mammals remains unknown. Nevertheless, these findings open up new avenues for investigating the structure-function relationship within the MPC complex.
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Affiliation(s)
| | | | - Jessica Escoffier
- the Swiss Centre for Applied Human Toxicology, and the Department of Genetic Medicine and Development, University of Geneva, 1211 Geneva 4, Switzerland
| | - Mayis Kaba
- the Swiss Centre for Applied Human Toxicology, and the Department of Genetic Medicine and Development, University of Geneva, 1211 Geneva 4, Switzerland
| | | | - Serge Nef
- the Swiss Centre for Applied Human Toxicology, and the Department of Genetic Medicine and Development, University of Geneva, 1211 Geneva 4, Switzerland
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Vanderperre B, Herzig S, Krznar P, Hörl M, Ammar Z, Montessuit S, Pierredon S, Zamboni N, Martinou JC. Embryonic Lethality of Mitochondrial Pyruvate Carrier 1 Deficient Mouse Can Be Rescued by a Ketogenic Diet. PLoS Genet 2016; 12:e1006056. [PMID: 27176894 PMCID: PMC4866774 DOI: 10.1371/journal.pgen.1006056] [Citation(s) in RCA: 53] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2015] [Accepted: 04/25/2016] [Indexed: 12/19/2022] Open
Abstract
Mitochondrial import of pyruvate by the mitochondrial pyruvate carrier (MPC) is a central step which links cytosolic and mitochondrial intermediary metabolism. To investigate the role of the MPC in mammalian physiology and development, we generated a mouse strain with complete loss of MPC1 expression. This resulted in embryonic lethality at around E13.5. Mouse embryonic fibroblasts (MEFs) derived from mutant mice displayed defective pyruvate-driven respiration as well as perturbed metabolic profiles, and both defects could be restored by reexpression of MPC1. Labeling experiments using 13C-labeled glucose and glutamine demonstrated that MPC deficiency causes increased glutaminolysis and reduced contribution of glucose-derived pyruvate to the TCA cycle. Morphological defects were observed in mutant embryonic brains, together with major alterations of their metabolome including lactic acidosis, diminished TCA cycle intermediates, energy deficit and a perturbed balance of neurotransmitters. Strikingly, these changes were reversed when the pregnant dams were fed a ketogenic diet, which provides acetyl-CoA directly to the TCA cycle and bypasses the need for a functional MPC. This allowed the normal gestation and development of MPC deficient pups, even though they all died within a few minutes post-delivery. This study establishes the MPC as a key player in regulating the metabolic state necessary for embryonic development, neurotransmitter balance and post-natal survival.
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Affiliation(s)
| | - Sébastien Herzig
- Department of Cell Biology, University of Geneva, Geneva, Switzerland
| | - Petra Krznar
- Institute of Molecular Systems Biology, ETH Zürich, Zürich, Switzerland
| | - Manuel Hörl
- Institute of Molecular Systems Biology, ETH Zürich, Zürich, Switzerland
| | - Zeinab Ammar
- Department of Cell Biology, University of Geneva, Geneva, Switzerland
| | - Sylvie Montessuit
- Department of Cell Biology, University of Geneva, Geneva, Switzerland
| | - Sandra Pierredon
- Department of Cell Biology, University of Geneva, Geneva, Switzerland
| | - Nicola Zamboni
- Institute of Molecular Systems Biology, ETH Zürich, Zürich, Switzerland
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Compan V, Pierredon S, Vanderperre B, Krznar P, Marchiq I, Zamboni N, Pouyssegur J, Martinou JC. Monitoring Mitochondrial Pyruvate Carrier Activity in Real Time Using a BRET-Based Biosensor: Investigation of the Warburg Effect. Mol Cell 2015; 59:491-501. [DOI: 10.1016/j.molcel.2015.06.035] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2015] [Revised: 05/22/2015] [Accepted: 06/26/2015] [Indexed: 02/04/2023]
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Vanderperre B, Bender T, Kunji ERS, Martinou JC. Mitochondrial pyruvate import and its effects on homeostasis. Curr Opin Cell Biol 2015; 33:35-41. [DOI: 10.1016/j.ceb.2014.10.008] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2014] [Revised: 10/30/2014] [Accepted: 10/31/2014] [Indexed: 12/15/2022]
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Vanderperre B, Lucier JF, Bissonnette C, Motard J, Tremblay G, Vanderperre S, Wisztorski M, Salzet M, Boisvert FM, Roucou X. Direct detection of alternative open reading frames translation products in human significantly expands the proteome. PLoS One 2013; 8:e70698. [PMID: 23950983 PMCID: PMC3741303 DOI: 10.1371/journal.pone.0070698] [Citation(s) in RCA: 143] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2013] [Accepted: 06/20/2013] [Indexed: 01/04/2023] Open
Abstract
