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Manohar S, Estrada ME, Uliana F, Vuina K, Alvarez PM, de Bruin RAM, Neurohr GE. Genome homeostasis defects drive enlarged cells into senescence. Mol Cell 2023; 83:4032-4046.e6. [PMID: 37977116 PMCID: PMC10659931 DOI: 10.1016/j.molcel.2023.10.018] [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: 09/12/2022] [Revised: 06/30/2023] [Accepted: 10/16/2023] [Indexed: 11/19/2023]
Abstract
Cellular senescence refers to an irreversible state of cell-cycle arrest and plays important roles in aging and cancer biology. Because senescence is associated with increased cell size, we used reversible cell-cycle arrests combined with growth rate modulation to study how excessive growth affects proliferation. We find that enlarged cells upregulate p21, which limits cell-cycle progression. Cells that re-enter the cell cycle encounter replication stress that is well tolerated in physiologically sized cells but causes severe DNA damage in enlarged cells, ultimately resulting in mitotic failure and permanent cell-cycle withdrawal. We demonstrate that enlarged cells fail to recruit 53BP1 and other non-homologous end joining (NHEJ) machinery to DNA damage sites and fail to robustly initiate DNA damage-dependent p53 signaling, rendering them highly sensitive to genotoxic stress. We propose that an impaired DNA damage response primes enlarged cells for persistent replication-acquired damage, ultimately leading to cell division failure and permanent cell-cycle exit.
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Affiliation(s)
- Sandhya Manohar
- Institute for Biochemistry, Department of Biology, ETH Zürich 8093, Zürich, Zürich, Switzerland
| | - Marianna E Estrada
- Institute for Biochemistry, Department of Biology, ETH Zürich 8093, Zürich, Zürich, Switzerland
| | - Federico Uliana
- Institute for Biochemistry, Department of Biology, ETH Zürich 8093, Zürich, Zürich, Switzerland
| | - Karla Vuina
- Laboratory for Molecular Cell Biology, University College London, London WC1E 6BT, UK
| | - Patricia Moyano Alvarez
- Institute for Biochemistry, Department of Biology, ETH Zürich 8093, Zürich, Zürich, Switzerland
| | - Robertus A M de Bruin
- Laboratory for Molecular Cell Biology, University College London, London WC1E 6BT, UK; UCL Cancer Institute, University College London, London WC1E 6BT, UK
| | - Gabriel E Neurohr
- Institute for Biochemistry, Department of Biology, ETH Zürich 8093, Zürich, Zürich, Switzerland.
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Scalia P, Williams SJ, Fujita-Yamaguchi Y, Giordano A. Cell cycle control by the insulin-like growth factor signal: at the crossroad between cell growth and mitotic regulation. Cell Cycle 2023; 22:1-37. [PMID: 36005738 PMCID: PMC9769454 DOI: 10.1080/15384101.2022.2108117] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
In proliferating cells and tissues a number of checkpoints (G1/S and G2/M) preceding cell division (M-phase) require the signal provided by growth factors present in serum. IGFs (I and II) have been demonstrated to constitute key intrinsic components of the peptidic active fraction of mammalian serum. In vivo genetic ablation studies have shown that the cellular signal triggered by the IGFs through their cellular receptors represents a non-replaceable requirement for cell growth and cell cycle progression. Retroactive and current evaluation of published literature sheds light on the intracellular circuitry activated by these factors providing us with a better picture of the pleiotropic mechanistic actions by which IGFs regulate both cell size and mitogenesis under developmental growth as well as in malignant proliferation. The present work aims to summarize the cumulative knowledge learned from the IGF ligands/receptors and their intracellular signaling transducers towards control of cell size and cell-cycle with particular focus to their actionable circuits in human cancer. Furthermore, we bring novel perspectives on key functional discriminants of the IGF growth-mitogenic pathway allowing re-evaluation on some of its signal components based upon established evidences.
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Affiliation(s)
- Pierluigi Scalia
- ISOPROG-Somatolink EPFP Research Network, Philadelphia, PA, USA, Caltanissetta, Italy,CST, Biology, Sbarro Institute for Cancer Research and Molecular Medicine, Temple University, Philadelphia, PA, United states,CONTACT Pierluigi Scalia ISOPROG-Somatolink EPFP Research Network, Philadelphia, PA9102, USA
| | - Stephen J Williams
- ISOPROG-Somatolink EPFP Research Network, Philadelphia, PA, USA, Caltanissetta, Italy,CST, Biology, Sbarro Institute for Cancer Research and Molecular Medicine, Temple University, Philadelphia, PA, United states
| | - Yoko Fujita-Yamaguchi
- Arthur Riggs Diabetes & Metabolism Research Institute, Beckman Research Institute of City of Hope, Duarte, CA, USA
| | - Antonio Giordano
- ISOPROG-Somatolink EPFP Research Network, Philadelphia, PA, USA, Caltanissetta, Italy,School of Medical Biotechnology, University of Siena, Italy
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Gorgisen G, Aydin M, Mboma O, Gökyildirim MY, Chao CM. The Role of Insulin Receptor Substrate Proteins in Bronchopulmonary Dysplasia and Asthma: New Potential Perspectives. Int J Mol Sci 2022; 23:ijms231710113. [PMID: 36077511 PMCID: PMC9456457 DOI: 10.3390/ijms231710113] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2022] [Revised: 08/30/2022] [Accepted: 09/01/2022] [Indexed: 01/12/2023] Open
Abstract
Insulin receptor substrates (IRSs) are proteins that are involved in signaling through the insulin receptor (IR) and insulin-like growth factor (IGFR). They can also interact with other receptors including growth factor receptors. Thus, they represent a critical node for the transduction and regulation of multiple signaling pathways in response to extracellular stimuli. In addition, IRSs play a central role in processes such as inflammation, growth, metabolism, and proliferation. Previous studies have highlighted the role of IRS proteins in lung diseases, in particular asthma. Further, the members of the IRS family are the common proteins of the insulin growth factor signaling cascade involved in lung development and disrupted in bronchopulmonary dysplasia (BPD). However, there is no study focusing on the relationship between IRS proteins and BPD yet. Unfortunately, there is still a significant gap in knowledge in this field. Thus, in this review, we aimed to summarize the current knowledge with the major goal of exploring the possible roles of IRS in BPD and asthma to foster new perspectives for further investigations.
