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Coulombe B, Durcan TM, Bernard G, Moursli A, Poitras C, Faubert D, Pinard M. The 37TrillionCells initiative for improving global healthcare via cell-based interception and precision medicine: focus on neurodegenerative diseases. Mol Brain 2024; 17:18. [PMID: 38605409 PMCID: PMC11007934 DOI: 10.1186/s13041-024-01088-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2024] [Accepted: 03/15/2024] [Indexed: 04/13/2024] Open
Abstract
One of the main burdens in the treatment of diseases is imputable to the delay between the appearance of molecular dysfunctions in the first affected disease cells and their presence in sufficient number for detection in specific tissues or organs. This delay obviously plays in favor of disease progression to an extent that makes efficient treatments difficult, as they arrive too late. The development of a novel medical strategy, termed cell-based interception and precision medicine, seeks to identify dysfunctional cells early, when tissue damages are not apparent and symptoms not yet present, and develop therapies to treat diseases early. Central to this strategy is the use of single-cell technologies that allow detection of molecular changes in cells at the time of phenotypical bifurcation from health to disease. In this article we describe a general procedure to support such an approach applied to neurodegenerative disorders. This procedure combines four components directed towards highly complementary objectives: 1) a high-performance single-cell proteomics (SCP) method (Detect), 2) the development of disease experimental cell models and predictive computational models of cell trajectories (Understand), 3) the discovery of specific targets and personalized therapies (Cure), and 4) the creation of a community of collaborating laboratories to accelerate the development of this novel medical paradigm (Collaborate). A global initiative named 37TrillionCells (37TC) was launched to advance the development of cell-based interception and precision medicine.
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Affiliation(s)
- Benoit Coulombe
- Translational Proteomics Laboratory, Institut de Recherches Cliniques de Montréal, Montreal, QC, H2W 1R7, Canada.
- Department of Biochemistry and Molecular Medicine, Université de Montréal, Montreal, QC, Canada.
| | - Thomas M Durcan
- The Neuro's Early Drug Discovery Unit (EDDU), McGill University, Montreal, Canada
| | - Geneviève Bernard
- Departments of Neurology and Neurosurgery, Pediatrics and Human Genetics, McGill University, Montreal, Canada
- Department Specialized Medicine, Division of Medical Genetics, McGill University Health Centre, Montreal, Canada
- Child Health and Human Development Program, Research Institute of the McGill University Health Centre, Montreal, Canada
| | - Asmae Moursli
- Translational Proteomics Laboratory, Institut de Recherches Cliniques de Montréal, Montreal, QC, H2W 1R7, Canada
| | - Christian Poitras
- Translational Proteomics Laboratory, Institut de Recherches Cliniques de Montréal, Montreal, QC, H2W 1R7, Canada
| | - Denis Faubert
- Mass Spectrometry and Proteomics Platform, Institut de Recherches Cliniques de Montréal, Montreal, QC, H2W1R7, Canada
| | - Maxime Pinard
- Translational Proteomics Laboratory, Institut de Recherches Cliniques de Montréal, Montreal, QC, H2W 1R7, Canada
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Shepelev NM, Kurochkina AO, Dontsova OA, Rubtsova MP. PRPF19 mRNA Encodes a Small Open Reading Frame That Is Important for Viability of Human Cells. DOKL BIOCHEM BIOPHYS 2024; 515:41-47. [PMID: 38472668 PMCID: PMC11021245 DOI: 10.1134/s1607672923700722] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2023] [Revised: 12/25/2023] [Accepted: 12/28/2023] [Indexed: 03/14/2024]
Abstract
High-throughput ribosome profiling demonstrates the translation of thousands of small open reading frames located in the 5' untranslated regions of messenger RNAs (upstream ORFs). Upstream ORF can both perform a regulatory function by influencing the translation of the downstream main ORF and encode a small functional protein or microprotein. In this work, we showed that the 5' untranslated region of the PRPF19 mRNA encodes an upstream ORF that is translated in human cells. Inactivation of this upstream ORF reduces the viability of human cells.
