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Bergeron JJM. Proteomics Impact on Cell Biology to Resolve Cell Structure and Function. Mol Cell Proteomics 2024; 23:100758. [PMID: 38574860 PMCID: PMC11070594 DOI: 10.1016/j.mcpro.2024.100758] [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: 02/07/2024] [Revised: 03/23/2024] [Accepted: 03/26/2024] [Indexed: 04/06/2024] Open
Abstract
The acceleration of advances in proteomics has enabled integration with imaging at the EM and light microscopy levels, cryo-EM of protein structures, and artificial intelligence with proteins comprehensively and accurately resolved for cell structures at nanometer to subnanometer resolution. Proteomics continues to outpace experimentally based structural imaging, but their ultimate integration is a path toward the goal of a compendium of all proteins to understand mechanistically cell structure and function.
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Affiliation(s)
- John J M Bergeron
- Department of Medicine, McGill University Hospital Research Institute, Montreal, Quebec, Canada.
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2
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Busselez J, Uzbekov RE, Franco B, Pancione M. New insights into the centrosome-associated spliceosome components as regulators of ciliogenesis and tissue identity. WILEY INTERDISCIPLINARY REVIEWS. RNA 2023; 14:e1776. [PMID: 36717357 DOI: 10.1002/wrna.1776] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/06/2022] [Revised: 12/20/2022] [Accepted: 12/27/2022] [Indexed: 02/01/2023]
Abstract
Biomolecular condensates are membrane-less assemblies of proteins and nucleic acids. Centrosomes are biomolecular condensates that play a crucial role in nuclear division, cytoskeletal remodeling, and cilia formation in animal cells. Spatial omics technology is providing new insights into the dynamic exchange of spliceosome components between the nucleus and the centrosome/cilium. Intriguingly, centrosomes are emerging as cytoplasmic sites for information storage, enriched with RNA molecules and RNA-processing proteins. Furthermore, growing evidence supports the view that nuclear spliceosome components assembled at the centrosome function as potential coordinators of splicing subprograms, pluripotency, and cell differentiation. In this article, we first discuss the current understanding of the centrosome/cilium complex, which controls both stem cell differentiation and pluripotency. We next explore the molecular mechanisms that govern splicing factor assembly and disassembly around the centrosome and examine how RNA processing pathways contribute to ciliogenesis. Finally, we discuss numerous unresolved compelling questions regarding the centrosome-associated spliceosome components and transcript variants within the cytoplasm as sources of RNA-based secondary messages in the regulation of cell identity and cell fate determination. This article is categorized under: RNA-Based Catalysis > RNA Catalysis in Splicing and Translation RNA Interactions with Proteins and Other Molecules > RNA-Protein Complexes RNA Processing > Splicing Regulation/Alternative Splicing RNA Processing > RNA Processing.
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Affiliation(s)
- Johan Busselez
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Illkirch-Graffenstaden, France
| | - Rustem E Uzbekov
- Faculté de Médecine, Université de Tours, Tours, France
- Faculty of Bioengineering and Bioinformatics, Moscow State University, Moscow, Russia
| | - Brunella Franco
- Telethon Institute of Genetics and Medicine (TIGEM), Naples, Italy
- Department of Translational Medicine, Medical Genetics, University of Naples "Federico II", Naples, Italy
- Scuola Superiore Meridionale (SSM, School of Advanced Studies), Genomics and Experimental Medicine program, University of Naples Federico II, Naples, Italy
| | - Massimo Pancione
- Department of Sciences and Technologies, University of Sannio, Benevento, Italy
- Department of Biochemistry and Molecular Biology, Faculty of Pharmacy, Complutense University Madrid, Madrid, Spain
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3
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Cerulo L, Pezzella N, Caruso FP, Parente P, Remo A, Giordano G, Forte N, Busselez J, Boschi F, Galiè M, Franco B, Pancione M. Single-cell proteo-genomic reveals a comprehensive map of centrosome-associated spliceosome components. iScience 2023; 26:106602. [PMID: 37250316 PMCID: PMC10214398 DOI: 10.1016/j.isci.2023.106602] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2022] [Revised: 01/16/2023] [Accepted: 03/29/2023] [Indexed: 05/31/2023] Open
Abstract
Ribonucleoprotein (RNP) condensates are crucial for controlling RNA metabolism and splicing events in animal cells. We used spatial proteomics and transcriptomic to elucidate RNP interaction networks at the centrosome, the main microtubule-organizing center in animal cells. We found a number of cell-type specific centrosome-associated spliceosome interactions localized in subcellular structures involved in nuclear division and ciliogenesis. A component of the nuclear spliceosome BUD31 was validated as an interactor of the centriolar satellite protein OFD1. Analysis of normal and disease cohorts identified the cholangiocarcinoma as target of centrosome-associated spliceosome alterations. Multiplexed single-cell fluorescent microscopy for the centriole linker CEP250 and spliceosome components including BCAS2, BUD31, SRSF2 and DHX35 recapitulated bioinformatic predictions on the centrosome-associated spliceosome components tissue-type specific composition. Collectively, centrosomes and cilia act as anchor for cell-type specific spliceosome components, and provide a helpful reference for explore cytoplasmic condensates functions in defining cell identity and in the origin of rare diseases.
