1
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Chadha Y, Khurana A, Schmoller KM. Eukaryotic cell size regulation and its implications for cellular function and dysfunction. Physiol Rev 2024; 104:1679-1717. [PMID: 38900644 DOI: 10.1152/physrev.00046.2023] [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: 12/26/2023] [Revised: 05/24/2024] [Accepted: 06/19/2024] [Indexed: 06/22/2024] Open
Abstract
Depending on cell type, environmental inputs, and disease, the cells in the human body can have widely different sizes. In recent years, it has become clear that cell size is a major regulator of cell function. However, we are only beginning to understand how the optimization of cell function determines a given cell's optimal size. Here, we review currently known size control strategies of eukaryotic cells and the intricate link of cell size to intracellular biomolecular scaling, organelle homeostasis, and cell cycle progression. We detail the cell size-dependent regulation of early development and the impact of cell size on cell differentiation. Given the importance of cell size for normal cellular physiology, cell size control must account for changing environmental conditions. We describe how cells sense environmental stimuli, such as nutrient availability, and accordingly adapt their size by regulating cell growth and cell cycle progression. Moreover, we discuss the correlation of pathological states with misregulation of cell size and how for a long time this was considered a downstream consequence of cellular dysfunction. We review newer studies that reveal a reversed causality, with misregulated cell size leading to pathophysiological phenotypes such as senescence and aging. In summary, we highlight the important roles of cell size in cellular function and dysfunction, which could have major implications for both diagnostics and treatment in the clinic.
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Affiliation(s)
- Yagya Chadha
- Institute of Functional Epigenetics, Molecular Targets and Therapeutics Center, Helmholtz Zentrum München, Neuherberg, Germany
| | - Arohi Khurana
- Institute of Functional Epigenetics, Molecular Targets and Therapeutics Center, Helmholtz Zentrum München, Neuherberg, Germany
| | - Kurt M Schmoller
- Institute of Functional Epigenetics, Molecular Targets and Therapeutics Center, Helmholtz Zentrum München, Neuherberg, Germany
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2
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Vidal PJ, Pérez AP, Yahya G, Aldea M. Transcriptomic balance and optimal growth are determined by cell size. Mol Cell 2024; 84:3288-3301.e3. [PMID: 39084218 DOI: 10.1016/j.molcel.2024.07.005] [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: 03/04/2024] [Revised: 06/11/2024] [Accepted: 07/08/2024] [Indexed: 08/02/2024]
Abstract
Cell size and growth are intimately related across the evolutionary scale, but whether cell size is important to attain maximal growth or fitness is still an open question. We show that growth rate is a non-monotonic function of cell volume, with maximal values around the critical size of wild-type yeast cells. The transcriptome of yeast and mouse cells undergoes a relative inversion in response to cell size, which we associate theoretically and experimentally with the necessary genome-wide diversity in RNA polymerase II affinity for promoters. Although highly expressed genes impose strong negative effects on fitness when the DNA/mass ratio is reduced, transcriptomic alterations mimicking the relative inversion by cell size strongly restrain cell growth. In all, our data indicate that cells set the critical size to obtain a properly balanced transcriptome and, as a result, maximize growth and fitness during proliferation.
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Affiliation(s)
- Pedro J Vidal
- Molecular Biology Institute of Barcelona (IBMB), CSIC, 08028 Barcelona, Catalonia, Spain
| | - Alexis P Pérez
- Molecular Biology Institute of Barcelona (IBMB), CSIC, 08028 Barcelona, Catalonia, Spain; Department of Basic Sciences, Universitat Internacional de Catalunya, 08195 Sant Cugat del Vallès, Barcelona, Spain
| | - Galal Yahya
- Molecular Biology Institute of Barcelona (IBMB), CSIC, 08028 Barcelona, Catalonia, Spain; Department of Microbiology and Immunology, School of Pharmacy, Zagazig University, 44511 Zagazig, Egypt.
| | - Martí Aldea
- Molecular Biology Institute of Barcelona (IBMB), CSIC, 08028 Barcelona, Catalonia, Spain; Department of Basic Sciences, Universitat Internacional de Catalunya, 08195 Sant Cugat del Vallès, Barcelona, Spain.
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3
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Yu JB, Padanilam BJ, Kim J. Activation of Yes-Associated Protein Is Indispensable for Transformation of Kidney Fibroblasts into Myofibroblasts during Repeated Administration of Cisplatin. Cells 2024; 13:1475. [PMID: 39273045 PMCID: PMC11393901 DOI: 10.3390/cells13171475] [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: 05/23/2024] [Revised: 08/22/2024] [Accepted: 08/30/2024] [Indexed: 09/15/2024] Open
Abstract
Cisplatin is a potent chemotherapy medication that is used to treat various types of cancer. However, it can cause nephrotoxic side effects, which lead to acute kidney injury (AKI) and subsequent chronic kidney disease (CKD). Although a clinically relevant in vitro model of CKD induced by repeated administration of low-dose cisplatin (RAC) has been established, its underlying mechanisms remain poorly understood. Here, we compared single administration of high-dose cisplatin (SAC) to repeated administration of low-dose cisplatin (RAC) in myofibroblast transformation and cellular morphology in a normal rat kidney fibroblast NRK-49F cell line. RAC instead of SAC transformed the fibroblasts into myofibroblasts as determined by α-smooth muscle actin, enlarged cell size as represented by F-actin staining, and increased cell flattening as expressed by the semidiameter ratio of attached cells to floated cells. Those phenomena, as well as cellular senescence, were significantly detected from the time right before the second administration of cisplatin. Interestingly, inhibition of the interaction between Yes-associated protein (YAP) and the transcriptional enhanced associated domain (TEAD) using Verteporfin remarkedly reduced cell size, cellular senescence, and myofibroblast transformation during RAC. These findings collectively suggest that YAP activation is indispensable for cellular hypertrophy, senescence, and myofibroblast transformation during RAC in kidney fibroblasts.
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Affiliation(s)
- Jia-Bin Yu
- Interdisciplinary Graduate Program in Advanced Convergence Technology & Science, Jeju National University, Jeju 63243, Republic of Korea
| | - Babu J Padanilam
- Department of Urology, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Jinu Kim
- Interdisciplinary Graduate Program in Advanced Convergence Technology & Science, Jeju National University, Jeju 63243, Republic of Korea
- Department of Anatomy, College of Medicine, Jeju National University, Jeju 63243, Republic of Korea
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4
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Huang YT, Hesting LL, Calvi BR. An unscheduled switch to endocycles induces a reversible senescent arrest that impairs growth of the Drosophila wing disc. PLoS Genet 2024; 20:e1011387. [PMID: 39226333 PMCID: PMC11398662 DOI: 10.1371/journal.pgen.1011387] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2024] [Revised: 09/13/2024] [Accepted: 08/06/2024] [Indexed: 09/05/2024] Open
Abstract
A programmed developmental switch to G / S endocycles results in tissue growth through an increase in cell size. Unscheduled, induced endocycling cells (iECs) promote wound healing but also contribute to cancer. Much remains unknown, however, about how these iECs affect tissue growth. Using the D. melanogaster wing disc as model, we find that populations of iECs initially increase in size but then subsequently undergo a heterogenous arrest that causes severe tissue undergrowth. iECs acquired DNA damage and activated a Jun N-terminal kinase (JNK) pathway, but, unlike other stressed cells, were apoptosis-resistant and not eliminated from the epithelium. Instead, iECs entered a JNK-dependent and reversible senescent-like arrest. Senescent iECs promoted division of diploid neighbors, but this compensatory proliferation did not rescue tissue growth. Our study has uncovered unique attributes of iECs and their effects on tissue growth that have important implications for understanding their roles in wound healing and cancer.
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Affiliation(s)
- Yi-Ting Huang
- Department of Biology, Simon Cancer Center, Indiana University, Bloomington, Indiana, United States of America
| | - Lauren L Hesting
- Department of Biology, Simon Cancer Center, Indiana University, Bloomington, Indiana, United States of America
| | - Brian R Calvi
- Department of Biology, Simon Cancer Center, Indiana University, Bloomington, Indiana, United States of America
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5
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Lanz MC, Zhang S, Swaffer MP, Ziv I, Götz LH, Kim J, McCarthy F, Jarosz DF, Elias JE, Skotheim JM. Genome dilution by cell growth drives starvation-like proteome remodeling in mammalian and yeast cells. Nat Struct Mol Biol 2024:10.1038/s41594-024-01353-z. [PMID: 39048803 DOI: 10.1038/s41594-024-01353-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2023] [Accepted: 06/12/2024] [Indexed: 07/27/2024]
Abstract
Cell size is tightly controlled in healthy tissues and single-celled organisms, but it remains unclear how cell size influences physiology. Increasing cell size was recently shown to remodel the proteomes of cultured human cells, demonstrating that large and small cells of the same type can be compositionally different. In the present study, we utilize the natural heterogeneity of hepatocyte ploidy and yeast genetics to establish that the ploidy-to-cell size ratio is a highly conserved determinant of proteome composition. In both mammalian and yeast cells, genome dilution by cell growth elicits a starvation-like phenotype, suggesting that growth in large cells is restricted by genome concentration in a manner that mimics a limiting nutrient. Moreover, genome dilution explains some proteomic changes ascribed to yeast aging. Overall, our data indicate that genome concentration drives changes in cell composition independently of external environmental cues.
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Affiliation(s)
- Michael C Lanz
- Department of Biology, Stanford University, Stanford, CA, USA.
- Chan Zuckerberg Biohub San Francisco, Stanford University, Stanford, CA, USA.
| | - Shuyuan Zhang
- Department of Biology, Stanford University, Stanford, CA, USA
| | | | - Inbal Ziv
- Department of Chemical and Systems Biology, Stanford University, Stanford, CA, USA
| | | | - Jacob Kim
- Department of Biology, Stanford University, Stanford, CA, USA
- Department of Chemical and Systems Biology, Stanford University, Stanford, CA, USA
| | - Frank McCarthy
- Chan Zuckerberg Biohub San Francisco, Stanford University, Stanford, CA, USA
| | - Daniel F Jarosz
- Department of Chemical and Systems Biology, Stanford University, Stanford, CA, USA
- Department of Developmental Biology, Stanford University, Stanford, CA, USA
| | - Joshua E Elias
- Chan Zuckerberg Biohub San Francisco, Stanford University, Stanford, CA, USA
| | - Jan M Skotheim
- Department of Biology, Stanford University, Stanford, CA, USA.
