1
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Dixon JC, Frick CL, Leveille CL, Garrison P, Lee PA, Mogre SS, Morris B, Nivedita N, Vasan R, Chen J, Fraser CL, Gamlin CR, Harris LK, Hendershott MC, Johnson GT, Klein KN, Oluoch SA, Thirstrup DJ, Sluzewski MF, Wilhelm L, Yang R, Toloudis DM, Viana MP, Theriot JA, Rafelski SM. Colony context and size-dependent compensation mechanisms give rise to variations in nuclear growth trajectories. Cell Syst 2025; 16:101265. [PMID: 40315848 DOI: 10.1016/j.cels.2025.101265] [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: 07/24/2024] [Revised: 12/10/2024] [Accepted: 03/28/2025] [Indexed: 05/04/2025]
Abstract
To investigate how cellular variations arise across spatiotemporal scales in a population of identical healthy cells, we performed a data-driven analysis of nuclear growth variations in hiPS cell colonies as a model system. We generated a 3D timelapse dataset of thousands of nuclei over multiple days and developed open-source tools for image and data analysis and feature-based timelapse data exploration. Together, these data, tools, and workflows comprise a framework for systematic quantitative analysis of dynamics at individual and population levels, and the analysis further highlights important aspects to consider when interpreting timelapse data. We found that individual nuclear volume growth trajectories arise from short-timescale variations attributable to their spatiotemporal context within the colony. We identified a time-invariant volume compensation relationship between nuclear growth duration and starting volume across the population. Notably, we discovered that inheritance plays a crucial role in determining these two key nuclear growth features while other growth features are determined by their spatiotemporal context and are not inherited.
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Affiliation(s)
- Julie C Dixon
- Allen Institute for Cell Science, 615 Westlake Ave N, Seattle, WA 98109, USA
| | - Christopher L Frick
- Allen Institute for Cell Science, 615 Westlake Ave N, Seattle, WA 98109, USA
| | | | - Philip Garrison
- Allen Institute for Cell Science, 615 Westlake Ave N, Seattle, WA 98109, USA
| | - Peyton A Lee
- Allen Institute for Cell Science, 615 Westlake Ave N, Seattle, WA 98109, USA
| | - Saurabh S Mogre
- Allen Institute for Cell Science, 615 Westlake Ave N, Seattle, WA 98109, USA
| | - Benjamin Morris
- Allen Institute for Cell Science, 615 Westlake Ave N, Seattle, WA 98109, USA
| | - Nivedita Nivedita
- Allen Institute for Cell Science, 615 Westlake Ave N, Seattle, WA 98109, USA
| | - Ritvik Vasan
- Allen Institute for Cell Science, 615 Westlake Ave N, Seattle, WA 98109, USA
| | - Jianxu Chen
- Allen Institute for Cell Science, 615 Westlake Ave N, Seattle, WA 98109, USA
| | - Cameron L Fraser
- Allen Institute for Cell Science, 615 Westlake Ave N, Seattle, WA 98109, USA
| | - Clare R Gamlin
- Allen Institute for Cell Science, 615 Westlake Ave N, Seattle, WA 98109, USA
| | - Leigh K Harris
- Allen Institute for Cell Science, 615 Westlake Ave N, Seattle, WA 98109, USA
| | | | - Graham T Johnson
- Allen Institute for Cell Science, 615 Westlake Ave N, Seattle, WA 98109, USA
| | - Kyle N Klein
- Allen Institute for Cell Science, 615 Westlake Ave N, Seattle, WA 98109, USA
| | - Sandra A Oluoch
- Allen Institute for Cell Science, 615 Westlake Ave N, Seattle, WA 98109, USA
| | - Derek J Thirstrup
- Allen Institute for Cell Science, 615 Westlake Ave N, Seattle, WA 98109, USA
| | - M Filip Sluzewski
- Allen Institute for Cell Science, 615 Westlake Ave N, Seattle, WA 98109, USA
| | - Lyndsay Wilhelm
- Allen Institute for Cell Science, 615 Westlake Ave N, Seattle, WA 98109, USA
| | - Ruian Yang
- Allen Institute for Cell Science, 615 Westlake Ave N, Seattle, WA 98109, USA
| | - Daniel M Toloudis
- Allen Institute for Cell Science, 615 Westlake Ave N, Seattle, WA 98109, USA
| | - Matheus P Viana
- Allen Institute for Cell Science, 615 Westlake Ave N, Seattle, WA 98109, USA
| | - Julie A Theriot
- Department of Biology and Howard Hughes Medical Institute, University of Washington, Seattle, WA 98195, USA
| | - Susanne M Rafelski
- Allen Institute for Cell Science, 615 Westlake Ave N, Seattle, WA 98109, USA.
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2
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Toscano E, Cimmino E, Boccia A, Sepe L, Paolella G. Cell populations simulated in silico within SimulCell accurately reproduce the behaviour of experimental cell cultures. NPJ Syst Biol Appl 2025; 11:48. [PMID: 40379622 DOI: 10.1038/s41540-025-00518-w] [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: 11/27/2024] [Accepted: 04/08/2025] [Indexed: 05/19/2025] Open
Abstract
In silico simulations are used to understand cell behaviour by means of different approaches and tools, which range from reproducing average population trends to building lattice-based models to, more recently, creating populations of individual cell agents whose mass, volume and morphology behave according to more or less precise rules and models. In this work, a new agent-based simulator, SimulCell, was conceived, developed and used to predict the behaviour of eukaryotic cell cultures while growing attached to a flat surface. The system, starting from time-lapse microscopy experiments, uses growth, proliferation and migration models to create synthetic populations closely resembling original cultures. Support for cell-cell and cell-environment interaction makes cell agents able to react to changes in medium composition and other events, such as physical damage or chemical modifications occurring in the culture plate. The simulator is accessible through a web application and generates data that can be shown as tables and graphs or exported for further analyses.
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Affiliation(s)
- Elvira Toscano
- CEINGE Biotecnologie Avanzate Franco Salvatore, Naples, Italy
- Department of Molecular Medicine and Medical Biotechnology, Università Degli Studi di Napoli "Federico II", Naples, Italy
| | - Elena Cimmino
- Department of Molecular Medicine and Medical Biotechnology, Università Degli Studi di Napoli "Federico II", Naples, Italy
| | - Angelo Boccia
- CEINGE Biotecnologie Avanzate Franco Salvatore, Naples, Italy
| | - Leandra Sepe
- Department of Molecular Medicine and Medical Biotechnology, Università Degli Studi di Napoli "Federico II", Naples, Italy
| | - Giovanni Paolella
- CEINGE Biotecnologie Avanzate Franco Salvatore, Naples, Italy.
- Department of Molecular Medicine and Medical Biotechnology, Università Degli Studi di Napoli "Federico II", Naples, Italy.