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Affiliation(s)
- Luigi Cerulo
- Bioinformatics Laboratory, BIOGEM scrl, Ariano Irpino, Avellino, Italy
- Department of Sciences and Technologies, University of Sannio, Benevento, Italy
| | - Nunziana Pezzella
- Telethon Institute of Genetics and Medicine (TIGEM), Via Campi Flegrei, 34, Pozzuoli, 80078 Naples, Italy
- School for Advanced Studies, Genomics and Experimental Medicine Program, Naples, Italy
| | - Francesca Pia Caruso
- Bioinformatics Laboratory, BIOGEM scrl, Ariano Irpino, Avellino, Italy
- Department of Sciences and Technologies, University of Sannio, Benevento, Italy
| | - Paola Parente
- Unit of Pathology, Fondazione IRCCS Casa Sollievo della Sofferenza, San Giovanni Rotondo, Foggia, Italy
| | - Andrea Remo
- Pathology Unit, Mater Salutis Hospital AULSS9, “Scaligera”, 37122 Verona, Italy
| | - Guido Giordano
- Unit of Medical Oncology and Biomolecular Therapy, Department of Medical and Surgical Sciences, University of Foggia, Policlinico Riuniti, 71122 Foggia, Italy
| | - Nicola Forte
- Department of Clinical Pathology, Fatebenefratelli Hospital, 82100 Benevento, Italy
| | - Johan Busselez
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Illkirch, France
| | - Federico Boschi
- Department of Computer Science, University of Verona, Strada Le Grazie 8, Verona, Italy
| | - Mirco Galiè
- Department of Neuroscience, Biomedicine and Movement, University of Verona, Verona, Italy
| | - Brunella Franco
- Telethon Institute of Genetics and Medicine (TIGEM), Via Campi Flegrei, 34, Pozzuoli, 80078 Naples, Italy
- School for Advanced Studies, Genomics and Experimental Medicine Program, Naples, Italy
- Medical Genetics, Department of Translational Medicine, University of Naples “Federico II”, Via Sergio Pansini, 80131 Naples, Italy
| | - Massimo Pancione
- Department of Sciences and Technologies, University of Sannio, Benevento, Italy
- Department of Biochemistry and Molecular Biology, Faculty of Pharmacy, Complutense University Madrid, 28040 Madrid, Spain
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4
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Mahen R. cNap1 bridges centriole contact sites to maintain centrosome cohesion. PLoS Biol 2022; 20:e3001854. [PMID: 36282799 PMCID: PMC9595518 DOI: 10.1371/journal.pbio.3001854] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2021] [Accepted: 09/27/2022] [Indexed: 11/06/2022] Open
Abstract
Centrioles are non-membrane-bound organelles that participate in fundamental cellular processes through their ability to form physical contacts with other structures. During interphase, two mature centrioles can associate to form a single centrosome—a phenomenon known as centrosome cohesion. Centrosome cohesion is important for processes such as cell migration, and yet how it is maintained is unclear. Current models indicate that pericentriolar fibres termed rootlets, also known as the centrosome linker, entangle to maintain centriole proximity. Here, I uncover a centriole–centriole contact site and mechanism of centrosome cohesion based on coalescence of the proximal centriole component cNap1. Using live-cell imaging of endogenously tagged cNap1, I show that proximal centrioles form dynamic contacts in response to physical force from the cytoskeleton. Expansion microscopy reveals that cNap1 bridges between these contact sites, physically linking proximal centrioles on the nanoscale. Fluorescence correlation spectroscopy (FCS)-calibrated imaging shows that cNap1 accumulates at nearly micromolar concentrations on proximal centrioles, corresponding to a few hundred protein copy numbers. When ectopically tethered to organelles such as lysosomes, cNap1 forms viscous and cohesive assemblies that promote organelle spatial proximity. These results suggest a mechanism of centrosome cohesion by cNap1 at the proximal centriole and illustrate how a non-membrane-bound organelle forms organelle contact sites. During interphase, two mature centrioles can associate to form a single centrosome; this "centrosome cohesion" is important for processes such as cell migration, but how is it maintained? This study combines live cell quantitative imaging, expansion microscopy and ectopic tethering to provide insights into the mechanisms by which centrioles maintain spatial proximity inside human cells.