- Chan Zuckerberg Biohub San Francisco, Stanford University, Stanford, CA, USA.
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6
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McLellan JL, Hanson KK. Differential effects of translation inhibitors on Plasmodium berghei liver stage parasites. Life Sci Alliance 2024; 7:e202302540. [PMID: 38575357 PMCID: PMC10994859 DOI: 10.26508/lsa.202302540] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2023] [Revised: 03/19/2024] [Accepted: 03/19/2024] [Indexed: 04/06/2024] Open
Abstract
Increasing numbers of antimalarial compounds are being identified that converge mechanistically at inhibition of cytoplasmic translation, regardless of the molecular target or mechanism. A deeper understanding of how their effectiveness as liver stage translation inhibitors relates to their chemoprotective potential could prove useful. Here, we probed that relationship using the Plasmodium berghei-HepG2 liver stage infection model. After determining translation inhibition EC50s for five compounds, we tested them at equivalent effective concentrations to compare the parasite response to, and recovery from, a brief period of translation inhibition in early schizogony, followed by parasites to 120 h post-infection to assess antiplasmodial effects of the treatment. We show compound-specific heterogeneity in single parasite and population responses to translation inhibitor treatment, with no single metric strongly correlated to the release of hepatic merozoites for all compounds. We also demonstrate that DDD107498 is capable of exerting antiplasmodial effects on translationally arrested liver stage parasites and uncover unexpected growth dynamics during the liver stage. Our results demonstrate that translation inhibition efficacy does not determine antiplasmodial efficacy for these compounds.
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Affiliation(s)
- James L McLellan
- https://ror.org/01kd65564 Department of Molecular Microbiology and Immunology and STCEID, University of Texas at San Antonio, San Antonio, TX, USA
| | - Kirsten K Hanson
- https://ror.org/01kd65564 Department of Molecular Microbiology and Immunology and STCEID, University of Texas at San Antonio, San Antonio, TX, USA
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7
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Manohar S, Neurohr GE. Too big not to fail: emerging evidence for size-induced senescence. FEBS J 2024; 291:2291-2305. [PMID: 37986656 DOI: 10.1111/febs.16983] [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: 07/18/2023] [Revised: 10/02/2023] [Accepted: 10/17/2023] [Indexed: 11/22/2023]
Abstract
Cellular senescence refers to a permanent and stable state of cell cycle exit. This process plays an important role in many cellular functions, including tumor suppression. It was first noted that senescence is associated with increased cell size in the early 1960s; however, how this contributes to permanent cell cycle exit was poorly understood until recently. In this review, we discuss new findings that identify increased cell size as not only a consequence but also a cause of permanent cell cycle exit. We highlight recent insights into how increased cell size alters normal cellular physiology and creates homeostatic imbalances that contribute to senescence induction. Finally, we focus on the potential clinical implications of these findings in the context of cell cycle arrest-causing cancer therapeutics and speculate on how tumor cell size changes may impact outcomes in patients treated with these drugs.
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Affiliation(s)
- Sandhya Manohar
- Department of Biology, Institute for Biochemistry, ETH Zürich, Switzerland
| | - Gabriel E Neurohr
- Department of Biology, Institute for Biochemistry, ETH Zürich, Switzerland
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8
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Meng Y, Zhang J, Liu Y, Zhu Y, Lv H, Xia F, Guo Q, Shi Q, Qiu C, Wang J. The biomedical application of inorganic metal nanoparticles in aging and aging-associated diseases. J Adv Res 2024:S2090-1232(24)00213-3. [PMID: 38821357 DOI: 10.1016/j.jare.2024.05.023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Revised: 05/10/2024] [Accepted: 05/22/2024] [Indexed: 06/02/2024] Open
Abstract
Aging and aging-associated diseases (AAD), including neurodegenerative disease, cancer, cardiovascular diseases, and diabetes, are inevitable process. With the gradual improvement of life style, life expectancy is gradually extended. However, the extended lifespan has not reduced the incidence of disease, and most elderly people are in ill-health state in their later years. Hence, understanding aging and AAD are significant for reducing the burden of the elderly. Inorganic metal nanoparticles (IMNPs) predominantly include gold, silver, iron, zinc, titanium, thallium, platinum, cerium, copper NPs, which has been widely used to prevent and treat aging and AAD due to their superior properties (essential metal ions for human body, easily synthesis and modification, magnetism). Therefore, a systematic review of common morphological alternations of senescent cells, altered genes and signal pathways in aging and AAD, and biomedical applications of IMNPs in aging and AAD is crucial for the further research and development of IMNPs in aging and AAD. This review focus on the existing research on cellular senescence, aging and AAD, as well as the applications of IMNPs in aging and AAD in the past decade. This review aims to provide cutting-edge knowledge involved with aging and AAD, the application of IMNPs in aging and AAD to promote the biomedical application of IMNPs in aging and AAD.
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Affiliation(s)
- Yuqing Meng
- State Key Laboratory for Quality Ensurance and Sustainable Use of Dao-di Herbs, Artemisinin Research Center, and Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China
| | - Junzhe Zhang
- State Key Laboratory for Quality Ensurance and Sustainable Use of Dao-di Herbs, Artemisinin Research Center, and Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China
| | - Yanqing Liu
- State Key Laboratory for Quality Ensurance and Sustainable Use of Dao-di Herbs, Artemisinin Research Center, and Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China
| | - Yongping Zhu
- State Key Laboratory for Quality Ensurance and Sustainable Use of Dao-di Herbs, Artemisinin Research Center, and Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China
| | - Haining Lv
- State Key Laboratory for Quality Ensurance and Sustainable Use of Dao-di Herbs, Artemisinin Research Center, and Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China
| | - Fei Xia
- State Key Laboratory for Quality Ensurance and Sustainable Use of Dao-di Herbs, Artemisinin Research Center, and Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China
| | - Qiuyan Guo
- State Key Laboratory for Quality Ensurance and Sustainable Use of Dao-di Herbs, Artemisinin Research Center, and Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China
| | - Qianli Shi
- State Key Laboratory for Quality Ensurance and Sustainable Use of Dao-di Herbs, Artemisinin Research Center, and Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China
| | - Chong Qiu
- State Key Laboratory for Quality Ensurance and Sustainable Use of Dao-di Herbs, Artemisinin Research Center, and Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China.
| | - Jigang Wang
- Department of Urology, Shenzhen Clinical Research Centre for Geriatrics, Shenzhen People's Hospital; The First Affiliated Hospital, Southern University of Science and Technology, Shenzhen 518020, Guangdong, China; State Key Laboratory of Antiviral Drugs, School of Pharmacy, Henan University, Kaifeng 475004, China.
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9
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Xie S, Zhang S, de Medeiros G, Liberali P, Skotheim JM. The G1/S transition in mammalian stem cells in vivo is autonomously regulated by cell size. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.09.588781. [PMID: 38645246 PMCID: PMC11030448 DOI: 10.1101/2024.04.09.588781] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/23/2024]
Abstract
Cell growth and division must be coordinated to maintain a stable cell size, but how this coordination is implemented in multicellular tissues remains unclear. In unicellular eukaryotes, autonomous cell size control mechanisms couple cell growth and division with little extracellular input. However, in multicellular tissues we do not know if autonomous cell size control mechanisms operate the same way or whether cell growth and cell cycle progression are separately controlled by cell-extrinsic signals. Here, we address this question by tracking single epidermal stem cells growing in adult mice. We find that a cell-autonomous size control mechanism, dependent on the RB pathway, sets the timing of S phase entry based on the cell's current size. Cell-extrinsic variations in the cellular microenvironment affect cell growth rates but not this autonomous coupling. Our work reassesses long-standing models of cell cycle regulation within complex metazoan tissues and identifies cell-autonomous size control as a critical mechanism regulating cell divisions in vivo and thereby a major contributor to stem cell heterogeneity.
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10
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Carpenter LC, Pérez-Verdugo F, Banerjee S. Mechanical control of cell proliferation patterns in growing epithelial monolayers. Biophys J 2024; 123:909-919. [PMID: 38449309 PMCID: PMC10995431 DOI: 10.1016/j.bpj.2024.03.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2023] [Revised: 01/13/2024] [Accepted: 03/01/2024] [Indexed: 03/08/2024] Open
Abstract
Cell proliferation plays a crucial role in regulating tissue homeostasis and development. However, our understanding of how cell proliferation is controlled in densely packed tissues is limited. Here we develop a computational framework to predict the patterns of cell proliferation in growing epithelial tissues, connecting single-cell behaviors and cell-cell interactions to tissue-level growth. Our model incorporates probabilistic rules governing cell growth, division, and elimination, also taking into account their feedback with tissue mechanics. In particular, cell growth is suppressed and apoptosis is enhanced in regions of high cell density. With these rules and model parameters calibrated using experimental data for epithelial monolayers, we predict how tissue confinement influences cell size and proliferation dynamics and how single-cell physical properties influence the spatiotemporal patterns of tissue growth. In this model, mechanical feedback between tissue confinement and cell growth leads to enhanced cell proliferation at tissue boundaries, whereas cell growth in the bulk is arrested, recapitulating experimental observations in epithelial tissues. By tuning cellular elasticity and contact inhibition of proliferation we can regulate the emergent patterns of cell proliferation, ranging from uniform growth at low contact inhibition to localized growth at higher contact inhibition. We show that the cell size threshold at G1/S transition governs the homeostatic cell density and tissue turnover rate, whereas the mechanical state of the tissue governs the dynamics of tissue growth. In particular, we find that the cellular parameters affecting tissue pressure play a significant role in determining the overall growth rate. Our computational study thus underscores the impact of cell mechanical properties on the spatiotemporal patterns of cell proliferation in growing epithelial tissues.
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Affiliation(s)
- Logan C Carpenter
- Department of Physics, Carnegie Mellon University, Pittsburgh, Pennsylvania
| | | | - Shiladitya Banerjee
- Department of Physics, Carnegie Mellon University, Pittsburgh, Pennsylvania.
