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Simerzin A, Ackerman EE, Fujimaki K, Kohler RH, Iwamoto Y, Heltberg MS, Jambhekar A, Weissleder R, Lahav G. Cell confluency affects p53 dynamics in response to DNA damage. Mol Biol Cell 2025; 36:br16. [PMID: 40202833 DOI: 10.1091/mbc.e24-09-0394] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/11/2025] Open
Abstract
The tumor suppressor protein p53 plays a key role in the cellular response to DNA damage. In response to DNA double-strand breaks (DSB), cultured cells exhibit oscillations of p53 levels, which impact gene expression and cell fate. The dynamics of p53 in vivo have only been studied in fixed tissues or using reporters for p53's transcriptional activity. Here we established breast tumors expressing a fluorescent reporter for p53 levels and employed intravital imaging to quantify its dynamics in response to DSB in vivo. Our findings revealed large heterogeneity among individual cells, with most cells exhibiting a single prolonged pulse. We then tested how p53 dynamics might change under high cell confluency, one factor that differs between cell culture and tissues. We revealed that highly confluent cultured breast cancer cells also show one broad p53 pulse instead of oscillations. Through mathematical modeling, sensitivity analysis, and live-cell imaging, we identified low levels of the phosphatase Wip1, a transcriptional target and negative regulator of p53, as a key contributor to these dynamics. Because high cell confluency better reflects the microenvironment of tissues, the impact of cell confluency on p53 dynamics may have important consequences for cancerous tissues responding to DNA damage-inducing therapies.
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Affiliation(s)
- Alina Simerzin
- Department of Systems Biology, Blavatnik Institute at Harvard Medical School, Boston, MA 02115
| | - Emily E Ackerman
- Department of Systems Biology, Blavatnik Institute at Harvard Medical School, Boston, MA 02115
| | - Kotaro Fujimaki
- Department of Systems Biology, Blavatnik Institute at Harvard Medical School, Boston, MA 02115
| | - Rainer H Kohler
- Center for Systems Biology, Massachusetts General Hospital, Boston, MA 02114
| | - Yoshiko Iwamoto
- Center for Systems Biology, Massachusetts General Hospital, Boston, MA 02114
| | - Mathias S Heltberg
- Department of Systems Biology, Blavatnik Institute at Harvard Medical School, Boston, MA 02115
- Niels Bohr Institute, University of Copenhagen, Copenhagen, Denmark 2100
| | - Ashwini Jambhekar
- Department of Systems Biology, Blavatnik Institute at Harvard Medical School, Boston, MA 02115
| | - Ralph Weissleder
- Center for Systems Biology, Massachusetts General Hospital, Boston, MA 02114
| | - Galit Lahav
- Department of Systems Biology, Blavatnik Institute at Harvard Medical School, Boston, MA 02115
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2
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Janes KA, Lazzara MJ. Systems Biology of the Cancer Cell. Annu Rev Biomed Eng 2025; 27:1-28. [PMID: 39689262 DOI: 10.1146/annurev-bioeng-103122-030552] [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: 12/19/2024]
Abstract
Questions in cancer have engaged systems biologists for decades. During that time, the quantity of molecular data has exploded, but the need for abstractions, formal models, and simplifying insights has remained the same. This review brings together classic breakthroughs and recent findings in the field of cancer systems biology, focusing on cancer cell pathways for tumorigenesis and therapeutic response. Cancer cells mutate and transduce information from their environment to alter gene expression, metabolism, and phenotypic states. Understanding the molecular architectures that make each of these steps possible is a long-term goal of cancer systems biology pursued by iterating between quantitative models and experiments. We argue that such iteration is the best path to deploying targeted therapies intelligently so that each patient receives the maximum benefit for their cancer.
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Affiliation(s)
- Kevin A Janes
- Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, Virginia, USA
- Department of Biomedical Engineering, University of Virginia, Charlottesville, Virginia, USA; ,
| | - Matthew J Lazzara
- Department of Chemical Engineering, University of Virginia, Charlottesville, Virginia, USA
- Department of Biomedical Engineering, University of Virginia, Charlottesville, Virginia, USA; ,
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3
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Abuetabh Y, Wu HH, Al Yousef H, Persad S, Schlosser MP, Eisenstat DD, Sergi CM, Leng R. Deciphering UBE4B phosphorylation dynamics: a key mechanism in p53 accumulation and cancer cell response to DNA damage. Cell Death Discov 2025; 11:131. [PMID: 40175346 PMCID: PMC11965332 DOI: 10.1038/s41420-025-02441-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2024] [Revised: 03/21/2025] [Accepted: 03/25/2025] [Indexed: 04/04/2025] Open
Abstract
The p53 tumor suppressor protein plays a crucial role in detecting and eliminating various oncogenic threats by promoting processes such as cell cycle arrest, DNA repair, senescence, and apoptosis. UBE4B is essential for negatively regulating p53 during normal conditions and following DNA damage. In previous studies, we demonstrated that UBE4B targets phosphorylated p53 for degradation in response to DNA damage. However, the regulation of UBE4B in relation to DNA damage in cancer is not well understood. In this study, we show that the UBE4B protein is regulated through a phosphorylation and dephosphorylation mechanism in response to DNA damage. Phosphorylation of UBE4B reduces its binding affinity to p53, leading to an accumulation of p53 in the cell. Wip1 plays a crucial role in the dephosphorylation of UBE4B, which stabilizes the activity of the UBE4B protein in response to DNA damage. UBE4B is primarily phosphorylated through ATR-mediated signaling, which reduces its binding affinity with p53, resulting in the accumulation and activation of p53. When Wip1 is inhibited, there is a significant increase in UBE4B phosphorylation, leading to more p53 accumulation and a reduction in cell growth. Therefore, understanding how UBE4B is regulated in cancer cells in response to DNA-damaging agents could help develop new therapeutic strategies to improve the prognosis for cancer patients.
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Affiliation(s)
- Yasser Abuetabh
- 370 Heritage Medical Research Center, Department of Laboratory Medicine and Pathology, University of Alberta, Edmonton, AB, T6G 2S2, Canada
| | - H Helena Wu
- 370 Heritage Medical Research Center, Department of Laboratory Medicine and Pathology, University of Alberta, Edmonton, AB, T6G 2S2, Canada
| | - Habib Al Yousef
- 370 Heritage Medical Research Center, Department of Laboratory Medicine and Pathology, University of Alberta, Edmonton, AB, T6G 2S2, Canada
| | - Sujata Persad
- Department of Pediatrics, University of Alberta, 11405 - 87 Ave., Edmonton, AB, T6G 1C9, Canada
| | - Mary-Pat Schlosser
- Department of Pediatrics, University of Alberta, 11405 - 87 Ave., Edmonton, AB, T6G 1C9, Canada
| | - David D Eisenstat
- Department of Pediatrics, University of Alberta, 11405 - 87 Ave., Edmonton, AB, T6G 1C9, Canada
- Department of Oncology, Cross Cancer Institute, 11560 University Ave., University of Alberta, Edmonton, AB, T6G 1Z2, Canada
- Department of Medical Genetics, University of Alberta, 8613 114 Street, Edmonton, AB, T6G 2H7, Canada
- Murdoch Children's Research Institute, Department of Paediatrics, University of Melbourne, 50 Flemington Road, Parkville, VIC, 3052, Australia
| | - Consolato M Sergi
- Division of Anatomical Pathology, Children's Hospital of Eastern Ontario (CHEO), University of Ottawa, 401 Smyth Road Ottawa, Ottawa, ON, K1H 8L1, Canada
| | - Roger Leng
- 370 Heritage Medical Research Center, Department of Laboratory Medicine and Pathology, University of Alberta, Edmonton, AB, T6G 2S2, Canada.