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3
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Bu X, Ashby N, Vitali T, Lee S, Gottumukkala A, Yun K, Tabbara S, Latham P, Teal C, Chung I. Cell crowding activates pro-invasive mechanotransduction pathway in high-grade DCIS via TRPV4 inhibition and cell volume reduction. eLife 2025; 13:RP100490. [PMID: 40256993 PMCID: PMC12011371 DOI: 10.7554/elife.100490] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/22/2025] Open
Abstract
Cell crowding is a common microenvironmental factor influencing various disease processes, but its role in promoting cell invasiveness remains unclear. This study investigates the biomechanical changes induced by cell crowding, focusing on pro-invasive cell volume reduction in ductal carcinoma in situ (DCIS). Crowding specifically enhanced invasiveness in high-grade DCIS cells through significant volume reduction compared to hyperplasia-mimicking or normal cells. Mass spectrometry revealed that crowding selectively relocated ion channels, including TRPV4, to the plasma membrane in high-grade DCIS cells. TRPV4 inhibition triggered by crowding decreased intracellular calcium levels, reduced cell volume, and increased invasion and motility. During this process, TRPV4 membrane relocation primed the channel for later activation, compensating for calcium loss. Analyses of patient-derived breast cancer tissues confirmed that plasma membrane-associated TRPV4 is specific to high-grade DCIS and indicates the presence of a pro-invasive cell volume reduction mechanotransduction pathway. Hyperosmotic conditions and pharmacologic TRPV4 inhibition mimicked crowding-induced effects, while TRPV4 activation reversed them. Silencing TRPV4 diminished mechanotransduction in high-grade DCIS cells, reducing calcium depletion, volume reduction, and motility. This study uncovers a novel pro-invasive mechanotransduction pathway driven by cell crowding and identifies TRPV4 as a potential biomarker for predicting invasion risk in DCIS patients.
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Affiliation(s)
- Xiangning Bu
- Department of Anatomy and Cell Biology, School of Medicine and Health Sciences, George Washington UniversityWashington, DCUnited States
| | - Nathanael Ashby
- Department of Anatomy and Cell Biology, School of Medicine and Health Sciences, George Washington UniversityWashington, DCUnited States
| | - Teresa Vitali
- Department of Anatomy and Cell Biology, School of Medicine and Health Sciences, George Washington UniversityWashington, DCUnited States
| | - Sulgi Lee
- Department of Anatomy and Cell Biology, School of Medicine and Health Sciences, George Washington UniversityWashington, DCUnited States
| | - Ananya Gottumukkala
- Department of Anatomy and Cell Biology, School of Medicine and Health Sciences, George Washington UniversityWashington, DCUnited States
- Thomas Jefferson High School for Science and TechnologyAlexandriaUnited States
| | - Kangsun Yun
- Department of Anatomy and Cell Biology, School of Medicine and Health Sciences, George Washington UniversityWashington, DCUnited States
| | - Sana Tabbara
- Department of Pathology, George Washington Medical Faculty AssociatesWashington, DCUnited States
| | - Patricia Latham
- Department of Pathology, George Washington Medical Faculty AssociatesWashington, DCUnited States
| | - Christine Teal
- Department of Surgery, George Washington Medical Faculty AssociatesWashington, DCUnited States
| | - Inhee Chung
- Department of Anatomy and Cell Biology, School of Medicine and Health Sciences, George Washington UniversityWashington, DCUnited States
- Department of Biomedical Engineering, GW School of Engineering and Applied Science, George Washington UniversityWashington, DCUnited States
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4
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Sharma S, Berger H, Meyer T, Teruel MN. Inactivation of CDK4/6, CDK2, and ERK in G1-phase triggers differentiation commitment. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2025:2025.04.07.647597. [PMID: 40291750 PMCID: PMC12026982 DOI: 10.1101/2025.04.07.647597] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/30/2025]
Abstract
Terminal cell differentiation, a process vital for tissue development and regeneration where progenitor cells acquire specialized functions and permanently exit the cell cycle, is still poorly understood at the molecular level. Using live-cell imaging and adipogenesis as a model, we demonstrate that the initial stage involves a variable number of cell divisions driven by redundant CDK4/6 or CDK2 activation.. Subsequently, a delayed decrease in cyclin D1 and an increase in p27 levels leads to the attenuation of CDK4/6 and CDK2 activity. This results in G1 lengthening and the induction of PPARG, the master regulator of adipogenesis. PPARG then induces p21, and later p18, culminating in the irreversible inactivation of CDK4/6 and CDK2, and thus, permanent cell cycle exit. However, contrary to expectation, CDK inactivation alone is not sufficient to trigger commitment to differentiation and functional specialization; ERK inactivation is also required. Our study establishes that the coordinated activation and subsequent delayed inactivation of CDK4/6, CDK2, and ERK are crucial determinants for irreversible cell cycle exit and differentiation commitment in terminal cell differentiation.
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5
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Rega C, Tsitsa I, Roumeliotis TI, Krystkowiak I, Portillo M, Yu L, Vorhauser J, Pines J, Mansfeld J, Choudhary J, Davey NE. High resolution profiling of cell cycle-dependent protein and phosphorylation abundance changes in non-transformed cells. Nat Commun 2025; 16:2579. [PMID: 40089461 PMCID: PMC11910661 DOI: 10.1038/s41467-025-57537-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2024] [Accepted: 02/24/2025] [Indexed: 03/17/2025] Open
Abstract
The cell cycle governs a precise series of molecular events, regulated by coordinated changes in protein and phosphorylation abundance, that culminates in the generation of two daughter cells. Here, we present a proteomic and phosphoproteomic analysis of the human cell cycle in hTERT-RPE-1 cells using deep quantitative mass spectrometry by isobaric labelling. By analysing non-transformed cells and improving the temporal resolution and coverage of key cell cycle regulators, we present a dataset of cell cycle-dependent protein and phosphorylation site oscillation that offers a foundational reference for investigating cell cycle regulation. These data reveal regulatory intricacies including proteins and phosphorylation sites exhibiting cell cycle-dependent oscillation, and proteins targeted for degradation during mitotic exit. Integrated with complementary resources, our data link cycle-dependent abundance dynamics to functional changes and are accessible through the Cell Cycle database (CCdb), an interactive web-based resource for the cell cycle community.
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Affiliation(s)
- Camilla Rega
- Division of Cancer Biology, The Institute of Cancer Research, London, UK
| | - Ifigenia Tsitsa
- Division of Cancer Biology, The Institute of Cancer Research, London, UK
| | | | | | - Maria Portillo
- Division of Cancer Biology, The Institute of Cancer Research, London, UK
| | - Lu Yu
- Division of Cancer Biology, The Institute of Cancer Research, London, UK
| | - Julia Vorhauser
- Division of Cancer Biology, The Institute of Cancer Research, London, UK
| | - Jonathon Pines
- Division of Cancer Biology, The Institute of Cancer Research, London, UK
| | - Jörg Mansfeld
- Division of Cancer Biology, The Institute of Cancer Research, London, UK
| | - Jyoti Choudhary
- Division of Cancer Biology, The Institute of Cancer Research, London, UK
| | - Norman E Davey
- Division of Cancer Biology, The Institute of Cancer Research, London, UK.