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11
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Pinto SC, Stojilković B, Zhang X, Sablowski R. Plant cell size: Links to cell cycle, differentiation and ploidy. CURRENT OPINION IN PLANT BIOLOGY 2024; 78:102527. [PMID: 38484440 DOI: 10.1016/j.pbi.2024.102527] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/23/2024] [Revised: 02/23/2024] [Accepted: 02/28/2024] [Indexed: 04/07/2024]
Abstract
Cell size affects many processes, including exchange of nutrients and external signals, cell division and tissue mechanics. Across eukaryotes, cells have evolved mechanisms that assess their own size to inform processes such as cell cycle progression or gene expression. Here, we review recent progress in understanding plant cell size regulation and its implications, relating these findings to work in other eukaryotes. Highlights include use of DNA contents as reference point to control the cell cycle in shoot meristems, a size-dependent cell fate decision during stomatal development and insights into the interconnection between ploidy, cell size and cell wall mechanics.
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Affiliation(s)
- Sara C Pinto
- Cell and Developmental Biology, John Innes Centre, Norwich, UK
| | | | - Xinyu Zhang
- Cell and Developmental Biology, John Innes Centre, Norwich, UK
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12
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Huang YT, Hesting LL, Calvi BR. An unscheduled switch to endocycles induces a reversible senescent arrest that impairs growth of the Drosophila wing disc. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.14.585098. [PMID: 38559130 PMCID: PMC10980049 DOI: 10.1101/2024.03.14.585098] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
A programmed developmental switch to G / S endocycles results in tissue growth through an increase in cell size. Unscheduled, induced endocycling cells (iECs) promote wound healing but also contribute to cancer. Much remains unknown, however, about how these iECs affect tissue growth. Using the D. melanogasterwing disc as model, we find that populations of iECs initially increase in size but then subsequently undergo a heterogenous arrest that causes severe tissue undergrowth. iECs acquired DNA damage and activated a Jun N-terminal kinase (JNK) pathway, but, unlike other stressed cells, were apoptosis-resistant and not eliminated from the epithelium. Instead, iECs entered a JNK-dependent and reversible senescent-like arrest. Senescent iECs promoted division of diploid neighbors, but this compensatory proliferation did not rescue tissue growth. Our study has uncovered unique attributes of iECs and their effects on tissue growth that have important implications for understanding their roles in wound healing and cancer.
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Affiliation(s)
- Yi-Ting Huang
- Department of Biology, Simon Cancer Center, Indiana University, Bloomington, IN 47405
| | - Lauren L. Hesting
- Department of Biology, Simon Cancer Center, Indiana University, Bloomington, IN 47405
| | - Brian R. Calvi
- Department of Biology, Simon Cancer Center, Indiana University, Bloomington, IN 47405
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13
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Foy R, Lew KX, Saurin AT. The search for CDK4/6 inhibitor biomarkers has been hampered by inappropriate proliferation assays. NPJ Breast Cancer 2024; 10:19. [PMID: 38438376 PMCID: PMC10912267 DOI: 10.1038/s41523-024-00624-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2023] [Accepted: 02/16/2024] [Indexed: 03/06/2024] Open
Abstract
CDK4/6 inhibitors are effective at treating advanced HR+ /HER2- breast cancer, however biomarkers that can predict response are urgently needed. We demonstrate here that previous large-scale screens designed to identify which tumour types or genotypes are most sensitive to CDK4/6 inhibitors have misrepresented the responsive cell lines because of a reliance on metabolic proliferation assays. CDK4/6-inhibited cells arrest in G1 but continue to grow in size, thereby producing more mitochondria. We show that this growth obscures the arrest using ATP-based proliferation assays but not if DNA-based assays are used instead. Furthermore, lymphoma lines, previously identified as the most sensitive, simply appear to respond the best using ATP-based assays because they fail to overgrow during the G1 arrest. Similarly, the CDK4/6 inhibitor abemaciclib appears to inhibit proliferation better than palbociclib because it also restricts cellular overgrowth through off-target effects. DepMap analysis of screening data using reliable assay types, demonstrates that palbociclib-sensitive cell types are also sensitive to Cyclin D1, CDK4 and CDK6 knockout/knockdown, whereas the palbociclib-resistant lines are sensitive to Cyclin E1, CDK2 and SKP2 knockout/knockdown. Potential biomarkers of palbociclib-sensitive cells are increased expression of CCND1 and RB1, and reduced expression of CCNE1 and CDKN2A. Probing DepMap with similar data from metabolic assays fails to reveal these associations. Together, this demonstrates why CDK4/6 inhibitors, and any other anti-cancer drugs that arrest the cell cycle but permit continued cell growth, must now be re-screened against a wide-range of cell types using an appropriate proliferation assay. This would help to better inform clinical trials and to identify much needed biomarkers of response.
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Affiliation(s)
- Reece Foy
- Cellular and Systems Medicine, Jacqui Wood Cancer Centre, School of Medicine, University of Dundee, Dundee, DD1 9SY, UK.
| | - Kah Xin Lew
- Cellular and Systems Medicine, Jacqui Wood Cancer Centre, School of Medicine, University of Dundee, Dundee, DD1 9SY, UK
| | - Adrian T Saurin
- Cellular and Systems Medicine, Jacqui Wood Cancer Centre, School of Medicine, University of Dundee, Dundee, DD1 9SY, UK.
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14
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Zheng Y, Su Z, Liu D, Huang B, Mu Q, Li Y, Wen D. Metagenomics reveals the influence of small microplastics on microbial communities in coastal sediments. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 914:169982. [PMID: 38215846 DOI: 10.1016/j.scitotenv.2024.169982] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/11/2023] [Revised: 01/04/2024] [Accepted: 01/05/2024] [Indexed: 01/14/2024]
Abstract
The ecological impact of microplastics (MPs) in coastal environments has been widely studied. However, the influence of small microplastics in the actual environment is often overlooked due to measurement challenges. In this study, Hangzhou Bay (HZB), China, was selected as our study area. High-throughput metagenomic sequencing and micro-Raman spectrometry were employed to analyze the microbial communities and microplastics of coastal sediment samples, respectively. We aimed to explore the ecological impact of MPs with small sizes (≤ 100 μm) in real coastal sediment environments. Our results revealed that as microplastic size decreased, the environmental behavior of MPs underwent alterations. In the coastal sediments, no significant correlations were observed between the detected MPs and the whole microbial communities, but small MPs posed potential hazards to eukaryotic communities. Moreover, these small MPs were more prone to microbial degradation and significantly affected carbon metabolism in the habitat. This study is the first to reveal the comprehensive impact of small MPs on microbial communities in a real coastal sediment environment.
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Affiliation(s)
- Yuhan Zheng
- College of Environmental Sciences and Engineering, Peking University, Beijing 100871, China
| | - Zhiguo Su
- School of Environment, Tsinghua University, Beijing 100084, China
| | - Dantong Liu
- China Aviation Planning and Design Institute(Group)CO., LTD, Beijing 100120, China
| | - Bei Huang
- Marine Ecological Environmental Monitoring Center of Zhejiang Province, Zhoushan 316021, China
| | - Qinglin Mu
- Marine Ecological Environmental Monitoring Center of Zhejiang Province, Zhoushan 316021, China
| | - Yunong Li
- College of Environmental Sciences and Engineering, Peking University, Beijing 100871, China
| | - Donghui Wen
- College of Environmental Sciences and Engineering, Peking University, Beijing 100871, China.
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15
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Sugiyama H, Goto Y, Kondo Y, Coudreuse D, Aoki K. Live-cell imaging defines a threshold in CDK activity at the G2/M transition. Dev Cell 2024; 59:545-557.e4. [PMID: 38228139 DOI: 10.1016/j.devcel.2023.12.014] [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: 04/12/2023] [Revised: 10/05/2023] [Accepted: 12/21/2023] [Indexed: 01/18/2024]
Abstract
Cyclin-dependent kinase (CDK) determines the temporal ordering of the cell cycle phases. However, despite significant progress in studying regulators of CDK and phosphorylation patterns of CDK substrates at the population level, it remains elusive how CDK regulators coordinately affect CDK activity at the single-cell level and how CDK controls the temporal order of cell cycle events. Here, we elucidate the dynamics of CDK activity in fission yeast and mammalian cells by developing a CDK activity biosensor, Eevee-spCDK. We find that although CDK activity does not necessarily correlate with cyclin levels, it converges to the same level around mitotic onset in several mutant backgrounds, including pom1Δ cells and wee1 or cdc25 overexpressing cells. These data provide direct evidence that cells enter the M phase when CDK activity reaches a high threshold, consistent with the quantitative model of cell cycle progression in fission yeast.
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Affiliation(s)
- Hironori Sugiyama
- Quantitative Biology Research Group, Exploratory Research Center on Life and Living Systems (ExCELLS), National Institutes of Natural Sciences, 5-1 Higashiyama, Myodaiji-cho, Okazaki, Aichi 444-8787, Japan
| | - Yuhei Goto
- Quantitative Biology Research Group, Exploratory Research Center on Life and Living Systems (ExCELLS), National Institutes of Natural Sciences, 5-1 Higashiyama, Myodaiji-cho, Okazaki, Aichi 444-8787, Japan; Division of Quantitative Biology, National Institute for Basic Biology, National Institutes of Natural Sciences, 5-1 Higashiyama, Myodaiji-cho, Okazaki, Aichi 444-8787, Japan; Basic Biology Program, Graduate Institute for Advanced Studies, SOKENDAI, 5-1 Higashiyama, Myodaiji-cho, Okazaki, Aichi 444-8787, Japan
| | - Yohei Kondo
- Quantitative Biology Research Group, Exploratory Research Center on Life and Living Systems (ExCELLS), National Institutes of Natural Sciences, 5-1 Higashiyama, Myodaiji-cho, Okazaki, Aichi 444-8787, Japan; Division of Quantitative Biology, National Institute for Basic Biology, National Institutes of Natural Sciences, 5-1 Higashiyama, Myodaiji-cho, Okazaki, Aichi 444-8787, Japan; Basic Biology Program, Graduate Institute for Advanced Studies, SOKENDAI, 5-1 Higashiyama, Myodaiji-cho, Okazaki, Aichi 444-8787, Japan
| | - Damien Coudreuse
- Institute of Biochemistry and Cellular Genetics, UMR 5095, CNRS, Bordeaux University, 33077 Bordeaux, France
| | - Kazuhiro Aoki
- Quantitative Biology Research Group, Exploratory Research Center on Life and Living Systems (ExCELLS), National Institutes of Natural Sciences, 5-1 Higashiyama, Myodaiji-cho, Okazaki, Aichi 444-8787, Japan; Division of Quantitative Biology, National Institute for Basic Biology, National Institutes of Natural Sciences, 5-1 Higashiyama, Myodaiji-cho, Okazaki, Aichi 444-8787, Japan; Basic Biology Program, Graduate Institute for Advanced Studies, SOKENDAI, 5-1 Higashiyama, Myodaiji-cho, Okazaki, Aichi 444-8787, Japan.