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Affiliation(s)
- N M Shepelev
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Moscow, Russia
- Department of Chemistry, Moscow State University, Moscow, Russia
| | - A O Kurochkina
- Department of Chemistry, Moscow State University, Moscow, Russia
| | - O A Dontsova
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Moscow, Russia
- Department of Chemistry, Moscow State University, Moscow, Russia
- Belozersky Institute of Physico-Chemical Biology, Moscow, Russia
- Skolkovo Institute of Science and Technology, Center for Molecular and Cellular Biology, Moscow, Russia
| | - M P Rubtsova
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Moscow, Russia.
- Department of Chemistry, Moscow State University, Moscow, Russia.
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Frommelt F, Fossati A, Uliana F, Wendt F, Xue P, Heusel M, Wollscheid B, Aebersold R, Ciuffa R, Gstaiger M. DIP-MS: ultra-deep interaction proteomics for the deconvolution of protein complexes. Nat Methods 2024; 21:635-647. [PMID: 38532014 PMCID: PMC11009110 DOI: 10.1038/s41592-024-02211-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2023] [Accepted: 02/14/2024] [Indexed: 03/28/2024]
Abstract
Most proteins are organized in macromolecular assemblies, which represent key functional units regulating and catalyzing most cellular processes. Affinity purification of the protein of interest combined with liquid chromatography coupled to tandem mass spectrometry (AP-MS) represents the method of choice to identify interacting proteins. The composition of complex isoforms concurrently present in the AP sample can, however, not be resolved from a single AP-MS experiment but requires computational inference from multiple time- and resource-intensive reciprocal AP-MS experiments. Here we introduce deep interactome profiling by mass spectrometry (DIP-MS), which combines AP with blue-native-PAGE separation, data-independent acquisition with mass spectrometry and deep-learning-based signal processing to resolve complex isoforms sharing the same bait protein in a single experiment. We applied DIP-MS to probe the organization of the human prefoldin family of complexes, resolving distinct prefoldin holo- and subcomplex variants, complex-complex interactions and complex isoforms with new subunits that were experimentally validated. Our results demonstrate that DIP-MS can reveal proteome modularity at unprecedented depth and resolution.
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Affiliation(s)
- Fabian Frommelt
- Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland.
| | - Andrea Fossati
- Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA
- J. David Gladstone Institutes, San Francisco, CA, USA
| | - Federico Uliana
- Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland
- Department of Biology, Institute of Biochemistry, ETH Zurich, Zurich, Switzerland
| | - Fabian Wendt
- Department of Health Sciences and Technology (D-HEST), Institute of Translational Medicine (ITM), ETH Zurich, Zurich, Switzerland
| | - Peng Xue
- Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland
- Guangzhou National Laboratory, Guang Zhou, China
| | - Moritz Heusel
- Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland
| | - Bernd Wollscheid
- Department of Health Sciences and Technology (D-HEST), Institute of Translational Medicine (ITM), ETH Zurich, Zurich, Switzerland
| | - Ruedi Aebersold
- Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland
| | - Rodolfo Ciuffa
- Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland
| | - Matthias Gstaiger
- Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland.
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Pinard M, Moursli A, Coulombe B. Drugs targeting the particle for arrangement of quaternary structure (PAQosome) and protein complex assembly. Expert Opin Drug Discov 2024; 19:57-71. [PMID: 37840283 DOI: 10.1080/17460441.2023.2267974] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2023] [Accepted: 10/04/2023] [Indexed: 10/17/2023]
Abstract
INTRODUCTION The PAQosome is a 12-subunit complex that acts as a co-factor of the molecular chaperones HSP90 and HSP70. This co-chaperone has been shown to participate in assembly and maturation of several protein complexes, including nuclear RNA polymerases, RNA processing factors, the ribosome, PIKKs, and others. Subunits of the PAQosome, adaptors, and clients have been reported to be involved in various diseases, making them interesting targets for drug discovery. AREA COVERED In this review, the authors cover the detailed mechanisms of PAQosome and chaperone function. Specifically, the authors summarize the status of the PAQosome and some related chaperones and co-chaperones as candidate targets for drug discovery. Indeed, a number of compounds are currently being tested for the development of treatments against diseases, such as cancers and neurodegenerative conditions. EXPERT OPINION Searching for new drugs targeting the PAQosome requires a better understanding of PAQosome subunit interactions and the discovery of new interaction partners. Thus, PAQosome subunit crystallization is an important experiment to initiate virtual screening against new target and the development of in silico tools such as AlphaFold-multimer could accelerate the search for new interaction partner and determine more rapidly the interaction pocket needed for virtual drug screening.