A fully mature mRNA is usually associated to a reference open reading frame encoding a single protein. Yet, mature mRNAs contain unconventional alternative open reading frames (AltORFs) located in untranslated regions (UTRs) or overlapping the reference ORFs (RefORFs) in non-canonical +2 and +3 reading frames. Although recent ribosome profiling and footprinting approaches have suggested the significant use of unconventional translation initiation sites in mammals, direct evidence of large-scale alternative protein expression at the proteome level is still lacking. To determine the contribution of alternative proteins to the human proteome, we generated a database of predicted human AltORFs revealing a new proteome mainly composed of small proteins with a median length of 57 amino acids, compared to 344 amino acids for the reference proteome. We experimentally detected a total of 1,259 alternative proteins by mass spectrometry analyses of human cell lines, tissues and fluids. In plasma and serum, alternative proteins represent up to 55% of the proteome and may be a potential unsuspected new source for biomarkers. We observed constitutive co-expression of RefORFs and AltORFs from endogenous genes and from transfected cDNAs, including tumor suppressor p53, and provide evidence that out-of-frame clones representing AltORFs are mistakenly rejected as false positive in cDNAs screening assays. Functional importance of alternative proteins is strongly supported by significant evolutionary conservation in vertebrates, invertebrates, and yeast. Our results imply that coding of multiple proteins in a single gene by the use of AltORFs may be a common feature in eukaryotes, and confirm that translation of unconventional ORFs generates an as yet unexplored proteome.
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Affiliation(s)
- Benoît Vanderperre
- Département de biochimie, Faculté de Médecine et des Sciences de la Santé, Université de Sherbrooke, Québec, Canada
| | - Jean-François Lucier
- Département de microbiologie, Faculté de Médecine et des Sciences de la Santé, Université de Sherbrooke, Québec, Canada
| | - Cyntia Bissonnette
- Département de biochimie, Faculté de Médecine et des Sciences de la Santé, Université de Sherbrooke, Québec, Canada
| | - Julie Motard
- Département de biochimie, Faculté de Médecine et des Sciences de la Santé, Université de Sherbrooke, Québec, Canada
| | - Guillaume Tremblay
- Département de biochimie, Faculté de Médecine et des Sciences de la Santé, Université de Sherbrooke, Québec, Canada
| | - Solène Vanderperre
- Département de biochimie, Faculté de Médecine et des Sciences de la Santé, Université de Sherbrooke, Québec, Canada
| | - Maxence Wisztorski
- PRISM, Laboratoire de Protéomique, Réponse Inflammatoire, Spectrométrie de Masse, EA 4550, SN3, Université Lille 1, Villeneuve d'Ascq, France
| | - Michel Salzet
- PRISM, Laboratoire de Protéomique, Réponse Inflammatoire, Spectrométrie de Masse, EA 4550, SN3, Université Lille 1, Villeneuve d'Ascq, France
| | - François-Michel Boisvert
- Département d'anatomie et de biologie cellulaire, Faculté de Médecine et des Sciences de la Santé, Université de Sherbrooke, Québec, Canada
| | - Xavier Roucou
- Département de biochimie, Faculté de Médecine et des Sciences de la Santé, Université de Sherbrooke, Québec, Canada
- * E-mail:
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14
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Vanderperre B, Lucier JF, Roucou X. HAltORF: a database of predicted out-of-frame alternative open reading frames in human. Database (Oxford) 2012; 2012:bas025. [PMID: 22613085 PMCID: PMC3356836 DOI: 10.1093/database/bas025] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Human alternative open reading frames (HAltORF) is a publicly available and searchable online database referencing putative products of out-of-frame alternative translation initiation (ATI) in human mRNAs. Out-of-frame ATI is a process by which a single mRNA encodes independent proteins, when distinct initiation codons located in different reading frames are recognized by a ribosome to initiate translation. This mechanism is largely used in viruses to increase the coding potential of small viral genomes. There is increasing evidence that out-of-frame ATI is also used in eukaryotes, including human, and may contribute to the diversity of the human proteome. HAltORF is the first web-based searchable database that allows thorough investigation in the human transcriptome of out-of-frame alternative open reading frames with a start codon located in a strong Kozak context, and are thus the more likely to be expressed. It is also the first large scale study on the human transcriptome to successfully predict the expression of out-of-frame ATI protein products that were previously discovered experimentally. HAltORF will be a useful tool for the identification of human genes with multiple coding sequences, and will help to better define and understand the complexity of the human proteome. Database URL:http://haltorf.roucoulab.com/.