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16
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Liu X, Yan J, Kirschner MW. Cell size homeostasis is tightly controlled throughout the cell cycle. PLoS Biol 2024; 22:e3002453. [PMID: 38180950 PMCID: PMC10769027 DOI: 10.1371/journal.pbio.3002453] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2023] [Accepted: 11/28/2023] [Indexed: 01/07/2024] Open
Abstract
To achieve a stable size distribution over multiple generations, proliferating cells require a means of counteracting stochastic noise in the rate of growth, the time spent in various phases of the cell cycle, and the imprecision in the placement of the plane of cell division. In the most widely accepted model, cell size is thought to be regulated at the G1/S transition, such that cells smaller than a critical size pause at the end of G1 phase until they have accumulated mass to a predetermined size threshold, at which point the cells proceed through the rest of the cell cycle. However, a model, based solely on a specific size checkpoint at G1/S, cannot readily explain why cells with deficient G1/S control mechanisms are still able to maintain a very stable cell size distribution. Furthermore, such a model would not easily account for stochastic variation in cell size during the subsequent phases of the cell cycle, which cannot be anticipated at G1/S. To address such questions, we applied computationally enhanced quantitative phase microscopy (ceQPM) to populations of cultured human cell lines, which enables highly accurate measurement of cell dry mass of individual cells throughout the cell cycle. From these measurements, we have evaluated the factors that contribute to maintaining cell mass homeostasis at any point in the cell cycle. Our findings reveal that cell mass homeostasis is accurately maintained, despite disruptions to the normal G1/S machinery or perturbations in the rate of cell growth. Control of cell mass is generally not confined to regulation of the G1 length. Instead mass homeostasis is imposed throughout the cell cycle. In the cell lines examined, we find that the coefficient of variation (CV) in dry mass of cells in the population begins to decline well before the G1/S transition and continues to decline throughout S and G2 phases. Among the different cell types tested, the detailed response of cell growth rate to cell mass differs. However, in general, when it falls below that for exponential growth, the natural increase in the CV of cell mass is effectively constrained. We find that both mass-dependent cell cycle regulation and mass-dependent growth rate modulation contribute to reducing cell mass variation within the population. Through the interplay and coordination of these 2 processes, accurate cell mass homeostasis emerges. Such findings reveal previously unappreciated and very general principles of cell size control in proliferating cells. These same regulatory processes might also be operative in terminally differentiated cells. Further quantitative dynamical studies should lead to a better understanding of the underlying molecular mechanisms of cell size control.
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Affiliation(s)
- Xili Liu
- Department of Systems Biology, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Jiawei Yan
- Department of Chemistry, Stanford University, Stanford, California, United States of America
| | - Marc W. Kirschner
- Department of Systems Biology, Harvard Medical School, Boston, Massachusetts, United States of America
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17
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Rong Y, Darnell AM, Sapp KM, Vander Heiden MG, Spencer SL. Cells use multiple mechanisms for cell-cycle arrest upon withdrawal of individual amino acids. Cell Rep 2023; 42:113539. [PMID: 38070134 PMCID: PMC11238304 DOI: 10.1016/j.celrep.2023.113539] [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: 04/17/2023] [Revised: 09/29/2023] [Accepted: 11/17/2023] [Indexed: 12/30/2023] Open
Abstract
Amino acids are required for cell growth and proliferation, but it remains unclear when and how amino acid availability impinges on the proliferation-quiescence decision. Here, we used time-lapse microscopy and single-cell tracking of cyclin-dependent kinase 2 (CDK2) activity to assess the response of individual cells to withdrawal of single amino acids and found strikingly different cell-cycle effects depending on the amino acid. For example, upon leucine withdrawal, MCF10A cells complete two cell cycles and then enter a CDK2-low quiescence, whereas lysine withdrawal causes immediate cell-cycle stalling. Methionine withdrawal triggers a restriction point phenotype similar to serum starvation or Mek inhibition: upon methionine withdrawal, cells complete their current cell cycle and enter a CDK2-low quiescence after mitosis. Modulation of restriction point regulators p21/p27 or cyclin D1 enables short-term rescue of proliferation under methionine and leucine withdrawal, and to a lesser extent lysine withdrawal, revealing a checkpoint connecting nutrient signaling to cell-cycle entry.
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Affiliation(s)
- Yao Rong
- Department of Molecular, Cellular, and Developmental Biology and BioFrontiers Institute, University of Colorado Boulder, Boulder, CO 80303, USA
| | - Alicia M Darnell
- Koch Institute for Integrative Cancer Research, Cambridge, MA, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Kiera M Sapp
- Koch Institute for Integrative Cancer Research, Cambridge, MA, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Matthew G Vander Heiden
- Koch Institute for Integrative Cancer Research, Cambridge, MA, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Dana-Farber Cancer Institute, Boston, MA 02215, USA; Broad Institute, Cambridge, MA 02139, USA
| | - Sabrina L Spencer
- Department of Biochemistry and BioFrontiers Institute, University of Colorado Boulder, Boulder, CO 80303, USA.
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18
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McLellan JL, Hanson KK. Translation inhibition efficacy does not determine the Plasmodium berghei liver stage antiplasmodial efficacy of protein synthesis inhibitors. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.12.07.570699. [PMID: 38106175 PMCID: PMC10723475 DOI: 10.1101/2023.12.07.570699] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2023]
Abstract
Protein synthesis is a core cellular process, necessary throughout the complex lifecycle of Plasmodium parasites, thus specific translation inhibitors would be a valuable class of antimalarial drugs, capable of both treating symptomatic infections in the blood and providing chemoprotection by targeting the initial parasite population in the liver, preventing both human disease and parasite transmission back to the mosquito host. As increasing numbers of antiplasmodial compounds are identified that converge mechanistically at inhibition of cytoplasmic translation, regardless of molecular target or mechanism, it would be useful to gain deeper understanding of how their effectiveness as liver stage translation inhibitors relates to their chemoprotective potential. Here, we probed that relationship using the P. berghei-HepG2 liver stage infection model. Using o-propargyl puromycin-based labeling of the nascent proteome in P. berghei-infected HepG2 monolayers coupled with automated confocal feedback microscopy to generate unbiased, single parasite image sets of P. berghei liver stage translation, we determined translation inhibition EC50s for five compounds, encompassing parasite-specific aminoacyl tRNA synthetase inhibitors, compounds targeting the ribosome in both host and parasite, as well as DDD107498, which targets Plasmodium eEF2, and is a leading antimalarial candidate compound being clinically developed as cabamiquine. Compounds were then tested at equivalent effective concentrations to compare the parasite response to, and recovery from, a brief period of translation inhibition in early schizogony, with parasites followed up to 120 hours post-infection to assess liver stage antiplasmodial effects of the treatment. Our data conclusively show that translation inhibition efficacy per se does not determine a translation inhibitor's antiplasmodial efficacy. DDD107498 was the least effective translation inhibitor, yet exerted the strongest antimalarial effects at both 5x- and 10x EC50 concentrations. We show compound-specific heterogeneity in single parasite and population responses to translation inhibitor treatment, with no single metric strongly correlated to release of hepatic merozoites for all compound, demonstrate that DDD107498 is capable of exerting antiplasmodial effects on translationally arrested liver stage parasites, and uncover unexpected growth dynamics during the liver stage. Our results demonstrate that translation inhibition efficacy cannot function as a proxy for antiplasmodial effectiveness, and highlight the importance of exploring the ultimate, as well as proximate, mechanisms of action of these compounds on liver stage parasites.
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Affiliation(s)
- James L. McLellan
- University of Texas at San Antonio, Department of Molecular Microbiology and Immunology and STCEID, San Antonio TX, USA
| | - Kirsten K. Hanson
- University of Texas at San Antonio, Department of Molecular Microbiology and Immunology and STCEID, San Antonio TX, USA
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19
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Swaffer MP, Marinov GK, Zheng H, Fuentes Valenzuela L, Tsui CY, Jones AW, Greenwood J, Kundaje A, Greenleaf WJ, Reyes-Lamothe R, Skotheim JM. RNA polymerase II dynamics and mRNA stability feedback scale mRNA amounts with cell size. Cell 2023; 186:5254-5268.e26. [PMID: 37944513 DOI: 10.1016/j.cell.2023.10.012] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2022] [Revised: 07/16/2023] [Accepted: 10/10/2023] [Indexed: 11/12/2023]
Abstract
A fundamental feature of cellular growth is that total protein and RNA amounts increase with cell size to keep concentrations approximately constant. A key component of this is that global transcription rates increase in larger cells. Here, we identify RNA polymerase II (RNAPII) as the limiting factor scaling mRNA transcription with cell size in budding yeast, as transcription is highly sensitive to the dosage of RNAPII but not to other components of the transcriptional machinery. Our experiments support a dynamic equilibrium model where global RNAPII transcription at a given size is set by the mass action recruitment kinetics of unengaged nucleoplasmic RNAPII to the genome. However, this only drives a sub-linear increase in transcription with size, which is then partially compensated for by a decrease in mRNA decay rates as cells enlarge. Thus, limiting RNAPII and feedback on mRNA stability work in concert to scale mRNA amounts with cell size.
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Affiliation(s)
| | - Georgi K Marinov
- Department of Genetics, Stanford University, Stanford, CA 94305, USA
| | - Huan Zheng
- Department of Biology, McGill University, Montreal, QC H3G 0B1, Canada
| | | | - Crystal Yee Tsui
- Department of Biology, Stanford University, Stanford, CA 94305, USA
| | | | | | - Anshul Kundaje
- Department of Genetics, Stanford University, Stanford, CA 94305, USA
| | | | | | - Jan M Skotheim
- Department of Biology, Stanford University, Stanford, CA 94305, USA; Chan Zuckerberg Biohub, San Francisco, CA 94158, USA.