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Affiliation(s)
- Maxime Pinard
- Translational Proteomics Laboratory, Institut de Recherches Cliniques de Montréal, Montréal, Québec, Canada
| | - Asmae Moursli
- Translational Proteomics Laboratory, Institut de Recherches Cliniques de Montréal, Montréal, Québec, Canada
| | - Benoit Coulombe
- Translational Proteomics Laboratory, Institut de Recherches Cliniques de Montréal, Montréal, Québec, Canada
- Department of Biochemistry and Molecular Medicine, Université de Montréal, Montréal, Québec, Canada
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Antonio LM, Martins GH, Aragão AZB, Quel NG, Zazeri G, Houry WA, Ramos CHI. Unveiling the Role of Sorghum RPAP3 in the Function of R2TP Complex: Insights into Protein Assembly in Plants. PLANTS (BASEL, SWITZERLAND) 2023; 12:2925. [PMID: 37631136 PMCID: PMC10458388 DOI: 10.3390/plants12162925] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Revised: 08/04/2023] [Accepted: 08/10/2023] [Indexed: 08/27/2023]
Abstract
The chaperone R2TP has multiple subunits that assist in the proper folding, assembly, and stabilization of various protein complexes in cells and its study can offer valuable insights into the regulation and maintenance of protein assemblies in plant systems. The 'T' component of R2TP is Tah1 in yeast, consisting of 111 residues, while its counterpart in humans is RPAP3, with 665 residues. RPAP3 acts as a co-chaperone of Hsp90 and facilitates interactions between RUVBL proteins and other complex components, enhancing the recruitment of client proteins by the R2TP complex. These facts further underscore the relevance of studying this complex in different organisms. The putative gene corresponding to the RPAP3 in Sorghum bicolor, a monocotyledon plant, was cloned, and the protein (396 residues) purified for biochemical characterization. SbRPAP3 exists as a folded monomer and has a RPAP3 domain, which is present in human RPAP3 but absent in yeast Tah1. SbRPAP3 retains its functional capabilities, including binding with RUVBLs, Hsp90, and Hsp70. By elucidating the role of RPAP3 in plant R2TP complex, we can further comprehend the molecular mechanisms underlying plant-specific protein assembly and contribute to advancements in plant biology and biotechnological applications.
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Affiliation(s)
- Larissa Machado Antonio
- Institute of Chemistry, University of Campinas—UNICAMP, Campinas 13100-104, SP, Brazil; (L.M.A.); (G.H.M.); (A.Z.B.A.); (N.G.Q.); (G.Z.)
| | - Gustavo Henrique Martins
- Institute of Chemistry, University of Campinas—UNICAMP, Campinas 13100-104, SP, Brazil; (L.M.A.); (G.H.M.); (A.Z.B.A.); (N.G.Q.); (G.Z.)
| | - Annelize Zambon Barbosa Aragão
- Institute of Chemistry, University of Campinas—UNICAMP, Campinas 13100-104, SP, Brazil; (L.M.A.); (G.H.M.); (A.Z.B.A.); (N.G.Q.); (G.Z.)
| | - Natália Galdi Quel
- Institute of Chemistry, University of Campinas—UNICAMP, Campinas 13100-104, SP, Brazil; (L.M.A.); (G.H.M.); (A.Z.B.A.); (N.G.Q.); (G.Z.)