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6
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Shanabag A, Armand J, Son E, Yang HW. Targeting CDK4/6 in breast cancer. Exp Mol Med 2025; 57:312-322. [PMID: 39930131 PMCID: PMC11873051 DOI: 10.1038/s12276-025-01395-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2024] [Revised: 11/15/2024] [Accepted: 11/17/2024] [Indexed: 03/04/2025] Open
Abstract
Dysregulation of the cell cycle machinery, particularly the overactivation of cyclin-dependent kinases 4 and 6 (CDK4/6), is a hallmark of breast cancer pathogenesis. The introduction of CDK4/6 inhibitors has transformed the treatment landscape for hormone receptor-positive breast cancer by effectively targeting abnormal cell cycle progression. However, despite their initial clinical success, drug resistance remains a significant challenge, with no reliable biomarkers available to predict treatment response or guide strategies for managing resistant populations. Consequently, numerous studies have sought to investigate the mechanisms driving resistance to optimize the therapeutic use of CDK4/6 inhibitors and improve patient outcomes. Here we examine the molecular mechanisms regulating the cell cycle, current clinical applications of CDK4/6 inhibitors in breast cancer, and key mechanisms contributing to drug resistance. Furthermore, we discuss emerging predictive biomarkers and highlight potential directions for overcoming resistance and enhancing therapeutic efficacy.
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Affiliation(s)
- Anusha Shanabag
- Department of Pathology and Cell Biology, Columbia University, New York, NY, USA
| | - Jessica Armand
- Department of Pathology and Cell Biology, Columbia University, New York, NY, USA
- Herbert Irving Comprehensive Cancer Center, Columbia University, New York, NY, USA
| | - Eugene Son
- Department of Pathology and Cell Biology, Columbia University, New York, NY, USA
| | - Hee Won Yang
- Department of Pathology and Cell Biology, Columbia University, New York, NY, USA.
- Herbert Irving Comprehensive Cancer Center, Columbia University, New York, NY, USA.
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7
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Beckers D, Jainarayanan AK, Dustin ML, Capera J. T Cell Resistance: On the Mechanisms of T Cell Non-activation. Immune Netw 2024; 24:e42. [PMID: 39801736 PMCID: PMC11711127 DOI: 10.4110/in.2024.24.e42] [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: 07/22/2024] [Revised: 10/28/2024] [Accepted: 11/12/2024] [Indexed: 01/16/2025] Open
Abstract
Immunological tolerance is a fundamental arm of any functioning immune system. Not only does tolerance mitigate collateral damage from host immune responses, but in doing so permits a robust response sufficient to clear infection as necessary. Yet, despite occupying such a cornerstone, research aiming to unravel the intricacies of tolerance induction is mired by interchangeable and often misused terminologies, with markers and mechanistic pathways that beg the question of redundancy. In this review we aim to define these boarders by providing new perspectives to long-standing theories of tolerance. Given the central role of T cells in enforcing immune cascades, in this review we choose to explore immunological tolerance through the perspective of T cell 'resistance to activation,' to delineate the contexts in which one tolerance mechanism has evolved over the other. By clarifying the important biological markers and cellular players underpinning T cell resistance to activation, we aim to encourage more purposeful and directed research into tolerance and, more-over, potential therapeutic strategies in autoimmune diseases and cancer. The tolerance field is in much need of reclassification and consideration, and in this review, we hope to open that conversation.
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Affiliation(s)
- Daniel Beckers
- The Kennedy Institute of Rheumatology, Nuffield Department of Orthopaedics Rheumatology & Musculoskeletal Sciences, University of Oxford, Oxford OX3 7FY, United Kingdom
| | - Ashwin K. Jainarayanan
- The Kennedy Institute of Rheumatology, Nuffield Department of Orthopaedics Rheumatology & Musculoskeletal Sciences, University of Oxford, Oxford OX3 7FY, United Kingdom
| | - Michael L. Dustin
- The Kennedy Institute of Rheumatology, Nuffield Department of Orthopaedics Rheumatology & Musculoskeletal Sciences, University of Oxford, Oxford OX3 7FY, United Kingdom
| | - Jesusa Capera
- The Kennedy Institute of Rheumatology, Nuffield Department of Orthopaedics Rheumatology & Musculoskeletal Sciences, University of Oxford, Oxford OX3 7FY, United Kingdom
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8
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Rizzo HE, Zhang AL, Gardel ML. Mechanochemical control systems regulating animal cell size. Curr Opin Cell Biol 2024; 91:102443. [PMID: 39504614 DOI: 10.1016/j.ceb.2024.102443] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2024] [Revised: 09/27/2024] [Accepted: 10/08/2024] [Indexed: 11/08/2024]
Abstract
Cell size regulation arises from physical manifestations of cell proliferation and metabolic pathways. On one hand, coordination between these systems yields a constant cell size over generations to maintain cell size homeostasis. However, active regulation of cell size is crucial to physiology and to establish broad variation of cell sizes within an individual organism, and is accomplished via physical and biochemical pathways modulated by myriad intrinsic and extrinsic cues. In this review, we explore recent data elucidating the mechanobiological regulation of the volume of animal cells and its coordination with metabolic and proliferative pathways.
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Affiliation(s)
- Heather E Rizzo
- Department of Molecular Genetics and Cell Biology, University of Chicago, Chicago, IL 60637, USA
| | - Andy L Zhang
- Department of Physics, The University of Chicago, Chicago, IL 60637, USA
| | - Margaret L Gardel
- Department of Molecular Genetics and Cell Biology, University of Chicago, Chicago, IL 60637, USA; Department of Physics, The University of Chicago, Chicago, IL 60637, USA; Pritzker School of Molecular Engineering, University of Chicago, Chicago, IL 60613, USA; CZ Biohub Chicago, LLC, Chicago, IL 60642, USA.
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9
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Höllring K, Nuić L, Rogić L, Kaliman S, Gehrer S, Wollnik C, Rehfeldt F, Hubert M, Smith AS. Capturing the mechanosensitivity of cell proliferation in models of epithelium. Proc Natl Acad Sci U S A 2024; 121:e2308126121. [PMID: 39467136 PMCID: PMC11551403 DOI: 10.1073/pnas.2308126121] [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: 05/15/2023] [Accepted: 07/23/2024] [Indexed: 10/30/2024] Open
Abstract
Despite the primary role of cell proliferation in tissue development and homeostatic maintenance, the interplay between cell density, cell mechanoresponse, and cell growth and division is not yet understood. In this article, we address this issue by reporting on an experimental investigation of cell proliferation on all time- and length-scales of the development of a model tissue, grown on collagen-coated glass or deformable substrates. Through extensive data analysis, we demonstrate the relation between mechanoresponse and probability for cell division, as a function of the local cell density. Motivated by these results, we construct a minimal model of cell division in tissue environment that can recover the data. By parameterizing the growth and the dividing phases of the cell cycle, and introducing such a proliferation model in dissipative particle dynamics simulations, we recover the mechanoresponsive, time-dependent density profiles in 2D tissues growing to macroscopic scales. The importance of separating the cell population into growing and dividing cells, each characterized by a particular time scale, is further emphasized by calculations of density profiles based on adapted Fisher-Kolmogorov equations. Together, these results show that the mechanoresponse on the level of a constitutive cell and its proliferation results in a matrix-sensitive active pressure. The latter evokes massive cooperative displacement of cells in the invading tissue and is a key factor for developing large-scale structures in the steady state.