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20
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Wilson GA, Vuina K, Sava G, Huard C, Meneguello L, Coulombe-Huntington J, Bertomeu T, Maizels RJ, Lauring J, Kriston-Vizi J, Tyers M, Ali S, Bertoli C, de Bruin RAM. Active growth signaling promotes senescence and cancer cell sensitivity to CDK7 inhibition. Mol Cell 2023; 83:4078-4092.e6. [PMID: 37977119 DOI: 10.1016/j.molcel.2023.10.017] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Revised: 07/25/2023] [Accepted: 10/16/2023] [Indexed: 11/19/2023]
Abstract
Tumor growth is driven by continued cellular growth and proliferation. Cyclin-dependent kinase 7's (CDK7) role in activating mitotic CDKs and global gene expression makes it therefore an attractive target for cancer therapies. However, what makes cancer cells particularly sensitive to CDK7 inhibition (CDK7i) remains unclear. Here, we address this question. We show that CDK7i, by samuraciclib, induces a permanent cell-cycle exit, known as senescence, without promoting DNA damage signaling or cell death. A chemogenetic genome-wide CRISPR knockout screen identified that active mTOR (mammalian target of rapamycin) signaling promotes samuraciclib-induced senescence. mTOR inhibition decreases samuraciclib sensitivity, and increased mTOR-dependent growth signaling correlates with sensitivity in cancer cell lines. Reverting a growth-promoting mutation in PIK3CA to wild type decreases sensitivity to CDK7i. Our work establishes that enhanced growth alone promotes CDK7i sensitivity, providing an explanation for why some cancers are more sensitive to CDK inhibition than normally growing cells.
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Affiliation(s)
- Gemma A Wilson
- Laboratory for Molecular Cell Biology, University College London, London, UK
| | - Karla Vuina
- Laboratory for Molecular Cell Biology, University College London, London, UK
| | - Georgina Sava
- Division of Cancer, Department of Surgery & Cancer, Imperial College London, London, UK
| | - Caroline Huard
- Institute for Research in Immunology and Cancer, Université de Montréal, Montréal, QC, Canada
| | - Leticia Meneguello
- Laboratory for Molecular Cell Biology, University College London, London, UK; UCL Cancer Institute, University College London, London, UK
| | - Jasmin Coulombe-Huntington
- Institute for Research in Immunology and Cancer, Université de Montréal, Montréal, QC, Canada; Department of Bioengineering, McGill University, Montréal, QC, Canada
| | - Thierry Bertomeu
- Institute for Research in Immunology and Cancer, Université de Montréal, Montréal, QC, Canada
| | - Rory J Maizels
- Laboratory for Molecular Cell Biology, University College London, London, UK
| | - Josh Lauring
- Janssen Research and Development, the Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, Baltimore, MD, USA
| | - Janos Kriston-Vizi
- Laboratory for Molecular Cell Biology, University College London, London, UK
| | - Mike Tyers
- Institute for Research in Immunology and Cancer, Université de Montréal, Montréal, QC, Canada; Hospital for Sick Children, University of Toronto, Toronto, ON, Canada
| | - Simak Ali
- Division of Cancer, Department of Surgery & Cancer, Imperial College London, London, UK
| | - Cosetta Bertoli
- Laboratory for Molecular Cell Biology, University College London, London, UK.
| | - Robertus A M de Bruin
- Laboratory for Molecular Cell Biology, University College London, London, UK; UCL Cancer Institute, University College London, London, UK.
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21
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Foy R, Crozier L, Pareri AU, Valverde JM, Park BH, Ly T, Saurin AT. Oncogenic signals prime cancer cells for toxic cell overgrowth during a G1 cell cycle arrest. Mol Cell 2023; 83:4047-4061.e6. [PMID: 37977117 DOI: 10.1016/j.molcel.2023.10.020] [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: 07/10/2023] [Accepted: 10/17/2023] [Indexed: 11/19/2023]
Abstract
CDK4/6 inhibitors are remarkable anti-cancer drugs that can arrest tumor cells in G1 and induce their senescence while causing only relatively mild toxicities in healthy tissues. How they achieve this mechanistically is unclear. We show here that tumor cells are specifically vulnerable to CDK4/6 inhibition because during the G1 arrest, oncogenic signals drive toxic cell overgrowth. This overgrowth causes permanent cell cycle withdrawal by either preventing progression from G1 or inducing genotoxic damage during the subsequent S-phase and mitosis. Inhibiting or reverting oncogenic signals that converge onto mTOR can rescue this excessive growth, DNA damage, and cell cycle exit in cancer cells. Conversely, inducing oncogenic signals in non-transformed cells can drive these toxic phenotypes and sensitize the cells to CDK4/6 inhibition. Together, this demonstrates that cell cycle arrest and oncogenic cell growth is a synthetic lethal combination that is exploited by CDK4/6 inhibitors to induce tumor-specific toxicity.
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Affiliation(s)
- Reece Foy
- Cellular and Systems Medicine, Jacqui Wood Cancer Centre, School of Medicine, University of Dundee, Dundee DD1 9SY, UK
| | - Lisa Crozier
- Cellular and Systems Medicine, Jacqui Wood Cancer Centre, School of Medicine, University of Dundee, Dundee DD1 9SY, UK
| | - Aanchal U Pareri
- Cellular and Systems Medicine, Jacqui Wood Cancer Centre, School of Medicine, University of Dundee, Dundee DD1 9SY, UK
| | - Juan Manuel Valverde
- Cellular and Systems Medicine, Jacqui Wood Cancer Centre, School of Medicine, University of Dundee, Dundee DD1 9SY, UK
| | - Ben Ho Park
- Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Tony Ly
- Molecular Cell and Developmental Biology, School of Life Sciences, University of Dundee, Dundee DD1 5EH, UK
| | - Adrian T Saurin
- Cellular and Systems Medicine, Jacqui Wood Cancer Centre, School of Medicine, University of Dundee, Dundee DD1 9SY, UK.
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22
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Emenecker RJ, Guadalupe K, Shamoon NM, Sukenik S, Holehouse AS. Sequence-ensemble-function relationships for disordered proteins in live cells. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.29.564547. [PMID: 37961106 PMCID: PMC10634935 DOI: 10.1101/2023.10.29.564547] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2023]
Abstract
Intrinsically disordered protein regions (IDRs) are ubiquitous across all kingdoms of life and play a variety of essential cellular roles. IDRs exist in a collection of structurally distinct conformers known as an ensemble. An IDR's amino acid sequence determines its ensemble, which in turn can play an important role in dictating molecular function. Yet a clear link connecting IDR sequence, its ensemble properties, and its molecular function in living cells has not been directly established. Here, we set out to test this sequence-ensemble-function paradigm using a novel computational method (GOOSE) that enables the rational design of libraries of IDRs by systematically varying specific sequence properties. Using ensemble FRET, we measured the ensemble dimensions of a library of rationally designed IDRs in human-derived cell lines, revealing how IDR sequence influences ensemble dimensions in situ. Furthermore, we show that the interplay between sequence and ensemble can tune an IDR's ability to sense changes in cell volume - a de novo molecular function for these synthetic sequences. Our results establish biophysical rules for intracellular sequence-ensemble relationships, enable a new route for understanding how IDR sequences map to function in live cells, and set the ground for the design of synthetic IDRs with de novo function.
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Affiliation(s)
- Ryan J. Emenecker
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO
- Center for Biomolecular Condensates (CBC), Washington University in St. Louis, St. Louis, MO
| | - Karina Guadalupe
- Department of Chemistry and Biochemistry, University of California, Merced, CA
- Center for Cellular and Biomolecular Machines, University of California, Merced, CA
| | - Nora M. Shamoon
- Center for Cellular and Biomolecular Machines, University of California, Merced, CA
- Quantitative Systems Biology Program, University of California, Merced, CA
| | - Shahar Sukenik
- Department of Chemistry and Biochemistry, University of California, Merced, CA
- Center for Cellular and Biomolecular Machines, University of California, Merced, CA
- Quantitative Systems Biology Program, University of California, Merced, CA
- Health Sciences Research Institute, University of California, Merced, CA
| | - Alex S. Holehouse
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO
- Center for Biomolecular Condensates (CBC), Washington University in St. Louis, St. Louis, MO
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23
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Mouton SN, Boersma AJ, Veenhoff LM. A physicochemical perspective on cellular ageing. Trends Biochem Sci 2023; 48:949-962. [PMID: 37716870 DOI: 10.1016/j.tibs.2023.08.007] [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: 04/21/2023] [Revised: 08/17/2023] [Accepted: 08/18/2023] [Indexed: 09/18/2023]
Abstract
Cellular ageing described at the molecular level is a multifactorial process that leads to a spectrum of ageing trajectories. There has been recent discussion about whether a decline in physicochemical homeostasis causes aberrant phase transitions, which are a driver of ageing. Indeed, the function of all biological macromolecules, regardless of their participation in biomolecular condensates, depends on parameters such as pH, crowding, and redox state. We expand on the physicochemical homeostasis hypothesis and summarise recent evidence that the intracellular milieu influences molecular processes involved in ageing.
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Affiliation(s)
- Sara N Mouton
- European Research Institute for the Biology of Ageing, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands.
| | - Arnold J Boersma
- Cellular Protein Chemistry, Bijvoet Centre for Biomolecular Research, Faculty of Science, Utrecht University, Utrecht, The Netherlands
| | - Liesbeth M Veenhoff
- European Research Institute for the Biology of Ageing, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands.
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24
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Lanz MC, Zhang S, Swaffer MP, Hernández Götz L, McCarty F, Ziv I, Jarosz DF, Elias JE, Skotheim JM. Genome dilution by cell growth drives starvation-like proteome remodeling in mammalian and yeast cells. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.16.562558. [PMID: 37905015 PMCID: PMC10614910 DOI: 10.1101/2023.10.16.562558] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/02/2023]
Abstract
Cell size is tightly controlled in healthy tissues and single-celled organisms, but it remains unclear how size influences cell physiology. Increasing cell size was recently shown to remodel the proteomes of cultured human cells, demonstrating that large and small cells of the same type can be biochemically different. Here, we corroborate these results in mouse hepatocytes and extend our analysis using yeast. We find that size-dependent proteome changes are highly conserved and mostly independent of metabolic state. As eukaryotic cells grow larger, the dilution of the genome elicits a starvation-like proteome phenotype, suggesting that growth in large cells is limited by the genome in a manner analogous to a limiting nutrient. We also demonstrate that the proteomes of replicatively-aged yeast are primarily determined by their large size. Overall, our data suggest that genome concentration is a universal determinant of proteome content in growing cells.