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Affiliation(s)
- Gokhan Gorgisen
- Department of Medical Genetics, Faculty of Medicine, Van Yüzüncü Yil University, Van 65080, Turkey
| | - Malik Aydin
- Laboratory of Experimental Pediatric Pneumology and Allergology, Center for Biomedical Education and Research, School of Life Sciences (ZBAF), Faculty of Health, Witten/Herdecke University, 58455 Witten, Germany
- Center for Child and Adolescent Medicine, Center for Clinical and Translational Research (CCTR), Helios University Hospital Wuppertal, Witten/Herdecke University, 42283 Wuppertal, Germany
| | - Olivier Mboma
- Laboratory of Experimental Pediatric Pneumology and Allergology, Center for Biomedical Education and Research, School of Life Sciences (ZBAF), Faculty of Health, Witten/Herdecke University, 58455 Witten, Germany
- Center for Child and Adolescent Medicine, Center for Clinical and Translational Research (CCTR), Helios University Hospital Wuppertal, Witten/Herdecke University, 42283 Wuppertal, Germany
| | - Mira Y. Gökyildirim
- Department of Pediatrics, University Medical Center Rostock, University of Rostock, 18057 Rostock, Germany
| | - Cho-Ming Chao
- Department of Pediatrics, University Medical Center Rostock, University of Rostock, 18057 Rostock, Germany
- Cardio-Pulmonary Institute (CPI), Universities of Giessen and Marburg Lung Center (UGMLC), Member of the German Center for Lung Research (DZL), Justus Liebig University Giessen, 35390 Giessen, Germany
- Correspondence: ; Tel.: +49-641-9946735
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Kelly V, Al-Rawi A, Lewis D, Kustatscher G, Ly T. Low Cell Number Proteomic Analysis Using In-Cell Protease Digests Reveals a Robust Signature for Cell Cycle State Classification. Mol Cell Proteomics 2022; 21:100169. [PMID: 34742921 PMCID: PMC8760417 DOI: 10.1016/j.mcpro.2021.100169] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2021] [Revised: 09/02/2021] [Accepted: 10/25/2021] [Indexed: 12/04/2022] Open
Abstract
Comprehensive proteome analysis of rare cell phenotypes remains a significant challenge. We report a method for low cell number MS-based proteomics using protease digestion of mildly formaldehyde-fixed cells in cellulo, which we call the "in-cell digest." We combined this with averaged MS1 precursor library matching to quantitatively characterize proteomes from low cell numbers of human lymphoblasts. About 4500 proteins were detected from 2000 cells, and 2500 proteins were quantitated from 200 lymphoblasts. The ease of sample processing and high sensitivity makes this method exceptionally suited for the proteomic analysis of rare cell states, including immune cell subsets and cell cycle subphases. To demonstrate the method, we characterized the proteome changes across 16 cell cycle states (CCSs) isolated from an asynchronous TK6 cells, avoiding synchronization. States included late mitotic cells present at extremely low frequency. We identified 119 pseudoperiodic proteins that vary across the cell cycle. Clustering of the pseudoperiodic proteins showed abundance patterns consistent with "waves" of protein degradation in late S, at the G2&M border, midmitosis, and at mitotic exit. These clusters were distinguished by significant differences in predicted nuclear localization and interaction with the anaphase-promoting complex/cyclosome. The dataset also identifies putative anaphase-promoting complex/cyclosome substrates in mitosis and the temporal order in which they are targeted for degradation. We demonstrate that a protein signature made of these 119 high-confidence cell cycle-regulated proteins can be used to perform unbiased classification of proteomes into CCSs. We applied this signature to 296 proteomes that encompass a range of quantitation methods, cell types, and experimental conditions. The analysis confidently assigns a CCS for 49 proteomes, including correct classification for proteomes from synchronized cells. We anticipate that this robust cell cycle protein signature will be crucial for classifying cell states in single-cell proteomes.
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Affiliation(s)
- Van Kelly
- Wellcome Centre for Cell Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, UK; Institute of Quantitative Biology, Biochemistry and Biotechnology, University of Edinburgh, Edinburgh, UK
| | - Aymen Al-Rawi
- Wellcome Centre for Cell Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, UK
| | - David Lewis
- Wellcome Centre for Cell Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, UK
| | - Georg Kustatscher
- Institute of Quantitative Biology, Biochemistry and Biotechnology, University of Edinburgh, Edinburgh, UK
| | - Tony Ly
- Wellcome Centre for Cell Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, UK; Centre for Gene Regulation and Expression, School of Life Sciences, University of Dundee, Dundee, UK.
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