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Affiliation(s)
- Kevin Höllring
- Physics Underlying Life Sciences Group, Department of Physics, Interdisciplinary Center for Nanostructured Films, Friedrich-Alexander Universität Erlangen-Nürnberg, Erlangen91058, Germany
| | - Lovro Nuić
- Group for Computational Life Sciences, Division of Physical Chemistry, Ruđer Bošković Institute, Zagreb10000, Croatia
| | - Luka Rogić
- Group for Computational Life Sciences, Division of Physical Chemistry, Ruđer Bošković Institute, Zagreb10000, Croatia
| | - Sara Kaliman
- Physics Underlying Life Sciences Group, Department of Physics, Interdisciplinary Center for Nanostructured Films, Friedrich-Alexander Universität Erlangen-Nürnberg, Erlangen91058, Germany
| | - Simone Gehrer
- Physics Underlying Life Sciences Group, Department of Physics, Interdisciplinary Center for Nanostructured Films, Friedrich-Alexander Universität Erlangen-Nürnberg, Erlangen91058, Germany
| | - Carina Wollnik
- Faculty of Physics, University of Göttingen, Third Institute of Physics-Biophysics, Göttingen37077, Germany
| | - Florian Rehfeldt
- Faculty of Physics, University of Göttingen, Third Institute of Physics-Biophysics, Göttingen37077, Germany
- Department of Physics, University of Bayreuth, Experimental Physics 1, Bayreuth95440, Germany
| | - Maxime Hubert
- Physics Underlying Life Sciences Group, Department of Physics, Interdisciplinary Center for Nanostructured Films, Friedrich-Alexander Universität Erlangen-Nürnberg, Erlangen91058, Germany
- Group for Computational Life Sciences, Division of Physical Chemistry, Ruđer Bošković Institute, Zagreb10000, Croatia
| | - Ana-Sunčana Smith
- Physics Underlying Life Sciences Group, Department of Physics, Interdisciplinary Center for Nanostructured Films, Friedrich-Alexander Universität Erlangen-Nürnberg, Erlangen91058, Germany
- Group for Computational Life Sciences, Division of Physical Chemistry, Ruđer Bošković Institute, Zagreb10000, Croatia
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10
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Ferrick KR, Fan Y, Ratnayeke N, Teruel MN, Meyer T. Transient proliferation by reversible YAP and mitogen-control of the cyclin D1/p27 ratio. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.10.11.617852. [PMID: 39416132 PMCID: PMC11482934 DOI: 10.1101/2024.10.11.617852] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 10/19/2024]
Abstract
Hippo-YAP signaling orchestrates epithelial tissue repair and is therefore an attractive target in regenerative medicine. Yet it is unresolved how YAP integrates with mitogen signaling and contact inhibition to control the underlying transient proliferative response. Here we show that reduced contact inhibition, increased mitogen signaling, and YAP-TEAD activation converge on increasing the nuclear cyclin D1/p27 protein ratio during G1 phase, towards a threshold ratio that dictates whether individual cells enter or exit the cell cycle. YAP increases this ratio indirectly, in concert with mitogen signaling, by increasing EGFR and other receptors that signal primarily through ERK. After a delay, contact inhibition suppresses YAP activity which gradually downregulates mitogen signaling and the cyclin D1/p27 ratio. Increasing YAP activity by ablating the suppressor Merlin/NF2 reveals a balancing mechanism in which YAP suppression and contact inhibition of proliferation can be recovered but only at higher local cell density. Thus, critical for tissue repair, robust proliferation responses result from the YAP-induced and receptor-mediated prolonged increase in the cyclin D1/p27 ratio, which is only reversed by delayed suppression of receptor signaling after contact inhibition of YAP.
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Affiliation(s)
- Katherine R. Ferrick
- Department of Cell and Developmental Biology, Weill Cornell Medicine, New York, NY, USA
- Department of Chemical and Systems Biology, Stanford Medicine, Stanford, CA, USA
| | - Yilin Fan
- Department of Cell and Developmental Biology, Weill Cornell Medicine, New York, NY, USA
- Department of Chemical and Systems Biology, Stanford Medicine, Stanford, CA, USA
- Current: Department of Pathology and Center for Cancer Research, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Nalin Ratnayeke
- Department of Cell and Developmental Biology, Weill Cornell Medicine, New York, NY, USA
- Department of Chemical and Systems Biology, Stanford Medicine, Stanford, CA, USA
- Current: Cancer Biology and Genetics Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Mary N. Teruel
- Department of Biochemistry, Weill Cornell Medicine, New York, NY, USA
| | - Tobias Meyer
- Department of Cell and Developmental Biology, Weill Cornell Medicine, New York, NY, USA
- Department of Chemical and Systems Biology, Stanford Medicine, Stanford, CA, USA
- Lead contact
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11
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Leung CWB, Wall J, Esashi F. From rest to repair: Safeguarding genomic integrity in quiescent cells. DNA Repair (Amst) 2024; 142:103752. [PMID: 39167890 DOI: 10.1016/j.dnarep.2024.103752] [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: 05/16/2024] [Revised: 08/12/2024] [Accepted: 08/12/2024] [Indexed: 08/23/2024]
Abstract
Quiescence is an important non-pathological state in which cells pause cell cycle progression temporarily, sometimes for decades, until they receive appropriate proliferative stimuli. Quiescent cells make up a significant proportion of the body, and maintaining genomic integrity during quiescence is crucial for tissue structure and function. While cells in quiescence are spared from DNA damage associated with DNA replication or mitosis, they are still exposed to various sources of endogenous DNA damage, including those induced by normal transcription and metabolism. As such, it is vital that cells retain their capacity to effectively repair lesions that may occur and return to the cell cycle without losing their cellular properties. Notably, while DNA repair pathways are often found to be downregulated in quiescent cells, emerging evidence suggests the presence of active or differentially regulated repair mechanisms. This review aims to provide a current understanding of DNA repair processes during quiescence in mammalian systems and sheds light on the potential pathological consequences of inefficient or inaccurate repair in quiescent cells.
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Affiliation(s)
| | - Jacob Wall
- Sir William Dunn School of Pathology, South Parks Road, Oxford, UK
| | - Fumiko Esashi
- Sir William Dunn School of Pathology, South Parks Road, Oxford, UK.