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25
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Williamson D, Tasker-Brown W, Murray JAH, Jones AR, Band LR. Modelling how plant cell-cycle progression leads to cell size regulation. PLoS Comput Biol 2023; 19:e1011503. [PMID: 37862377 PMCID: PMC10653611 DOI: 10.1371/journal.pcbi.1011503] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Revised: 11/16/2023] [Accepted: 09/07/2023] [Indexed: 10/22/2023] Open
Abstract
Populations of cells typically maintain a consistent size, despite cell division rarely being precisely symmetrical. Therefore, cells must possess a mechanism of "size control", whereby the cell volume at birth affects cell-cycle progression. While size control mechanisms have been elucidated in a number of other organisms, it is not yet clear how this mechanism functions in plants. Here, we present a mathematical model of the key interactions in the plant cell cycle. Model simulations reveal that the network of interactions exhibits limit-cycle solutions, with biological switches underpinning both the G1/S and G2/M cell-cycle transitions. Embedding this network model within growing cells, we test hypotheses as to how cell-cycle progression can depend on cell size. We investigate two different mechanisms at both the G1/S and G2/M transitions: (i) differential expression of cell-cycle activator and inhibitor proteins (with synthesis of inhibitor proteins being independent of cell size), and (ii) equal inheritance of inhibitor proteins after cell division. The model demonstrates that both these mechanisms can lead to larger daughter cells progressing through the cell cycle more rapidly, and can thus contribute to cell-size control. To test how these features enable size homeostasis over multiple generations, we then simulated these mechanisms in a cell-population model with multiple rounds of cell division. These simulations suggested that integration of size-control mechanisms at both G1/S and G2/M provides long-term cell-size homeostasis. We concluded that while both size independence and equal inheritance of inhibitor proteins can reduce variations in cell size across individual cell-cycle phases, combining size-control mechanisms at both G1/S and G2/M is essential to maintain size homeostasis over multiple generations. Thus, our study reveals how features of the cell-cycle network enable cell-cycle progression to depend on cell size, and provides a mechanistic understanding of how plant cell populations maintain consistent size over generations.
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Affiliation(s)
- Daniel Williamson
- Centre for Mathematical Medicine and Biology, School of Mathematical Sciences, University of Nottingham, Nottingham, United Kingdom
| | - William Tasker-Brown
- Cardiff School of Biosciences, Cardiff University, Sir Martin Evans Building, Museum Avenue, Cardiff, United Kingdom
| | - James A. H. Murray
- Cardiff School of Biosciences, Cardiff University, Sir Martin Evans Building, Museum Avenue, Cardiff, United Kingdom
| | - Angharad R. Jones
- Cardiff School of Biosciences, Cardiff University, Sir Martin Evans Building, Museum Avenue, Cardiff, United Kingdom
| | - Leah R. Band
- Centre for Mathematical Medicine and Biology, School of Mathematical Sciences, University of Nottingham, Nottingham, United Kingdom
- Division of Plant and Crop Sciences, School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough, United Kingdom
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26
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Gong Y, Dale R, Fung HF, Amador GO, Smit ME, Bergmann DC. A cell size threshold triggers commitment to stomatal fate in Arabidopsis. SCIENCE ADVANCES 2023; 9:eadf3497. [PMID: 37729402 PMCID: PMC10881030 DOI: 10.1126/sciadv.adf3497] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Accepted: 08/15/2023] [Indexed: 09/22/2023]
Abstract
How flexible developmental programs integrate information from internal and external factors to modulate stem cell behavior is a fundamental question in developmental biology. Cells of the Arabidopsis stomatal lineage modify the balance of stem cell proliferation and differentiation to adjust the size and cell type composition of mature leaves. Here, we report that meristemoids, one type of stomatal lineage stem cell, trigger the transition from asymmetric self-renewing divisions to commitment and terminal differentiation by crossing a critical cell size threshold. Through computational simulation, we demonstrate that this cell size-mediated transition allows robust, yet flexible termination of stem cell proliferation, and we observe adjustments in the number of divisions before the differentiation threshold under several genetic manipulations. We experimentally evaluate several mechanisms for cell size sensing, and our data suggest that this stomatal lineage transition is dependent on a nuclear factor that is sensitive to DNA content.
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Affiliation(s)
- Yan Gong
- Department of Biology, Stanford University, Stanford, CA 94305, USA
| | - Renee Dale
- Donald Danforth Plant Science Center, St. Louis, MO 63132 USA
| | - Hannah F. Fung
- Department of Biology, Stanford University, Stanford, CA 94305, USA
| | - Gabriel O. Amador
- Department of Developmental Biology, Stanford University, Stanford, CA 94305, USA
| | - Margot E. Smit
- Department of Biology, Stanford University, Stanford, CA 94305, USA
- Howard Hughes Medical Institute, Stanford University, Stanford, CA 94305, USA
| | - Dominique C. Bergmann
- Department of Biology, Stanford University, Stanford, CA 94305, USA
- Howard Hughes Medical Institute, Stanford University, Stanford, CA 94305, USA
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27
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Devany J, Falk MJ, Holt LJ, Murugan A, Gardel ML. Epithelial tissue confinement inhibits cell growth and leads to volume-reducing divisions. Dev Cell 2023; 58:1462-1476.e8. [PMID: 37339629 PMCID: PMC10528006 DOI: 10.1016/j.devcel.2023.05.018] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Revised: 05/12/2023] [Accepted: 05/26/2023] [Indexed: 06/22/2023]
Abstract
Cell proliferation is a central process in tissue development, homeostasis, and disease, yet how proliferation is regulated in the tissue context remains poorly understood. Here, we introduce a quantitative framework to elucidate how tissue growth dynamics regulate cell proliferation. Using MDCK epithelial monolayers, we show that a limiting rate of tissue expansion creates confinement that suppresses cell growth; however, this confinement does not directly affect the cell cycle. This leads to uncoupling between rates of cell growth and division in epithelia and, thereby, reduces cell volume. Division becomes arrested at a minimal cell volume, which is consistent across diverse epithelia in vivo. Here, the nucleus approaches the minimum volume capable of packaging the genome. Loss of cyclin D1-dependent cell-volume regulation results in an abnormally high nuclear-to-cytoplasmic volume ratio and DNA damage. Overall, we demonstrate how epithelial proliferation is regulated by the interplay between tissue confinement and cell-volume regulation.
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Affiliation(s)
- John Devany
- Department of Physics, The University of Chicago, Chicago, IL 60637, USA; James Franck Institute, The University of Chicago, Chicago, IL 60637, USA; Institute for Biophysical Dynamics, The University of Chicago, Chicago, IL 60637, USA
| | - Martin J Falk
- Department of Physics, The University of Chicago, Chicago, IL 60637, USA; James Franck Institute, The University of Chicago, Chicago, IL 60637, USA
| | - Liam J Holt
- Institute for Systems Genetics, New York University, Grossman School of Medicine, New York, NY 10016, USA
| | - Arvind Murugan
- Department of Physics, The University of Chicago, Chicago, IL 60637, USA; James Franck Institute, The University of Chicago, Chicago, IL 60637, USA
| | - Margaret L Gardel
- Department of Physics, The University of Chicago, Chicago, IL 60637, USA; James Franck Institute, The University of Chicago, Chicago, IL 60637, USA; Institute for Biophysical Dynamics, The University of Chicago, Chicago, IL 60637, USA; Pritzker School of Molecular Engineering, The University of Chicago, Chicago, IL 60637, USA.
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28
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Ashraf HM, Fernandez B, Spencer SL. The intensities of canonical senescence biomarkers integrate the duration of cell-cycle withdrawal. Nat Commun 2023; 14:4527. [PMID: 37500655 PMCID: PMC10374620 DOI: 10.1038/s41467-023-40132-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2022] [Accepted: 07/10/2023] [Indexed: 07/29/2023] Open
Abstract
Senescence, a state of irreversible cell-cycle withdrawal, is difficult to distinguish from quiescence, a state of reversible cell-cycle withdrawal. This difficulty arises because quiescent and senescent cells are defined by overlapping biomarkers, raising the question of whether these states are truly distinct. To address this, we use single-cell time-lapse imaging to distinguish slow-cycling cells that spend long periods in quiescence from cells that never cycle after recovery from senescence-inducing treatments, followed by staining for various senescence biomarkers. We find that the staining intensity of multiple senescence biomarkers is graded rather than binary and reflects the duration of cell-cycle withdrawal, rather than senescence per se. Together, our data show that quiescent and apparent senescent cells are nearly molecularly indistinguishable from each other at a snapshot in time. This suggests that cell-cycle withdrawal itself is graded rather than binary, where the intensities of senescence biomarkers integrate the duration of past cell-cycle withdrawal.
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Affiliation(s)
- Humza M Ashraf
- Department of Biochemistry, University of Colorado, Boulder, CO, 80303, USA
- BioFrontiers Institute, University of Colorado, Boulder, CO, 80303, USA
| | - Brianna Fernandez
- Department of Biochemistry, University of Colorado, Boulder, CO, 80303, USA
- BioFrontiers Institute, University of Colorado, Boulder, CO, 80303, USA
| | - Sabrina L Spencer
- Department of Biochemistry, University of Colorado, Boulder, CO, 80303, USA.
- BioFrontiers Institute, University of Colorado, Boulder, CO, 80303, USA.
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29
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Carpenter LC, Pérez-Verdugo F, Banerjee S. Mechanical control of cell proliferation patterns in growing tissues. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.07.25.550581. [PMID: 37546964 PMCID: PMC10402015 DOI: 10.1101/2023.07.25.550581] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/08/2023]
Abstract
Cell proliferation plays a crucial role in regulating tissue homeostasis and development. However, our understanding of how cell proliferation is controlled in densely packed tissues is limited. Here we develop a computational framework to predict the patterns of cell proliferation in growing tissues, connecting single-cell behaviors and cell-cell interactions to tissue-level growth. Our model incorporates probabilistic rules governing cell growth, division, and elimination, while also taking into account their feedback with tissue mechanics. In particular, cell growth is suppressed and apoptosis is enhanced in regions of high cell density. With these rules and model parameters calibrated using experimental data, we predict how tissue confinement influences cell size and proliferation dynamics, and how single-cell physical properties influence the spatiotemporal patterns of tissue growth. Our findings indicate that mechanical feedback between tissue confinement and cell growth leads to enhanced cell proliferation at tissue boundaries, whereas cell growth in the bulk is arrested. By tuning cellular elasticity and contact inhibition of proliferation we can regulate the emergent patterns of cell proliferation, ranging from uniform growth at low contact inhibition to localized growth at higher contact inhibition. Furthermore, mechanical state of the tissue governs the dynamics of tissue growth, with cellular parameters affecting tissue pressure playing a significant role in determining the overall growth rate. Our computational study thus underscores the impact of cell mechanical properties on the spatiotemporal patterns of cell proliferation in growing tissues.