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4
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Venkatachalapathy H, Dallon S, Yang Z, Azarin SM, Sarkar CA, Batchelor E. Pulsed stimuli enable p53 phase resetting to synchronize single cells and modulate cell fate. Mol Syst Biol 2025; 21:390-412. [PMID: 40033003 PMCID: PMC11965341 DOI: 10.1038/s44320-025-00091-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2023] [Revised: 02/03/2025] [Accepted: 02/10/2025] [Indexed: 03/05/2025] Open
Abstract
Oscillatory p53 expression occurs in individual cells responding to DNA breaks. While the majority of cells exhibit the same qualitative response, quantitative features of the oscillations (e.g., amplitude or period) can be highly variable between cells, generating heterogeneity in downstream cell fate responses. Since heterogeneity can be detrimental to therapies based on DNA damage, methods to induce synchronization of p53 oscillations across cells in a population have the potential to generate more predictable responses to DNA-damaging treatments. Using mathematical modeling and time-lapse microscopy, we demonstrated that p53 oscillations can be synchronized through the phenomenon of phase resetting. Surprisingly, p53 oscillations were synchronized over a wider range of damage-induction frequencies than predicted computationally. Recapitulating the range of synchronizing frequencies required, non-intuitively, a less robust oscillator. We showed that p53 phase resetting altered the expression of downstream targets responsible for cell fate depending on target mRNA stability. This study demonstrates that p53 oscillations can be phase reset and highlights the potential of driving p53 dynamics to reduce cellular variability and synchronize cell fate responses to DNA damage.
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Affiliation(s)
- Harish Venkatachalapathy
- Department of Integrative Biology and Physiology, University of Minnesota, Minneapolis, MN, 55455, USA
- Department of Chemical Engineering and Materials Science, University of Minnesota, Minneapolis, MN, 55455, USA
| | - Samuel Dallon
- Department of Biomedical Engineering, University of Minnesota, Minneapolis, MN, 55455, USA
| | - Zhilin Yang
- Laboratory of Cell Biology, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, 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.
| | - Eric Batchelor
- Department of Integrative Biology and Physiology, University of Minnesota, Minneapolis, MN, 55455, USA.
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Yuan HH, Yin H, Marincas M, Xie LL, Bu LL, Guo MH, Zheng XL. From DNA Repair to Redox Signaling: The Multifaceted Role of APEX1 (Apurinic/Apyrimidinic Endonuclease 1) in Cardiovascular Health and Disease. Int J Mol Sci 2025; 26:3034. [PMID: 40243693 PMCID: PMC11988304 DOI: 10.3390/ijms26073034] [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: 02/13/2025] [Revised: 03/17/2025] [Accepted: 03/20/2025] [Indexed: 04/18/2025] Open
Abstract
Apurinic/apyrimidinic endonuclease 1 (APEX1) serves as a potent regulatory factor in innate immunity, exhibiting both redox and endonuclease activities. Its redox function enables the regulation of transcription factors such as NF-κB or STAT3, whereas its endonuclease activity recognizes apurinic/apyrimidinic (AP) sites in damaged DNA lesions during base excision repair (BER) and double-stranded DNA repair, thereby I confirm.anti-inflammatory, antioxidative stress and antiapoptotic effects. APEX1 is expressed in a variety of cell types that constitute the cardiovascular system, including cardiomyocytes, endothelial cells, smooth muscle cells, and immune cells. Emerging genetic and experimental evidence points towards the functional roles of APEX1 in the pathophysiology of cardiovascular diseases, including neointimal formation and atherosclerosis. This review aims to present comprehensive coverage of the up-to-date literature concerning the molecular and cellular functions of APEX1, with a particular focus on how APEX1 contributes to the (dys)functions of different cell types during the pathogenesis of cardiovascular diseases. Furthermore, we underscore the potential of APEX1 as a therapeutic target for the treatment of cardiovascular diseases.
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Affiliation(s)
- Huan-Huan Yuan
- Key Laboratory of Hunan Province for Integrated Traditional Chinese and Western Medicine on Prevention and Treatment of Cardio-Cerebral Diseases, College of Integrated Traditional Chinese and Western Medicine, Hunan University of Chinese Medicine, Changsha 410208, China
- Department of Biochemistry & Molecular Biology, Libin Cardiovascular Institute, Cumming School of Medicine, University of Calgary, Calgary, AB T2N 4Z6, Canada
| | - Hao Yin
- Robarts Research Institute, Schulich School of Medicine and Dentistry, Western University, 1151 Richmond St. N., London, ON N6A 5B7, Canada
| | - Mara Marincas
- Department of Biochemistry & Molecular Biology, Libin Cardiovascular Institute, Cumming School of Medicine, University of Calgary, Calgary, AB T2N 4Z6, Canada
| | - Ling-Li Xie
- Key Laboratory of Hunan Province for Integrated Traditional Chinese and Western Medicine on Prevention and Treatment of Cardio-Cerebral Diseases, College of Integrated Traditional Chinese and Western Medicine, Hunan University of Chinese Medicine, Changsha 410208, China
- Department of Biochemistry & Molecular Biology, Libin Cardiovascular Institute, Cumming School of Medicine, University of Calgary, Calgary, AB T2N 4Z6, Canada
| | - Lan-Lan Bu
- Key Laboratory of Hunan Province for Integrated Traditional Chinese and Western Medicine on Prevention and Treatment of Cardio-Cerebral Diseases, College of Integrated Traditional Chinese and Western Medicine, Hunan University of Chinese Medicine, Changsha 410208, China
| | - Min-Hua Guo
- Key Laboratory of Hunan Province for Integrated Traditional Chinese and Western Medicine on Prevention and Treatment of Cardio-Cerebral Diseases, College of Integrated Traditional Chinese and Western Medicine, Hunan University of Chinese Medicine, Changsha 410208, China
| | - Xi-Long Zheng
- Department of Biochemistry & Molecular Biology, Libin Cardiovascular Institute, Cumming School of Medicine, University of Calgary, Calgary, AB T2N 4Z6, Canada
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6
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Givré A, Colman-Lerner A, Ponce Dawson S. Amplitude and frequency encoding result in qualitatively distinct informational landscapes in cell signaling. Sci Rep 2025; 15:8075. [PMID: 40057610 PMCID: PMC11890874 DOI: 10.1038/s41598-025-92424-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2024] [Accepted: 02/27/2025] [Indexed: 05/13/2025] Open
Abstract
Cells continuously sense their surroundings to detect modifications and generate responses. Very often changes in extracellular concentrations initiate signaling cascades that eventually result in changes in gene expression. Increasing stimulus strengths can be encoded in increasing concentration amplitudes or increasing activation frequencies of intermediaries of the pathway. In this paper we show that the different way in which amplitude and frequency encoding map environmental changes endow cells with qualitatively different information transmission capabilities. While amplitude encoding is optimal for a limited range of stimuli strengths, frequency encoding can transmit information with equal reliability over much broader ranges. The qualitative difference between the two strategies stems from the scale invariant discriminating power of the first transducing step in frequency codification. The apparently redundant combination of both strategies in some cell types may then serve the purpose of expanding the span over which stimulus strengths can be reliably discriminated. In this paper we discuss a possible example of this mechanism in yeast.
