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Pereira CD, Espadas G, Martins F, Bertrand AT, Servais L, Sabidó E, Chevalier P, da Cruz e Silva OA, Rebelo S. Quantitative proteome analysis of LAP1-deficient human fibroblasts: A pilot approach for predicting the signaling pathways deregulated in LAP1-associated diseases. Biochem Biophys Rep 2024; 39:101757. [PMID: 39035020 PMCID: PMC11260385 DOI: 10.1016/j.bbrep.2024.101757] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2024] [Revised: 06/11/2024] [Accepted: 06/14/2024] [Indexed: 07/23/2024] Open
Abstract
Lamina-associated polypeptide 1 (LAP1), a ubiquitously expressed nuclear envelope protein, appears to be essential for the maintenance of cell homeostasis. Although rare, mutations in the human LAP1-encoding TOR1AIP1 gene cause severe diseases and can culminate in the premature death of affected individuals. Despite there is increasing evidence of the pathogenicity of TOR1AIP1 mutations, the current knowledge on LAP1's physiological roles in humans is limited; hence, investigation is required to elucidate the critical functions of this protein, which can be achieved by uncovering the molecular consequences of LAP1 depletion, a topic that remains largely unexplored. In this work, the proteome of patient-derived LAP1-deficient fibroblasts carrying a pathological TOR1AIP1 mutation (LAP1 E482A) was quantitatively analyzed to identify global changes in protein abundance levels relatively to control fibroblasts. An in silico functional enrichment analysis of the mass spectrometry-identified differentially expressed proteins was also performed, along with additional in vitro functional assays, to unveil the biological processes that are potentially dysfunctional in LAP1 E482A fibroblasts. Collectively, our findings suggest that LAP1 deficiency may induce significant alterations in various cellular activities, including DNA repair, messenger RNA degradation/translation, proteostasis and glutathione metabolism/antioxidant response. This study sheds light on possible new functions of human LAP1 and could set the basis for subsequent in-depth mechanistic investigations. Moreover, by identifying deregulated signaling pathways in LAP1-deficient cells, our work may offer valuable molecular targets for future disease-modifying therapies for TOR1AIP1-associated nuclear envelopathies.
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Affiliation(s)
- Cátia D. Pereira
- Institute of Biomedicine (iBiMED), Department of Medical Sciences, University of Aveiro, 3810-193, Aveiro, Portugal
| | - Guadalupe Espadas
- Center for Genomics Regulation, The Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
- Universitat Pompeu Fabra, Barcelona, Spain
| | - Filipa Martins
- Institute of Biomedicine (iBiMED), Department of Medical Sciences, University of Aveiro, 3810-193, Aveiro, Portugal
| | - Anne T. Bertrand
- Sorbonne Université, Inserm, Institut de Myologie, Centre de Recherche en Myologie, Paris, France
| | - Laurent Servais
- MDUK Oxford Neuromuscular Center, Department of Paediatrics, University of Oxford and NIHR Oxford Biomedical Research Center, Oxford, OX3 9DU, United Kingdom
- Neuromuscular Center, Division of Paediatrics, University Hospital of Liège and University of Liège, 4000, Liège, Belgium
| | - Eduard Sabidó
- Center for Genomics Regulation, The Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
- Universitat Pompeu Fabra, Barcelona, Spain
| | - Philippe Chevalier
- Université Claude Bernard Lyon 1, Lyon, France
- Hospices Civils de Lyon, Lyon, France
| | - Odete A.B. da Cruz e Silva
- Institute of Biomedicine (iBiMED), Department of Medical Sciences, University of Aveiro, 3810-193, Aveiro, Portugal
| | - Sandra Rebelo
- Institute of Biomedicine (iBiMED), Department of Medical Sciences, University of Aveiro, 3810-193, Aveiro, Portugal
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Sciandra F, Desiderio C, Vincenzoni F, Viscuso S, Bozzi M, Hübner W, Jimenez-Gutierrez GE, Cisneros B, Brancaccio A. Analysis of the GFP-labelled β-dystroglycan interactome in HEK-293 transfected cells reveals novel intracellular networks. Biochem Biophys Res Commun 2024; 703:149656. [PMID: 38364681 DOI: 10.1016/j.bbrc.2024.149656] [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: 11/29/2023] [Revised: 01/19/2024] [Accepted: 02/06/2024] [Indexed: 02/18/2024]
