1
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Holtzen SE, Navid E, Kainov JD, Palmer AE. Transient Zn 2+ deficiency induces replication stress and compromises daughter cell proliferation. Proc Natl Acad Sci U S A 2024; 121:e2321216121. [PMID: 38687796 PMCID: PMC11087780 DOI: 10.1073/pnas.2321216121] [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: 12/09/2023] [Accepted: 03/13/2024] [Indexed: 05/02/2024] Open
Abstract
Cells must replicate their genome quickly and accurately, and they require metabolites and cofactors to do so. Ionic zinc (Zn2+) is an essential micronutrient that is required for hundreds of cellular processes, including DNA synthesis and adequate proliferation. Deficiency in this micronutrient impairs DNA synthesis and inhibits proliferation, but the mechanism is unknown. Using fluorescent reporters to track single cells via long-term live-cell imaging, we find that Zn2+ is required at the G1/S transition and during S phase for timely completion of S phase. A short pulse of Zn2+ deficiency impairs DNA synthesis and increases markers of replication stress. These markers of replication stress are reversed upon resupply of Zn2+. Finally, we find that if Zn2+ is chelated during the mother cell's S phase, daughter cells enter a transient quiescent state, maintained by sustained expression of p21, which disappears upon reentry into the cell cycle. In summary, short pulses of mild Zn2+ deficiency in S phase specifically induce replication stress, which causes downstream proliferation impairments in daughter cells.
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Affiliation(s)
- Samuel E. Holtzen
- Department of Molecular Cellular and Developmental Biology, University of Colorado, Boulder, CO80309
| | - Elnaz Navid
- Department of Biochemistry, University of Colorado, Boulder, CO80309
| | - Joseph D. Kainov
- Department of Biochemistry, University of Colorado, Boulder, CO80309
| | - Amy E. Palmer
- Department of Biochemistry, University of Colorado, Boulder, CO80309
- BioFrontiers Institute, University of Colorado, Boulder, CO80309
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2
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McKenney C, Lendner Y, Guerrero Zuniga A, Sinha N, Veresko B, Aikin TJ, Regot S. CDK4/6 activity is required during G 2 arrest to prevent stress-induced endoreplication. Science 2024; 384:eadi2421. [PMID: 38696576 DOI: 10.1126/science.adi2421] [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: 04/12/2023] [Accepted: 03/05/2024] [Indexed: 05/04/2024]
Abstract
Cell cycle events are coordinated by cyclin-dependent kinases (CDKs) to ensure robust cell division. CDK4/6 and CDK2 regulate the growth 1 (G1) to synthesis (S) phase transition of the cell cycle by responding to mitogen signaling, promoting E2F transcription and inhibition of the anaphase-promoting complex. We found that this mechanism was still required in G2-arrested cells to prevent cell cycle exit after the S phase. This mechanism revealed a role for CDK4/6 in maintaining the G2 state, challenging the notion that the cell cycle is irreversible and that cells do not require mitogens after passing the restriction point. Exit from G2 occurred during ribotoxic stress and was actively mediated by stress-activated protein kinases. Upon relief of stress, a significant fraction of cells underwent a second round of DNA replication that led to whole-genome doubling.
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Affiliation(s)
- Connor McKenney
- Department of Molecular Biology and Genetics, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Department of Oncology, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
- The Biochemistry, Cellular, and Molecular Biology Graduate Program, Johns Hopkins University, Baltimore, MD, USA
| | - Yovel Lendner
- Department of Molecular Biology and Genetics, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Department of Oncology, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Adler Guerrero Zuniga
- Department of Molecular Biology and Genetics, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Department of Oncology, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
- The Biochemistry, Cellular, and Molecular Biology Graduate Program, Johns Hopkins University, Baltimore, MD, USA
| | - Niladri Sinha
- Department of Molecular Biology and Genetics, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Benjamin Veresko
- Department of Molecular Biology and Genetics, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Department of Oncology, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Timothy J Aikin
- Department of Molecular Biology and Genetics, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Department of Oncology, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
- The Biochemistry, Cellular, and Molecular Biology Graduate Program, Johns Hopkins University, Baltimore, MD, USA
| | - Sergi Regot
- Department of Molecular Biology and Genetics, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Department of Oncology, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
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3
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Guerrero Zuniga A, Aikin TJ, McKenney C, Lendner Y, Phung A, Hook PW, Meltzer A, Timp W, Regot S. Sustained ERK signaling promotes G2 cell cycle exit and primes cells for whole-genome duplication. Dev Cell 2024:S1534-5807(24)00200-4. [PMID: 38640927 DOI: 10.1016/j.devcel.2024.03.032] [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: 10/28/2022] [Revised: 01/30/2024] [Accepted: 03/25/2024] [Indexed: 04/21/2024]
Abstract
Whole-genome duplication (WGD) is a frequent event in cancer evolution that fuels chromosomal instability. WGD can result from mitotic errors or endoreduplication, yet the molecular mechanisms that drive WGD remain unclear. Here, we use live single-cell analysis to characterize cell-cycle dynamics upon aberrant Ras-ERK signaling. We find that sustained ERK signaling in human cells leads to reactivation of the APC/C in G2, resulting in tetraploid G0-like cells that are primed for WGD. This process is independent of DNA damage or p53 but dependent on p21. Transcriptomics analysis and live-cell imaging showed that constitutive ERK activity promotes p21 expression, which is necessary and sufficient to inhibit CDK activity and which prematurely activates the anaphase-promoting complex (APC/C). Finally, either loss of p53 or reduced ERK signaling allowed for endoreduplication, completing a WGD event. Thus, sustained ERK signaling-induced G2 cell cycle exit represents an alternative path to WGD.
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Affiliation(s)
- Adler Guerrero Zuniga
- Department of Molecular Biology and Genetics, The Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Department of Oncology, The Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; The Biochemistry, Cellular and Molecular Biology Graduate Program, The Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Timothy J Aikin
- Department of Molecular Biology and Genetics, The Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Department of Oncology, The Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; The Biochemistry, Cellular and Molecular Biology Graduate Program, The Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Connor McKenney
- Department of Molecular Biology and Genetics, The Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Department of Oncology, The Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; The Biochemistry, Cellular and Molecular Biology Graduate Program, The Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Yovel Lendner
- Department of Molecular Biology and Genetics, The Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Department of Oncology, The Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Alain Phung
- Department of Molecular Biology and Genetics, The Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Department of Oncology, The Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Paul W Hook
- Department of Biomedical Engineering, The Johns Hopkins University, Baltimore, MD 21205, USA
| | - Amy Meltzer
- Department of Biomedical Engineering, The Johns Hopkins University, Baltimore, MD 21205, USA
| | - Winston Timp
- Department of Biomedical Engineering, The Johns Hopkins University, Baltimore, MD 21205, USA
| | - Sergi Regot
- Department of Molecular Biology and Genetics, The Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Department of Oncology, The Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.
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4
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Kawabata T, Sekiya R, Goto S, Li TS. Chronic replication stress invokes mitochondria dysfunction via impaired parkin activity. Sci Rep 2024; 14:7877. [PMID: 38570643 PMCID: PMC10991263 DOI: 10.1038/s41598-024-58656-w] [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] [Accepted: 04/02/2024] [Indexed: 04/05/2024] Open
Abstract
Replication stress is a major contributor to tumorigenesis because it provides a source of chromosomal rearrangements via recombination events. PARK2, which encodes parkin, a regulator of mitochondrial homeostasis, is located on one of the common fragile sites that are prone to rearrangement by replication stress, indicating that replication stress may potentially impact mitochondrial homeostasis. Here, we show that chronic low-dose replication stress causes a fixed reduction in parkin expression, which is associated with mitochondrial dysfunction, indicated by an increase in mtROS. Consistent with the major role of parkin in mitophagy, reduction in parkin protein expression was associated with a slight decrease in mitophagy and changes in mitochondrial morphology. In contrast, cells expressing ectopic PARK2 gene does not show mtROS increases and changes in mitochondrial morphology even after exposure to chronic replication stress, suggesting that intrinsic fragility at PARK2 loci associated with parkin reduction is responsible for mitochondrial dysfunction caused by chronic replication stress. As endogenous replication stress and mitochondrial dysfunction are both involved in multiple pathophysiology, our data support the therapeutic development of recovery of parkin expression in human healthcare.
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Affiliation(s)
- Tsuyoshi Kawabata
- Department of Stem Cell Biology, Atomic Bomb Disease Institute, Nagasaki University, Nagasaki, Japan.
| | - Reiko Sekiya
- Department of Stem Cell Biology, Atomic Bomb Disease Institute, Nagasaki University, Nagasaki, Japan
| | - Shinji Goto
- Department of Stem Cell Biology, Atomic Bomb Disease Institute, Nagasaki University, Nagasaki, Japan
| | - Tao-Sheng Li
- Department of Stem Cell Biology, Atomic Bomb Disease Institute, Nagasaki University, Nagasaki, Japan
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5
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Zikry TM, Wolff SC, Ranek JS, Davis HM, Naugle A, Luthra N, Whitman AA, Kedziora KM, Stallaert W, Kosorok MR, Spanheimer PM, Purvis JE. Cell cycle plasticity underlies fractional resistance to palbociclib in ER+/HER2- breast tumor cells. Proc Natl Acad Sci U S A 2024; 121:e2309261121. [PMID: 38324568 PMCID: PMC10873600 DOI: 10.1073/pnas.2309261121] [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: 06/06/2023] [Accepted: 01/05/2024] [Indexed: 02/09/2024] Open
Abstract
The CDK4/6 inhibitor palbociclib blocks cell cycle progression in Estrogen receptor-positive, human epidermal growth factor 2 receptor-negative (ER+/HER2-) breast tumor cells. Despite the drug's success in improving patient outcomes, a small percentage of tumor cells continues to divide in the presence of palbociclib-a phenomenon we refer to as fractional resistance. It is critical to understand the cellular mechanisms underlying fractional resistance because the precise percentage of resistant cells in patient tissue is a strong predictor of clinical outcomes. Here, we hypothesize that fractional resistance arises from cell-to-cell differences in core cell cycle regulators that allow a subset of cells to escape CDK4/6 inhibitor therapy. We used multiplex, single-cell imaging to identify fractionally resistant cells in both cultured and primary breast tumor samples resected from patients. Resistant cells showed premature accumulation of multiple G1 regulators including E2F1, retinoblastoma protein, and CDK2, as well as enhanced sensitivity to pharmacological inhibition of CDK2 activity. Using trajectory inference approaches, we show how plasticity among cell cycle regulators gives rise to alternate cell cycle "paths" that allow individual tumor cells to escape palbociclib treatment. Understanding drivers of cell cycle plasticity, and how to eliminate resistant cell cycle paths, could lead to improved cancer therapies targeting fractionally resistant cells to improve patient outcomes.
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Affiliation(s)
- Tarek M. Zikry
- Computational Medicine Program, University of North Carolina at Chapel Hill, Chapel Hill, NC27599
- Department of Biostatistics, Gillings School of Global Public Health, University of North Carolina, Chapel Hill, NC27599
| | - Samuel C. Wolff
- Computational Medicine Program, University of North Carolina at Chapel Hill, Chapel Hill, NC27599
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC27599
| | - Jolene S. Ranek
- Computational Medicine Program, University of North Carolina at Chapel Hill, Chapel Hill, NC27599
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC27599
| | - Harris M. Davis
- Computational Medicine Program, University of North Carolina at Chapel Hill, Chapel Hill, NC27599
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC27599
| | - Ander Naugle
- Computational Medicine Program, University of North Carolina at Chapel Hill, Chapel Hill, NC27599
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC27599
| | - Namit Luthra
- Computational Medicine Program, University of North Carolina at Chapel Hill, Chapel Hill, NC27599
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC27599
| | - Austin A. Whitman
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC27599
| | - Katarzyna M. Kedziora
- Center for Biologic Imaging, Department of Cell Biology, University of Pittsburg, Pittsburgh, PA15620
| | - Wayne Stallaert
- Department of Computational and Systems Biology, University of Pittsburg, Pittsburgh, PA15620
| | - Michael R. Kosorok
- Department of Biostatistics, Gillings School of Global Public Health, University of North Carolina, Chapel Hill, NC27599
| | - Philip M. Spanheimer
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC27599
- Department of Surgery, University of North Carolina at Chapel Hill, Chapel Hill, NC27599
| | - Jeremy E. Purvis
- Computational Medicine Program, University of North Carolina at Chapel Hill, Chapel Hill, NC27599
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC27599
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC27599
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6
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Thoma OM, Naschberger E, Kubánková M, Larafa I, Kramer V, Menchicchi B, Merkel S, Britzen-Laurent N, Jefremow A, Grützmann R, Koop K, Neufert C, Atreya R, Guck J, Stürzl M, Neurath MF, Waldner MJ. p21 Prevents the Exhaustion of CD4 + T Cells Within the Antitumor Immune Response Against Colorectal Cancer. Gastroenterology 2024; 166:284-297.e11. [PMID: 37734420 DOI: 10.1053/j.gastro.2023.09.017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Revised: 08/30/2023] [Accepted: 09/05/2023] [Indexed: 09/23/2023]
Abstract
BACKGROUND & AIMS T cells are crucial for the antitumor response against colorectal cancer (CRC). T-cell reactivity to CRC is nevertheless limited by T-cell exhaustion. However, molecular mechanisms regulating T-cell exhaustion are only poorly understood. METHODS We investigated the functional role of cyclin-dependent kinase 1a (Cdkn1a or p21) in cluster of differentiation (CD) 4+ T cells using murine CRC models. Furthermore, we evaluated the expression of p21 in patients with stage I to IV CRC. In vitro coculture models were used to understand the effector function of p21-deficient CD4+ T cells. RESULTS We observed that the activation of cell cycle regulator p21 is crucial for CD4+ T-cell cytotoxic function and that p21 deficiency in type 1 helper T cells (Th1) leads to increased tumor growth in murine CRC. Similarly, low p21 expression in CD4+ T cells infiltrated into tumors of CRC patients is associated with reduced cancer-related survival. In mouse models of CRC, p21-deficient Th1 cells show signs of exhaustion, where an accumulation of effector/effector memory T cells and CD27/CD28 loss are predominant. Immune reconstitution of tumor-bearing Rag1-/- mice using ex vivo-treated p21-deficient T cells with palbociclib, an inhibitor of cyclin-dependent kinase 4/6, restored cytotoxic function and prevented exhaustion of p21-deficient CD4+ T cells as a possible concept for future immunotherapy of human disease. CONCLUSIONS Our data reveal the importance of p21 in controlling the cell cycle and preventing exhaustion of Th1 cells. Furthermore, we unveil the therapeutic potential of cyclin-dependent kinase inhibitors such as palbociclib to reduce T-cell exhaustion for future treatment of patients with colorectal cancer.