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Affiliation(s)
- Alan Givré
- Departamento de Física, Facultad de Ciencias Exactas y Naturales, UBA, Buenos Aires, Argentina
- Instituto de Física de Buenos Aires (IFIBA), CONICET-UBA, Buenos Aires, Argentina
| | - Alejandro Colman-Lerner
- Departamento de Fisiología, Departamento de Fisiología, Biología Molecular y Celular, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina
- Instituto de Fisiología, Biología Molecular y Neurociencias (IFIBYNE), CONICET-UBA, Buenos Aires, Argentina
| | - Silvina Ponce Dawson
- Departamento de Física, Facultad de Ciencias Exactas y Naturales, UBA, Buenos Aires, Argentina.
- Instituto de Física de Buenos Aires (IFIBA), CONICET-UBA, Buenos Aires, Argentina.
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7
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Rosen SJ, Witteveen O, Baxter N, Lach RS, Bauer M, Wilson MZ. Anti-resonance in developmental signaling regulates cell fate decisions. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2025:2025.02.04.636331. [PMID: 39990305 PMCID: PMC11844363 DOI: 10.1101/2025.02.04.636331] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 02/25/2025]
Abstract
Cells process dynamic signaling inputs to regulate fate decisions during development. While oscillations or waves in key developmental pathways, such as Wnt, have been widely observed, the principles governing how cells decode these signals remain unclear. By leveraging optogenetic control of the Wnt signaling pathway in both HEK293T cells and H9 human embryonic stem cells, we systematically map the relationship between signal frequency and downstream pathway activation. We find that cells exhibit a minimal response to Wnt at certain frequencies, a behavior we term anti-resonance. We developed both detailed biochemical and simplified hidden variable models that explain how anti-resonance emerges from the interplay between fast and slow pathway dynamics. Remarkably, we find that frequency directly influences cell fate decisions involved in human gastrulation; signals delivered at anti-resonant frequencies result in dramatically reduced mesoderm differentiation. Our work reveals a previously unknown mechanism of how cells decode dynamic signals and how anti-resonance may filter against spurious activation. These findings establish new insights into how cells decode dynamic signals with implications for tissue engineering, regenerative medicine, and cancer biology.
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Affiliation(s)
- Samuel J. Rosen
- Interdisciplinary Program in Quantitative Biosciences, University of California Santa Barbara, Santa Barbara, CA, USA
| | - Olivier Witteveen
- Department of Bionanoscience, Kavli Institute of Nanoscience Delft, Technische Universiteit Delft, Van der Maasweg 9, 2629 HZ Delft, the Netherlands
| | - Naomi Baxter
- Department of Molecular, Cellular, and Development Biology, University of California Santa Barbara, Santa Barbara, CA, USA
| | - Ryan S. Lach
- Integrated Biosciences, Inc., Redwood City, CA, USA
| | - Marianne Bauer
- Department of Bionanoscience, Kavli Institute of Nanoscience Delft, Technische Universiteit Delft, Van der Maasweg 9, 2629 HZ Delft, the Netherlands
| | - Maxwell Z. Wilson
- Center for Bioengineering, University of California Santa Barbara, Santa Barbara, CA, USA
- Interdisciplinary Program in Quantitative Biosciences, University of California Santa Barbara, Santa Barbara, CA, USA
- Department of Molecular, Cellular, and Development Biology, University of California Santa Barbara, Santa Barbara, CA, USA
- Neuroscience Research Institute, University of California Santa Barbara, Santa Barbara, CA, USA
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8
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Nakamura E, Blanchini F, Giordano G, Hoffmann A, Franco E. Temporal dose inversion properties of adaptive biomolecular circuits. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2025:2025.02.10.636967. [PMID: 39990486 PMCID: PMC11844413 DOI: 10.1101/2025.02.10.636967] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 02/25/2025]
Abstract
Cells have the capacity to encode and decode information in the temporal features of molecular signals. Many pathways, for example, generate either sustained or pulsatile responses depending on the context, and such diverse temporal behaviors have a profound impact on cell fate. Here we focus on how molecular pathways can convert the temporal features of dynamic signals, in particular how they can convert transient signals into persistent downstream events and vice versa. We describe this type of behavior as temporal dose inversion, and we demonstrate that it can be achieved through adaptive molecular circuits. We consider motifs known as incoherent feedforward loop (IFFL) and negative feedback loop (NFL), and identify parametric conditions that enable temporal dose inversion. We next consider more complex versions of these circuits that could be realized using enzymatic signaling and gene regulatory networks, finding that both circuits can exhibit temporal dose inversion. Finally, we consider a generalized IFFL topology, and we find that both the time delay in the inhibition pathway and the relative signal intensities of the activation and inhibition signals are key determinants for temporal dose inversion. Our investigation expands the potential use of adaptive circuits as signal processing units and contributes to our understanding of the role of adaptive circuits in nature.
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Affiliation(s)
- Eiji Nakamura
- Department of Mechanical and Aerospace Engineering, University of California, Los Angeles, USA
| | - Franco Blanchini
- Department of Mathematics, Computer Science and Physics, University of Udine, Italy
| | - Giulia Giordano
- Department of Industrial Engineering, University of Trento, Italy
| | - Alexander Hoffmann
- Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, USA
| | - Elisa Franco
- Department of Mechanical and Aerospace Engineering, University of California, Los Angeles, USA
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9
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Hsieh FS, Nguyen DPM, Heltberg MS, Wu CC, Lee YC, Jensen MH, Chen SH. Plausible, robust biological oscillations through allelic buffering. Cell Syst 2024; 15:1018-1032.e12. [PMID: 39504970 DOI: 10.1016/j.cels.2024.10.002] [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: 12/30/2023] [Revised: 08/12/2024] [Accepted: 10/10/2024] [Indexed: 11/08/2024]
Abstract
Biological oscillators can specify time- and dose-dependent functions via dedicated control of their oscillatory dynamics. However, how biological oscillators, which recurrently activate noisy biochemical processes, achieve robust oscillations remains unclear. Here, we characterize the long-term oscillations of p53 and its negative feedback regulator Mdm2 in single cells after DNA damage. Whereas p53 oscillates regularly, Mdm2 from a single MDM2 allele exhibits random unresponsiveness to ∼9% of p53 pulses. Using allelic-specific imaging of MDM2 activity, we show that MDM2 alleles buffer each other to maintain p53 pulse amplitude. Removal of MDM2 allelic buffering cripples the robustness of p53 amplitude, thereby elevating p21 levels and cell-cycle arrest. In silico simulations support that allelic buffering enhances the robustness of biological oscillators and broadens their plausible biochemical space. Our findings show how allelic buffering ensures robust p53 oscillations, highlighting the potential importance of allelic buffering for the emergence of robust biological oscillators during evolution. A record of this paper's transparent peer review process is included in the supplemental information.
