1
|
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.
Collapse
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
| |
Collapse
|
2
|
Flores-Martin JB, Bonnet LV, Palandri A, Zamanillo Hermida S, Hallak MH, Galiano MR. The 19S proteasome subunit Rpt5 reversibly associates with cold-stable microtubules in glial cells at low temperatures. FEBS Lett 2022; 596:1165-1177. [PMID: 35114005 DOI: 10.1002/1873-3468.14307] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Accepted: 01/19/2022] [Indexed: 11/12/2022]
Abstract
The ubiquitin-proteasome system (UPS) degrades intracellular proteins through the 26S proteasome. We analyzed how cold stress affects the UPS in glial cells. Together with a reduction in the 20S proteolytic activity and increased levels of polyubiquitinated proteins, exposure of glial cell cultures to cold induces a partial disassembly of the 26S proteasome. In particular, we found that Rpt5, a subunit of the 19S proteasome, relocates to cold-stable microtubules, although no apparent cytoskeletal redistribution was detected for other analyzed subunits of the 19S or 20S complexes. Furthermore, we demonstrate that both the expression of the microtubule-associated protein MAP6 and the post-translational acetylation of α-tubulin modulate the association of Rpt5 with microtubules. This reversible association could be related to functional preservation of the proteolytic complex during cold stress.
Collapse
Affiliation(s)
- Jésica B Flores-Martin
- Facultad de Ciencias Químicas, Departamento de Química Biológica Ranwel Caputto, Centro de Investigaciones en Química Biológica de Córdoba (CIQUIBIC-CONICET), Universidad Nacional de Córdoba, 5000, Córdoba, Argentina
| | - Laura V Bonnet
- Facultad de Ciencias Químicas, Departamento de Química Biológica Ranwel Caputto, Centro de Investigaciones en Química Biológica de Córdoba (CIQUIBIC-CONICET), Universidad Nacional de Córdoba, 5000, Córdoba, Argentina
| | - Anabela Palandri
- Facultad de Ciencias Químicas, Departamento de Química Biológica Ranwel Caputto, Centro de Investigaciones en Química Biológica de Córdoba (CIQUIBIC-CONICET), Universidad Nacional de Córdoba, 5000, Córdoba, Argentina
| | - Sofía Zamanillo Hermida
- Facultad de Ciencias Químicas, Departamento de Química Biológica Ranwel Caputto, Centro de Investigaciones en Química Biológica de Córdoba (CIQUIBIC-CONICET), Universidad Nacional de Córdoba, 5000, Córdoba, Argentina
| | - Marta H Hallak
- Facultad de Ciencias Químicas, Departamento de Química Biológica Ranwel Caputto, Centro de Investigaciones en Química Biológica de Córdoba (CIQUIBIC-CONICET), Universidad Nacional de Córdoba, 5000, Córdoba, Argentina
| | - Mauricio R Galiano
- Facultad de Ciencias Químicas, Departamento de Química Biológica Ranwel Caputto, Centro de Investigaciones en Química Biológica de Córdoba (CIQUIBIC-CONICET), Universidad Nacional de Córdoba, 5000, Córdoba, Argentina
| |
Collapse
|
3
|
Kita AM, Swider ZT, Erofeev I, Halloran MC, Goryachev AB, Bement WM. Spindle-F-actin interactions in mitotic spindles in an intact vertebrate epithelium. Mol Biol Cell 2019; 30:1645-1654. [PMID: 31091161 PMCID: PMC6727749 DOI: 10.1091/mbc.e19-02-0126] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022] Open
Abstract
Mitotic spindles are well known to be assembled from and dependent on microtubules. In contrast, whether actin filaments (F-actin) are required for or are even present in mitotic spindles has long been controversial. Here we have developed improved methods for simultaneously preserving F-actin and microtubules in fixed samples and exploited them to demonstrate that F-actin is indeed associated with mitotic spindles in intact Xenopus laevis embryonic epithelia. We also find that there is an “F-actin cycle,” in which the distribution and organization of spindle F-actin changes over the course of the cell cycle. Live imaging using a probe for F-actin reveals that at least two pools of F-actin are associated with mitotic spindles: a relatively stable internal network of cables that moves in concert with and appears to be linked to spindles, and F-actin “fingers” that rapidly extend from the cell cortex toward the spindle and make transient contact with the spindle poles. We conclude that there is a robust endoplasmic F-actin network in normal vertebrate epithelial cells and that this network is also a component of mitotic spindles. More broadly, we conclude that there is far more internal F-actin in epithelial cells than is commonly believed.