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12
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Dixon JC, Frick CL, Leveille CL, Garrison P, Lee PA, Mogre SS, Morris B, Nivedita N, Vasan R, Chen J, Fraser CL, Gamlin CR, Harris LK, Hendershott MC, Johnson GT, Klein KN, Oluoch SA, Thirstrup DJ, Sluzewski MF, Wilhelm L, Yang R, Toloudis DM, Viana MP, Theriot JA, Rafelski SM. Colony context and size-dependent compensation mechanisms give rise to variations in nuclear growth trajectories. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.28.601071. [PMID: 38979140 PMCID: PMC11230432 DOI: 10.1101/2024.06.28.601071] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/10/2024]
Abstract
To investigate the fundamental question of how cellular variations arise across spatiotemporal scales in a population of identical healthy cells, we focused on nuclear growth in hiPS cell colonies as a model system. We generated a 3D timelapse dataset of thousands of nuclei over multiple days, and developed open-source tools for image and data analysis and an interactive timelapse viewer for exploring quantitative features of nuclear size and shape. We performed a data-driven analysis of nuclear growth variations across timescales. We found that individual nuclear volume growth trajectories arise from short timescale variations attributable to their spatiotemporal context within the colony. We identified a strikingly time-invariant volume compensation relationship between nuclear growth duration and starting volume across the population. Notably, we discovered that inheritance plays a crucial role in determining these two key nuclear growth features while other growth features are determined by their spatiotemporal context and are not inherited.
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Affiliation(s)
- Julie C. Dixon
- Allen Institute for Cell Science, 615 Westlake Ave N, Seattle, WA, 98109, USA
- These authors contributed equally to this work
| | - Christopher L. Frick
- Allen Institute for Cell Science, 615 Westlake Ave N, Seattle, WA, 98109, USA
- These authors contributed equally to this work
| | - Chantelle L. Leveille
- Allen Institute for Cell Science, 615 Westlake Ave N, Seattle, WA, 98109, USA
- These authors contributed equally to this work
| | - Philip Garrison
- Allen Institute for Cell Science, 615 Westlake Ave N, Seattle, WA, 98109, USA
- These authors contributed equally to this work
| | - Peyton A. Lee
- Allen Institute for Cell Science, 615 Westlake Ave N, Seattle, WA, 98109, USA
- These authors contributed equally to this work
| | - Saurabh S. Mogre
- Allen Institute for Cell Science, 615 Westlake Ave N, Seattle, WA, 98109, USA
- These authors contributed equally to this work
| | - Benjamin Morris
- Allen Institute for Cell Science, 615 Westlake Ave N, Seattle, WA, 98109, USA
- These authors contributed equally to this work
| | - Nivedita Nivedita
- Allen Institute for Cell Science, 615 Westlake Ave N, Seattle, WA, 98109, USA
- These authors contributed equally to this work
| | - Ritvik Vasan
- Allen Institute for Cell Science, 615 Westlake Ave N, Seattle, WA, 98109, USA
- These authors contributed equally to this work
| | - Jianxu Chen
- Allen Institute for Cell Science, 615 Westlake Ave N, Seattle, WA, 98109, USA
- Present address: Leibniz-Institut fur Analytische Wissenschaften – ISAS – e.V., Dortmund, 44139, Germany
| | - Cameron L. Fraser
- Allen Institute for Cell Science, 615 Westlake Ave N, Seattle, WA, 98109, USA
| | - Clare R. Gamlin
- Allen Institute for Cell Science, 615 Westlake Ave N, Seattle, WA, 98109, USA
| | - Leigh K. Harris
- Allen Institute for Cell Science, 615 Westlake Ave N, Seattle, WA, 98109, USA
| | | | - Graham T. Johnson
- Allen Institute for Cell Science, 615 Westlake Ave N, Seattle, WA, 98109, USA
| | - Kyle N. Klein
- Allen Institute for Cell Science, 615 Westlake Ave N, Seattle, WA, 98109, USA
| | - Sandra A. Oluoch
- Allen Institute for Cell Science, 615 Westlake Ave N, Seattle, WA, 98109, USA
| | - Derek J. Thirstrup
- Allen Institute for Cell Science, 615 Westlake Ave N, Seattle, WA, 98109, USA
| | - M. Filip Sluzewski
- Allen Institute for Cell Science, 615 Westlake Ave N, Seattle, WA, 98109, USA
| | - Lyndsay Wilhelm
- Allen Institute for Cell Science, 615 Westlake Ave N, Seattle, WA, 98109, USA
| | - Ruian Yang
- Allen Institute for Cell Science, 615 Westlake Ave N, Seattle, WA, 98109, USA
| | - Daniel M. Toloudis
- Allen Institute for Cell Science, 615 Westlake Ave N, Seattle, WA, 98109, USA
| | - Matheus P. Viana
- Allen Institute for Cell Science, 615 Westlake Ave N, Seattle, WA, 98109, USA
| | - Julie A. Theriot
- Department of Biology and Howard Hughes Medical Institute, University of Washington, Seattle, WA 98195, USA
| | - Susanne M. Rafelski
- Allen Institute for Cell Science, 615 Westlake Ave N, Seattle, WA, 98109, USA
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13
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Fulman-Levy H, Cohen-Harazi R, Levi B, Argaev-Frenkel L, Abramovich I, Gottlieb E, Hofmann S, Koman I, Nesher E. Metabolic alterations and cellular responses to β-Hydroxybutyrate treatment in breast cancer cells. Cancer Metab 2024; 12:16. [PMID: 38812058 PMCID: PMC11134656 DOI: 10.1186/s40170-024-00339-1] [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: 07/18/2023] [Accepted: 03/18/2024] [Indexed: 05/31/2024] Open
Abstract
BACKGROUND The ketogenic diet (KD), based on high fat (over 70% of daily calories), low carbohydrate, and adequate protein intake, has become popular due to its potential therapeutic benefits for several diseases including cancer. Under KD and starvation conditions, the lack of carbohydrates promotes the production of ketone bodies (KB) from fats by the liver as an alternative source of metabolic energy. KD and starvation may affect the metabolism in cancer cells, as well as tumor characteristics. The aim of this study is to evaluate the effect of KD conditions on a wide variety of aspects of breast cancer cells in vitro. METHODS Using two cancer and one non-cancer breast cell line, we evaluate the effect of β-hydroxybutyrate (βHb) treatment on cell growth, survival, proliferation, colony formation, and migration. We also assess the effect of KB on metabolic profile of the cells. Using RNAseq analysis, we elucidate the effect of βHb on the gene expression profile. RESULTS Significant effects were observed following treatment by βHb which include effects on viability, proliferation, and colony formation of MCF7 cells, and different effects on colony formation of MDA-MB-231 cells, with no such effects on non-cancer HB2 cells. We found no changes in glucose intake or lactate output following βHb treatment as measured by LC-MS, but an increase in reactive oxygen species (ROS) level was detected. RNAseq analysis demonstrated significant changes in genes involved in lipid metabolism, cancer, and oxidative phosphorylation. CONCLUSIONS Based on our results, we conclude that differential response of cancer cell lines to βHb treatment, as alternative energy source or signal to alter lipid metabolism and oncogenicity, supports the need for a personalized approach to breast cancer patient treatment.