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Affiliation(s)
- Feng-Shu Hsieh
- Lab for Cell Dynamics, Institute of Molecular Biology, Academia Sinica, Taipei 115, Taiwan
| | - Duy P M Nguyen
- Lab for Cell Dynamics, Institute of Molecular Biology, Academia Sinica, Taipei 115, Taiwan
| | - Mathias S Heltberg
- Niels Bohr Institute, University of Copenhagen, Copenhagen 2100, Denmark
| | - Chia-Chou Wu
- Lab for Cell Dynamics, Institute of Molecular Biology, Academia Sinica, Taipei 115, Taiwan; National Center for Theoretical Sciences, Physics Division, Complex Systems, Taipei 10617, Taiwan
| | - Yi-Chen Lee
- Lab for Cell Dynamics, Institute of Molecular Biology, Academia Sinica, Taipei 115, Taiwan
| | - Mogens H Jensen
- Niels Bohr Institute, University of Copenhagen, Copenhagen 2100, Denmark
| | - Sheng-Hong Chen
- Lab for Cell Dynamics, Institute of Molecular Biology, Academia Sinica, Taipei 115, Taiwan; National Center for Theoretical Sciences, Physics Division, Complex Systems, Taipei 10617, Taiwan.
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10
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Jiménez A, Lucchetti A, Heltberg MS, Moretto L, Sanchez C, Jambhekar A, Jensen MH, Lahav G. Entrainment and multi-stability of the p53 oscillator in human cells. Cell Syst 2024; 15:956-968.e3. [PMID: 39368467 DOI: 10.1016/j.cels.2024.09.001] [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: 01/09/2024] [Revised: 06/25/2024] [Accepted: 09/12/2024] [Indexed: 10/07/2024]
Abstract
The tumor suppressor p53 responds to cellular stress and activates transcription programs critical for regulating cell fate. DNA damage triggers oscillations in p53 levels with a robust period. Guided by the theory of synchronization and entrainment, we developed a mathematical model and experimental system to test the ability of the p53 oscillator to entrain to external drug pulses of various periods and strengths. We found that the p53 oscillator can be locked and entrained to a wide range of entrainment modes. External periods far from p53's natural oscillations increased the heterogeneity between individual cells whereas stronger inputs reduced it. Single-cell measurements allowed deriving the phase response curves (PRCs) and multiple Arnold tongues of p53. In addition, multi-stability and non-linear behaviors were mathematically predicted and experimentally detected, including mode hopping, period doubling, and chaos. Our work revealed critical dynamical properties of the p53 oscillator and provided insights into understanding and controlling it. A record of this paper's transparent peer review process is included in the supplemental information.
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Affiliation(s)
- Alba Jiménez
- Department of Systems Biology, Blavatnik Institute at Harvard Medical School, Boston, MA 02115, USA
| | - Alessandra Lucchetti
- Department of Systems Biology, Blavatnik Institute at Harvard Medical School, Boston, MA 02115, USA; Niels Bohr Institute, University of Copenhagen, Copenhagen 2100, Denmark
| | - Mathias S Heltberg
- Department of Systems Biology, Blavatnik Institute at Harvard Medical School, Boston, MA 02115, USA; Niels Bohr Institute, University of Copenhagen, Copenhagen 2100, Denmark
| | - Liv Moretto
- Niels Bohr Institute, University of Copenhagen, Copenhagen 2100, Denmark
| | - Carlos Sanchez
- Department of Systems Biology, Blavatnik Institute at Harvard Medical School, Boston, MA 02115, USA
| | - Ashwini Jambhekar
- Department of Systems Biology, Blavatnik Institute at Harvard Medical School, Boston, MA 02115, USA
| | - Mogens H Jensen
- Niels Bohr Institute, University of Copenhagen, Copenhagen 2100, Denmark.
| | - Galit Lahav
- Department of Systems Biology, Blavatnik Institute at Harvard Medical School, Boston, MA 02115, USA.
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11
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Liu TT, Wang Q, Zhou Y, Ye B, Liu T, Yan L, Fan J, Xu J, Zhou Y, Xia Z, Deng X. Discovery of a Meisoindigo-Derived PROTAC as the ATM Degrader: Revolutionizing Colorectal Cancer Therapy via Synthetic Lethality with ATR Inhibitors. J Med Chem 2024; 67:7620-7634. [PMID: 38634707 DOI: 10.1021/acs.jmedchem.4c00454] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/19/2024]
Abstract
Meisoindigo (Mei) has long been recognized in chronic myeloid leukemia (CML) treatment. To elucidate its molecular target and mechanisms, we embarked on designing and synthesizing a series of Mei-derived PROTACs. Through this endeavor, VHL-type PROTAC 9b was identified to be highly cytotoxic against SW620, SW480, and K562 cells. Employing DiaPASEF-based quantitative proteomic analysis, in combination with extensive validation assays, we unveiled that 9b potently and selectively degraded ATM across SW620 and SW480 cells in a ubiquitin-proteasome-dependent manner. 9b-induced selective ATM degradation prompted DNA damage response cascades, thereby leading to the cell cycle arrest and cell apoptosis. This pioneering discovery renders the advent of ATM degradation for anti-cancer therapy. Notably, 9b-induced ATM degradation synergistically enhanced the efficacy of ATR inhibitor AZD6738 both in vitro and in vivo. This work establishes the synthetic lethality-inducing properties of ATR inhibitors in the ATM-deficient context, thereby providing new avenues to innovative therapies for colorectal cancer.