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Affiliation(s)
- Oana-Maria Thoma
- Department of Medicine 1, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany; German Center for Immunotherapy, Deutsches Zentrum Immuntherapie (DZI), University Hospital Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany; Comprehensive Cancer Center Erlangen-EMN (CCC ER-EMN), Erlangen, Germany.
| | - Elisabeth Naschberger
- Comprehensive Cancer Center Erlangen-EMN (CCC ER-EMN), Erlangen, Germany; Division of Molecular and Experimental Surgery, Department of Surgery, University Hospital Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
| | - Markéta Kubánková
- Max Planck Institute for the Science of Light & Max-Planck-Zentrum für Physik und Medizin, Erlangen, Germany
| | - Imen Larafa
- Department of Medicine 1, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany; German Center for Immunotherapy, Deutsches Zentrum Immuntherapie (DZI), University Hospital Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany; Comprehensive Cancer Center Erlangen-EMN (CCC ER-EMN), Erlangen, Germany
| | - Viktoria Kramer
- Department of Medicine 1, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany; German Center for Immunotherapy, Deutsches Zentrum Immuntherapie (DZI), University Hospital Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany; Comprehensive Cancer Center Erlangen-EMN (CCC ER-EMN), Erlangen, Germany
| | - Bianca Menchicchi
- Department of Medicine 1, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany; German Center for Immunotherapy, Deutsches Zentrum Immuntherapie (DZI), University Hospital Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany; Comprehensive Cancer Center Erlangen-EMN (CCC ER-EMN), Erlangen, Germany
| | - Susanne Merkel
- Comprehensive Cancer Center Erlangen-EMN (CCC ER-EMN), Erlangen, Germany; Department of Surgery, University Hospital Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
| | - Nathalie Britzen-Laurent
- Comprehensive Cancer Center Erlangen-EMN (CCC ER-EMN), Erlangen, Germany; Department of Surgery, University Hospital Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
| | - André Jefremow
- Department of Medicine 1, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany; German Center for Immunotherapy, Deutsches Zentrum Immuntherapie (DZI), University Hospital Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany; Comprehensive Cancer Center Erlangen-EMN (CCC ER-EMN), Erlangen, Germany
| | - Robert Grützmann
- Comprehensive Cancer Center Erlangen-EMN (CCC ER-EMN), Erlangen, Germany; Department of Surgery, University Hospital Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
| | - Kristina Koop
- Department of Medicine 1, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany; German Center for Immunotherapy, Deutsches Zentrum Immuntherapie (DZI), University Hospital Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany; Comprehensive Cancer Center Erlangen-EMN (CCC ER-EMN), Erlangen, Germany
| | - Clemens Neufert
- Department of Medicine 1, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany; German Center for Immunotherapy, Deutsches Zentrum Immuntherapie (DZI), University Hospital Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany; Comprehensive Cancer Center Erlangen-EMN (CCC ER-EMN), Erlangen, Germany
| | - Raja Atreya
- Department of Medicine 1, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany; German Center for Immunotherapy, Deutsches Zentrum Immuntherapie (DZI), University Hospital Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany; Comprehensive Cancer Center Erlangen-EMN (CCC ER-EMN), Erlangen, Germany
| | - Jochen Guck
- Max Planck Institute for the Science of Light & Max-Planck-Zentrum für Physik und Medizin, Erlangen, Germany
| | - Michael Stürzl
- Comprehensive Cancer Center Erlangen-EMN (CCC ER-EMN), Erlangen, Germany; Division of Molecular and Experimental Surgery, Department of Surgery, University Hospital Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
| | - Markus F Neurath
- Department of Medicine 1, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany; German Center for Immunotherapy, Deutsches Zentrum Immuntherapie (DZI), University Hospital Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany; Comprehensive Cancer Center Erlangen-EMN (CCC ER-EMN), Erlangen, Germany
| | - Maximilian J Waldner
- Department of Medicine 1, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany; German Center for Immunotherapy, Deutsches Zentrum Immuntherapie (DZI), University Hospital Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany; Comprehensive Cancer Center Erlangen-EMN (CCC ER-EMN), Erlangen, Germany; Erlangen Graduate School in Advanced Optical Technologies (SAOT), Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
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7
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Diehl FF, Sapp KM, Vander Heiden MG. The bidirectional relationship between metabolism and cell cycle control. Trends Cell Biol 2024; 34:136-149. [PMID: 37385879 DOI: 10.1016/j.tcb.2023.05.012] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Revised: 05/30/2023] [Accepted: 05/31/2023] [Indexed: 07/01/2023]
Abstract
The relationship between metabolism and cell cycle progression is complex and bidirectional. Cells must rewire metabolism to meet changing biosynthetic demands across cell cycle phases. In turn, metabolism can influence cell cycle progression through direct regulation of cell cycle proteins, through nutrient-sensing signaling pathways, and through its impact on cell growth, which is linked to cell division. Furthermore, metabolism is a key player in mediating quiescence-proliferation transitions in physiologically important cell types, such as stem cells. How metabolism impacts cell cycle progression, exit, and re-entry, as well as how these processes impact metabolism, is not fully understood. Recent advances uncovering mechanistic links between cell cycle regulators and metabolic processes demonstrate a complex relationship between metabolism and cell cycle control, with many questions remaining.
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Affiliation(s)
- Frances F Diehl
- Department of Molecular Biology and Genetics, Howard Hughes Medical Institute, Johns Hopkins University School of Medicine, Baltimore, MD, USA; Koch Institute for Integrative Cancer Research and the Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Kiera M Sapp
- Koch Institute for Integrative Cancer Research and the Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Matthew G Vander Heiden
- Koch Institute for Integrative Cancer Research and the Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA; Dana-Farber Cancer Institute, Boston, MA, USA.
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8
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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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9
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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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10
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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 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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11
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Holtzen SE, Navid E, Kainov JD, Palmer AE. Transient Zn 2+ deficiency induces replication stress and compromises daughter cell proliferation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.12.08.570860. [PMID: 38106081 PMCID: PMC10723434 DOI: 10.1101/2023.12.08.570860] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2023]
Abstract
Cells must replicate their genome quickly and accurately, and they require metabolites and cofactors to do so. Ionic zinc (Zn2+) is an essential micronutrient that is required for hundreds of cellular processes, including DNA synthesis and adequate proliferation. Deficiency in this micronutrient impairs DNA synthesis and inhibits proliferation, but the mechanism is unknown. Using fluorescent reporters to track single cells via long-term live-cell imaging, we find that Zn2+ is required at the G1/S transition and during S-phase for timely completion of S-phase. A short pulse of Zn2+ deficiency impairs DNA synthesis and increases markers of replication stress. These markers of replication stress are reversed upon resupply of Zn2+. Finally, we find that if Zn2+ is removed during the mother cell's S-phase, daughter cells enter a transient quiescent state, maintained by sustained expression of p21, which disappears upon reentry into the cell cycle. In summary, short pulses of mild Zn2+ deficiency in S-phase specifically induce replication stress, which causes downstream proliferation impairments in daughter cells.
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Affiliation(s)
- Samuel E. Holtzen
- Department of Molecular Cellular and Developmental Biology and BioFrontiers Institute, University of Colorado Boulder, Boulder, CO, 80309
- Department of Biochemistry, University of Colorado, Boulder, CO, 80309
| | - Elnaz Navid
- Department of Biochemistry, University of Colorado, Boulder, CO, 80309
| | - Joseph D. Kainov
- Department of Biochemistry, University of Colorado, Boulder, CO, 80309
| | - Amy E. Palmer
- Department of Biochemistry, University of Colorado, Boulder, CO, 80309
- Department of Biochemistry and BioFrontiers Institute, University of Colorado, Boulder, CO, 80309
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12
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Dludla PV, Cirilli I, Marcheggiani F, Silvestri S, Orlando P, Muvhulawa N, Moetlediwa MT, Nkambule BB, Mazibuko-Mbeje SE, Hlengwa N, Hanser S, Ndwandwe D, Marnewick JL, Basson AK, Tiano L. Bioactive Properties, Bioavailability Profiles, and Clinical Evidence of the Potential Benefits of Black Pepper ( Piper nigrum) and Red Pepper ( Capsicum annum) against Diverse Metabolic Complications. Molecules 2023; 28:6569. [PMID: 37764345 PMCID: PMC10534530 DOI: 10.3390/molecules28186569] [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: 07/23/2023] [Revised: 08/29/2023] [Accepted: 09/07/2023] [Indexed: 09/29/2023] Open
Abstract
The consumption of food-derived products, including the regular intake of pepper, is increasingly evaluated for its potential benefits in protecting against diverse metabolic complications. The current study made use of prominent electronic databases including PubMed, Google Scholar, and Scopus to retrieve clinical evidence linking the intake of black and red pepper with the amelioration of metabolic complications. The findings summarize evidence supporting the beneficial effects of black pepper (Piper nigrum L.), including its active ingredient, piperine, in improving blood lipid profiles, including reducing circulating levels of total cholesterol, low-density lipoprotein cholesterol, and triglycerides in overweight and obese individuals. The intake of piperine was also linked with enhanced antioxidant and anti-inflammatory properties by increasing serum levels of superoxide dismutase while reducing those of malonaldehyde and C-reactive protein in individuals with metabolic syndrome. Evidence summarized in the current review also indicates that red pepper (Capsicum annum), together with its active ingredient, capsaicin, could promote energy expenditure, including limiting energy intake, which is likely to contribute to reduced fat mass in overweight and obese individuals. Emerging clinical evidence also indicates that pepper may be beneficial in alleviating complications linked with other chronic conditions, including osteoarthritis, oropharyngeal dysphagia, digestion, hemodialysis, and neuromuscular fatigue. Notably, the beneficial effects of pepper or its active ingredients appear to be more pronounced when used in combination with other bioactive compounds. The current review also covers essential information on the metabolism and bioavailability profiles of both pepper species and their main active ingredients, which are all necessary to understand their potential beneficial effects against metabolic diseases.
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Affiliation(s)
- Phiwayinkosi V. Dludla
- Cochrane South Africa, South African Medical Research Council, Tygerberg 7505, South Africa; (N.M.); (D.N.)
- Department of Biochemistry and Microbiology, University of Zululand, KwaDlangezwa 3886, South Africa; (N.H.); (A.K.B.)
| | - Ilenia Cirilli
- Department of Life and Environmental Sciences, Polytechnic University of Marche, 60131 Ancona, Italy; (I.C.); (F.M.); (S.S.); (P.O.); (L.T.)
| | - Fabio Marcheggiani
- Department of Life and Environmental Sciences, Polytechnic University of Marche, 60131 Ancona, Italy; (I.C.); (F.M.); (S.S.); (P.O.); (L.T.)
| | - Sonia Silvestri
- Department of Life and Environmental Sciences, Polytechnic University of Marche, 60131 Ancona, Italy; (I.C.); (F.M.); (S.S.); (P.O.); (L.T.)
| | - Patrick Orlando
- Department of Life and Environmental Sciences, Polytechnic University of Marche, 60131 Ancona, Italy; (I.C.); (F.M.); (S.S.); (P.O.); (L.T.)
| | - Ndivhuwo Muvhulawa
- Cochrane South Africa, South African Medical Research Council, Tygerberg 7505, South Africa; (N.M.); (D.N.)