Abstract
Dystroglycan (DG) is a cell adhesion complex that is widely expressed in tissues. It is composed by two subunits, α-DG, a highly glycosylated protein that interacts with several extracellular matrix proteins, and transmembrane β-DG whose, cytodomain binds to the actin cytoskeleton. Glycosylation of α-DG is crucial for functioning as a receptor for its multiple extracellular binding partners. Perturbation of α-DG glycosylation is the central event in the pathogenesis of severe pathologies such as muscular dystrophy and cancer. β-DG acts as a scaffold for several cytoskeletal and nuclear proteins and very little is known about the fine regulation of some of these intracellular interactions and how they are perturbed in diseases. To start filling this gap by identifying uncharacterized intracellular networks preferentially associated with β-DG, HEK-293 cells were transiently transfected with a plasmid carrying the β-DG subunit with GFP fused at its C-terminus. With this strategy, we aimed at forcing β-DG to occupy multiple intracellular locations instead of sitting tightly at its canonical plasma membrane milieu, where it is commonly found in association with α-DG. Immunoprecipitation by anti-GFP antibodies followed by shotgun proteomic analysis led to the identification of an interactome formed by 313 exclusive protein matches for β-DG binding. A series of already known β-DG interactors have been found, including ezrin and emerin, whilst significant new matches, which include potential novel β-DG interactors and their related networks, were identified in diverse subcellular compartments, such as cytoskeleton, endoplasmic reticulum/Golgi, mitochondria, nuclear membrane and the nucleus itself. Of particular interest amongst the novel identified matches, Lamina-Associated Polypeptide-1B (LAP1B), an inner nuclear membrane protein, whose mutations are known to cause nuclear envelopathies characterized by muscular dystrophy, was found to interact with β-DG in HEK-293 cells. This evidence was confirmed by immunoprecipitation, Western blotting and immunofluorescence experiments. We also found by immunofluorescence experiments that LAP1B looses its nuclear envelope localization in C2C12 DG-knock-out cells, suggesting that LAP1B requires β-DG for a proper nuclear localization. These results expand the role of β-DG as a nuclear scaffolding protein and provide novel evidence of a possible link between dystroglycanopathies and nuclear envelopathies displaying with muscular dystrophy.
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Affiliation(s)
- Francesca Sciandra
- Istituto di Scienze e Tecnologie Chimiche "Giulio Natta"- SCITEC (CNR), Largo F. Vito, 00168, Roma, Italy
| | - Claudia Desiderio
- Istituto di Scienze e Tecnologie Chimiche "Giulio Natta"- SCITEC (CNR), Largo F. Vito, 00168, Roma, Italy
| | - Federica Vincenzoni
- Dipartimento di Scienze biotecnologiche di base, cliniche intensivologiche e perioperatorie, Sezione di Biochimica e Biochimica Clinica, Università Cattolica del Sacro Cuore, Largo F. Vito 1, 00168, Roma, Italy; Fondazione Policlinico Universitario A. Gemelli IRCCS, Roma, Italy
| | - Simona Viscuso
- Dipartimento di Scienze biotecnologiche di base, cliniche intensivologiche e perioperatorie, Sezione di Biochimica e Biochimica Clinica, Università Cattolica del Sacro Cuore, Largo F. Vito 1, 00168, Roma, Italy
| | - Manuela Bozzi
- Istituto di Scienze e Tecnologie Chimiche "Giulio Natta"- SCITEC (CNR), Largo F. Vito, 00168, Roma, Italy; Dipartimento di Scienze biotecnologiche di base, cliniche intensivologiche e perioperatorie, Sezione di Biochimica e Biochimica Clinica, Università Cattolica del Sacro Cuore, Largo F. Vito 1, 00168, Roma, Italy
| | - Wolfgang Hübner
- Biomolecular Photonics, University of Bielefeld, 33615, Bielefeld, Germany
| | | | - Bulmaro Cisneros
- Departamento de Genética y Biología Molecular, CINVESTAV Zacatenco IPN, Ciudad de México, 07360, Mexico
| | - Andrea Brancaccio
- Istituto di Scienze e Tecnologie Chimiche "Giulio Natta"- SCITEC (CNR), Largo F. Vito, 00168, Roma, Italy; School of Biochemistry, University of Bristol, BS8 1TD, UK.