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Affiliation(s)
- Robert Mahen
- The Medical Research Council Cancer Unit, University of Cambridge, Hills Road, Cambridge, United Kingdom
- Photonics Group, Department of Physics, Imperial College London, London, United Kingdom
- * E-mail:
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5
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Martin-Cofreces NB, Chichon FJ, Calvo E, Torralba D, Bustos-Moran E, Dosil SG, Rojas-Gomez A, Bonzon-Kulichenko E, Lopez JA, Otón J, Sorrentino A, Zabala JC, Vernos I, Vazquez J, Valpuesta JM, Sanchez-Madrid F. The chaperonin CCT controls T cell receptor-driven 3D configuration of centrioles. SCIENCE ADVANCES 2020; 6:eabb7242. [PMID: 33268369 PMCID: PMC7821906 DOI: 10.1126/sciadv.abb7242] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/13/2020] [Accepted: 10/19/2020] [Indexed: 05/17/2023]
Abstract
T lymphocyte activation requires the formation of immune synapses (IS) with antigen-presenting cells. The dynamics of membrane receptors, signaling scaffolds, microfilaments, and microtubules at the IS determine the potency of T cell activation and subsequent immune response. Here, we show that the cytosolic chaperonin CCT (chaperonin-containing TCP1) controls the changes in reciprocal orientation of the centrioles and polarization of the tubulin dynamics induced by T cell receptor in T lymphocytes forming an IS. CCT also controls the mitochondrial ultrastructure and the metabolic status of T cells, regulating the de novo synthesis of tubulin as well as posttranslational modifications (poly-glutamylation, acetylation, Δ1 and Δ2) of αβ-tubulin heterodimers, fine-tuning tubulin dynamics. These changes ultimately determine the function and organization of the centrioles, as shown by three-dimensional reconstruction of resting and stimulated primary T cells using cryo-soft x-ray tomography. Through this mechanism, CCT governs T cell activation and polarity.
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Affiliation(s)
- N B Martin-Cofreces
- Immunology Service, Hospital Universitario de la Princesa, UAM, IIS-IP. Madrid, 28006 Spain.
- Area of Vascular Pathophysiology, Laboratory of Intercellular Communication, Fundación Centro Nacional de Investigaciones Cardiovasculares-Carlos III, Madrid, 28029 Spain
- Centro de Investigación Biomédica en Red de Enfermedades Cardiovasculares (CIBERCV), 28029 Spain
| | - F J Chichon
- Department of Macromolecular Structure, Computational Systems Biology Group, Centro Nacional de Biotecnología (CNB-CSIC), Madrid, 28049, Spain
| | - E Calvo
- Centro de Investigación Biomédica en Red de Enfermedades Cardiovasculares (CIBERCV), 28029 Spain
- Laboratory of Cardiovascular Proteomics. Fundación Centro Nacional de Investigaciones Cardiovasculares-Carlos III, Madrid, 28029 Spain
| | - D Torralba
- Immunology Service, Hospital Universitario de la Princesa, UAM, IIS-IP. Madrid, 28006 Spain
- Area of Vascular Pathophysiology, Laboratory of Intercellular Communication, Fundación Centro Nacional de Investigaciones Cardiovasculares-Carlos III, Madrid, 28029 Spain
| | - E Bustos-Moran
- Immunology Service, Hospital Universitario de la Princesa, UAM, IIS-IP. Madrid, 28006 Spain
- Area of Vascular Pathophysiology, Laboratory of Intercellular Communication, Fundación Centro Nacional de Investigaciones Cardiovasculares-Carlos III, Madrid, 28029 Spain
| | - S G Dosil
- Immunology Service, Hospital Universitario de la Princesa, UAM, IIS-IP. Madrid, 28006 Spain
- Area of Vascular Pathophysiology, Laboratory of Intercellular Communication, Fundación Centro Nacional de Investigaciones Cardiovasculares-Carlos III, Madrid, 28029 Spain
| | - A Rojas-Gomez
- Immunology Service, Hospital Universitario de la Princesa, UAM, IIS-IP. Madrid, 28006 Spain
- Area of Vascular Pathophysiology, Laboratory of Intercellular Communication, Fundación Centro Nacional de Investigaciones Cardiovasculares-Carlos III, Madrid, 28029 Spain
| | - E Bonzon-Kulichenko