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Affiliation(s)
- Hadas Fulman-Levy
- Department of Molecular Biology, Ariel University, Ariel, 4070000, Israel
- Institute for Personalized and Translational Medicine, Ariel University, Ariel, 4070000, Israel
| | - Raichel Cohen-Harazi
- Institute for Personalized and Translational Medicine, Ariel University, Ariel, 4070000, Israel
| | - Bar Levi
- Department of Molecular Biology, Ariel University, Ariel, 4070000, Israel
| | - Lital Argaev-Frenkel
- Institute for Personalized and Translational Medicine, Ariel University, Ariel, 4070000, Israel
| | - Ifat Abramovich
- Rappaport Faculty of Medicine and Research Institute, Technion, Haifa, 3525422, Israel
| | - Eyal Gottlieb
- Rappaport Faculty of Medicine and Research Institute, Technion, Haifa, 3525422, Israel
| | - Sarah Hofmann
- Medical Faculty Mannheim, Heidelberg University, 68167 , Mannheim, Germany
| | - Igor Koman
- Department of Molecular Biology, Ariel University, Ariel, 4070000, Israel.
- Institute for Personalized and Translational Medicine, Ariel University, Ariel, 4070000, Israel.
| | - Elimelech Nesher
- Department of Molecular Biology, Ariel University, Ariel, 4070000, Israel.
- Institute for Personalized and Translational Medicine, Ariel University, Ariel, 4070000, Israel.
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14
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Yang HW. Investigating Heterogeneous Cell-Cycle Progression Using Single-Cell Imaging Approaches. Methods Mol Biol 2024; 2740:263-273. [PMID: 38393481 DOI: 10.1007/978-1-0716-3557-5_16] [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] [Indexed: 02/25/2024]
Abstract
Investigating cell-cycle progression has been challenging due to the complex interconnectivity of regulatory processes and inherent cell-to-cell heterogeneity, which often require synchronization procedures. However, recent advancements in cell-cycle sensors and single-cell imaging techniques have turned this heterogeneity into an advantage for investigating the molecular mechanisms underlying diverse responses. This has led to significant progress in our understanding of cell-cycle regulation. In this paper, we present a comprehensive live single-cell imaging workflow that leverages cutting-edge live-cell sensors. These advanced single-cell imaging procedures provide promising opportunities for elucidating the molecular mechanisms underpinnings of heterogeneous responses in cell-cycle progression.
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Affiliation(s)
- Hee Won Yang
- Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, NY, USA.
- Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY, USA.
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15
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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: 5] [Impact Index Per Article: 2.5] [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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16
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Ram A, Murphy D, DeCuzzi N, Patankar M, Hu J, Pargett M, Albeck JG. A guide to ERK dynamics, part 2: downstream decoding. Biochem J 2023; 480:1909-1928. [PMID: 38038975 PMCID: PMC10754290 DOI: 10.1042/bcj20230277] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2023] [Revised: 11/03/2023] [Accepted: 11/09/2023] [Indexed: 12/02/2023]
Abstract
Signaling by the extracellular signal-regulated kinase (ERK) pathway controls many cellular processes, including cell division, death, and differentiation. In this second installment of a two-part review, we address the question of how the ERK pathway exerts distinct and context-specific effects on multiple processes. We discuss how the dynamics of ERK activity induce selective changes in gene expression programs, with insights from both experiments and computational models. With a focus on single-cell biosensor-based studies, we summarize four major functional modes for ERK signaling in tissues: adjusting the size of cell populations, gradient-based patterning, wave propagation of morphological changes, and diversification of cellular gene expression states. These modes of operation are disrupted in cancer and other related diseases and represent potential targets for therapeutic intervention. By understanding the dynamic mechanisms involved in ERK signaling, there is potential for pharmacological strategies that not only simply inhibit ERK, but also restore functional activity patterns and improve disease outcomes.
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Affiliation(s)
- Abhineet Ram
- Department of Molecular and Cellular Biology, University of California, Davis, CA, U.S.A
| | - Devan Murphy
- Department of Molecular and Cellular Biology, University of California, Davis, CA, U.S.A
| | - Nicholaus DeCuzzi
- Department of Molecular and Cellular Biology, University of California, Davis, CA, U.S.A
| | - Madhura Patankar
- Department of Molecular and Cellular Biology, University of California, Davis, CA, U.S.A
| | - Jason Hu
- Department of Molecular and Cellular Biology, University of California, Davis, CA, U.S.A
| | - Michael Pargett
- Department of Molecular and Cellular Biology, University of California, Davis, CA, U.S.A
| | - John G. Albeck
- Department of Molecular and Cellular Biology, University of California, Davis, CA, U.S.A
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17
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Simonov YP, Tatarskiy VV, Georgieva SG, Soshnikova NV. Contact Inhibition of Proliferation Is Accompanied by Expression of the PHF10D Subunit of the Chromatin Remodeling Complex PBAF in Mouse and Human Cell Lines. DOKL BIOCHEM BIOPHYS 2023; 513:S18-S22. [PMID: 38189884 DOI: 10.1134/s1607672923700667] [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: 11/03/2023] [Revised: 11/17/2023] [Accepted: 11/17/2023] [Indexed: 01/09/2024]
Abstract
PHF10 is a subunit of the PBAF complex, which regulates the expression of many genes in developing and maturing organisms. PHF10 has four isoforms that differ in domain structure. The PHF10A isoform, containing a DPF domain at the C-terminus and 46 amino acids at the N-terminus, is necessary for the expression of proliferation genes; the functions of the other isoforms are less studied. In this work, we have established that, upon contact inhibition of mouse and human cell proliferation caused by the establishment of a tight junction and adherence junction between cells, the expression of the PHF10A isoform stops and instead the PHF10D isoform is expressed, which does not contain DPF-domain and N-terminal sequence. The function of the PHF10D isoform may be associated with the establishment of intercellular contacts.
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Affiliation(s)
- Yu P Simonov
- Department of Transcription Factors, Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | - V V Tatarskiy
- Institute of Gene Biology, Russian Academy of Sciences, Moscow, Russia
| | - S G Georgieva
- Department of Transcription Factors, Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | - N V Soshnikova
- Department of Transcription Factors, Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia.
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia.
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18
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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: 20] [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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19
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Liu C, Kudo T, Ye X, Gascoigne K. Cell-to-cell variability in Myc dynamics drives transcriptional heterogeneity in cancer cells. Cell Rep 2023; 42:112401. [PMID: 37060565 DOI: 10.1016/j.celrep.2023.112401] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Revised: 03/07/2023] [Accepted: 03/31/2023] [Indexed: 04/16/2023] Open
Abstract
Cell-to-cell heterogeneity is vital for tumor evolution and survival. How cancer cells achieve and exploit this heterogeneity remains an active area of research. Here, we identify c-Myc as a highly heterogeneously expressed transcription factor and an orchestrator of transcriptional and phenotypic diversity in cancer cells. By monitoring endogenous c-Myc protein in individual living cells, we report the surprising pulsatile nature of c-Myc expression and the extensive cell-to-cell variability in its dynamics. We further show that heterogeneity in c-Myc dynamics leads to variable target gene transcription and that timing of c-Myc expression predicts cell-cycle progression rates and drug sensitivities. Together, our data advocate for a model in which cancer cells increase the heterogeneity of functionally diverse transcription factors such as c-Myc to rapidly survey transcriptional landscapes and survive stress.