Collapse
Affiliation(s)
- Angela M Kita
- Cellular and Molecular Biology Graduate Program, University of Wisconsin-Madison, Madison, WI 53706.,Laboratory of Cell and Molecular Biology, University of Wisconsin-Madison, Madison, WI 53706
| | - Zachary T Swider
- Cellular and Molecular Biology Graduate Program, University of Wisconsin-Madison, Madison, WI 53706.,Laboratory of Cell and Molecular Biology, University of Wisconsin-Madison, Madison, WI 53706
| | - Ivan Erofeev
- Centre for Synthetic and Systems Biology, University of Edinburgh, Edinburgh EH9 3JD, United Kingdom
| | - Mary C Halloran
- Department of Integrative Biology, University of Wisconsin-Madison, Madison, WI 53706.,Department of Neuroscience, University of Wisconsin-Madison, Madison, WI 53706
| | - Andrew B Goryachev
- Centre for Synthetic and Systems Biology, University of Edinburgh, Edinburgh EH9 3JD, United Kingdom
| | - William M Bement
- Cellular and Molecular Biology Graduate Program, University of Wisconsin-Madison, Madison, WI 53706.,Laboratory of Cell and Molecular Biology, University of Wisconsin-Madison, Madison, WI 53706.,Department of Integrative Biology, University of Wisconsin-Madison, Madison, WI 53706
| |
Collapse
|
4
|
Bonnet F, Molina A, Roussat M, Azais M, Bel-Vialar S, Gautrais J, Pituello F, Agius E. Neurogenic decisions require a cell cycle independent function of the CDC25B phosphatase. eLife 2018; 7:32937. [PMID: 29969095 PMCID: PMC6051746 DOI: 10.7554/elife.32937] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2017] [Accepted: 06/08/2018] [Indexed: 01/06/2023] Open
Abstract
A fundamental issue in developmental biology and in organ homeostasis is understanding the molecular mechanisms governing the balance between stem cell maintenance and differentiation into a specific lineage. Accumulating data suggest that cell cycle dynamics play a major role in the regulation of this balance. Here we show that the G2/M cell cycle regulator CDC25B phosphatase is required in mammals to finely tune neuronal production in the neural tube. We show that in chick neural progenitors, CDC25B activity favors fast nuclei departure from the apical surface in early G1, stimulates neurogenic divisions and promotes neuronal differentiation. We design a mathematical model showing that within a limited period of time, cell cycle length modifications cannot account for changes in the ratio of the mode of division. Using a CDC25B point mutation that cannot interact with CDK, we show that part of CDC25B activity is independent of its action on the cell cycle.
Collapse
Affiliation(s)
- Frédéric Bonnet
- Centre de Biologie du Développement, Centre de Biologie Intégrative, Université de Toulouse, CNRS, UPS, Toulouse, France
| | - Angie Molina
- Centre de Biologie du Développement, Centre de Biologie Intégrative, Université de Toulouse, CNRS, UPS, Toulouse, France
| | - Mélanie Roussat
- Centre de Biologie du Développement, Centre de Biologie Intégrative, Université de Toulouse, CNRS, UPS, Toulouse, France
| | - Manon Azais
- Centre de Recherches sur la Cognition Animale, Centre de Biologie Intégrative., Université de Toulouse, CNRS, UPS, Toulouse, France
| | - Sophie Bel-Vialar
- Centre de Biologie du Développement, Centre de Biologie Intégrative, Université de Toulouse, CNRS, UPS, Toulouse, France
| | - Jacques Gautrais
- Centre de Recherches sur la Cognition Animale, Centre de Biologie Intégrative., Université de Toulouse, CNRS, UPS, Toulouse, France
| | - Fabienne Pituello
- Centre de Biologie du Développement, Centre de Biologie Intégrative, Université de Toulouse, CNRS, UPS, Toulouse, France
| | - Eric Agius
- Centre de Biologie du Développement, Centre de Biologie Intégrative, Université de Toulouse, CNRS, UPS, Toulouse, France
| |
Collapse
|
5
|
Kiss KP, Varga G, Mikala G, Balassa K, Bors A, Kovy P, Meggyesi N, Kozma A, Csacsovszki O, Remenyi P, Valyi-Nagy I, Tordai A, Masszi T, Andrikovics H. The adverse effect of FOPNL genomic variant is reversed by bortezomib-based treatment protocols in multiple myeloma. Leuk Lymphoma 2017; 59:710-716. [PMID: 28691553 DOI: 10.1080/10428194.2017.1346250] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
Fibroblast growth factor receptor 1 oncogene partner N-terminal like gene (FOPNL) rs72773978 polymorphism was identified as an adverse prognostic factor in multiple myeloma (MM). We aimed to investigate the associations of rs72773978 with clinical characteristics and treatment outcome in 373 Hungarian MM patients. In our cohort, FOPNL polymorphism showed differential prognostic effect that depended on the treatment applied. Among patients treated with non-proteasome inhibitor (PI)-based therapy, carriership of the minor allele was significantly associated with adverse overall survival (p=.022). In contrast, the adverse effect was overcome by the application of PI-containing treatment (p=.048). Multivariate analyses revealed the independent adverse effect of rs72773978 on survival in the non-PI-treated group (p=.045), but not in PI treatment (OS: p=.093). We confirmed the adverse prognostic effect of rs72773978 associated with non-PI-based treatment regimens. Our results point to the importance of genotypic prognostic information associated with complex clinical background MM.