- Department of Biochemistry, North-West University, Mafikeng Campus, Mmabatho 2735, South Africa; (M.T.M.); (S.E.M.-M.)
| | - Marakiya T. Moetlediwa
- Department of Biochemistry, North-West University, Mafikeng Campus, Mmabatho 2735, South Africa; (M.T.M.); (S.E.M.-M.)
| | - Bongani B. Nkambule
- School of Laboratory Medicine and Medical Sciences, University of KwaZulu-Natal, Durban 4000, South Africa;
| | - Sithandiwe E. Mazibuko-Mbeje
- Department of Biochemistry, North-West University, Mafikeng Campus, Mmabatho 2735, South Africa; (M.T.M.); (S.E.M.-M.)
| | - Nokulunga Hlengwa
- Department of Biochemistry and Microbiology, University of Zululand, KwaDlangezwa 3886, South Africa; (N.H.); (A.K.B.)
| | - Sidney Hanser
- Department of Physiology and Environmental Health, University of Limpopo, Sovenga 0727, South Africa;
| | - Duduzile Ndwandwe
- Cochrane South Africa, South African Medical Research Council, Tygerberg 7505, South Africa; (N.M.); (D.N.)
| | - Jeanine L. Marnewick
- Applied Microbial and Health Biotechnology Institute, Cape Peninsula University of Technology, Bellville 7535, South Africa;
| | - Albertus K. Basson
- Department of Biochemistry and Microbiology, University of Zululand, KwaDlangezwa 3886, South Africa; (N.H.); (A.K.B.)
| | - Luca Tiano
- Department of Life and Environmental Sciences, Polytechnic University of Marche, 60131 Ancona, Italy; (I.C.); (F.M.); (S.S.); (P.O.); (L.T.)
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13
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Milletti G, Colicchia V, Cecconi F. Cyclers' kinases in cell division: from molecules to cancer therapy. Cell Death Differ 2023; 30:2035-2052. [PMID: 37516809 PMCID: PMC10482880 DOI: 10.1038/s41418-023-01196-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2023] [Revised: 07/08/2023] [Accepted: 07/18/2023] [Indexed: 07/31/2023] Open
Abstract
Faithful eucaryotic cell division requires spatio-temporal orchestration of multiple sequential events. To ensure the dynamic nature of these molecular and morphological transitions, a swift modulation of key regulatory pathways is necessary. The molecular process that most certainly fits this description is phosphorylation, the post-translational modification provided by kinases, that is crucial to allowing the progression of the cell cycle and that culminates with the separation of two identical daughter cells. In detail, from the early stages of the interphase to the cytokinesis, each critical step of this process is tightly regulated by multiple families of kinases including the Cyclin-dependent kinases (CDKs), kinases of the Aurora, Polo, Wee1 families, and many others. While cell-cycle-related CDKs control the timing of the different phases, preventing replication machinery errors, the latter modulate the centrosome cycle and the spindle function, avoiding karyotypic abnormalities typical of chromosome instability. Such chromosomal abnormalities may result from replication stress (RS) and chromosome mis-segregation and are considered a hallmark of poor prognosis, therapeutic resistance, and metastasis in cancer patients. Here, we discuss recent advances in the understanding of how different families of kinases concur to govern cell cycle, preventing RS and mitotic infidelity. Additionally, considering the growing number of clinical trials targeting these molecules, we review to what extent and in which tumor context cell-cycle-related kinases inhibitors are worth exploiting as an effective therapeutic strategy.
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Affiliation(s)
- Giacomo Milletti
- DNA Replication and Cancer Group, Danish Cancer Institute, 2100, Copenhagen, Denmark.
- Department of Pediatric Hematology and Oncology and of Cell and Gene Therapy, IRCCS Ospedale Pediatrico Bambino Gesù, Rome, Italy.
| | - Valeria Colicchia
- Department of Biology, University of Rome Tor Vergata, Rome, Italy
- IRBM S.p.A., Via Pontina Km 30.60, 00070, Pomezia, Italy
| | - Francesco Cecconi
- Cell Stress and Survival Group, Center for Autophagy, Recycling and Disease (CARD), Danish Cancer Institute, Copenhagen, Denmark.
- Università Cattolica del Sacro Cuore and Fondazione Policlinico Universitario Agostino Gemelli IRCCS, Rome, Italy.
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14
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Cassidy T. A Continuation Technique for Maximum Likelihood Estimators in Biological Models. Bull Math Biol 2023; 85:90. [PMID: 37650951 PMCID: PMC10471725 DOI: 10.1007/s11538-023-01200-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2023] [Accepted: 08/14/2023] [Indexed: 09/01/2023]
Abstract
Estimating model parameters is a crucial step in mathematical modelling and typically involves minimizing the disagreement between model predictions and experimental data. This calibration data can change throughout a study, particularly if modelling is performed simultaneously with the calibration experiments, or during an on-going public health crisis as in the case of the COVID-19 pandemic. Consequently, the optimal parameter set, or maximal likelihood estimator (MLE), is a function of the experimental data set. Here, we develop a numerical technique to predict the evolution of the MLE as a function of the experimental data. We show that, when considering perturbations from an initial data set, our approach is significantly more computationally efficient that re-fitting model parameters while producing acceptable model fits to the updated data. We use the continuation technique to develop an explicit functional relationship between fit model parameters and experimental data that can be used to measure the sensitivity of the MLE to experimental data. We then leverage this technique to select between model fits with similar information criteria, a priori determine the experimental measurements to which the MLE is most sensitive, and suggest additional experiment measurements that can resolve parameter uncertainty.
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Affiliation(s)
- Tyler Cassidy
- School of Mathematics, University of Leeds, Leeds, LS2 9JT, UK.
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15
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Hoffman TE, Nangia V, Ill CR, Passanisi VJ, Armstrong C, Yang C, Spencer SL. Multiple cancers escape from multiple MAPK pathway inhibitors and use DNA replication stress signaling to tolerate aberrant cell cycles. Sci Signal 2023; 16:eade8744. [PMID: 37527351 DOI: 10.1126/scisignal.ade8744] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Accepted: 07/13/2023] [Indexed: 08/03/2023]
Abstract
Many cancers harbor pro-proliferative mutations of the mitogen-activated protein kinase (MAPK) pathway. In BRAF-driven melanoma cells treated with BRAF inhibitors, subpopulations of cells escape drug-induced quiescence through a nongenetic manner of adaptation and resume slow proliferation. Here, we found that this phenomenon is common to many cancer types driven by EGFR, KRAS, or BRAF mutations in response to multiple, clinically approved MAPK pathway inhibitors. In 2D cultures and 3D spheroid models of various cancer cell lines, a subset of cells escaped drug-induced quiescence within 4 days to resume proliferation. These "escapee" cells exhibited DNA replication deficits, accumulated DNA lesions, and mounted a stress response that depended on the ataxia telangiectasia and RAD3-related (ATR) kinase. We further identified that components of the Fanconi anemia (FA) DNA repair pathway are recruited to sites of mitotic DNA synthesis (MiDAS) in escapee cells, enabling successful completion of cell division. Analysis of patient tumor samples and clinical data correlated disease progression with an increase in DNA replication stress response factors. Our findings suggest that many MAPK pathway-mutant cancers rapidly escape drug action and that suppressing early stress tolerance pathways may achieve more durable clinical responses to MAPK pathway inhibitors.
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Affiliation(s)
- Timothy E Hoffman
- Department of Biochemistry and Biofrontiers Institute, University of Colorado Boulder, Boulder, CO 80303, USA
| | - Varuna Nangia
- Department of Biochemistry and Biofrontiers Institute, University of Colorado Boulder, Boulder, CO 80303, USA
- Medical Scientist Training Program, University of Colorado-Anschutz Medical School, Aurora, CO 80045, USA
| | - C Ryland Ill
- Department of Biochemistry and Biofrontiers Institute, University of Colorado Boulder, Boulder, CO 80303, USA
| | - Victor J Passanisi
- Department of Biochemistry and Biofrontiers Institute, University of Colorado Boulder, Boulder, CO 80303, USA
| | - Claire Armstrong
- Department of Biochemistry and Biofrontiers Institute, University of Colorado Boulder, Boulder, CO 80303, USA
| | - Chen Yang
- Department of Biochemistry and Biofrontiers Institute, University of Colorado Boulder, Boulder, CO 80303, USA
- Molecular Cellular and Developmental Biology, University of Colorado Boulder, Boulder, CO 80303, 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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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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17
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Armstrong C, Passanisi VJ, Ashraf HM, Spencer SL. Cyclin E/CDK2 and feedback from soluble histone protein regulate the S phase burst of histone biosynthesis. Cell Rep 2023; 42:112768. [PMID: 37428633 PMCID: PMC10440735 DOI: 10.1016/j.celrep.2023.112768] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2022] [Revised: 04/17/2023] [Accepted: 06/23/2023] [Indexed: 07/12/2023] Open
Abstract
Faithful DNA replication requires that cells fine-tune their histone pool in coordination with cell-cycle progression. Replication-dependent histone biosynthesis is initiated at a low level upon cell-cycle commitment, followed by a burst at the G1/S transition, but it remains unclear how exactly the cell regulates this burst in histone biosynthesis as DNA replication begins. Here, we use single-cell time-lapse imaging to elucidate the mechanisms by which cells modulate histone production during different phases of the cell cycle. We find that CDK2-mediated phosphorylation of NPAT at the restriction point triggers histone transcription, which results in a burst of histone mRNA precisely at the G1/S phase boundary. Excess soluble histone protein further modulates histone abundance by promoting the degradation of histone mRNA for the duration of S phase. Thus, cells regulate their histone production in strict coordination with cell-cycle progression by two distinct mechanisms acting in concert.
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Affiliation(s)
- Claire Armstrong
- Department of Biochemistry, University of Colorado Boulder, Boulder, CO 80303, USA; BioFrontiers Institute, University of Colorado Boulder, Boulder, CO 80303, USA
| | - Victor J Passanisi
- Department of Biochemistry, University of Colorado Boulder, Boulder, CO 80303, USA; BioFrontiers Institute, University of Colorado Boulder, Boulder, CO 80303, USA
| | - Humza M Ashraf
- Department of Biochemistry, University of Colorado Boulder, Boulder, CO 80303, USA; BioFrontiers Institute, University of Colorado Boulder, Boulder, CO 80303, USA
| | - Sabrina L Spencer
- Department of Biochemistry, University of Colorado Boulder, Boulder, CO 80303, USA; BioFrontiers Institute, University of Colorado Boulder, Boulder, CO 80303, USA.
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18
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Zheng D, Mao Y, Gao Y, He F, Ma J. Daughter cell fate choice instructed preemptively by mother cells facing nutrient limitation. iScience 2023; 26:107198. [PMID: 37485365 PMCID: PMC10359942 DOI: 10.1016/j.isci.2023.107198] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Revised: 02/03/2023] [Accepted: 06/20/2023] [Indexed: 07/25/2023] Open
Abstract
Nutrients are vital to cellular activities, yet it is largely unknown how individual cells respond to nutrient deprivation. Live imaging results show that unlike the removal of amino acids or glutamine that immediately halts cell cycle progression, glucose withdrawal does not prevent cells from completing their current cycle. Although cells that begin to experience glucose withdrawal in S phase give rise to daughter cells with an equal choice of proliferation or quiescence, those enduring such experience in G1 phase give rise to daughter cells that predominantly enter quiescence. This fate choice difference stems from p21 protein accumulated during G2/M of the latter cells. Induced degradation of p21 permits daughter cells to enter S phase but with a consequent accumulation of DNA damage. These results suggest that mother cells that begin to experience glucose limitation in G1 phase take preemptive steps toward preventing daughter cells from making a harmful choice.
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Affiliation(s)
- Dianpeng Zheng
- Women’s Hospital and Institute of Genetics, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310058, China
- Zhejiang Provincial Key Laboratory of Genetic and Developmental Disorder, Hangzhou, Zhejiang 310058, China
| | - Yaowen Mao
- Women’s Hospital and Institute of Genetics, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310058, China
- Zhejiang Provincial Key Laboratory of Genetic and Developmental Disorder, Hangzhou, Zhejiang 310058, China
| | - Yinglong Gao
- Zhejiang Provincial Key Laboratory of Genetic and Developmental Disorder, Hangzhou, Zhejiang 310058, China
- National Clinical Research Center for Child Health, Children’s Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310052, China
| | - Feng He
- Women’s Hospital and Institute of Genetics, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310058, China
- Zhejiang Provincial Key Laboratory of Genetic and Developmental Disorder, Hangzhou, Zhejiang 310058, China
- National Clinical Research Center for Child Health, Children’s Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310052, China
| | - Jun Ma
- Women’s Hospital and Institute of Genetics, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310058, China
- Zhejiang Provincial Key Laboratory of Genetic and Developmental Disorder, Hangzhou, Zhejiang 310058, China
- National Clinical Research Center for Child Health, Children’s Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310052, China
- Women’s Reproductive Health Research Laboratory of Zhejiang Province, Hangzhou, Zhejiang 310006, China
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19
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Arora M, Moser J, Hoffman TE, Watts LP, Min M, Musteanu M, Rong Y, Ill CR, Nangia V, Schneider J, Sanclemente M, Lapek J, Nguyen L, Niessen S, Dann S, VanArsdale T, Barbacid M, Miller N, Spencer SL. Rapid adaptation to CDK2 inhibition exposes intrinsic cell-cycle plasticity. Cell 2023; 186:2628-2643.e21. [PMID: 37267950 DOI: 10.1016/j.cell.2023.05.013] [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: 11/03/2020] [Revised: 10/10/2022] [Accepted: 05/10/2023] [Indexed: 06/04/2023]
Abstract
CDK2 is a core cell-cycle kinase that phosphorylates many substrates to drive progression through the cell cycle. CDK2 is hyperactivated in multiple cancers and is therefore an attractive therapeutic target. Here, we use several CDK2 inhibitors in clinical development to interrogate CDK2 substrate phosphorylation, cell-cycle progression, and drug adaptation in preclinical models. Whereas CDK1 is known to compensate for loss of CDK2 in Cdk2-/- mice, this is not true of acute inhibition of CDK2. Upon CDK2 inhibition, cells exhibit a rapid loss of substrate phosphorylation that rebounds within several hours. CDK4/6 activity backstops inhibition of CDK2 and sustains the proliferative program by maintaining Rb1 hyperphosphorylation, active E2F transcription, and cyclin A2 expression, enabling re-activation of CDK2 in the presence of drug. Our results augment our understanding of CDK plasticity and indicate that co-inhibition of CDK2 and CDK4/6 may be required to suppress adaptation to CDK2 inhibitors currently under clinical assessment.