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Affiliation(s)
- Logan C Carpenter
- Department of Physics, Carnegie Mellon University, Pittsburgh, PA 15213, USA
| | | | - Shiladitya Banerjee
- Department of Physics, Carnegie Mellon University, Pittsburgh, PA 15213, USA
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30
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Ji X, Lin J. Implications of differential size-scaling of cell-cycle regulators on cell size homeostasis. PLoS Comput Biol 2023; 19:e1011336. [PMID: 37506170 PMCID: PMC10411824 DOI: 10.1371/journal.pcbi.1011336] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2022] [Revised: 08/09/2023] [Accepted: 07/07/2023] [Indexed: 07/30/2023] Open
Abstract
Accurate timing of division and size homeostasis is crucial for cells. A potential mechanism for cells to decide the timing of division is the differential scaling of regulatory protein copy numbers with cell size. However, it remains unclear whether such a mechanism can lead to robust growth and division, and how the scaling behaviors of regulatory proteins influence the cell size distribution. Here we study a mathematical model combining gene expression and cell growth, in which the cell-cycle activators scale superlinearly with cell size while the inhibitors scale sublinearly. The cell divides once the ratio of their concentrations reaches a threshold value. We find that the cell can robustly grow and divide within a finite range of the threshold value with the cell size proportional to the ploidy. In a stochastic version of the model, the cell size at division is uncorrelated with that at birth. Also, the more differential the cell-size scaling of the cell-cycle regulators is, the narrower the cell-size distribution is. Intriguingly, our model with multiple regulators rationalizes the observation that after the deletion of a single regulator, the coefficient of variation of cell size remains roughly the same though the average cell size changes significantly. Our work reveals that the differential scaling of cell-cycle regulators provides a robust mechanism of cell size control.
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Affiliation(s)
- Xiangrui Ji
- Yuanpei College, Peking University, Beijing, China
| | - Jie Lin
- Center for Quantitative Biology, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China
- Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China
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31
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Fung HF, Bergmann DC. Function follows form: How cell size is harnessed for developmental decisions. Eur J Cell Biol 2023; 102:151312. [PMID: 36989838 DOI: 10.1016/j.ejcb.2023.151312] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Revised: 03/16/2023] [Accepted: 03/22/2023] [Indexed: 03/29/2023] Open
Abstract
Cell size has profound effects on biological function, influencing a wide range of processes, including biosynthetic capacity, metabolism, and nutrient uptake. As a result, size is typically maintained within a narrow, population-specific range through size control mechanisms, which are an active area of study. While the physiological consequences of cell size are relatively well-characterized, less is known about its developmental consequences, and specifically its effects on developmental transitions. In this review, we compare systems where cell size is linked to developmental transitions, paying particular attention to examples from plants. We conclude by proposing that size can offer a simple readout of complex inputs, enabling flexible decisions during plant development.
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32
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Ashraf HM, Fernandez B, Spencer SL. The intensities of canonical senescence biomarkers integrate the duration of cell-cycle withdrawal. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.03.18.533242. [PMID: 36993379 PMCID: PMC10055273 DOI: 10.1101/2023.03.18.533242] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/31/2023]
Abstract
Senescence, a state of permanent cell-cycle withdrawal, is difficult to distinguish from quiescence, a transient state of cell-cycle withdrawal. This difficulty arises because quiescent and senescent cells are defined by overlapping biomarkers, raising the question of whether quiescence and senescence are truly distinct states. To address this, we used single-cell time-lapse imaging to distinguish slow-cycling quiescent cells from bona fide senescent cells after chemotherapy treatment, followed immediately by staining for various senescence biomarkers. We found that the staining intensity of multiple senescence biomarkers is graded rather than binary and primarily reflects the duration of cell-cycle withdrawal, rather than senescence per se. Together, our data suggest that quiescence and senescence are not distinct cellular states but rather fall on a continuum of cell-cycle withdrawal, where the intensities of canonical senescence biomarkers reflect the likelihood of cell-cycle re-entry.
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33
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Chaillot J, Cook MA, Sellam A. Novel determinants of cell size homeostasis in the opportunistic yeast Candida albicans. Curr Genet 2023; 69:67-75. [PMID: 36449086 DOI: 10.1007/s00294-022-01260-0] [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: 11/18/2022] [Revised: 11/21/2022] [Accepted: 11/23/2022] [Indexed: 12/05/2022]
Abstract
The basis for commitment to cell division in late G1 phase, called Start in yeast, is a critical but still poorly understood aspect of eukaryotic cell proliferation. Most dividing cells accumulate mass and grow to a critical cell size before traversing the cell cycle. This size threshold couples cell growth to division and thereby establishes long-term size homeostasis. At present, mechanisms involved in cell size homeostasis in fungal pathogens are not well described. Our previous survey of the size phenome in Candida albicans focused on 279 unique mutants enriched mainly in kinases and transcription factors (Sellam et al. PLoS Genet 15:e1008052, 2019). To uncover novel size regulators in C. albicans and highlight potential innovation within cell size control in pathogenic fungi, we expanded our genetic survey of cell size to include 1301 strains from the GRACE (Gene Replacement and Conditional Expression) collection. The current investigation uncovered both known and novel biological processes required for cell size homeostasis in C. albicans. We also confirmed the plasticity of the size control network as few C. albicans size genes overlapped with those of the budding yeast Saccharomyces cerevisiae. Many new size genes of C. albicans were associated with biological processes that were not previously linked to cell size control and offer an opportunity for future investigation. Additional work is needed to understand if mitochondrial activity is a critical element of the metric that dictates cell size in C. albicans and whether modulation of the onset of actomyosin ring constriction is an additional size checkpoint.
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Affiliation(s)
- Julien Chaillot
- Department of Microbiology, Infectious Diseases and Immunology, Faculty of Medicine, Université Laval, Quebec City, QC, Canada
- Centre de Recherche Paul Pascal, Unité Mixte de Recherche 5031, Université de Bordeaux, Centre National de la Recherche Scientifique, 33600, Pessac, France
| | - Michael A Cook
- Department of Biochemistry and Biomedical Sciences, David Braley Center for Antibiotic Discovery, Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, ON, Canada
| | - Adnane Sellam
- Montreal Heart Institute, Université de Montréal, Montréal, QC, Canada.
- Department of Microbiology, Infectious Diseases and Immunology, Faculty of Medicine, Université de Montréal, Montréal, QC, Canada.
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34
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Balachandra S, Sarkar S, Amodeo AA. The Nuclear-to-Cytoplasmic Ratio: Coupling DNA Content to Cell Size, Cell Cycle, and Biosynthetic Capacity. Annu Rev Genet 2022; 56:165-185. [PMID: 35977407 PMCID: PMC10165727 DOI: 10.1146/annurev-genet-080320-030537] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Though cell size varies between different cells and across species, the nuclear-to-cytoplasmic (N/C) ratio is largely maintained across species and within cell types. A cell maintains a relatively constant N/C ratio by coupling DNA content, nuclear size, and cell size. We explore how cells couple cell division and growth to DNA content. In some cases, cells use DNA as a molecular yardstick to control the availability of cell cycle regulators. In other cases, DNA sets a limit for biosynthetic capacity. Developmentally programmed variations in the N/C ratio for a given cell type suggest that a specific N/C ratio is required to respond to given physiological demands. Recent observations connecting decreased N/C ratios with cellular senescence indicate that maintaining the proper N/C ratio is essential for proper cellular functioning. Together, these findings suggest a causative, not simply correlative, role for the N/C ratio in regulating cell growth and cell cycle progression.
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Affiliation(s)
- Shruthi Balachandra
- Department of Biological Sciences, Dartmouth College, Hanover, New Hampshire, USA; ,
| | - Sharanya Sarkar
- Department of Microbiology and Immunology, Dartmouth College, Hanover, New Hampshire, USA;
| | - Amanda A Amodeo
- Department of Biological Sciences, Dartmouth College, Hanover, New Hampshire, USA; ,
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35
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Borowik AK, Davidyan A, Peelor FF, Voloviceva E, Doidge SM, Bubak MP, Mobley CB, McCarthy JJ, Dupont-Versteegden EE, Miller BF. Skeletal Muscle Nuclei in Mice are not Post-mitotic. FUNCTION 2022; 4:zqac059. [PMID: 36569816 PMCID: PMC9772608 DOI: 10.1093/function/zqac059] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2022] [Revised: 11/15/2022] [Accepted: 11/16/2022] [Indexed: 11/23/2022] Open
Abstract
The skeletal muscle research field generally accepts that nuclei in skeletal muscle fibers (ie, myonuclei) are post-mitotic and unable to proliferate. Because our deuterium oxide (D2O) labeling studies showed DNA synthesis in skeletal muscle tissue, we hypothesized that resident myonuclei can replicate in vivo. To test this hypothesis, we used a mouse model that temporally labeled myonuclei with GFP followed by D2O labeling during normal cage activity, functional overload, and with satellite cell ablation. During normal cage activity, we observed deuterium enrichment into myonuclear DNA in 7 out of 7 plantaris (PLA), 6 out of 6 tibialis anterior (TA), 5 out of 7 gastrocnemius (GAST), and 7 out of 7 quadriceps (QUAD). The average fractional synthesis rates (FSR) of DNA in myonuclei were: 0.0202 ± 0.0093 in PLA, 0.0239 ± 0.0040 in TA, 0.0076 ± 0. 0058 in GAST, and 0.0138 ± 0.0039 in QUAD, while there was no replication in myonuclei from EDL. These FSR values were largely reproduced in the overload and satellite cell ablation conditions, although there were higher synthesis rates in the overloaded PLA muscle. We further provided evidence that myonuclear replication is through endoreplication, which results in polyploidy. These novel findings contradict the dogma that skeletal muscle nuclei are post-mitotic and open potential avenues to harness the intrinsic replicative ability of myonuclei for muscle maintenance and growth.