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Affiliation(s)
- Ting-Ting Liu
- Xiangya School of Pharmaceutical Sciences, Hunan Key Laboratory of Diagnostic and Therapeutic Drug Research for Chronic Diseases, Central South University, Changsha, Hunan 410013, China
| | - Qing Wang
- Xiangya School of Pharmaceutical Sciences, Hunan Key Laboratory of Diagnostic and Therapeutic Drug Research for Chronic Diseases, Central South University, Changsha, Hunan 410013, China
| | - Yuxing Zhou
- Xiangya School of Pharmaceutical Sciences, Hunan Key Laboratory of Diagnostic and Therapeutic Drug Research for Chronic Diseases, Central South University, Changsha, Hunan 410013, China
| | - Baixin Ye
- Bone Marrow Transplantation Center, the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 311106, China
| | - Tingting Liu
- Xiangya School of Pharmaceutical Sciences, Hunan Key Laboratory of Diagnostic and Therapeutic Drug Research for Chronic Diseases, Central South University, Changsha, Hunan 410013, China
| | - Linyang Yan
- Xiangya School of Pharmaceutical Sciences, Hunan Key Laboratory of Diagnostic and Therapeutic Drug Research for Chronic Diseases, Central South University, Changsha, Hunan 410013, China
| | - Jinbao Fan
- Xiangya School of Pharmaceutical Sciences, Hunan Key Laboratory of Diagnostic and Therapeutic Drug Research for Chronic Diseases, Central South University, Changsha, Hunan 410013, China
| | - Jiahao Xu
- Xiangya School of Pharmaceutical Sciences, Hunan Key Laboratory of Diagnostic and Therapeutic Drug Research for Chronic Diseases, Central South University, Changsha, Hunan 410013, China
| | - Yingjun Zhou
- Xiangya School of Pharmaceutical Sciences, Hunan Key Laboratory of Diagnostic and Therapeutic Drug Research for Chronic Diseases, Central South University, Changsha, Hunan 410013, China
| | - Zanxian Xia
- School of Life Sciences, Central South University, Changsha, Hunan 410013, China
| | - Xu Deng
- Xiangya School of Pharmaceutical Sciences, Hunan Key Laboratory of Diagnostic and Therapeutic Drug Research for Chronic Diseases, Central South University, Changsha, Hunan 410013, China
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12
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Kandouz M. Cell Death, by Any Other Name…. Cells 2024; 13:325. [PMID: 38391938 PMCID: PMC10886887 DOI: 10.3390/cells13040325] [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: 12/31/2023] [Revised: 02/04/2024] [Accepted: 02/06/2024] [Indexed: 02/24/2024] Open
Abstract
Studies trying to understand cell death, this ultimate biological process, can be traced back to a century ago. Yet, unlike many other fashionable research interests, research on cell death is more alive than ever. New modes of cell death are discovered in specific contexts, as are new molecular pathways. But what is "cell death", really? This question has not found a definitive answer yet. Nevertheless, part of the answer is irreversibility, whereby cells can no longer recover from stress or injury. Here, we identify the most distinctive features of different modes of cell death, focusing on the executive final stages. In addition to the final stages, these modes can differ in their triggering stimulus, thus referring to the initial stages. Within this framework, we use a few illustrative examples to examine how intercellular communication factors in the demise of cells. First, we discuss the interplay between cell-cell communication and cell death during a few steps in the early development of multicellular organisms. Next, we will discuss this interplay in a fully developed and functional tissue, the gut, which is among the most rapidly renewing tissues in the body and, therefore, makes extensive use of cell death. Furthermore, we will discuss how the balance between cell death and communication is modified during a pathological condition, i.e., colon tumorigenesis, and how it could shed light on resistance to cancer therapy. Finally, we briefly review data on the role of cell-cell communication modes in the propagation of cell death signals and how this has been considered as a potential therapeutic approach. Far from vainly trying to provide a comprehensive review, we launch an invitation to ponder over the significance of cell death diversity and how it provides multiple opportunities for the contribution of various modes of intercellular communication.
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Affiliation(s)
- Mustapha Kandouz
- Department of Pathology, School of Medicine, Wayne State University, 540 East Canfield Avenue, Detroit, MI 48201, USA;
- Karmanos Cancer Institute, Wayne State University, Detroit, MI 48201, USA
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13
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Tilden EI, Maduskar A, Oldenborg A, Sabatini BL, Chen Y. A Cre-dependent reporter mouse for quantitative real-time imaging of protein kinase A activity dynamics. Sci Rep 2024; 14:3054. [PMID: 38321128 PMCID: PMC10847463 DOI: 10.1038/s41598-024-53313-8] [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: 11/17/2023] [Accepted: 01/30/2024] [Indexed: 02/08/2024] Open
Abstract
Intracellular signaling dynamics play a crucial role in cell function. Protein kinase A (PKA) is a key signaling molecule that has diverse functions, from regulating metabolism and brain activity to guiding development and cancer progression. We previously developed an optical reporter, FLIM-AKAR, that allows for quantitative imaging of PKA activity via fluorescence lifetime imaging microscopy and photometry. However, using viral infection or electroporation for the delivery of FLIM-AKAR is invasive and results in variable expression. Here, we developed a reporter mouse, FL-AK, which expresses FLIM-AKAR in a Cre-dependent manner from the ROSA26 locus. FL-AK provides robust and consistent expression of FLIM-AKAR over time. Functionally, the mouse line reports an increase in PKA activity in response to activation of both Gαs and Gαq-coupled receptors in brain slices. In vivo, FL-AK reports PKA phosphorylation in response to neuromodulator receptor activation. Thus, FL-AK provides a quantitative, robust, and flexible method to reveal the dynamics of PKA activity in diverse cell types.
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Affiliation(s)
- Elizabeth I Tilden
- Department of Neuroscience, Washington University in St. Louis, St. Louis, MO, USA
- Ph.D. Program in Neuroscience, Washington University in St. Louis, St. Louis, MO, USA
| | - Aditi Maduskar
- Department of Neuroscience, Washington University in St. Louis, St. Louis, MO, USA
| | - Anna Oldenborg
- Department of Neuroscience, Washington University in St. Louis, St. Louis, MO, USA
| | - Bernardo L Sabatini
- Department of Neurobiology, Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, USA
| | - Yao Chen
- Department of Neuroscience, Washington University in St. Louis, St. Louis, MO, USA.
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14
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Shalwitz R, Day T, Ruehlmann AK, Julio L, Gordon S, Vandeuren A, Nelson M, Lyman M, Kelly K, Altvater A, Ondeck C, O'Brien S, Hamilton T, Hanson RL, Wayman K, Miller A, Shalwitz I, Batchelor E, McNutt P. Treatment of Sulfur Mustard Corneal Injury by Augmenting the DNA Damage Response (DDR): A Novel Approach. J Pharmacol Exp Ther 2024; 388:526-535. [PMID: 37977813 PMCID: PMC10801765 DOI: 10.1124/jpet.123.001686] [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: 01/27/2023] [Revised: 09/21/2023] [Accepted: 09/22/2023] [Indexed: 11/19/2023] Open
Abstract
Sulfur mustard (SM) is a highly reactive organic chemical has been used as a chemical warfare agent and terrorist threat since World War I. The cornea is highly sensitive to SM toxicity and exposure to low vapor doses can cause incapacitating acute injuries. Exposure to higher doses can elicit persistent secondary keratopathies that cause reduced quality of life and impaired or lost vision. Despite a century of research, there are no specific treatments for acute or persistent ocular SM injuries. SM cytotoxicity emerges, in part, through DNA alkylation and double-strand breaks (DSBs). Because DSBs can naturally be repaired by DNA damage response pathways with low efficiency, we hypothesized that enhancing the homologous recombination pathway could pose a novel approach to mitigate SM injury. Here, we demonstrate that a dilithium salt of adenosine diphosphoribose (INV-102) increases protein levels of p53 and Sirtuin 6, upregulates transcription of BRCA1/2, enhances γH2AX focus formation, and promotes assembly of repair complexes at DSBs. Based on in vitro evidence showing INV-102 enhancement of DNA damage response through both p53-dependent and p53-independent pathways, we next tested INV-102 in a rabbit preclinical model of corneal injury. In vivo studies demonstrate a marked reduction in the incidence and severity of secondary keratopathies in INV-102-treated eyes compared with vehicle-treated eyes when treatment was started 24 hours after SM vapor exposure. These results suggest DNA repair mechanisms are a viable therapeutic target for SM injury and suggest topical treatment with INV-102 is a promising approach for SM as well as other conditions associated with DSBs. SIGNIFICANCE STATEMENT: Sulfur mustard gas corneal injury currently has no therapeutic treatment. This study aims to show the therapeutic potential of activating the body's natural DNA damage response to activate tissue repair.