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Affiliation(s)
- Mansi Arora
- Department of Biochemistry and BioFrontiers Institute, University of Colorado-Boulder, Boulder, CO 80303, USA
| | - Justin Moser
- Department of Biochemistry and BioFrontiers Institute, University of Colorado-Boulder, Boulder, CO 80303, USA
| | - Timothy E Hoffman
- Department of Biochemistry and BioFrontiers Institute, University of Colorado-Boulder, Boulder, CO 80303, USA
| | - Lotte P Watts
- Department of Biochemistry and BioFrontiers Institute, University of Colorado-Boulder, Boulder, CO 80303, USA
| | - Mingwei Min
- Department of Biochemistry and BioFrontiers Institute, University of Colorado-Boulder, Boulder, CO 80303, USA; Guangzhou Laboratory, Guangzhou, Guangdong, China
| | - Monica Musteanu
- Experimental Oncology Group, Molecular Oncology Programme, Spanish National Cancer Research Centre, Madrid, Spain; Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Instituto de Salud Carlos III, 28029 Madrid, Spain
| | - Yao Rong
- Department of Biochemistry and BioFrontiers Institute, University of Colorado-Boulder, Boulder, CO 80303, USA; Department of Molecular, Cellular, and Developmental Biology and BioFrontiers Institute, University of Colorado-Boulder, Boulder, CO 80303, USA
| | - C Ryland Ill
- Department of Biochemistry and BioFrontiers Institute, University of Colorado-Boulder, Boulder, CO 80303, USA
| | - Varuna Nangia
- Department of Biochemistry and BioFrontiers Institute, University of Colorado-Boulder, Boulder, CO 80303, USA
| | - Jordan Schneider
- Department of Biochemistry and BioFrontiers Institute, University of Colorado-Boulder, Boulder, CO 80303, USA
| | - Manuel Sanclemente
- Experimental Oncology Group, Molecular Oncology Programme, Spanish National Cancer Research Centre, Madrid, Spain
| | - John Lapek
- Oncology Research & Development, Pfizer Worldwide Research & Development, San Diego, CA 92121, USA
| | - Lisa Nguyen
- Oncology Research & Development, Pfizer Worldwide Research & Development, San Diego, CA 92121, USA
| | - Sherry Niessen
- Oncology Research & Development, Pfizer Worldwide Research & Development, San Diego, CA 92121, USA
| | - Stephen Dann
- Oncology Research & Development, Pfizer Worldwide Research & Development, San Diego, CA 92121, USA
| | - Todd VanArsdale
- Oncology Research & Development, Pfizer Worldwide Research & Development, San Diego, CA 92121, USA
| | - Mariano Barbacid
- Experimental Oncology Group, Molecular Oncology Programme, Spanish National Cancer Research Centre, Madrid, Spain; Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Instituto de Salud Carlos III, 28029 Madrid, Spain
| | - Nichol Miller
- Oncology Research & Development, Pfizer Worldwide Research & Development, San Diego, CA 92121, USA
| | - Sabrina L Spencer
- Department of Biochemistry and BioFrontiers Institute, University of Colorado-Boulder, Boulder, CO 80303, USA.
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20
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Venkatachalapathy H, Brzakala C, Batchelor E, Azarin SM, Sarkar CA. Inertial effect of cell state velocity on the quiescence-proliferation fate decision in breast cancer. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.22.541793. [PMID: 37292599 PMCID: PMC10245870 DOI: 10.1101/2023.05.22.541793] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Energy landscapes can provide intuitive depictions of population heterogeneity and dynamics. However, it is unclear whether individual cell behavior, hypothesized to be determined by initial position and noise, is faithfully recapitulated. Using the p21-/Cdk2-dependent quiescence-proliferation decision in breast cancer dormancy as a testbed, we examined single-cell dynamics on the landscape when perturbed by hypoxia, a dormancy-inducing stress. Combining trajectory-based energy landscape generation with single-cell time-lapse microscopy, we found that initial position on a p21/Cdk2 landscape did not fully explain the observed cell-fate heterogeneity under hypoxia. Instead, cells with higher cell state velocities prior to hypoxia, influenced by epigenetic parameters, tended to remain proliferative under hypoxia. Thus, the fate decision on this landscape is significantly influenced by "inertia", a velocity-dependent ability to resist directional changes despite reshaping of the underlying landscape, superseding positional effects. Such inertial effects may markedly influence cell-fate trajectories in tumors and other dynamically changing microenvironments.
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Affiliation(s)
- Harish Venkatachalapathy
- Department of Chemical Engineering and Materials Science, University of Minnesota, Minneapolis, MN 55455, USA
| | - Cole Brzakala
- Department of Chemical Engineering and Materials Science, University of Minnesota, Minneapolis, MN 55455, USA
| | - Eric Batchelor
- Department of Integrative Biology and Physiology, University of Minnesota, Minneapolis, MN 55455, USA
| | - Samira M. Azarin
- Department of Chemical Engineering and Materials Science, University of Minnesota, Minneapolis, MN 55455, USA
| | - Casim A. Sarkar
- Department of Biomedical Engineering, University of Minnesota, Minneapolis, MN 55455, USA
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21
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Wiecek AJ, Cutty SJ, Kornai D, Parreno-Centeno M, Gourmet LE, Tagliazucchi GM, Jacobson DH, Zhang P, Xiong L, Bond GL, Barr AR, Secrier M. Genomic hallmarks and therapeutic implications of G0 cell cycle arrest in cancer. Genome Biol 2023; 24:128. [PMID: 37221612 PMCID: PMC10204193 DOI: 10.1186/s13059-023-02963-4] [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: 06/01/2022] [Accepted: 05/07/2023] [Indexed: 05/25/2023] Open
Abstract
BACKGROUND Therapy resistance in cancer is often driven by a subpopulation of cells that are temporarily arrested in a non-proliferative G0 state, which is difficult to capture and whose mutational drivers remain largely unknown. RESULTS We develop methodology to robustly identify this state from transcriptomic signals and characterise its prevalence and genomic constraints in solid primary tumours. We show that G0 arrest preferentially emerges in the context of more stable, less mutated genomes which maintain TP53 integrity and lack the hallmarks of DNA damage repair deficiency, while presenting increased APOBEC mutagenesis. We employ machine learning to uncover novel genomic dependencies of this process and validate the role of the centrosomal gene CEP89 as a modulator of proliferation and G0 arrest capacity. Lastly, we demonstrate that G0 arrest underlies unfavourable responses to various therapies exploiting cell cycle, kinase signalling and epigenetic mechanisms in single-cell data. CONCLUSIONS We propose a G0 arrest transcriptional signature that is linked with therapeutic resistance and can be used to further study and clinically track this state.
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Affiliation(s)
- Anna J. Wiecek
- UCL Genetics Institute, Department of Genetics, Evolution and Environment, University College London, London, UK
| | - Stephen J. Cutty
- Institute of Clinical Sciences, Faculty of Medicine, Imperial College London, London, UK
| | - Daniel Kornai
- UCL Genetics Institute, Department of Genetics, Evolution and Environment, University College London, London, UK
| | - Mario Parreno-Centeno
- UCL Genetics Institute, Department of Genetics, Evolution and Environment, University College London, London, UK
| | - Lucie E. Gourmet
- UCL Genetics Institute, Department of Genetics, Evolution and Environment, University College London, London, UK
| | | | - Daniel H. Jacobson
- UCL Genetics Institute, Department of Genetics, Evolution and Environment, University College London, London, UK
- UCL Cancer Institute, Paul O’Gorman Building, University College London, London, UK
| | - Ping Zhang
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Lingyun Xiong
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Gareth L. Bond
- Institute of Cancer and Genomic Sciences, University of Birmingham, Edgbaston, Birmingham, UK
| | - Alexis R. Barr
- Institute of Clinical Sciences, Faculty of Medicine, Imperial College London, London, UK
- Cell Cycle Control Team, MRC London Institute of Medical Sciences (LMS), London, UK
| | - Maria Secrier
- UCL Genetics Institute, Department of Genetics, Evolution and Environment, University College London, London, UK
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22
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Hoffman TE, Yang C, Nangia V, Ill CR, Spencer SL. Multiple cancer types rapidly escape from multiple MAPK inhibitors to generate mutagenesis-prone subpopulations. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.03.17.533211. [PMID: 36993538 PMCID: PMC10055235 DOI: 10.1101/2023.03.17.533211] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/31/2023]
Abstract
Many cancers harbor pro-proliferative mutations of the mitogen-activated protein kinase (MAPK) pathway and many targeted inhibitors now exist for clinical use, but drug resistance remains a major issue. We recently showed that BRAF-driven melanoma cells treated with BRAF inhibitors can non-genetically adapt to drug within 3-4 days to escape quiescence and resume slow proliferation. Here we show that this phenomenon is not unique to melanomas treated with BRAF inhibitors but rather is widespread across many clinical MAPK inhibitors and cancer types driven by EGFR, KRAS, and BRAF mutations. In all treatment contexts examined, a subset of cells can escape drug-induced quiescence within four days to resume proliferation. These escapee cells broadly experience aberrant DNA replication, accumulate DNA lesions, spend longer in G2-M cell cycle phases, and mount an ATR-dependent stress response. We further identify the Fanconi anemia (FA) DNA repair pathway as critical for successful mitotic completion in escapees. Long-term cultures, patient samples, and clinical data demonstrate a broad dependency on ATR- and FA-mediated stress tolerance. Together, these results highlight the pervasiveness with which MAPK-mutant cancers are able to rapidly escape drug and the importance of suppressing early stress tolerance pathways to potentially achieve more durable clinical responses to targeted MAPK pathway inhibitors.
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23
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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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24
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Armstrong C, Passanisi VJ, Ashraf HM, Spencer SL. Cyclin E/CDK2 and feedback from soluble histone protein regulate the S phase burst of histone biosynthesis. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.03.17.533218. [PMID: 36993620 PMCID: PMC10055190 DOI: 10.1101/2023.03.17.533218] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/19/2023]
Abstract
Faithful DNA replication requires that cells fine-tune their histone pool in coordination with cell-cycle progression. Replication-dependent histone biosynthesis is initiated at a low level upon cell-cycle commitment, followed by a burst at the G1/S transition, but it remains unclear how exactly the cell regulates this change in histone biosynthesis as DNA replication begins. Here, we use single-cell timelapse imaging to elucidate the mechanisms by which cells modulate histone production during different phases of the cell cycle. We find that CDK2-mediated phosphorylation of NPAT at the Restriction Point triggers histone transcription, which results in a burst of histone mRNA precisely at the G1/S phase boundary. Excess soluble histone protein further modulates histone abundance by promoting the degradation of histone mRNA for the duration of S phase. Thus, cells regulate their histone production in strict coordination with cell-cycle progression by two distinct mechanisms acting in concert.
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25
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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] [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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26
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Fischer M, Schade AE, Branigan TB, Müller GA, DeCaprio JA. Coordinating gene expression during the cell cycle. Trends Biochem Sci 2022; 47:1009-1022. [PMID: 35835684 DOI: 10.1016/j.tibs.2022.06.007] [Citation(s) in RCA: 53] [Impact Index Per Article: 26.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Revised: 06/08/2022] [Accepted: 06/14/2022] [Indexed: 02/08/2023]
Abstract
Cell cycle-dependent gene transcription is tightly controlled by the retinoblastoma (RB):E2F and DREAM complexes, which repress all cell cycle genes during quiescence. Cyclin-dependent kinase (CDK) phosphorylation of RB and DREAM allows for the expression of two gene sets. The first set of genes, with peak expression in G1/S, is activated by E2F transcription factors (TFs) and is required for DNA synthesis. The second set, with maximum expression during G2/M, is required for mitosis and is coordinated by the MuvB complex, together with B-MYB and Forkhead box M1 (FOXM1). In this review, we summarize the key findings that established the distinct control mechanisms regulating G1/S and G2/M gene expression in mammals and discuss recent advances in the understanding of the temporal control of these genes.
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Affiliation(s)
- Martin Fischer
- Computational Biology Group, Leibniz Institute on Aging - Fritz Lipmann Institute (FLI), 07745, Jena, Germany.
| | - Amy E Schade
- Genetics Division, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Timothy B Branigan
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Gerd A Müller
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, CA 95064, USA
| | - James A DeCaprio
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA.