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Affiliation(s)
- Agnieszka K Borowik
- Aging and Metabolism Research Program, Oklahoma Medical Research Foundation, 825 NE 13th St, Oklahoma City, OK 73104, USA
| | - Arik Davidyan
- Aging and Metabolism Research Program, Oklahoma Medical Research Foundation, 825 NE 13th St, Oklahoma City, OK 73104, USA
- Department of Biological Sciences, California State University Sacramento, 6000 J Street, Sacramento, CA, 95819, USA
| | - Frederick F Peelor
- Aging and Metabolism Research Program, Oklahoma Medical Research Foundation, 825 NE 13th St, Oklahoma City, OK 73104, USA
| | - Evelina Voloviceva
- Aging and Metabolism Research Program, Oklahoma Medical Research Foundation, 825 NE 13th St, Oklahoma City, OK 73104, USA
| | - Stephen M Doidge
- Aging and Metabolism Research Program, Oklahoma Medical Research Foundation, 825 NE 13th St, Oklahoma City, OK 73104, USA
| | - Matthew P Bubak
- Aging and Metabolism Research Program, Oklahoma Medical Research Foundation, 825 NE 13th St, Oklahoma City, OK 73104, USA
| | | | - John J McCarthy
- Center for Muscle Biology, University of Kentucky, Lexington, KY 40506, USA
- Department of Physiology, College of Medicine, University of Kentucky, Lexington, KY, 40506, USA
| | - Esther E Dupont-Versteegden
- Center for Muscle Biology, University of Kentucky, Lexington, KY 40506, USA
- Department of Physiology, College of Medicine, University of Kentucky, Lexington, KY, 40506, USA
- Department of Physical Therapy, College of Health Sciences, University of Kentucky, 900 S Limestone, Lexington, KY 40536, USA
| | - Benjamin F Miller
- Aging and Metabolism Research Program, Oklahoma Medical Research Foundation, 825 NE 13th St, Oklahoma City, OK 73104, USA
- Oklahoma City VA Medical Center, 921 NE 13th St, Oklahoma City, OK 73104, USA
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36
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Davies DM, van den Handel K, Bharadwaj S, Lengefeld J. Cellular enlargement - A new hallmark of aging? Front Cell Dev Biol 2022; 10:1036602. [PMID: 36438561 PMCID: PMC9688412 DOI: 10.3389/fcell.2022.1036602] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2022] [Accepted: 10/17/2022] [Indexed: 12/03/2023] Open
Abstract
Years of important research has revealed that cells heavily invest in regulating their size. Nevertheless, it has remained unclear why accurate size control is so important. Our recent study using hematopoietic stem cells (HSCs) in vivo indicates that cellular enlargement is causally associated with aging. Here, we present an overview of these findings and their implications. Furthermore, we performed a broad literature analysis to evaluate the potential of cellular enlargement as a new aging hallmark and to examine its connection to previously described aging hallmarks. Finally, we highlight interesting work presenting a correlation between cell size and age-related diseases. Taken together, we found mounting evidence linking cellular enlargement to aging and age-related diseases. Therefore, we encourage researchers from seemingly unrelated areas to take a fresh look at their data from the perspective of cell size.
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Affiliation(s)
- Daniel M. Davies
- Institute of Biotechnology, HiLIFE, University of Helsinki, Helsinki, Finland
| | - Kim van den Handel
- Institute of Biotechnology, HiLIFE, University of Helsinki, Helsinki, Finland
| | - Soham Bharadwaj
- Institute of Biotechnology, HiLIFE, University of Helsinki, Helsinki, Finland
| | - Jette Lengefeld
- Institute of Biotechnology, HiLIFE, University of Helsinki, Helsinki, Finland
- Center for Hematology and Regenerative Medicine, Department of Medicine Huddinge, Karolinska Institutet, Stockholm, Sweden
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37
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Yu JB, Lee DS, Padanilam BJ, Kim J. Repeated Administration of Cisplatin Transforms Kidney Fibroblasts through G2/M Arrest and Cellular Senescence. Cells 2022; 11:cells11213472. [PMID: 36359868 PMCID: PMC9655665 DOI: 10.3390/cells11213472] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Revised: 10/29/2022] [Accepted: 10/31/2022] [Indexed: 11/06/2022] Open
Abstract
Cisplatin is a potent chemotherapeutic used for the treatment of many types of cancer, but it has nephrotoxic side effects leading to acute kidney injury and subsequently chronic kidney disease (CKD). Previous work has focused on acute kidney tubular injury induced by cisplatin, whereas the chronic sequelae post-injury has not been well-explored. In the present study, we established a kidney fibroblast model of CKD induced by repeated administration of cisplatin (RAC) as a clinically relevant model. In NRK-49F rat kidney fibroblasts, RAC upregulated α-smooth muscle actin (α-SMA) and fibronectin proteins, suggesting that RAC induces kidney fibroblast-to-myofibroblast transformation. RAC also enhanced cell size, including the cell attachment surface area, nuclear area, and cell volume. Furthermore, RAC induced p21 expression and senescence-associated β-galactosidase activity, suggesting that kidney fibroblasts exposed to RAC develop a senescent phenotype. Inhibition of p21 reduced cellular senescence, hypertrophy, and myofibroblast transformation induced by RAC. Intriguingly, after RAC, kidney fibroblasts were arrested at the G2/M phase. Repeated treatment with paclitaxel as an inducer of G2/M arrest upregulated p21, α-SMA, and fibronectin in the kidney fibroblasts. Taken together, these data suggest that RAC transforms kidney fibroblasts into myofibroblasts through G2/M arrest and cellular senescence.
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Affiliation(s)
- Jia-Bin Yu
- Interdisciplinary Graduate Program in Advanced Convergence Technology & Science, Jeju National University, Jeju 63243, Korea
| | - Dong-Sun Lee
- Interdisciplinary Graduate Program in Advanced Convergence Technology & Science, Jeju National University, Jeju 63243, Korea
- Subtropical/Tropical Organism Gene Bank, Jeju National University, Jeju 63243, Korea
- Jeju Microbiome Research Center, Jeju National University, Jeju 63243, Korea
- Faculty of Biotechnology, College of Applied Life Sciences, SARI, Jeju National University, Jeju 63243, Korea
| | - Babu J. Padanilam
- Department of Urology, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Correspondence: (B.J.P.); (J.K.)
| | - Jinu Kim
- Interdisciplinary Graduate Program in Advanced Convergence Technology & Science, Jeju National University, Jeju 63243, Korea
- Department of Anatomy, Jeju National University College of Medicine, Jeju 63243, Korea
- Correspondence: (B.J.P.); (J.K.)
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38
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Liu X, Oh S, Kirschner MW. The uniformity and stability of cellular mass density in mammalian cell culture. Front Cell Dev Biol 2022; 10:1017499. [PMID: 36313562 PMCID: PMC9597509 DOI: 10.3389/fcell.2022.1017499] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2022] [Accepted: 09/23/2022] [Indexed: 12/04/2022] Open
Abstract
Cell dry mass is principally determined by the sum of biosynthesis and degradation. Measurable change in dry mass occurs on a time scale of hours. By contrast, cell volume can change in minutes by altering the osmotic conditions. How changes in dry mass and volume are coupled is a fundamental question in cell size control. If cell volume were proportional to cell dry mass during growth, the cell would always maintain the same cellular mass density, defined as cell dry mass dividing by cell volume. The accuracy and stability against perturbation of this proportionality has never been stringently tested. Normalized Raman Imaging (NoRI), can measure both protein and lipid dry mass density directly. Using this new technique, we have been able to investigate the stability of mass density in response to pharmaceutical and physiological perturbations in three cultured mammalian cell lines. We find a remarkably narrow mass density distribution within cells, that is, significantly tighter than the variability of mass or volume distribution. The measured mass density is independent of the cell cycle. We find that mass density can be modulated directly by extracellular osmolytes or by disruptions of the cytoskeleton. Yet, mass density is surprisingly resistant to pharmacological perturbations of protein synthesis or protein degradation, suggesting there must be some form of feedback control to maintain the homeostasis of mass density when mass is altered. By contrast, physiological perturbations such as starvation or senescence induce significant shifts in mass density. We have begun to shed light on how and why cell mass density remains fixed against some perturbations and yet is sensitive during transitions in physiological state.
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Affiliation(s)
| | | | - Marc W. Kirschner
- Department of Systems Biology, Harvard Medical School, Boston, MA, United States
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39
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Zhang S, Zatulovskiy E, Arand J, Sage J, Skotheim JM. The cell cycle inhibitor RB is diluted in G1 and contributes to controlling cell size in the mouse liver. Front Cell Dev Biol 2022; 10:965595. [PMID: 36092730 PMCID: PMC9452963 DOI: 10.3389/fcell.2022.965595] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2022] [Accepted: 07/27/2022] [Indexed: 12/14/2022] Open
Abstract
Every type of cell in an animal maintains a specific size, which likely contributes to its ability to perform its physiological functions. While some cell size control mechanisms are beginning to be elucidated through studies of cultured cells, it is unclear if and how such mechanisms control cell size in an animal. For example, it was recently shown that RB, the retinoblastoma protein, was diluted by cell growth in G1 to promote size-dependence of the G1/S transition. However, it remains unclear to what extent the RB-dilution mechanism controls cell size in an animal. We therefore examined the contribution of RB-dilution to cell size control in the mouse liver. Consistent with the RB-dilution model, genetic perturbations decreasing RB protein concentrations through inducible shRNA expression or through liver-specific Rb1 knockout reduced hepatocyte size, while perturbations increasing RB protein concentrations in an Fah -/- mouse model increased hepatocyte size. Moreover, RB concentration reflects cell size in G1 as it is lower in larger G1 hepatocytes. In contrast, concentrations of the cell cycle activators Cyclin D1 and E2f1 were relatively constant. Lastly, loss of Rb1 weakened cell size control, i.e., reduced the inverse correlation between how much cells grew in G1 and how large they were at birth. Taken together, our results show that an RB-dilution mechanism contributes to cell size control in the mouse liver by linking cell growth to the G1/S transition.
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Affiliation(s)
- Shuyuan Zhang
- Department of Biology, Stanford University, Stanford, CA, United States
| | | | - Julia Arand
- Departments of Pediatrics and Genetics, School of Medicine, Stanford University, Stanford, CA, United States
| | - Julien Sage
- Departments of Pediatrics and Genetics, School of Medicine, Stanford University, Stanford, CA, United States
| | - Jan M. Skotheim
- Department of Biology, Stanford University, Stanford, CA, United States
- Chan Zuckerberg Biohub, San Francisco, CA, United States
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