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Benarroch L, Madsen-Østerbye J, Abdelhalim M, Mamchaoui K, Ohana J, Bigot A, Mouly V, Bonne G, Bertrand AT, Collas P. Cellular and Genomic Features of Muscle Differentiation from Isogenic Fibroblasts and Myoblasts. Cells 2023; 12:1995. [PMID: 37566074 PMCID: PMC10417614 DOI: 10.3390/cells12151995] [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: 06/30/2023] [Revised: 07/27/2023] [Accepted: 07/31/2023] [Indexed: 08/12/2023] Open
Abstract
The ability to recapitulate muscle differentiation in vitro enables the exploration of mechanisms underlying myogenesis and muscle diseases. However, obtaining myoblasts from patients with neuromuscular diseases or from healthy subjects poses ethical and procedural challenges that limit such investigations. An alternative consists in converting skin fibroblasts into myogenic cells by forcing the expression of the myogenic regulator MYOD. Here, we directly compared cellular phenotype, transcriptome, and nuclear lamina-associated domains (LADs) in myo-converted human fibroblasts and myotubes differentiated from myoblasts. We used isogenic cells from a 16-year-old donor, ruling out, for the first time to our knowledge, genetic factors as a source of variations between the two myogenic models. We show that myo-conversion of fibroblasts upregulates genes controlling myogenic pathways leading to multinucleated cells expressing muscle cell markers. However, myotubes are more advanced in myogenesis than myo-converted fibroblasts at the phenotypic and transcriptomic levels. While most LADs are shared between the two cell types, each also displays unique domains of lamin A/C interactions. Furthermore, myotube-specific LADs are more gene-rich and less heterochromatic than shared LADs or LADs unique to myo-converted fibroblasts, and they uniquely sequester developmental genes. Thus, myo-converted fibroblasts and myotubes retain cell type-specific features of radial and functional genome organization. Our results favor a view of myo-converted fibroblasts as a practical model to investigate the phenotypic and genomic properties of muscle cell differentiation in normal and pathological contexts, but also highlight current limitations in using fibroblasts as a source of myogenic cells.
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Affiliation(s)
- Louise Benarroch
- Sorbonne Université, Inserm, Institut de Myologie, Centre de Recherche en Myologie, 75013 Paris, France; (L.B.); (K.M.); (J.O.); (A.B.); (V.M.); (G.B.)
| | - Julia Madsen-Østerbye
- Department of Molecular Medicine, Institute of Basic Medical Sciences, Faculty of Medicine, University of Oslo, 0372 Oslo, Norway; (J.M.-Ø.); (M.A.)
- Department of Immunology and Transfusion Medicine, Oslo University Hospital, 0372 Oslo, Norway
| | - Mohamed Abdelhalim
- Department of Molecular Medicine, Institute of Basic Medical Sciences, Faculty of Medicine, University of Oslo, 0372 Oslo, Norway; (J.M.-Ø.); (M.A.)
| | - Kamel Mamchaoui
- Sorbonne Université, Inserm, Institut de Myologie, Centre de Recherche en Myologie, 75013 Paris, France; (L.B.); (K.M.); (J.O.); (A.B.); (V.M.); (G.B.)
| | - Jessica Ohana
- Sorbonne Université, Inserm, Institut de Myologie, Centre de Recherche en Myologie, 75013 Paris, France; (L.B.); (K.M.); (J.O.); (A.B.); (V.M.); (G.B.)
| | - Anne Bigot
- Sorbonne Université, Inserm, Institut de Myologie, Centre de Recherche en Myologie, 75013 Paris, France; (L.B.); (K.M.); (J.O.); (A.B.); (V.M.); (G.B.)
| | - Vincent Mouly
- Sorbonne Université, Inserm, Institut de Myologie, Centre de Recherche en Myologie, 75013 Paris, France; (L.B.); (K.M.); (J.O.); (A.B.); (V.M.); (G.B.)
| | - Gisèle Bonne
- Sorbonne Université, Inserm, Institut de Myologie, Centre de Recherche en Myologie, 75013 Paris, France; (L.B.); (K.M.); (J.O.); (A.B.); (V.M.); (G.B.)
| | - Anne T. Bertrand
- Sorbonne Université, Inserm, Institut de Myologie, Centre de Recherche en Myologie, 75013 Paris, France; (L.B.); (K.M.); (J.O.); (A.B.); (V.M.); (G.B.)
| | - Philippe Collas
- Department of Molecular Medicine, Institute of Basic Medical Sciences, Faculty of Medicine, University of Oslo, 0372 Oslo, Norway; (J.M.-Ø.); (M.A.)
- Department of Immunology and Transfusion Medicine, Oslo University Hospital, 0372 Oslo, Norway
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