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27
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Hughes FA, Barr AR, Thomas P. Patterns of interdivision time correlations reveal hidden cell cycle factors. eLife 2022; 11:e80927. [PMID: 36377847 PMCID: PMC9822260 DOI: 10.7554/elife.80927] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2022] [Accepted: 11/14/2022] [Indexed: 11/16/2022] Open
Abstract
The time taken for cells to complete a round of cell division is a stochastic process controlled, in part, by intracellular factors. These factors can be inherited across cellular generations which gives rise to, often non-intuitive, correlation patterns in cell cycle timing between cells of different family relationships on lineage trees. Here, we formulate a framework of hidden inherited factors affecting the cell cycle that unifies known cell cycle control models and reveals three distinct interdivision time correlation patterns: aperiodic, alternator, and oscillator. We use Bayesian inference with single-cell datasets of cell division in bacteria, mammalian and cancer cells, to identify the inheritance motifs that underlie these datasets. From our inference, we find that interdivision time correlation patterns do not identify a single cell cycle model but generally admit a broad posterior distribution of possible mechanisms. Despite this unidentifiability, we observe that the inferred patterns reveal interpretable inheritance dynamics and hidden rhythmicity of cell cycle factors. This reveals that cell cycle factors are commonly driven by circadian rhythms, but their period may differ in cancer. Our quantitative analysis thus reveals that correlation patterns are an emergent phenomenon that impact cell proliferation and these patterns may be altered in disease.
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Affiliation(s)
- Fern A Hughes
- Department of Mathematics, Imperial College LondonLondonUnited Kingdom
- MRC London Institute of Medical SciencesLondonUnited Kingdom
| | - Alexis R Barr
- MRC London Institute of Medical SciencesLondonUnited Kingdom
- Institute of Clinical Sciences, Imperial College LondonLondonUnited Kingdom
| | - Philipp Thomas
- Department of Mathematics, Imperial College LondonLondonUnited Kingdom
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28
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Slade L, Biswas D, Kienesberger PC, Pulinilkunnil T. Loss of transcription factor EB dysregulates the G1/S transition and DNA replication in mammary epithelial cells. J Biol Chem 2022; 298:102692. [PMID: 36372230 PMCID: PMC9764199 DOI: 10.1016/j.jbc.2022.102692] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Revised: 10/25/2022] [Accepted: 10/27/2022] [Indexed: 11/13/2022] Open
Abstract
Triple-negative breast cancer (TNBC) poses significant challenges for treatment given the lack of targeted therapies and increased probability of relapse. It is pertinent to identify vulnerabilities in TNBC and develop newer treatments. Our prior research demonstrated that transcription factor EB (TFEB) is necessary for TNBC survival by regulating DNA repair, apoptosis signaling, and the cell cycle. However, specific mechanisms by which TFEB targets DNA repair and cell cycle pathways are unclear, and whether these effects dictate TNBC survival is yet to be determined. Here, we show that TFEB knockdown decreased the expression of genes and proteins involved in DNA replication and cell cycle progression in MDA-MB-231 TNBC cells. DNA replication was decreased in cells lacking TFEB, as measured by EdU incorporation. TFEB silencing in MDA-MB-231 and noncancerous MCF10A cells impaired progression through the S-phase following G1/S synchronization; however, this proliferation defect could not be rescued by co-knockdown of suppressor RB1. Instead, TFEB knockdown reduced origin licensing in G1 and early S-phase MDA-MB-231 cells. TFEB silencing was associated with replication stress in MCF10A but not in TNBC cells. Lastly, we identified that TFEB knockdown renders TNBC cells more sensitive to inhibitors of Aurora Kinase A, a protein facilitating mitosis. Thus, inhibition of TFEB impairs cell cycle progress by decreasing origin licensing, leading to delayed entry into the S-phase, while rendering TNBC cells sensitive to Aurora kinase A inhibitors and decreasing cell viability. In contrast, TFEB silencing in noncancerous cells is associated with replication stress and leads to G1/S arrest.
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29
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Jolly A, Fanti AK, Kongsaysak-Lengyel C, Claudino N, Gräßer I, Becker NB, Höfer T. CycleFlow simultaneously quantifies cell-cycle phase lengths and quiescence in vivo. CELL REPORTS METHODS 2022; 2:100315. [PMID: 36313807 PMCID: PMC9606136 DOI: 10.1016/j.crmeth.2022.100315] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/13/2020] [Revised: 07/25/2022] [Accepted: 09/14/2022] [Indexed: 11/16/2022]
Abstract
Populations of stem, progenitor, or cancer cells show proliferative heterogeneity in vivo, comprising proliferating and quiescent cells. Consistent quantification of the quiescent subpopulation and progression of the proliferating cells through the individual phases of the cell cycle has not been achieved. Here, we describe CycleFlow, a method that robustly infers this comprehensive information from standard pulse-chase experiments with thymidine analogs. Inference is based on a mathematical model of the cell cycle, with realistic waiting time distributions for the G1, S, and G2/M phases and a long-term quiescent G0 state. We validate CycleFlow with an exponentially growing cancer cell line in vitro. Applying it to T cell progenitors in steady state in vivo, we uncover strong proliferative heterogeneity, with a minority of CD4+CD8+ T cell progenitors cycling very rapidly and then entering quiescence. CycleFlow is suitable as a routine method for quantitative cell-cycle analysis.
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Affiliation(s)
- Adrien Jolly
- Division of Theoretical Systems Biology, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
| | - Ann-Kathrin Fanti
- Division of Cellular Immunology, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
| | | | - Nina Claudino
- Division of Theoretical Systems Biology, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
| | - Ines Gräßer
- Division of Theoretical Systems Biology, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
| | - Nils B. Becker
- Division of Theoretical Systems Biology, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
| | - Thomas Höfer
- Division of Theoretical Systems Biology, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
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30
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Stallaert W, Taylor SR, Kedziora KM, Taylor CD, Sobon HK, Young CL, Limas JC, Varblow Holloway J, Johnson MS, Cook JG, Purvis JE. The molecular architecture of cell cycle arrest. Mol Syst Biol 2022; 18:e11087. [PMID: 36161508 PMCID: PMC9511499 DOI: 10.15252/msb.202211087] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2022] [Revised: 09/07/2022] [Accepted: 09/09/2022] [Indexed: 11/09/2022] Open
Abstract
The cellular decision governing the transition between proliferative and arrested states is crucial to the development and function of every tissue. While the molecular mechanisms that regulate the proliferative cell cycle are well established, we know comparatively little about what happens to cells as they diverge into cell cycle arrest. We performed hyperplexed imaging of 47 cell cycle effectors to obtain a map of the molecular architecture that governs cell cycle exit and progression into reversible (“quiescent”) and irreversible (“senescent”) arrest states. Using this map, we found multiple points of divergence from the proliferative cell cycle; identified stress‐specific states of arrest; and resolved the molecular mechanisms governing these fate decisions, which we validated by single‐cell, time‐lapse imaging. Notably, we found that cells can exit into senescence from either G1 or G2; however, both subpopulations converge onto a single senescent state with a G1‐like molecular signature. Cells can escape from this “irreversible” arrest state through the upregulation of G1 cyclins. This map provides a more comprehensive understanding of the overall organization of cell proliferation and arrest.
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Affiliation(s)
- Wayne Stallaert
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.,Computational Medicine Program, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Sovanny R Taylor
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.,Computational Medicine Program, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Katarzyna M Kedziora
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.,Bioinformatics and Analytics Research Collaborative (BARC), University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Colin D Taylor
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.,Computational Medicine Program, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Holly K Sobon
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.,Computational Medicine Program, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Catherine L Young
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.,Computational Medicine Program, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Juanita C Limas
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Jonah Varblow Holloway
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.,Computational Medicine Program, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Martha S Johnson
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Jeanette Gowen Cook
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.,Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Jeremy E Purvis
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.,Computational Medicine Program, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
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31
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Diehl FF, Miettinen TP, Elbashir R, Nabel CS, Darnell AM, Do BT, Manalis SR, Lewis CA, Vander Heiden MG. Nucleotide imbalance decouples cell growth from cell proliferation. Nat Cell Biol 2022; 24:1252-1264. [PMID: 35927450 PMCID: PMC9359916 DOI: 10.1038/s41556-022-00965-1] [Citation(s) in RCA: 29] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2021] [Accepted: 06/21/2022] [Indexed: 12/26/2022]
Abstract
Nucleotide metabolism supports RNA synthesis and DNA replication to enable cell growth and division. Nucleotide depletion can inhibit cell growth and proliferation, but how cells sense and respond to changes in the relative levels of individual nucleotides is unclear. Moreover, the nucleotide requirement for biomass production changes over the course of the cell cycle, and how cells coordinate differential nucleotide demands with cell cycle progression is not well understood. Here we find that excess levels of individual nucleotides can inhibit proliferation by disrupting the relative levels of nucleotide bases needed for DNA replication and impeding DNA replication. The resulting purine and pyrimidine imbalances are not sensed by canonical growth regulatory pathways like mTORC1, Akt and AMPK signalling cascades, causing excessive cell growth despite inhibited proliferation. Instead, cells rely on replication stress signalling to survive during, and recover from, nucleotide imbalance during S phase. We find that ATR-dependent replication stress signalling is activated during unperturbed S phases and promotes nucleotide availability to support DNA replication. Together, these data reveal that imbalanced nucleotide levels are not detected until S phase, rendering cells reliant on replication stress signalling to cope with this metabolic problem and disrupting the coordination of cell growth and division.
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Affiliation(s)
- Frances F Diehl
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Teemu P Miettinen
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA
- Medical Research Council Laboratory for Molecular Cell Biology, University College London, London, UK
| | - Ryan Elbashir
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Christopher S Nabel
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA
- Massachusetts General Hospital Cancer Center, Boston, MA, USA
| | - Alicia M Darnell
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Brian T Do
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
- Harvard-MIT Health Sciences and Technology, Cambridge, MA, USA
| | - Scott R Manalis
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA
- Departments of Biological Engineering and Mechanical Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | | | - Matthew G Vander Heiden
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA.
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA.
- Dana-Farber Cancer Institute, Boston, MA, USA.
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32
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Macdougall LJ, Hoffman TE, Kirkpatrick BE, Fairbanks BD, Bowman CN, Spencer SL, Anseth KS. Intracellular Crowding by Bio-Orthogonal Hydrogel Formation Induces Reversible Molecular Stasis. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2022; 34:e2202882. [PMID: 35671709 PMCID: PMC9377388 DOI: 10.1002/adma.202202882] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/29/2022] [Revised: 05/19/2022] [Indexed: 05/22/2023]
Abstract
To survive extreme conditions, certain animals enter a reversible protective stasis through vitrification of the cytosol by polymeric molecules such as proteins and polysaccharides. In this work, synthetic gelation of the cytosol in living cells is used to induce reversible molecular stasis. Through the sequential lipofectamine-mediated transfection of complementary poly(ethylene glycol) macromers into mammalian cells, intracellular crosslinking occurs through bio-orthogonal strain-promoted azide-alkyne cycloaddition click reactions. This achieves efficient polymer uptake with minimal cell death (99% viable). Intracellular crosslinking decreases DNA replication and protein synthesis, and increases the quiescent population by 2.5-fold. Real-time tracking of single cells containing intracellular crosslinked polymers identifies increases in intermitotic time (15 h vs 19 h) and decreases in motility (30 µm h-1 vs 15 µm h-1 ). The cytosol viscosity increases threefold after intracellular crosslinking and results in disordered cytoskeletal structure in addition to the disruption of cellular coordination in a scratch assay. By incorporating photodegradable nitrobenzyl moieties into the polymer backbone, the effects of intracellular crosslinking are reversed upon exposure to light, thereby restoring proliferation (80% phospho-Rb+ cells), protein translation, and migration. Reversible intracellular crosslinking provides a novel method for dynamic manipulation of intracellular mechanics, altering essential processes that determine cellular function.