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Affiliation(s)
- Robert Shalwitz
- Invirsa, Inc., Columbus, Ohio (R.S., A.K.R., A.M., I.S.); Department of Biology, Northeastern University, Boston, Massachusetts (T.D., L.J., S.G., A.V.); Department of Integrative Biology and Physiology, University of Minnesota, Minneapolis, Minnesota (R.L.H., K.W., E.B.); United States Army Medical Research Institute for Chemical Defense, Gunpowder, Maryland (M.N., M.L., K.K., A.A., C.O., S.O., T.H., P.M.); and Wake Forest Institute for Regenerative Medicine, School of Medicine, Wake Forest University Health Sciences, Winston-Salem, North Carolina (S.O., C.O., P.M.)
| | - Tovah Day
- Invirsa, Inc., Columbus, Ohio (R.S., A.K.R., A.M., I.S.); Department of Biology, Northeastern University, Boston, Massachusetts (T.D., L.J., S.G., A.V.); Department of Integrative Biology and Physiology, University of Minnesota, Minneapolis, Minnesota (R.L.H., K.W., E.B.); United States Army Medical Research Institute for Chemical Defense, Gunpowder, Maryland (M.N., M.L., K.K., A.A., C.O., S.O., T.H., P.M.); and Wake Forest Institute for Regenerative Medicine, School of Medicine, Wake Forest University Health Sciences, Winston-Salem, North Carolina (S.O., C.O., P.M.)
| | - Anna Kotsakis Ruehlmann
- Invirsa, Inc., Columbus, Ohio (R.S., A.K.R., A.M., I.S.); Department of Biology, Northeastern University, Boston, Massachusetts (T.D., L.J., S.G., A.V.); Department of Integrative Biology and Physiology, University of Minnesota, Minneapolis, Minnesota (R.L.H., K.W., E.B.); United States Army Medical Research Institute for Chemical Defense, Gunpowder, Maryland (M.N., M.L., K.K., A.A., C.O., S.O., T.H., P.M.); and Wake Forest Institute for Regenerative Medicine, School of Medicine, Wake Forest University Health Sciences, Winston-Salem, North Carolina (S.O., C.O., P.M.)
| | - Lindsay Julio
- Invirsa, Inc., Columbus, Ohio (R.S., A.K.R., A.M., I.S.); Department of Biology, Northeastern University, Boston, Massachusetts (T.D., L.J., S.G., A.V.); Department of Integrative Biology and Physiology, University of Minnesota, Minneapolis, Minnesota (R.L.H., K.W., E.B.); United States Army Medical Research Institute for Chemical Defense, Gunpowder, Maryland (M.N., M.L., K.K., A.A., C.O., S.O., T.H., P.M.); and Wake Forest Institute for Regenerative Medicine, School of Medicine, Wake Forest University Health Sciences, Winston-Salem, North Carolina (S.O., C.O., P.M.)
| | - Shellaina Gordon
- Invirsa, Inc., Columbus, Ohio (R.S., A.K.R., A.M., I.S.); Department of Biology, Northeastern University, Boston, Massachusetts (T.D., L.J., S.G., A.V.); Department of Integrative Biology and Physiology, University of Minnesota, Minneapolis, Minnesota (R.L.H., K.W., E.B.); United States Army Medical Research Institute for Chemical Defense, Gunpowder, Maryland (M.N., M.L., K.K., A.A., C.O., S.O., T.H., P.M.); and Wake Forest Institute for Regenerative Medicine, School of Medicine, Wake Forest University Health Sciences, Winston-Salem, North Carolina (S.O., C.O., P.M.)
| | - Adrianna Vandeuren
- Invirsa, Inc., Columbus, Ohio (R.S., A.K.R., A.M., I.S.); Department of Biology, Northeastern University, Boston, Massachusetts (T.D., L.J., S.G., A.V.); Department of Integrative Biology and Physiology, University of Minnesota, Minneapolis, Minnesota (R.L.H., K.W., E.B.); United States Army Medical Research Institute for Chemical Defense, Gunpowder, Maryland (M.N., M.L., K.K., A.A., C.O., S.O., T.H., P.M.); and Wake Forest Institute for Regenerative Medicine, School of Medicine, Wake Forest University Health Sciences, Winston-Salem, North Carolina (S.O., C.O., P.M.)
| | - Marian Nelson
- Invirsa, Inc., Columbus, Ohio (R.S., A.K.R., A.M., I.S.); Department of Biology, Northeastern University, Boston, Massachusetts (T.D., L.J., S.G., A.V.); Department of Integrative Biology and Physiology, University of Minnesota, Minneapolis, Minnesota (R.L.H., K.W., E.B.); United States Army Medical Research Institute for Chemical Defense, Gunpowder, Maryland (M.N., M.L., K.K., A.A., C.O., S.O., T.H., P.M.); and Wake Forest Institute for Regenerative Medicine, School of Medicine, Wake Forest University Health Sciences, Winston-Salem, North Carolina (S.O., C.O., P.M.)
| | - Megan Lyman
- Invirsa, Inc., Columbus, Ohio (R.S., A.K.R., A.M., I.S.); Department of Biology, Northeastern University, Boston, Massachusetts (T.D., L.J., S.G., A.V.); Department of Integrative Biology and Physiology, University of Minnesota, Minneapolis, Minnesota (R.L.H., K.W., E.B.); United States Army Medical Research Institute for Chemical Defense, Gunpowder, Maryland (M.N., M.L., K.K., A.A., C.O., S.O., T.H., P.M.); and Wake Forest Institute for Regenerative Medicine, School of Medicine, Wake Forest University Health Sciences, Winston-Salem, North Carolina (S.O., C.O., P.M.)
| | - Kyle Kelly
- Invirsa, Inc., Columbus, Ohio (R.S., A.K.R., A.M., I.S.); Department of Biology, Northeastern University, Boston, Massachusetts (T.D., L.J., S.G., A.V.); Department of Integrative Biology and Physiology, University of Minnesota, Minneapolis, Minnesota (R.L.H., K.W., E.B.); United States Army Medical Research Institute for Chemical Defense, Gunpowder, Maryland (M.N., M.L., K.K., A.A., C.O., S.O., T.H., P.M.); and Wake Forest Institute for Regenerative Medicine, School of Medicine, Wake Forest University Health Sciences, Winston-Salem, North Carolina (S.O., C.O., P.M.)
| | - Amber Altvater
- Invirsa, Inc., Columbus, Ohio (R.S., A.K.R., A.M., I.S.); Department of Biology, Northeastern University, Boston, Massachusetts (T.D., L.J., S.G., A.V.); Department of Integrative Biology and Physiology, University of Minnesota, Minneapolis, Minnesota (R.L.H., K.W., E.B.); United States Army Medical Research Institute for Chemical Defense, Gunpowder, Maryland (M.N., M.L., K.K., A.A., C.O., S.O., T.H., P.M.); and Wake Forest Institute for Regenerative Medicine, School of Medicine, Wake Forest University Health Sciences, Winston-Salem, North Carolina (S.O., C.O., P.M.)
| | - Celinia Ondeck
- Invirsa, Inc., Columbus, Ohio (R.S., A.K.R., A.M., I.S.); Department of Biology, Northeastern University, Boston, Massachusetts (T.D., L.J., S.G., A.V.); Department of Integrative Biology and Physiology, University of Minnesota, Minneapolis, Minnesota (R.L.H., K.W., E.B.); United States Army Medical Research Institute for Chemical Defense, Gunpowder, Maryland (M.N., M.L., K.K., A.A., C.O., S.O., T.H., P.M.); and Wake Forest Institute for Regenerative Medicine, School of Medicine, Wake Forest University Health Sciences, Winston-Salem, North Carolina (S.O., C.O., P.M.)