| | - Gabriel Zazeri
- Institute of Chemistry, University of Campinas—UNICAMP, Campinas 13100-104, SP, Brazil; (L.M.A.); (G.H.M.); (A.Z.B.A.); (N.G.Q.); (G.Z.)
| | - Walid A. Houry
- Department of Biochemistry, University of Toronto, Toronto, ON M5G 1M1, Canada;
- Department of Chemistry, University of Toronto, Toronto, ON M5S 3H6, Canada
| | - Carlos Henrique Inacio Ramos
- Institute of Chemistry, University of Campinas—UNICAMP, Campinas 13100-104, SP, Brazil; (L.M.A.); (G.H.M.); (A.Z.B.A.); (N.G.Q.); (G.Z.)
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Pinard M, Dastpeyman S, Poitras C, Bernard G, Gauthier MS, Coulombe B. Riluzole partially restores RNA polymerase III complex assembly in cells expressing the leukodystrophy-causative variant POLR3B R103H. Mol Brain 2022; 15:98. [PMID: 36451185 PMCID: PMC9710144 DOI: 10.1186/s13041-022-00974-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2022] [Accepted: 10/16/2022] [Indexed: 12/12/2022] Open
Abstract
The mechanism of assembly of RNA polymerase III (Pol III), the 17-subunit enzyme that synthesizes tRNAs, 5 S rRNA, and other small-nuclear (sn) RNAs in eukaryotes, is not clearly understood. The recent discovery of the HSP90 co-chaperone PAQosome (Particle for Arrangement of Quaternary structure) revealed a function for this machinery in the biogenesis of nuclear RNA polymerases. However, the connection between Pol III subunits and the PAQosome during the assembly process remains unexplored. Here, we report the development of a mass spectrometry-based assay that allows the characterization of Pol III assembly. This assay was used to dissect the stages of Pol III assembly, to start defining the function of the PAQosome in this process, to dissect the assembly defects driven by the leukodystrophy-causative R103H substitution in POLR3B, and to discover that riluzole, an FDA-approved drug for alleviation of ALS symptoms, partly corrects these assembly defects. Together, these results shed new light on the mechanism and regulation of human nuclear Pol III biogenesis.
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Affiliation(s)
- Maxime Pinard
- grid.511547.30000 0001 2106 1695Translational Proteomics Laboratory, Institut de Recherches Cliniques de Montréal, Montréal, Québec Canada
| | - Samaneh Dastpeyman
- grid.511547.30000 0001 2106 1695Translational Proteomics Laboratory, Institut de Recherches Cliniques de Montréal, Montréal, Québec Canada
| | - Christian Poitras
- grid.511547.30000 0001 2106 1695Translational Proteomics Laboratory, Institut de Recherches Cliniques de Montréal, Montréal, Québec Canada
| | - Geneviève Bernard
- grid.63984.300000 0000 9064 4811Child Health and Human Development Program, Research Institute of the McGill University Health Centre, Montreal, Canada ,grid.14709.3b0000 0004 1936 8649Department of Neurology and Neurosurgery, McGill University, Montreal, Canada ,grid.14709.3b0000 0004 1936 8649Department of Human Genetics, McGill University, Montreal, Canada ,grid.14709.3b0000 0004 1936 8649Department of Pediatrics, McGill University, Montreal, Canada ,grid.63984.300000 0000 9064 4811Department of Specialized Medicine, Division of Medical Genetics, McGill University Health Center, Montreal, Canada
| | - Marie-Soleil Gauthier
- grid.511547.30000 0001 2106 1695Translational Proteomics Laboratory, Institut de Recherches Cliniques de Montréal, Montréal, Québec Canada
| | - Benoit Coulombe
- grid.511547.30000 0001 2106 1695Translational Proteomics Laboratory, Institut de Recherches Cliniques de Montréal, Montréal, Québec Canada ,grid.14848.310000 0001 2292 3357Department of Biochemistry and Molecular Medicine, Université de Montréal, Montréal, Québec Canada
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