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Affiliation(s)
- Laura J Macdougall
- Department of Chemical and Biological Engineering, University of Colorado Boulder, Boulder, CO, 80303, USA
- The BioFrontiers Institute, University of Colorado Boulder, Boulder, CO, 80303, USA
| | - Timothy E Hoffman
- The BioFrontiers Institute, University of Colorado Boulder, Boulder, CO, 80303, USA
- Department of Chemistry and Biochemistry, University of Colorado Boulder, Boulder, CO, 80303, USA
| | - Bruce E Kirkpatrick
- Department of Chemical and Biological Engineering, University of Colorado Boulder, Boulder, CO, 80303, USA
- The BioFrontiers Institute, University of Colorado Boulder, Boulder, CO, 80303, USA
- Medical Scientist Training Program, School of Medicine, University of Colorado, Aurora, CO, 80045, USA
| | - Benjamin D Fairbanks
- Department of Chemical and Biological Engineering, University of Colorado Boulder, Boulder, CO, 80303, USA
- Material Science and Engineering, University of Colorado Boulder, Boulder, CO, 80303, USA
| | - Christopher N Bowman
- Department of Chemical and Biological Engineering, University of Colorado Boulder, Boulder, CO, 80303, USA
- The BioFrontiers Institute, University of Colorado Boulder, Boulder, CO, 80303, USA
- Material Science and Engineering, University of Colorado Boulder, Boulder, CO, 80303, USA
| | - Sabrina L Spencer
- The BioFrontiers Institute, University of Colorado Boulder, Boulder, CO, 80303, USA
- Department of Chemistry and Biochemistry, University of Colorado Boulder, Boulder, CO, 80303, USA
| | - Kristi S Anseth
- Department of Chemical and Biological Engineering, University of Colorado Boulder, Boulder, CO, 80303, USA
- The BioFrontiers Institute, University of Colorado Boulder, Boulder, CO, 80303, USA
- Material Science and Engineering, University of Colorado Boulder, Boulder, CO, 80303, USA
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33
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Swadling JB, Warnecke T, Morris KL, Barr AR. Conserved Cdk inhibitors show unique structural responses to tyrosine phosphorylation. Biophys J 2022; 121:2312-2329. [PMID: 35614852 PMCID: PMC9279356 DOI: 10.1016/j.bpj.2022.05.024] [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: 06/25/2021] [Revised: 03/01/2022] [Accepted: 05/18/2022] [Indexed: 11/02/2022] Open
Abstract
Balanced proliferation-quiescence decisions are vital during normal development and in tissue homeostasis, and their dysregulation underlies tumorigenesis. Entry into proliferative cycles is driven by Cyclin/Cyclin-dependent kinases (Cdks). Conserved Cdk inhibitors (CKIs) p21Cip1/Waf1, p27Kip1, and p57Kip2 bind to Cyclin/Cdks and inhibit Cdk activity. p27 tyrosine phosphorylation, in response to mitogenic signaling, promotes activation of CyclinD/Cdk4 and CyclinA/Cdk2. Tyrosine phosphorylation is conserved in p21 and p57, although the number of sites differs. We use molecular-dynamics simulations to compare the structural changes in Cyclin/Cdk/CKI trimers induced by single and multiple tyrosine phosphorylation in CKIs and their impact on CyclinD/Cdk4 and CyclinA/Cdk2 activity. Despite shared structural features, CKI binding induces distinct structural responses in Cyclin/Cdks and the predicted effects of CKI tyrosine phosphorylation on Cdk activity are not conserved across CKIs. Our analyses suggest how CKIs may have evolved to be sensitive to different inputs to give context-dependent control of Cdk activity.
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Affiliation(s)
- Jacob B Swadling
- Institute of Clinical Sciences, Imperial College London, London, United Kingdom; MRC London Institute of Medical Sciences, London, United Kingdom.
| | - Tobias Warnecke
- Institute of Clinical Sciences, Imperial College London, London, United Kingdom; MRC London Institute of Medical Sciences, London, United Kingdom
| | - Kyle L Morris
- MRC London Institute of Medical Sciences, London, United Kingdom
| | - Alexis R Barr
- Institute of Clinical Sciences, Imperial College London, London, United Kingdom; MRC London Institute of Medical Sciences, London, United Kingdom.
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34
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Oncogenic RAS sensitizes cells to drug-induced replication stress via transcriptional silencing of P53. Oncogene 2022; 41:2719-2733. [PMID: 35393546 PMCID: PMC9076537 DOI: 10.1038/s41388-022-02291-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2021] [Revised: 03/17/2022] [Accepted: 03/21/2022] [Indexed: 11/09/2022]
Abstract
Cancer cells often experience high basal levels of DNA replication stress (RS), for example due to hyperactivation of oncoproteins like MYC or RAS. Therefore, cancer cells are considered to be sensitive to drugs that exacerbate the level of RS or block the intra S-phase checkpoint. Consequently, RS-inducing drugs including ATR and CHK1 inhibitors are used or evaluated as anti-cancer therapies. However, drug resistance and lack of biomarkers predicting therapeutic efficacy limit efficient use. This raises the question what determines sensitivity of individual cancer cells to RS. Here, we report that oncogenic RAS does not only enhance the sensitivity to ATR/CHK1 inhibitors by directly causing RS. Instead, we observed that HRASG12V dampens the activation of the P53-dependent transcriptional response to drug-induced RS, which in turn confers sensitivity to RS. We demonstrate that inducible expression of HRASG12V sensitized cells to ATR and CHK1 inhibitors. Using RNA-sequencing of FACS-sorted cells we discovered that P53 signaling is the sole transcriptional response to RS. However, oncogenic RAS attenuates the transcription of P53 and TGF-β pathway components which consequently dampens P53 target gene expression. Accordingly, live cell imaging showed that HRASG12V exacerbates RS in S/G2-phase, which could be rescued by stabilization of P53. Thus, our results demonstrate that transcriptional control of P53 target genes is the prime determinant in the response to ATR/CHK1 inhibitors and show that hyperactivation of the MAPK pathway impedes this response. Our findings suggest that the level of oncogenic MAPK signaling could predict sensitivity to intra-S-phase checkpoint inhibition in cancers with intact P53.
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35
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Wu G, Xiu H, Luo H, Ding Y, Li Y. A mathematical model for cell cycle control: graded response or quantized response. Cell Cycle 2022; 21:820-834. [PMID: 35107036 PMCID: PMC8973363 DOI: 10.1080/15384101.2022.2031770] [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: 09/17/2021] [Revised: 01/03/2022] [Accepted: 01/17/2022] [Indexed: 02/04/2023] Open
Abstract
Cell cycle is an important and complex biological system. A lot of efforts have been put in understanding cell cycle arrest for its vital role in clinical therapies. The cell-cycle-arrest outcomes upon stimulation are complicated. The response could be stringent or relaxed, and graded or quantized. A model fully addressing various cell-cycle-arrest outcomes is to be developed. Here, we developed a mathematical model of cell cycle control incorporating distinct characteristics of various cell-cycle-arrest outcomes. The model can simulate two typical properties of cell cycle arrest, quantized and graded. We also characterized the inheritable quiescence and refractory state, which were crucial in long-term response of the population. Then, we monitored cells respond to multiple stimulations, and the results indicated that cells responded to stimulations with small interval did not induce significantly sustained cell cycle arrest as the existence of refractory state. Our work will benefit fundamental research and make efforts to predicting outcomes of clinical therapeutics.
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Affiliation(s)
- Guoyu Wu
- School of Clinical Pharmacy, Guangdong Pharmaceutical University, Guangdong, China
- Key Specialty of Clinical Pharmacy, The First Affiliated Hospital of Guangdong Pharmaceutical University, Guangzhou, China
- NMPA Key Laboratory for Technology Research and Evaluation of Pharmacovigilance, Guangdong Pharmaceutical University, Guangzhou, China
- CONTACT Guoyu Wu
| | - Huiyu Xiu
- School of Clinical Pharmacy, Guangdong Pharmaceutical University, Guangdong, China
| | - Haiying Luo
- School of Clinical Pharmacy, Guangdong Pharmaceutical University, Guangdong, China
| | - Yu Ding
- School of Clinical Pharmacy, Guangdong Pharmaceutical University, Guangdong, China
| | - Yuchao Li
- MegaLab, MegaRobo Technologies Co., Ltd, Beijing, China
- Yuchao Li
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36
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The structure of the human cell cycle. Cell Syst 2022; 13:230-240.e3. [PMID: 34800361 PMCID: PMC8930470 DOI: 10.1016/j.cels.2021.10.007] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Revised: 08/16/2021] [Accepted: 10/26/2021] [Indexed: 01/01/2023]
Abstract
Understanding the organization of the cell cycle has been a longstanding goal in cell biology. We combined time-lapse microscopy, highly multiplexed single-cell imaging of 48 core cell cycle proteins, and manifold learning to render a visualization of the human cell cycle. This data-driven approach revealed the comprehensive "structure" of the cell cycle: a continuum of molecular states that cells occupy as they transition from one cell division to the next, or as they enter or exit cell cycle arrest. Paradoxically, progression deeper into cell cycle arrest was accompanied by increases in proliferative effectors such as CDKs and cyclins, which can drive cell cycle re-entry by overcoming p21 induction. The structure also revealed the molecular trajectories into senescence and the unique combination of molecular features that define this irreversibly arrested state. This approach will enable the comparison of alternative cell cycles during development, in response to environmental perturbation and in disease. A record of this paper's transparent peer review process is included in the supplemental information.
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37
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Crozier L, Foy R, Mouery BL, Whitaker RH, Corno A, Spanos C, Ly T, Gowen Cook J, Saurin AT. CDK4/6 inhibitors induce replication stress to cause long-term cell cycle withdrawal. EMBO J 2022; 41:e108599. [PMID: 35037284 PMCID: PMC8922273 DOI: 10.15252/embj.2021108599] [Citation(s) in RCA: 36] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2021] [Revised: 11/18/2021] [Accepted: 12/21/2021] [Indexed: 12/29/2022] Open
Abstract
CDK4/6 inhibitors arrest the cell cycle in G1-phase. They are approved to treat breast cancer and are also undergoing clinical trials against a range of other tumour types. To facilitate these efforts, it is important to understand why a cytostatic arrest in G1 causes long-lasting effects on tumour growth. Here, we demonstrate that a prolonged G1 arrest following CDK4/6 inhibition downregulates replisome components and impairs origin licencing. Upon release from that arrest, many cells fail to complete DNA replication and exit the cell cycle in a p53-dependent manner. If cells fail to withdraw from the cell cycle following DNA replication problems, they enter mitosis and missegregate chromosomes causing excessive DNA damage, which further limits their proliferative potential. These effects are observed in a range of tumour types, including breast cancer, implying that genotoxic stress is a common outcome of CDK4/6 inhibition. This unanticipated ability of CDK4/6 inhibitors to induce DNA damage now provides a rationale to better predict responsive tumour types and effective combination therapies, as demonstrated by the fact that CDK4/6 inhibition induces sensitivity to chemotherapeutics that also cause replication stress.
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Affiliation(s)
- Lisa Crozier
- Division of Cellular and Systems MedicineJacqui Wood Cancer CentreSchool of MedicineUniversity of DundeeDundeeUK
| | - Reece Foy
- Division of Cellular and Systems MedicineJacqui Wood Cancer CentreSchool of MedicineUniversity of DundeeDundeeUK
| | - Brandon L Mouery
- Curriculum in Genetics and Molecular BiologyUniversity of North Carolina at Chapel HillChapel HillNCUSA
| | - Robert H Whitaker
- Department of Biochemistry and BiophysicsUniversity of North Carolina at Chapel HillChapel HillNCUSA
| | - Andrea Corno
- Division of Cellular and Systems MedicineJacqui Wood Cancer CentreSchool of MedicineUniversity of DundeeDundeeUK
| | - Christos Spanos
- Wellcome Trust Centre for Cell BiologyUniversity of EdinburghEdinburghUK
| | - Tony Ly
- Wellcome Trust Centre for Cell BiologyUniversity of EdinburghEdinburghUK
- Present address:
Centre for Gene Regulation and ExpressionSchool of Life SciencesUniversity of DundeeDundeeUK
| | - Jeanette Gowen Cook
- Department of Biochemistry and BiophysicsUniversity of North Carolina at Chapel HillChapel HillNCUSA
| | - Adrian T Saurin
- Division of Cellular and Systems MedicineJacqui Wood Cancer CentreSchool of MedicineUniversity of DundeeDundeeUK
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38
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Gousias K, Theocharous T, Simon M. Mechanisms of Cell Cycle Arrest and Apoptosis in Glioblastoma. Biomedicines 2022; 10:biomedicines10030564. [PMID: 35327366 PMCID: PMC8945784 DOI: 10.3390/biomedicines10030564] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2021] [Revised: 02/10/2022] [Accepted: 02/26/2022] [Indexed: 12/13/2022] Open
Abstract
Cells of glioblastoma, the most frequent primary malignant brain tumor, are characterized by their rapid growth and infiltration of adjacent healthy brain parenchyma, which reflects their aggressive biological behavior. In order to maintain their excessive proliferation and invasion, glioblastomas exploit the innate biological capacities of the patients suffering from this tumor. The pathways involved in cell cycle regulation and apoptosis are the mechanisms most commonly affected. The following work reviews the regulatory pathways of cell growth in general as well as the dysregulated cell cycle and apoptosis relevant mechanisms observed in glioblastomas. We then describe the molecular targeting of the current established adjuvant therapy and present ongoing trials or completed studies on specific promising therapeutic agents that induce cell cycle arrest and apoptosis of glioblastoma cells.