| | - Sean O'Brien
- Invirsa, Inc., Columbus, Ohio (R.S., A.K.R., A.M., I.S.); Department of Biology, Northeastern University, Boston, Massachusetts (T.D., L.J., S.G., A.V.); Department of Integrative Biology and Physiology, University of Minnesota, Minneapolis, Minnesota (R.L.H., K.W., E.B.); United States Army Medical Research Institute for Chemical Defense, Gunpowder, Maryland (M.N., M.L., K.K., A.A., C.O., S.O., T.H., P.M.); and Wake Forest Institute for Regenerative Medicine, School of Medicine, Wake Forest University Health Sciences, Winston-Salem, North Carolina (S.O., C.O., P.M.)
| | - Tracey Hamilton
- Invirsa, Inc., Columbus, Ohio (R.S., A.K.R., A.M., I.S.); Department of Biology, Northeastern University, Boston, Massachusetts (T.D., L.J., S.G., A.V.); Department of Integrative Biology and Physiology, University of Minnesota, Minneapolis, Minnesota (R.L.H., K.W., E.B.); United States Army Medical Research Institute for Chemical Defense, Gunpowder, Maryland (M.N., M.L., K.K., A.A., C.O., S.O., T.H., P.M.); and Wake Forest Institute for Regenerative Medicine, School of Medicine, Wake Forest University Health Sciences, Winston-Salem, North Carolina (S.O., C.O., P.M.)
| | - Ryan L Hanson
- Invirsa, Inc., Columbus, Ohio (R.S., A.K.R., A.M., I.S.); Department of Biology, Northeastern University, Boston, Massachusetts (T.D., L.J., S.G., A.V.); Department of Integrative Biology and Physiology, University of Minnesota, Minneapolis, Minnesota (R.L.H., K.W., E.B.); United States Army Medical Research Institute for Chemical Defense, Gunpowder, Maryland (M.N., M.L., K.K., A.A., C.O., S.O., T.H., P.M.); and Wake Forest Institute for Regenerative Medicine, School of Medicine, Wake Forest University Health Sciences, Winston-Salem, North Carolina (S.O., C.O., P.M.)
| | - Kayla Wayman
- Invirsa, Inc., Columbus, Ohio (R.S., A.K.R., A.M., I.S.); Department of Biology, Northeastern University, Boston, Massachusetts (T.D., L.J., S.G., A.V.); Department of Integrative Biology and Physiology, University of Minnesota, Minneapolis, Minnesota (R.L.H., K.W., E.B.); United States Army Medical Research Institute for Chemical Defense, Gunpowder, Maryland (M.N., M.L., K.K., A.A., C.O., S.O., T.H., P.M.); and Wake Forest Institute for Regenerative Medicine, School of Medicine, Wake Forest University Health Sciences, Winston-Salem, North Carolina (S.O., C.O., P.M.)
| | - Alexandrea Miller
- Invirsa, Inc., Columbus, Ohio (R.S., A.K.R., A.M., I.S.); Department of Biology, Northeastern University, Boston, Massachusetts (T.D., L.J., S.G., A.V.); Department of Integrative Biology and Physiology, University of Minnesota, Minneapolis, Minnesota (R.L.H., K.W., E.B.); United States Army Medical Research Institute for Chemical Defense, Gunpowder, Maryland (M.N., M.L., K.K., A.A., C.O., S.O., T.H., P.M.); and Wake Forest Institute for Regenerative Medicine, School of Medicine, Wake Forest University Health Sciences, Winston-Salem, North Carolina (S.O., C.O., P.M.)
| | - Isaiah Shalwitz
- Invirsa, Inc., Columbus, Ohio (R.S., A.K.R., A.M., I.S.); Department of Biology, Northeastern University, Boston, Massachusetts (T.D., L.J., S.G., A.V.); Department of Integrative Biology and Physiology, University of Minnesota, Minneapolis, Minnesota (R.L.H., K.W., E.B.); United States Army Medical Research Institute for Chemical Defense, Gunpowder, Maryland (M.N., M.L., K.K., A.A., C.O., S.O., T.H., P.M.); and Wake Forest Institute for Regenerative Medicine, School of Medicine, Wake Forest University Health Sciences, Winston-Salem, North Carolina (S.O., C.O., P.M.)
| | - Eric Batchelor
- Invirsa, Inc., Columbus, Ohio (R.S., A.K.R., A.M., I.S.); Department of Biology, Northeastern University, Boston, Massachusetts (T.D., L.J., S.G., A.V.); Department of Integrative Biology and Physiology, University of Minnesota, Minneapolis, Minnesota (R.L.H., K.W., E.B.); United States Army Medical Research Institute for Chemical Defense, Gunpowder, Maryland (M.N., M.L., K.K., A.A., C.O., S.O., T.H., P.M.); and Wake Forest Institute for Regenerative Medicine, School of Medicine, Wake Forest University Health Sciences, Winston-Salem, North Carolina (S.O., C.O., P.M.)
| | - Patrick McNutt
- Invirsa, Inc., Columbus, Ohio (R.S., A.K.R., A.M., I.S.); Department of Biology, Northeastern University, Boston, Massachusetts (T.D., L.J., S.G., A.V.); Department of Integrative Biology and Physiology, University of Minnesota, Minneapolis, Minnesota (R.L.H., K.W., E.B.); United States Army Medical Research Institute for Chemical Defense, Gunpowder, Maryland (M.N., M.L., K.K., A.A., C.O., S.O., T.H., P.M.); and Wake Forest Institute for Regenerative Medicine, School of Medicine, Wake Forest University Health Sciences, Winston-Salem, North Carolina (S.O., C.O., P.M.)
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15
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Safieh J, Chazan A, Saleem H, Vyas P, Danin-Poleg Y, Ron D, Haran TE. A molecular mechanism for the "digital" response of p53 to stress. Proc Natl Acad Sci U S A 2023; 120:e2305713120. [PMID: 38015851 PMCID: PMC10710088 DOI: 10.1073/pnas.2305713120] [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: 04/09/2023] [Accepted: 10/25/2023] [Indexed: 11/30/2023] Open
Abstract
The tumor suppressor protein p53 accumulates in response to cellular stress and consequently orchestrates the expression of multiple genes in a p53-level and time-dependent manner to overcome stress consequences, for which a molecular mechanism is currently unknown. Previously, we reported that DNA torsional flexibility distinguishes among p53 response elements (REs) and that transactivation at basal p53 levels is correlated with p53 REs flexibility. Here, we calculated the flexibility of ~200 p53 REs. By connecting functional outcomes of p53-target genes' activation to the calculated flexibility of their REs, we show that genes known to belong to pathways that are activated rapidly upon stress contain REs that are significantly more flexible relative to REs of genes known to be involved in pathways that are activated later in the response to stress. The global structural properties of several p53 REs belonging to different pathways were experimentally validated. Additionally, reporter-gene expression driven by flexible p53 REs occurred at lower p53 levels and with faster rates than expression from rigid REs. Furthermore, analysis of published endogenous mRNA levels of p53-target genes as a function of REs' flexibility showed that early versus late genes differ significantly in their flexibility properties of their REs and that highly flexible p53 REs enable high-activation level exclusively to early-response genes. Overall, we demonstrate that DNA flexibility of p53 REs contributes significantly to functional selectivity in the p53 system by facilitating the initial steps of p53-dependent target-genes expression, thereby contributing to survival versus death decisions in the p53 system.