- Centro de Investigación Biomédica en Red de Enfermedades Cardiovasculares (CIBERCV), 28029 Spain
- Laboratory of Cardiovascular Proteomics. Fundación Centro Nacional de Investigaciones Cardiovasculares-Carlos III, Madrid, 28029 Spain
| | - J A Lopez
- Laboratory of Cardiovascular Proteomics. Fundación Centro Nacional de Investigaciones Cardiovasculares-Carlos III, Madrid, 28029 Spain
| | - J Otón
- Structural Studies Division, MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK
| | - A Sorrentino
- ALBA Synchrotron Light Source, Cerdanyola del Vallès, Barcelona 08290, Spain
| | - J C Zabala
- Departament of Molecular Biology, Facultad de Medicina, Universidad de Cantabria, Santander, 39005 Spain
| | - I Vernos
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr Aiguader 88, Barcelona, 08003, Spain
- Universitat Pompeu Fabra (UPF), Dr Aiguader 88, Barcelona 08003, Spain
- ICREA, Pg. Lluis Companys 23, Barcelona 08010, Spain
| | - J Vazquez
- Centro de Investigación Biomédica en Red de Enfermedades Cardiovasculares (CIBERCV), 28029 Spain
- Laboratory of Cardiovascular Proteomics. Fundación Centro Nacional de Investigaciones Cardiovasculares-Carlos III, Madrid, 28029 Spain
| | - J M Valpuesta
- Department of Macromolecular Structure, Computational Systems Biology Group, Centro Nacional de Biotecnología (CNB-CSIC), Madrid, 28049, Spain.
| | - F Sanchez-Madrid
- Immunology Service, Hospital Universitario de la Princesa, UAM, IIS-IP. Madrid, 28006 Spain.
- Area of Vascular Pathophysiology, Laboratory of Intercellular Communication, Fundación Centro Nacional de Investigaciones Cardiovasculares-Carlos III, Madrid, 28029 Spain
- Centro de Investigación Biomédica en Red de Enfermedades Cardiovasculares (CIBERCV), 28029 Spain
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Lins MP, Viana IMMN, Smaniotto S, Reis MDDS. Interactions between thymic endothelial cells and thymocytes are influenced by growth hormone. Growth Factors 2020; 38:177-188. [PMID: 34028312 DOI: 10.1080/08977194.2021.1924699] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 09/30/2022]
Abstract
Growth hormone (GH), in addition to its classic actions on growth and metabolism in the body, exerts pleiotropic effects on the immune system, particularly on the thymus. The aim of this study was to evaluate the influence of GH on the interactions between mature thymocytes and the thymic endothelium involved in the migratory process. To this end, fresh thymocytes (C57BL/6 mice) and the thymic endothelial cell line (tEnd.1) were used. In the cell adhesion assay, the GH-treated thymocytes adhered more to tEnd.1 cells. Additionally, there was an improvement in the deposition of fibronectin by tEnd.1 cells when co-cultured with GH-pre-treated thymocytes. Furthermore, GH induced thymocyte F-actin polymerization. In the transendothelial migration assay, a large number of GH-treated thymocytes, mainly the CD4-CD8+ subset, migrated towards the endothelium under the stimulus of insulin-like growth factor 1. In conclusion, we demonstrated the positive actions of GH in thymocyte/thymic endothelium interactions, including transendothelial migration.
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Affiliation(s)
- Marvin Paulo Lins
- Laboratory of Cell Biology, Institute of Biological and Health Sciences, Federal University of Alagoas, Maceió, Brazil
- Brazilian National Institute of Science and Technology on Neuroimmunomodulation (INCT-NIM), Rio de Janeiro, Brazil
| | | | - Salete Smaniotto
- Laboratory of Cell Biology, Institute of Biological and Health Sciences, Federal University of Alagoas, Maceió, Brazil
- Brazilian National Institute of Science and Technology on Neuroimmunomodulation (INCT-NIM), Rio de Janeiro, Brazil
| | - Maria Danielma Dos Santos Reis
- Laboratory of Cell Biology, Institute of Biological and Health Sciences, Federal University of Alagoas, Maceió, Brazil
- Brazilian National Institute of Science and Technology on Neuroimmunomodulation (INCT-NIM), Rio de Janeiro, Brazil
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