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Affiliation(s)
- Konstantinos Gousias
- Department of Neurosurgery, St. Marien Academic Hospital Lünen, KLW St. Paulus Corporation, 44534 Luenen, Germany;
- Medical School, Westfälische Wilhelms University of Muenster, 48149 Muenster, Germany
- Medical School, University of Nicosia, Nicosia 2414, Cyprus
- Correspondence: ; Tel.: +49-2306-773151
| | - Theocharis Theocharous
- Department of Neurosurgery, St. Marien Academic Hospital Lünen, KLW St. Paulus Corporation, 44534 Luenen, Germany;
| | - Matthias Simon
- Department of Neurosurgery, Bethel Clinic, University of Bielefeld Medical School, 33617 Bielefeld, Germany;
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39
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Connolly C, Takahashi S, Miura H, Hiratani I, Gilbert N, Donaldson AD, Hiraga SI. SAF-A promotes origin licensing and replication fork progression to ensure robust DNA replication. J Cell Sci 2022; 135:jcs258991. [PMID: 34888666 DOI: 10.1242/jcs.258991] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2021] [Accepted: 12/02/2021] [Indexed: 11/20/2022] Open
Abstract
The organisation of chromatin is closely intertwined with biological activities of chromosome domains, including transcription and DNA replication status. Scaffold-attachment factor A (SAF-A), also known as heterogeneous nuclear ribonucleoprotein U (HNRNPU), contributes to the formation of open chromatin structure. Here, we demonstrate that SAF-A promotes the normal progression of DNA replication and enables resumption of replication after inhibition. We report that cells depleted of SAF-A show reduced origin licensing in G1 phase and, consequently, reduced origin activation frequency in S phase. Replication forks also progress less consistently in cells depleted of SAF-A, contributing to reduced DNA synthesis rate. Single-cell replication timing analysis revealed two distinct effects of SAF-A depletion: first, the boundaries between early- and late-replicating domains become more blurred; and second, SAF-A depletion causes replication timing changes that tend to bring regions of discordant domain compartmentalisation and replication timing into concordance. Associated with these defects, SAF-A-depleted cells show elevated formation of phosphorylated histone H2AX (γ-H2AX) and tend to enter quiescence. Overall, we find that SAF-A protein promotes robust DNA replication to ensure continuing cell proliferation.
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Affiliation(s)
- Caitlin Connolly
- Institute of Medical Sciences, University of Aberdeen, Foresterhill, Aberdeen AB25 2ZD, UK
| | - Saori Takahashi
- RIKEN Center for Biosystems Dynamics Research, Kobe, Hyogo 650-0047, Japan
| | - Hisashi Miura
- RIKEN Center for Biosystems Dynamics Research, Kobe, Hyogo 650-0047, Japan
| | - Ichiro Hiratani
- RIKEN Center for Biosystems Dynamics Research, Kobe, Hyogo 650-0047, Japan
| | - Nick Gilbert
- MRC Human Genetics Unit, The University of Edinburgh, Crewe Rd, Edinburgh EH4 2XU, UK
| | - Anne D Donaldson
- Institute of Medical Sciences, University of Aberdeen, Foresterhill, Aberdeen AB25 2ZD, UK
| | - Shin-Ichiro Hiraga
- Institute of Medical Sciences, University of Aberdeen, Foresterhill, Aberdeen AB25 2ZD, UK
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40
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Pulianmackal AJ, Sun D, Yumoto K, Li Z, Chen YC, Patel MV, Wang Y, Yoon E, Pearson A, Yang Q, Taichman R, Cackowski FC, Buttitta LA. Monitoring Spontaneous Quiescence and Asynchronous Proliferation-Quiescence Decisions in Prostate Cancer Cells. Front Cell Dev Biol 2021; 9:728663. [PMID: 34957090 PMCID: PMC8703172 DOI: 10.3389/fcell.2021.728663] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2021] [Accepted: 11/19/2021] [Indexed: 11/13/2022] Open
Abstract
The proliferation-quiescence decision is a dynamic process that remains incompletely understood. Live-cell imaging with fluorescent cell cycle sensors now allows us to visualize the dynamics of cell cycle transitions and has revealed that proliferation-quiescence decisions can be highly heterogeneous, even among clonal cell lines in culture. Under normal culture conditions, cells often spontaneously enter non-cycling G0 states of varying duration and depth. This also occurs in cancer cells and G0 entry in tumors may underlie tumor dormancy and issues with cancer recurrence. Here we show that a cell cycle indicator previously shown to indicate G0 upon serum starvation, mVenus-p27K-, can also be used to monitor spontaneous quiescence in untransformed and cancer cell lines. We find that the duration of spontaneous quiescence in untransformed and cancer cells is heterogeneous and that a portion of this heterogeneity results from asynchronous proliferation-quiescence decisions in pairs of daughters after mitosis, where one daughter cell enters or remains in temporary quiescence while the other does not. We find that cancer dormancy signals influence both entry into quiescence and asynchronous proliferation-quiescence decisions after mitosis. Finally, we show that spontaneously quiescent prostate cancer cells exhibit altered expression of components of the Hippo pathway and are enriched for the stem cell markers CD133 and CD44. This suggests a hypothesis that dormancy signals could promote cancer recurrence by increasing the proportion of quiescent tumor cells poised for cell cycle re-entry with stem cell characteristics in cancer.
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Affiliation(s)
- Ajai J Pulianmackal
- Molecular, Cellular and Developmental Biology, University of Michigan, Ann Arbor, MI, United States
| | - Dan Sun
- Molecular, Cellular and Developmental Biology, University of Michigan, Ann Arbor, MI, United States
| | - Kenji Yumoto
- School of Dentistry, University of Michigan, Ann Arbor, MI, United States
| | - Zhengda Li
- Department of Biophysics, University of Michigan, Ann Arbor, MI, United States
| | - Yu-Chih Chen
- Department of Electrical Engineering and Computer Science, University of Michigan, Ann Arbor, MI, United States.,Department of Computational and Systems Biology, Hillman Cancer Center, University of Pittsburgh School of Medicine, Pittsburgh, PA, United States
| | - Meha V Patel
- Molecular, Cellular and Developmental Biology, University of Michigan, Ann Arbor, MI, United States
| | - Yu Wang
- School of Dentistry, University of Michigan, Ann Arbor, MI, United States
| | - Euisik Yoon
- Department of Electrical Engineering and Computer Science, University of Michigan, Ann Arbor, MI, United States.,Department of Biomedical Engineering, University of Michigan, Ann Arbor, MI, United States.,Center for Nanomedicine, Institute for Basic Science (IBS) and Graduate Program of Nano Biomedical Engineering (Nano BME), Advanced Science Institute, Yonsei University, Seoul, Korea, South Korea
| | - Alexander Pearson
- Department of Medicine, Section of Hematology/Oncology, University of Chicago Medical Center, Chicago, IL, United States
| | - Qiong Yang
- Department of Biophysics, University of Michigan, Ann Arbor, MI, United States
| | - Russell Taichman
- School of Dentistry, University of Michigan, Ann Arbor, MI, United States.,Department of Periodontology, School of Dentistry, University of Alabama at Birmingham, Birmingham, AL, United States
| | - Frank C Cackowski
- School of Dentistry, University of Michigan, Ann Arbor, MI, United States.,Department of Oncology, Karmanos Cancer Institute and Wayne State University, Detroit, MI, United States
| | - Laura A Buttitta
- Molecular, Cellular and Developmental Biology, University of Michigan, Ann Arbor, MI, United States
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41
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Jensen-Cody CW, Crooke AK, Rotti PG, Ievlev V, Shahin W, Park SY, Lynch TJ, Engelhardt JF. Lef-1 controls cell cycle progression in airway basal cells to regulate proliferation and differentiation. Stem Cells 2021; 39:1221-1235. [PMID: 33932322 PMCID: PMC8785221 DOI: 10.1002/stem.3386] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2021] [Accepted: 04/08/2021] [Indexed: 11/10/2022]
Abstract
The mammalian airways are lined by a continuous epithelial layer that is maintained by diverse populations of resident multipotent stem cells. These stem cells are responsible for replenishing the epithelium both at homeostasis and following injury, making them promising targets for stem cell and genetic-based therapies for a variety of respiratory diseases. However, the mechanisms that regulate when and how these stem cells proliferate, migrate, and differentiate remains incompletely understood. Here, we find that the high mobility group (HMG) domain transcription factor Lef-1 regulates proliferation and differentiation of mouse tracheal basal cells. We demonstrate that conditional deletion of Lef-1 stalls basal cell proliferation at the G1/S transition of the cell cycle, and that Lef-1 knockout cells are unable to maintain luminal tracheal cell types in long-term air-liquid interface culture. RNA sequencing analysis revealed that Lef-1 knockout (Lef-1KO) results in downregulation of key DNA damage response and cell cycle progression genes, including the kinase Chek1. Furthermore, chemical inhibition of Chek1 is sufficient to stall basal cell self-renewal in a similar fashion as Lef-1 deletion. Notably, the cell cycle block imposed by Lef-1KO in vitro is transient and basal cells eventually compensate to proliferate normally in a Chek1-independent manner. Finally, Lef-1KO cells were unable to fully regenerate tracheal epithelium following injury in vivo. These findings reveal that Lef-1 is essential for proper basal cell function. Thus, modulating Lef-1 function in airway basal cells may have applications in regenerative medicine.
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Affiliation(s)
- Chandler W Jensen-Cody
- Department of Anatomy & Cell Biology, University of Iowa, Carver College of Medicine, Iowa City, Iowa, USA
| | - Adrianne K Crooke
- Department of Anatomy & Cell Biology, University of Iowa, Carver College of Medicine, Iowa City, Iowa, USA
| | - Pavana G Rotti
- Department of Anatomy & Cell Biology, University of Iowa, Carver College of Medicine, Iowa City, Iowa, USA
| | - Vitaly Ievlev
- Department of Anatomy & Cell Biology, University of Iowa, Carver College of Medicine, Iowa City, Iowa, USA
| | - Weam Shahin
- Department of Anatomy & Cell Biology, University of Iowa, Carver College of Medicine, Iowa City, Iowa, USA
| | - Soo-Yeun Park
- Department of Anatomy & Cell Biology, University of Iowa, Carver College of Medicine, Iowa City, Iowa, USA
| | - Thomas J Lynch
- Department of Anatomy & Cell Biology, University of Iowa, Carver College of Medicine, Iowa City, Iowa, USA
| | - John F Engelhardt
- Department of Anatomy & Cell Biology, University of Iowa, Carver College of Medicine, Iowa City, Iowa, USA
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42
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Cassidy T, Nichol D, Robertson-Tessi M, Craig M, Anderson ARA. The role of memory in non-genetic inheritance and its impact on cancer treatment resistance. PLoS Comput Biol 2021; 17:e1009348. [PMID: 34460809 PMCID: PMC8432806 DOI: 10.1371/journal.pcbi.1009348] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Revised: 09/10/2021] [Accepted: 08/11/2021] [Indexed: 12/24/2022] Open
Abstract
Intra-tumour heterogeneity is a leading cause of treatment failure and disease progression in cancer. While genetic mutations have long been accepted as a primary mechanism of generating this heterogeneity, the role of phenotypic plasticity is becoming increasingly apparent as a driver of intra-tumour heterogeneity. Consequently, understanding the role of this plasticity in treatment resistance and failure is a key component of improving cancer therapy. We develop a mathematical model of stochastic phenotype switching that tracks the evolution of drug-sensitive and drug-tolerant subpopulations to clarify the role of phenotype switching on population growth rates and tumour persistence. By including cytotoxic therapy in the model, we show that, depending on the strategy of the drug-tolerant subpopulation, stochastic phenotype switching can lead to either transient or permanent drug resistance. We study the role of phenotypic heterogeneity in a drug-resistant, genetically homogeneous population of non-small cell lung cancer cells to derive a rational treatment schedule that drives population extinction and avoids competitive release of the drug-tolerant sub-population. This model-informed therapeutic schedule results in increased treatment efficacy when compared against periodic therapy, and, most importantly, sustained tumour decay without the development of resistance.
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Affiliation(s)
- Tyler Cassidy
- Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, New Mexico, United States of America
| | - Daniel Nichol
- Evolutionary Genomics and Modelling Lab, Centre for Evolution and Cancer, The Institute of Cancer Research, London, United Kingdom
| | - Mark Robertson-Tessi
- Department of Integrated Mathematical Oncology, H. Lee Moffitt Cancer Center, Tampa, Florida, United States of America
| | - Morgan Craig
- Département de mathématiques et de statistique, Université de Montréal, Montreal, Canada
- CHU Sainte-Justine, Montreal, Canada
| | - Alexander R. A. Anderson
- Department of Integrated Mathematical Oncology, H. Lee Moffitt Cancer Center, Tampa, Florida, United States of America
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43
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Abstract
The current model of replication-dependent (RD) histone biosynthesis posits that RD histone gene expression is coupled to DNA replication, occurring only in S phase of the cell cycle once DNA synthesis has begun. However, several key factors in the RD histone biosynthesis pathway are up-regulated by E2F or phosphorylated by CDK2, suggesting these processes may instead begin much earlier, at the point of cell-cycle commitment. In this study, we use both fixed- and live-cell imaging of human cells to address this question, revealing a hybrid model in which RD histone biosynthesis is first initiated in G1, followed by a strong increase in histone production in S phase of the cell cycle. This suggests a mechanism by which cells that have committed to the cell cycle build up an initial small pool of RD histones to be available for the start of DNA replication, before producing most of the necessary histones required in S phase. Thus, a clear distinction exists at completion of mitosis between cells that are born with the intention of proceeding through the cell cycle and replicating their DNA and cells that have chosen to exit the cell cycle and have no immediate need for histone synthesis.