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Affiliation(s)
- Chad Liu
- Department of Discovery Oncology, Genentech, Inc., South San Francisco, CA 94080, USA
| | - Takamasa Kudo
- Department of Cellular and Tissue Genomics, Genentech, Inc., South San Francisco, CA 94080, USA
| | - Xin Ye
- Department of Discovery Oncology, Genentech, Inc., South San Francisco, CA 94080, USA
| | - Karen Gascoigne
- Department of Discovery Oncology, Genentech, Inc., South San Francisco, CA 94080, USA.
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20
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Johnson MS, Cook JG. Cell cycle exits and U-turns: Quiescence as multiple reversible forms of arrest. Fac Rev 2023; 12:5. [PMID: 36923701 PMCID: PMC10009890 DOI: 10.12703/r/12-5] [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] [Indexed: 03/10/2023] Open
Abstract
Cell proliferation control is essential during development and for maintaining adult tissues. Loss of that control promotes not only oncogenesis when cells proliferate inappropriately but also developmental abnormalities or degeneration when cells fail to proliferate when and where needed. To ensure that cells are produced at the right place and time, an intricate balance of pro-proliferative and anti-proliferative signals impacts the probability that cells undergo cell cycle exit to quiescence, or G0 phase. This brief review describes recent advances in our understanding of how and when quiescence is initiated and maintained in mammalian cells. We highlight the growing appreciation for quiescence as a collection of context-dependent distinct states.
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Affiliation(s)
- Martha Sharisha Johnson
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, NC, USA
| | - Jeanette Gowen Cook
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, NC, USA
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21
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Lin X, Wang C, Fang F, Zhou S. A simple integrated microfluidic platform for the research of hydrogels containing gradients in cell density induced breast cancer electrochemotherapy. Talanta 2023; 253:123920. [PMID: 36122433 DOI: 10.1016/j.talanta.2022.123920] [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: 05/10/2022] [Revised: 08/28/2022] [Accepted: 09/04/2022] [Indexed: 12/13/2022]
Abstract
Cell density is important for tumour metastasis, treatment and prognosis. Characterizing changes in cell density for electrochemotherapy (ECT) can reveal sub-populations in pathological states, and adjust treatment program. In this work, a simple and convenient microfluidic platform was developed to study the effect cell density on ECT by integrating the improved cell gradient generator, cell culture chamber and indium tin oxide interdigital electrodes. Agarose, as extracellular matrix (ECM), was used to 3D cell culture to imitate in vivo microenvironment. The precision and reproducibility of cell density gradient with agarose solution were achieved because the hydrophobic modification of microchannels surface resulted in reducing cell adhesion and residue. ECT cytotoxicity assay with difference in cell densities was studied. The results showed that tumour cell density is one of the most factors for ECT treatment and ECT cytotoxicity has a certain of cell density-depended. But only electroporation on low cell density level, ECM would be one of the most key factors for ECT cytotoxicity, which would provide a new idea for chip-based cell assay in clinical diagnosis and drug screening in ordinary laboratories.
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Affiliation(s)
- Xuexia Lin
- Department of Chemical Engineering & Pharmaceutical Engineering, College of Chemical Engineering, Huaqiao University, Xiamen, 361021, PR China.
| | - Chenjing Wang
- Department of Chemical Engineering & Pharmaceutical Engineering, College of Chemical Engineering, Huaqiao University, Xiamen, 361021, PR China
| | - Feixiang Fang
- Department of Chemical Engineering & Pharmaceutical Engineering, College of Chemical Engineering, Huaqiao University, Xiamen, 361021, PR China
| | - Shufeng Zhou
- Department of Chemical Engineering & Pharmaceutical Engineering, College of Chemical Engineering, Huaqiao University, Xiamen, 361021, PR China
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22
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Mohammadi F, Visagan S, Gross SM, Karginov L, Lagarde JC, Heiser LM, Meyer AS. A lineage tree-based hidden Markov model quantifies cellular heterogeneity and plasticity. Commun Biol 2022; 5:1258. [PMID: 36396800 PMCID: PMC9671968 DOI: 10.1038/s42003-022-04208-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Accepted: 11/01/2022] [Indexed: 11/18/2022] Open
Abstract
Individual cells can assume a variety of molecular and phenotypic states and recent studies indicate that cells can rapidly adapt in response to therapeutic stress. Such phenotypic plasticity may confer resistance, but also presents opportunities to identify molecular programs that could be targeted for therapeutic benefit. Approaches to quantify tumor-drug responses typically focus on snapshot, population-level measurements. While informative, these methods lack lineage and temporal information, which are particularly critical for understanding dynamic processes such as cell state switching. As new technologies have become available to measure lineage relationships, modeling approaches will be needed to identify the forms of cell-to-cell heterogeneity present in these data. Here we apply a lineage tree-based adaptation of a hidden Markov model that employs single cell lineages as input to learn the characteristic patterns of phenotypic heterogeneity and state transitions. In benchmarking studies, we demonstrated that the model successfully classifies cells within experimentally-tractable dataset sizes. As an application, we analyzed experimental measurements in cancer and non-cancer cell populations under various treatments. We find evidence of multiple phenotypically distinct states, with considerable heterogeneity and unique drug responses. In total, this framework allows for the flexible modeling of single cell heterogeneity across lineages to quantify, understand, and control cell state switching.
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Affiliation(s)
- Farnaz Mohammadi
- Department of Bioengineering, University of California, Los Angeles, CA, USA
| | - Shakthi Visagan
- Department of Bioengineering, University of California, Los Angeles, CA, USA
| | - Sean M Gross
- Department of Biomedical Engineering, Oregon Health & Science University, Portland, OR, USA
| | - Luka Karginov
- Department of Bioengineering, University of Illinois, Urbana Champaign, IL, USA
| | - J C Lagarde
- Department of Bioengineering, University of California, Los Angeles, CA, USA
| | - Laura M Heiser
- Department of Biomedical Engineering, Oregon Health & Science University, Portland, OR, USA
| | - Aaron S Meyer
- Department of Bioengineering, University of California, Los Angeles, CA, USA.
- Department of Bioinformatics, University of California, Los Angeles, CA, USA.
- Jonsson Comprehensive Cancer Center, University of California, Los Angeles, CA, USA.
- Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, University of California, Los Angeles, CA, USA.