Collapse
Affiliation(s)
- Katalin Piroska Kiss
- a Laboratory of Molecular Diagnostics , Hungarian National Blood Transfusion Service , Budapest , Hungary
| | - Gergely Varga
- b 3rd Department of Internal Medicine , Semmelweis University , Budapest , Hungary
| | - Gabor Mikala
- c Department of Haematology and Stem Cell Transplantation , St. Istvan and St. Laszlo Hospital , Budapest , Hungary
| | - Katalin Balassa
- a Laboratory of Molecular Diagnostics , Hungarian National Blood Transfusion Service , Budapest , Hungary
| | - Andras Bors
- a Laboratory of Molecular Diagnostics , Hungarian National Blood Transfusion Service , Budapest , Hungary
| | - Petra Kovy
- a Laboratory of Molecular Diagnostics , Hungarian National Blood Transfusion Service , Budapest , Hungary
| | - Nora Meggyesi
- a Laboratory of Molecular Diagnostics , Hungarian National Blood Transfusion Service , Budapest , Hungary
| | - Andras Kozma
- c Department of Haematology and Stem Cell Transplantation , St. Istvan and St. Laszlo Hospital , Budapest , Hungary
| | - Otto Csacsovszki
- c Department of Haematology and Stem Cell Transplantation , St. Istvan and St. Laszlo Hospital , Budapest , Hungary
| | - Peter Remenyi
- c Department of Haematology and Stem Cell Transplantation , St. Istvan and St. Laszlo Hospital , Budapest , Hungary
| | - Istvan Valyi-Nagy
- c Department of Haematology and Stem Cell Transplantation , St. Istvan and St. Laszlo Hospital , Budapest , Hungary
| | - Attila Tordai
- d Department of Pathophysiology , Semmelweis University , Budapest , Hungary
| | - Tamas Masszi
- b 3rd Department of Internal Medicine , Semmelweis University , Budapest , Hungary.,c Department of Haematology and Stem Cell Transplantation , St. Istvan and St. Laszlo Hospital , Budapest , Hungary
| | - Hajnalka Andrikovics
- a Laboratory of Molecular Diagnostics , Hungarian National Blood Transfusion Service , Budapest , Hungary
| |
Collapse
|
6
|
Vora SM, Phillips BT. The benefits of local depletion: The centrosome as a scaffold for ubiquitin-proteasome-mediated degradation. Cell Cycle 2016; 15:2124-2134. [PMID: 27294844 DOI: 10.1080/15384101.2016.1196306] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022] Open
Abstract
The centrosome is the major microtubule-organizing center in animal cells but is dispensable for proper microtubule spindle formation in many biological contexts and is thus thought to fulfill additional functions. Recent observations suggest that the centrosome acts as a scaffold for proteasomal degradation in the cell to regulate a variety of biological processes including cell fate acquisition, cell cycle control, stress response, and cell morphogenesis. Here, we review the body of studies indicating a role for the centrosome in promoting proteasomal degradation of ubiquitin-proteasome substrates and explore the functional relevance of this system in different biological contexts. We discuss a potential role for the centrosome in coordinating local degradation of proteasomal substrates, allowing cells to achieve stringent spatiotemporal control over various signaling processes.
Collapse
Affiliation(s)
- Setu M Vora
- a Department of Biological Sciences, University of Iowa , Iowa City , IA , USA
| | - Bryan T Phillips
- a Department of Biological Sciences, University of Iowa , Iowa City , IA , USA
| |
Collapse
|