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44
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Brooks RF. Cell Cycle Commitment and the Origins of Cell Cycle Variability. Front Cell Dev Biol 2021; 9:698066. [PMID: 34368148 PMCID: PMC8343065 DOI: 10.3389/fcell.2021.698066] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2021] [Accepted: 06/22/2021] [Indexed: 11/13/2022] Open
Abstract
Exit of cells from quiescence following mitogenic stimulation is highly asynchronous, and there is a great deal of heterogeneity in the response. Even in a single, clonal population, some cells re-enter the cell cycle after a sub-optimal mitogenic signal while other, seemingly identical cells, do not, though they remain capable of responding to a higher level of stimulus. This review will consider the origins of this variability and heterogeneity, both in cells re-entering the cycle from quiescence and in the context of commitment decisions in continuously cycling populations. Particular attention will be paid to the role of two interacting molecular networks, namely the RB-E2F and APC/CCDH1 "switches." These networks have the property of bistability and it seems likely that they are responsible for dynamic behavior previously described kinetically by Transition Probability models of the cell cycle. The relationship between these switches and the so-called Restriction Point of the cell cycle will also be considered.
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Affiliation(s)
- Robert F Brooks
- Molecular and Clinical Sciences Research Institute, St George's, University of London, London, United Kingdom.,Department of Anatomy, King's College London, London, United Kingdom
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45
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Molecular control of cell density-mediated exit to quiescence. Cell Rep 2021; 36:109436. [PMID: 34320337 PMCID: PMC8924979 DOI: 10.1016/j.celrep.2021.109436] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2020] [Revised: 05/04/2021] [Accepted: 07/01/2021] [Indexed: 12/22/2022] Open
Abstract
Contact inhibition of cell proliferation regulates tissue size and prevents uncontrolled cell expansion. When cell density increases, contact inhibition can force proliferating cells into quiescence. Here we show that the variable memory of local cell density experienced by a mother cell controls the levels of the cyclin-dependent kinase (CDK) activator cyclin D1 and inhibitor p27 in newborn daughters, which direct cells to proliferation or quiescence. Much of this regulation can be explained by rapid suppression of ERK activity by high cell density in mothers, which leads to lower cyclin D1 and higher p27 levels in daughters. Strikingly, cell density and mitogen signals compete by shifting the ratio of cyclin D1/p27 levels below or above a single sharp threshold that controls the proliferation decision. Thus, the history of competing cell density and mitogen signals experienced by mothers is funneled into a precise activator-inhibitor balance that decides the fate of daughter cells. Using live single-cell microscopy, Fan and Meyer show that the decision of newborn daughter cells to proliferate or become quiescent is controlled by the memory of local cell density inherited from mother cells. This memory is mediated by an ultrasensitive activator-inhibitor balance between cyclin D1 and p27.
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46
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Lezaja A, Panagopoulos A, Wen Y, Carvalho E, Imhof R, Altmeyer M. RPA shields inherited DNA lesions for post-mitotic DNA synthesis. Nat Commun 2021; 12:3827. [PMID: 34158486 PMCID: PMC8219667 DOI: 10.1038/s41467-021-23806-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2020] [Accepted: 05/11/2021] [Indexed: 02/05/2023] Open
Abstract
The paradigm that checkpoints halt cell cycle progression for genome repair has been challenged by the recent discovery of heritable DNA lesions escaping checkpoint control. How such inherited lesions affect genome function and integrity is not well understood. Here, we identify a new class of heritable DNA lesions, which is marked by replication protein A (RPA), a protein primarily known for shielding single-stranded DNA in S/G2. We demonstrate that post-mitotic RPA foci occur at low frequency during unperturbed cell cycle progression, originate from the previous cell cycle, and are exacerbated upon replication stress. RPA-marked inherited ssDNA lesions are found at telomeres, particularly of ALT-positive cancer cells. We reveal that RPA protects these replication remnants in G1 to allow for post-mitotic DNA synthesis (post-MiDAS). Given that ALT-positive cancer cells exhibit high levels of replication stress and telomere fragility, targeting post-MiDAS might be a new therapeutic opportunity.
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Affiliation(s)
- Aleksandra Lezaja
- grid.7400.30000 0004 1937 0650Department of Molecular Mechanisms of Disease, University of Zurich, Zurich, Switzerland
| | - Andreas Panagopoulos
- grid.7400.30000 0004 1937 0650Department of Molecular Mechanisms of Disease, University of Zurich, Zurich, Switzerland
| | - Yanlin Wen
- grid.7400.30000 0004 1937 0650Department of Molecular Mechanisms of Disease, University of Zurich, Zurich, Switzerland
| | - Edison Carvalho
- grid.7400.30000 0004 1937 0650Department of Molecular Mechanisms of Disease, University of Zurich, Zurich, Switzerland
| | - Ralph Imhof
- grid.7400.30000 0004 1937 0650Department of Molecular Mechanisms of Disease, University of Zurich, Zurich, Switzerland
| | - Matthias Altmeyer
- grid.7400.30000 0004 1937 0650Department of Molecular Mechanisms of Disease, University of Zurich, Zurich, Switzerland
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47
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O'Connor SA, Feldman HM, Arora S, Hoellerbauer P, Toledo CM, Corrin P, Carter L, Kufeld M, Bolouri H, Basom R, Delrow J, McFaline-Figueroa JL, Trapnell C, Pollard SM, Patel A, Paddison PJ, Plaisier CL. Neural G0: a quiescent-like state found in neuroepithelial-derived cells and glioma. Mol Syst Biol 2021; 17:e9522. [PMID: 34101353 PMCID: PMC8186478 DOI: 10.15252/msb.20209522] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2020] [Revised: 04/30/2021] [Accepted: 05/14/2021] [Indexed: 12/13/2022] Open
Abstract
Single‐cell RNA sequencing has emerged as a powerful tool for resolving cellular states associated with normal and maligned developmental processes. Here, we used scRNA‐seq to examine the cell cycle states of expanding human neural stem cells (hNSCs). From these data, we constructed a cell cycle classifier that identifies traditional cell cycle phases and a putative quiescent‐like state in neuroepithelial‐derived cell types during mammalian neurogenesis and in gliomas. The Neural G0 markers are enriched with quiescent NSC genes and other neurodevelopmental markers found in non‐dividing neural progenitors. Putative glioblastoma stem‐like cells were significantly enriched in the Neural G0 cell population. Neural G0 cell populations and gene expression are significantly associated with less aggressive tumors and extended patient survival for gliomas. Genetic screens to identify modulators of Neural G0 revealed that knockout of genes associated with the Hippo/Yap and p53 pathways diminished Neural G0 in vitro, resulting in faster G1 transit, down‐regulation of quiescence‐associated markers, and loss of Neural G0 gene expression. Thus, Neural G0 represents a dynamic quiescent‐like state found in neuroepithelial‐derived cells and gliomas.
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Affiliation(s)
- Samantha A O'Connor
- School of Biological and Health Systems Engineering, Arizona State University, Tempe, AZ, USA
| | - Heather M Feldman
- Human Biology Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Sonali Arora
- Human Biology Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Pia Hoellerbauer
- Human Biology Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA.,Molecular and Cellular Biology Program, University of Washington, Seattle, WA, USA
| | - Chad M Toledo
- Human Biology Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA.,Molecular and Cellular Biology Program, University of Washington, Seattle, WA, USA
| | - Philip Corrin
- Human Biology Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Lucas Carter
- Human Biology Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Megan Kufeld
- Human Biology Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Hamid Bolouri
- Human Biology Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Ryan Basom
- Genomics and Bioinformatics Shared Resources, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Jeffrey Delrow
- Genomics and Bioinformatics Shared Resources, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | | | - Cole Trapnell
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Steven M Pollard
- Edinburgh CRUK Cancer Research Centre, MRC Centre for Regenerative Medicine, The University of Edinburgh, Edinburgh, UK
| | - Anoop Patel
- Human Biology Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA.,Department of Neurosurgery, University of Washington, Seattle, WA, USA
| | - Patrick J Paddison
- Human Biology Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA.,Molecular and Cellular Biology Program, University of Washington, Seattle, WA, USA
| | - Christopher L Plaisier
- School of Biological and Health Systems Engineering, Arizona State University, Tempe, AZ, USA
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48
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Pack LR, Daigh LH, Chung M, Meyer T. Clinical CDK4/6 inhibitors induce selective and immediate dissociation of p21 from cyclin D-CDK4 to inhibit CDK2. Nat Commun 2021; 12:3356. [PMID: 34099663 PMCID: PMC8184839 DOI: 10.1038/s41467-021-23612-z] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2020] [Accepted: 05/06/2021] [Indexed: 12/11/2022] Open
Abstract
Since their discovery as drivers of proliferation, cyclin-dependent kinases (CDKs) have been considered therapeutic targets. Small molecule inhibitors of CDK4/6 are used and tested in clinical trials to treat multiple cancer types. Despite their clinical importance, little is known about how CDK4/6 inhibitors affect the stability of CDK4/6 complexes, which bind cyclins and inhibitory proteins such as p21. We develop an assay to monitor CDK complex stability inside the nucleus. Unexpectedly, treatment with CDK4/6 inhibitors-palbociclib, ribociclib, or abemaciclib-immediately dissociates p21 selectively from CDK4 but not CDK6 complexes. This effect mediates indirect inhibition of CDK2 activity by p21 but not p27 redistribution. Our work shows that CDK4/6 inhibitors have two roles: non-catalytic inhibition of CDK2 via p21 displacement from CDK4 complexes, and catalytic inhibition of CDK4/6 independent of p21. By broadening the non-catalytic displacement to p27 and CDK6 containing complexes, next-generation CDK4/6 inhibitors may have improved efficacy and overcome resistance mechanisms.
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Affiliation(s)
- Lindsey R Pack
- Department of Chemical and Systems Biology, Stanford University, Stanford, CA, USA
| | - Leighton H Daigh
- Department of Chemical and Systems Biology, Stanford University, Stanford, CA, USA
| | - Mingyu Chung
- Department of Chemical and Systems Biology, Stanford University, Stanford, CA, USA
| | - Tobias Meyer
- Department of Chemical and Systems Biology, Stanford University, Stanford, CA, USA.
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49
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AHNAK controls 53BP1-mediated p53 response by restraining 53BP1 oligomerization and phase separation. Mol Cell 2021; 81:2596-2610.e7. [PMID: 33961796 PMCID: PMC8221568 DOI: 10.1016/j.molcel.2021.04.010] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2020] [Revised: 03/05/2021] [Accepted: 04/09/2021] [Indexed: 12/21/2022]
Abstract
p53-binding protein 1 (53BP1) regulates both the DNA damage response and p53 signaling. Although 53BP1's function is well established in DNA double-strand break repair, how its role in p53 signaling is modulated remains poorly understood. Here, we identify the scaffolding protein AHNAK as a G1 phase-enriched interactor of 53BP1. We demonstrate that AHNAK binds to the 53BP1 oligomerization domain and controls its multimerization potential. Loss of AHNAK results in hyper-accumulation of 53BP1 on chromatin and enhanced phase separation, culminating in an elevated p53 response, compromising cell survival in cancer cells but leading to senescence in non-transformed cells. Cancer transcriptome analyses indicate that AHNAK-53BP1 cooperation contributes to the suppression of p53 target gene networks in tumors and that loss of AHNAK sensitizes cells to combinatorial cancer treatments. These findings highlight AHNAK as a rheostat of 53BP1 function, which surveys cell proliferation by preventing an excessive p53 response.
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50
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Tian C, Yang C, Spencer SL. EllipTrack: A Global-Local Cell-Tracking Pipeline for 2D Fluorescence Time-Lapse Microscopy. Cell Rep 2021; 32:107984. [PMID: 32755578 DOI: 10.1016/j.celrep.2020.107984] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2019] [Revised: 05/29/2020] [Accepted: 07/09/2020] [Indexed: 12/12/2022] Open
Abstract
Time-lapse microscopy provides an unprecedented opportunity to monitor single-cell dynamics. However, tracking cells for long periods remains a technical challenge, especially for multi-day, large-scale movies with rapid cell migration, high cell density, and drug treatments that alter cell morphology/behavior. Here, we present EllipTrack, a global-local cell-tracking pipeline optimized for tracking such movies. EllipTrack first implements a global track-linking algorithm to construct tracks that maximize the probability of cell lineages. Tracking mistakes are then corrected with a local track-correction module in which tracks generated by the global algorithm are systematically examined and amended if a more probable alternative can be found. Through benchmarking, we show that EllipTrack outperforms state-of-the-art cell trackers and generates nearly error-free cell lineages for multiple large-scale movies. In addition, EllipTrack can adapt to time- and cell-density-dependent changes in cell migration speeds and requires minimal training datasets. EllipTrack is available at https://github.com/tianchengzhe/EllipTrack.
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Affiliation(s)
- Chengzhe Tian
- Department of Biochemistry, University of Colorado Boulder, Boulder, CO 80303, USA; BioFrontiers Institute, University of Colorado Boulder, Boulder, CO 80303, USA.
| | - Chen Yang
- Department of Molecular, Cellular, and Developmental Biology, University of Colorado Boulder, Boulder, CO 80303, USA; BioFrontiers Institute, University of Colorado Boulder, Boulder, CO 80303, USA
| | - Sabrina L Spencer
- Department of Biochemistry, University of Colorado Boulder, Boulder, CO 80303, USA; BioFrontiers Institute, University of Colorado Boulder, Boulder, CO 80303, USA.
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