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23
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Kim S, Leong A, Kim M, Yang HW. CDK4/6 initiates Rb inactivation and CDK2 activity coordinates cell-cycle commitment and G1/S transition. Sci Rep 2022; 12:16810. [PMID: 36207346 PMCID: PMC9546874 DOI: 10.1038/s41598-022-20769-5] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2021] [Accepted: 09/19/2022] [Indexed: 02/04/2023] Open
Abstract
External signaling controls cell-cycle entry until cells irreversibly commit to the cell cycle to ensure faithful DNA replication. This process is tightly regulated by cyclin-dependent kinases (CDKs) and the retinoblastoma protein (Rb). Here, using live-cell sensors for CDK4/6 and CDK2 activities, we propose that CDK4/6 initiates Rb inactivation and CDK2 activation, which coordinates the timing of cell-cycle commitment and sequential G1/S transition. Our data show that CDK4/6 activation induces Rb inactivation and thereby E2F activation, driving a gradual increase in CDK2 activity. We found that rapid CDK4/6 inhibition can reverse cell-cycle entry until CDK2 activity reaches to high levels. This suggests that high CDK2 activity is required to initiate CDK2-Rb positive feedback and CDK4/6-indpendent cell-cycle progression. Since CDK2 activation also facilitates initiation of DNA replication, the timing of CDK2-Rb positive feedback is coupled with the G1/S transition. Our experiments, which acutely increased CDK2 activity by cyclin E1 overexpression, indicate that cells commit to the cell cycle before triggering DNA replication. Together, our data suggest that CDK4/6 inactivates Rb to begin E2F and CDK2 activation, and high CDK2 activity is necessary and sufficient to generate a bistable switch for Rb phosphorylation before DNA replication. These findings highlight how cells initiate the cell cycle and subsequently commit to the cell cycle before the G1/S transition.
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Affiliation(s)
- Sungsoo Kim
- Department of Pathology and Cell Biology, Columbia University, New York, NY, 10032, USA
| | - Alessandra Leong
- Department of Pathology and Cell Biology, Columbia University, New York, NY, 10032, USA
| | - Minah Kim
- Department of Pathology and Cell Biology, Columbia University, New York, NY, 10032, USA.
- Herbert Irving Comprehensive Cancer Center, Columbia University, New York, NY, 10032, USA.
| | - Hee Won Yang
- Department of Pathology and Cell Biology, Columbia University, New York, NY, 10032, USA.
- Herbert Irving Comprehensive Cancer Center, Columbia University, New York, NY, 10032, USA.
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24
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Lim R, Banerjee A, Biswas R, Chari AN, Raghavan S. Mechanotransduction through adhesion molecules: Emerging roles in regulating the stem cell niche. Front Cell Dev Biol 2022; 10:966662. [PMID: 36172276 PMCID: PMC9511051 DOI: 10.3389/fcell.2022.966662] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2022] [Accepted: 07/18/2022] [Indexed: 11/23/2022] Open
Abstract
Stem cells have been shown to play an important role in regenerative medicine due to their proliferative and differentiation potential. The challenge, however, lies in regulating and controlling their potential for this purpose. Stem cells are regulated by growth factors as well as an array of biochemical and mechanical signals. While the role of biochemical signals and growth factors in regulating stem cell homeostasis is well explored, the role of mechanical signals has only just started to be investigated. Stem cells interact with their niche or to other stem cells via adhesion molecules that eventually transduce mechanical cues to maintain their homeostatic function. Here, we present a comprehensive review on our current understanding of the influence of the forces perceived by cell adhesion molecules on the regulation of stem cells. Additionally, we provide insights on how this deeper understanding of mechanobiology of stem cells has translated toward therapeutics.
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Affiliation(s)
- Ryan Lim
- A∗STAR Skin Research Lab (ASRL), Agency for Science, Technology and Research (A*STAR) 8A Biomedical Grove, Singapore, Singapore
| | - Avinanda Banerjee
- A∗STAR Skin Research Lab (ASRL), Agency for Science, Technology and Research (A*STAR) 8A Biomedical Grove, Singapore, Singapore
| | - Ritusree Biswas
- Institute for Stem Cell Science and Regenerative Medicine (inStem), GKVK Campus, Bangalore, India
- Sastra University, Thanjavur, TN, India
| | - Anana Nandakumar Chari
- A∗STAR Skin Research Lab (ASRL), Agency for Science, Technology and Research (A*STAR) 8A Biomedical Grove, Singapore, Singapore
| | - Srikala Raghavan
- A∗STAR Skin Research Lab (ASRL), Agency for Science, Technology and Research (A*STAR) 8A Biomedical Grove, Singapore, Singapore
- Institute for Stem Cell Science and Regenerative Medicine (inStem), GKVK Campus, Bangalore, India
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Chu W, Hu G, Peng L, Zhang W, Ma Z. The use of a novel deer antler decellularized cartilage-derived matrix scaffold for repair of osteochondral defects. J Biol Eng 2021; 15:23. [PMID: 34479610 PMCID: PMC8414868 DOI: 10.1186/s13036-021-00274-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Accepted: 08/16/2021] [Indexed: 01/17/2023] Open
Abstract
Background The physiologic regenerative capacity of cartilage is severely limited. Current studies on the repair of osteochondral defects (OCDs) have mainly focused on the regeneration of cartilage tissues. The antler cartilage is a unique regenerative cartilage that has the potential for cartilage repair. Methods Antler decellularized cartilage-derived matrix scaffolds (adCDMs) were prepared by combining freezing-thawing and enzymatic degradation. Their DNA, glycosaminoglycans (GAGs), and collagen content were then detected. Biosafety and biocompatibility were evaluated by pyrogen detection, hemolysis analysis, cytotoxicity evaluation, and subcutaneous implantation experiments. adCDMs were implanted into rabbit articular cartilage defects for 2 months to evaluate their therapeutic effects. Results AdCDMs were observed to be rich in collagen and GAGs and devoid of cells. AdCDMs were also determined to have good biosafety and biocompatibility. Both four- and eight-week treatments of OCDs showed a flat and smooth surface of the healing cartilage at the adCDMs filled site. The international cartilage repair society scores (ICRS) of adCDMs were significantly higher than those of controls (porcine dCDMs and normal saline) (p < 0.05). The repaired tissue in the adCDM group was fibrotic with high collagen, specifically, type II collagen. Conclusions We concluded that adCDMs could achieve excellent cartilage regeneration repair in a rabbit knee OCDs model. Our study stresses the importance and benefits of adCDMs in bone formation and overall anatomical reconstitution, and it provides a novel source for developing cartilage-regenerating repair materials. Supplementary Information The online version contains supplementary material available at 10.1186/s13036-021-00274-5.
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Affiliation(s)
- Wenhui Chu
- School of Life Science, Taizhou University, 1139 Shifu Avenue, Jiaojiang District, Zhejiang, 318000, Taizhou, China
| | - Gaowei Hu
- School of Life Science, Taizhou University, 1139 Shifu Avenue, Jiaojiang District, Zhejiang, 318000, Taizhou, China
| | - Lin Peng
- School of Life Science, Taizhou University, 1139 Shifu Avenue, Jiaojiang District, Zhejiang, 318000, Taizhou, China
| | - Wei Zhang
- Post-Doctoral Innovation Site, Jinan University Affiliation, Yuanzhi Health Technology Co, Ltd, Hengqin New District, 519000, Zhuhai, Guangdong, China. .,Medical Imaging Center, The First Affiliated Hospital of Jinan University, Jinan University, 613 Huangpu Avenue West, Tianhe District, Guangdong, 510080, Guangzhou, China.
| | - Zhe Ma
- School of Life Science, Taizhou University, 1139 Shifu Avenue, Jiaojiang District, Zhejiang, 318000, Taizhou, China.
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