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Affiliation(s)
- Benoît Vanderperre
- Département de Biochimie, Faculté de Médecine et des Sciences de la Santé, Université de Sherbrooke, Québec, Canada
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Vanderperre B, Staskevicius AB, Tremblay G, McCoy M, O'Neill MA, Cashman NR, Roucou X. An overlapping reading frame in the PRNP gene encodes a novel polypeptide distinct from the prion protein. FASEB J 2011; 25:2373-86. [PMID: 21478263 DOI: 10.1096/fj.10-173815] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
The prion protein gene PRNP directs the synthesis of one of the most intensively studied mammalian proteins, the prion protein (PrP). Yet the physiological function of PrP has remained elusive and has created controversies in the literature. We found a downstream alternative translation initiation AUG codon surrounded by an optimal Kozak sequence in the +3 reading frame of PRNP. The corresponding alternative open reading frame encodes a polypeptide termed alternative prion protein (AltPrP) with a completely different amino acid sequence from PrP. We introduced a hemagglutinin (HA) tag in frame with AltPrP in PrP cDNAs from different species to test the expression of this novel polypeptide using anti-HA antibodies. AltPrP is constitutively coexpressed with human, bovine, sheep, and deer PrP. AltPrP is localized at the mitochondria and is up-regulated by endoplasmic reticulum stress and proteasomal inhibition. Generation of anti-AltPrP antibodies allowed us to test for endogenous expression of AltPrP in wild-type human cells expressing PrP. By transfecting cells with siRNA against PrP mRNA, we repressed expression of both PrP and AltPrP, confirming endogenous expression of AltPrP from PRNP. AltPrP was also detected in human brain homogenate, primary neurons, and peripheral blood mononuclear cells. These results demonstrate an unexpected function for PRNP, which, in addition to plasma membrane-anchored PrP, also encodes a second polypeptide termed AltPrP.
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Affiliation(s)
- Benoît Vanderperre
- Department of Biochemistry, Faculty of Medicine, University of Sherbrooke, 3001 12ème Avenue Nord, Sherbrooke, QC, J1H 5N4, Canada
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Beaudoin S, Vanderperre B, Grenier C, Tremblay I, Leduc F, Roucou X. A large ribonucleoprotein particle induced by cytoplasmic PrP shares striking similarities with the chromatoid body, an RNA granule predicted to function in posttranscriptional gene regulation. Biochim Biophys Acta 2008; 1793:335-45. [PMID: 19014979 DOI: 10.1016/j.bbamcr.2008.10.009] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/15/2008] [Revised: 09/23/2008] [Accepted: 10/14/2008] [Indexed: 01/08/2023]
Abstract
The observation that PrP is present in the cytosol of some neurons and non-neuronal cells and that the N-terminal signal peptide is slightly inefficient has brought speculations concerning a possible function of the protein in the cytosol. Here, we show that cells expressing a cytosolic form of PrP termed cyPrP display a large juxtanuclear cytoplasmic RNA organelle. Although cyPrP spontaneously forms aggresomes, we used several mutants to demonstrate that the assembly of this RNA organelle is independent from cyPrP aggregation. Components of the organelle fall into three classes: mRNAs; proteins, including the RNAseIII family polymerase Dicer, the decapping enzyme Dcp1a, the DEAD-box RNA helicase DDX6, and the small nuclear ribonucleoprotein-associated proteins SmB/B'/N; and non-coding RNAs, including rRNA 5S, tRNAs, U1 small nuclear RNA, and microRNAs. This composition is similar to RNA granules or chromatoid bodies from germ cells, or planarian stem cells and neurons, which are large ribonucleoprotein complexes predicted to function in RNA processing and posttranscriptional gene regulation. The domain of PrP encompassing residues 30 to 49 is essential for the formation of the RNA particle. Our findings confirm the intriguing relation between PrP and RNA in cells, and underscore an unexpected function for cytosolic PrP: assembling a large RNA processing center which we have termed PrP-RNP for PrP-induced ribonucleoprotein particle.
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Affiliation(s)
- Simon Beaudoin
- Department of Biochemistry, Faculty of Medicine, University of Sherbrooke, 3001 12(ème) avenue nord, Sherbrooke, Québec, Canada J1H 5N4
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