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Affiliation(s)
- Jessy Safieh
- Department of Biology, Technion, Technion City, Haifa2300003, Israel
| | - Ariel Chazan
- Department of Biology, Technion, Technion City, Haifa2300003, Israel
| | - Hanna Saleem
- Department of Biology, Technion, Technion City, Haifa2300003, Israel
| | - Pratik Vyas
- Department of Biology, Technion, Technion City, Haifa2300003, Israel
| | - Yael Danin-Poleg
- Department of Biology, Technion, Technion City, Haifa2300003, Israel
| | - Dina Ron
- Department of Biology, Technion, Technion City, Haifa2300003, Israel
| | - Tali E. Haran
- Department of Biology, Technion, Technion City, Haifa2300003, Israel
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16
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Venkatachalapathy H, Yang Z, Azarin SM, Sarkar CA, Batchelor E. Pulsed stimuli entrain p53 to synchronize single cells and modulate cell-fate determination. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.24.563786. [PMID: 37961090 PMCID: PMC10634792 DOI: 10.1101/2023.10.24.563786] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2023]
Abstract
Entrainment to an external stimulus enables a synchronized oscillatory response across a population of cells, increasing coherent responses by reducing cell-to-cell heterogeneity. It is unclear whether the property of entrainability extends to systems where responses are intrinsic to the individual cell, rather than dependent on coherence across a population of cells. Using a combination of mathematical modeling, time-lapse fluorescence microscopy, and single-cell tracking, we demonstrated that p53 oscillations triggered by DNA double-strand breaks (DSBs) can be entrained with a periodic damage stimulus, despite such synchrony not known to function in effective DNA damage responses. Surprisingly, p53 oscillations were experimentally entrained over a wider range of DSB frequencies than predicted by an established computational model for the system. We determined that recapitulating the increased range of entrainment frequencies required, non-intuitively, a less robust oscillator and wider steady-state valley on the energy landscape. Further, we show that p53 entrainment can lead to altered expression dynamics of downstream targets responsible for cell fate in a manner dependent on target mRNA stability. Overall, this study demonstrates that entrainment can occur in a biological oscillator despite the apparent lack of an evolutionary advantage conferred through synchronized responses and highlights the potential of externally entraining p53 dynamics to reduce cellular variability and synchronize cell-fate responses for therapeutic outcomes.
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17
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Tilden EI, Maduskar A, Oldenborg A, Sabatini BL, Chen Y. A Cre-dependent reporter mouse for quantitative real-time imaging of Protein Kinase A activity dynamics. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.31.565028. [PMID: 37961214 PMCID: PMC10635033 DOI: 10.1101/2023.10.31.565028] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2023]
Abstract
Intracellular signaling dynamics play a crucial role in cell function. Protein kinase A (PKA) is a key signaling molecule that has diverse functions, from regulating metabolism and brain activity to guiding development and cancer progression. We previously developed an optical reporter, FLIM-AKAR, that allows for quantitative imaging of PKA activity via fluorescence lifetime imaging microscopy and photometry. However, using viral infection or electroporation for the delivery of FLIM-AKAR is invasive, cannot easily target sparse or hard-to-transfect/infect cell types, and results in variable expression. Here, we developed a reporter mouse, FL-AK, which expresses FLIM-AKAR in a Cre-dependent manner from the ROSA26 locus. FL-AK provides robust and consistent expression of FLIM-AKAR over time. Functionally, the mouse line reports an increase in PKA activity in response to activation of both Gαs and Gαq-coupled receptors in brain slices. In vivo, FL-AK reports PKA phosphorylation in response to neuromodulator receptor activation. Thus, FL-AK provides a quantitative, robust, and flexible method to reveal the dynamics of PKA activity in diverse cell types.
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Affiliation(s)
- Elizabeth I. Tilden
- Department of Neuroscience, Washington University in St. Louis, St. Louis, MO, United States
- Ph. D. Program in Neuroscience, Washington University in St. Louis
| | - Aditi Maduskar
- Department of Neuroscience, Washington University in St. Louis, St. Louis, MO, United States
| | - Anna Oldenborg
- Department of Neuroscience, Washington University in St. Louis, St. Louis, MO, United States
| | - Bernardo L. Sabatini
- Howard Hughes Medical Institute, Department of Neurobiology, Harvard Medical School, Boston, MA, United States
| | - Yao Chen
- Department of Neuroscience, Washington University in St. Louis, St. Louis, MO, United States
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18
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Marques JF, Kops GJPL. Permission to pass: on the role of p53 as a gatekeeper for aneuploidy. Chromosome Res 2023; 31:31. [PMID: 37864038 PMCID: PMC10589155 DOI: 10.1007/s10577-023-09741-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Revised: 09/25/2023] [Accepted: 10/03/2023] [Indexed: 10/22/2023]
Abstract
Aneuploidy-the karyotype state in which the number of chromosomes deviates from a multiple of the haploid chromosome set-is common in cancer, where it is thought to facilitate tumor initiation and progression. However, it is poorly tolerated in healthy cells: during development and tissue homeostasis, aneuploid cells are efficiently cleared from the population. It is still largely unknown how cancer cells become, and adapt to being, aneuploid. P53, the gatekeeper of the genome, has been proposed to guard against aneuploidy. Aneuploidy in cancer genomes strongly correlates with mutations in TP53, and p53 is thought to prevent the propagation of aneuploid cells. Whether p53 also participates in preventing the mistakes in cell division that lead to aneuploidy is still under debate. In this review, we summarize the current understanding of the role of p53 in protecting cells from aneuploidy, and we explore the consequences of functional p53 loss for the propagation of aneuploidy in cancer.
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Affiliation(s)
- Joana F Marques
- Royal Netherlands Academy of Arts and Sciences (KNAW), Hubrecht Institute, Uppsalalaan 8, 3584CT, Utrecht, the Netherlands
- University Medical Center Utrecht, Heidelberglaan 100, 3584CX, Utrecht, the Netherlands
- Oncode Institute, Jaarbeursplein 6, 3521AL, Utrecht, the Netherlands
| | - Geert J P L Kops
- Royal Netherlands Academy of Arts and Sciences (KNAW), Hubrecht Institute, Uppsalalaan 8, 3584CT, Utrecht, the Netherlands.
- University Medical Center Utrecht, Heidelberglaan 100, 3584CX, Utrecht, the Netherlands.
- Oncode Institute, Jaarbeursplein 6, 3521AL, Utrecht, the Netherlands.
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19
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Tran AP, Tralie CJ, Reyes J, Moosmüller C, Belkhatir Z, Kevrekidis IG, Levine AJ, Deasy JO, Tannenbaum AR. Long-term p21 and p53 dynamics regulate the frequency of mitosis events and cell cycle arrest following radiation damage. Cell Death Differ 2023; 30:660-672. [PMID: 36182991 PMCID: PMC9984379 DOI: 10.1038/s41418-022-01069-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2022] [Revised: 09/12/2022] [Accepted: 09/14/2022] [Indexed: 11/07/2022] Open
Abstract
Radiation exposure of healthy cells can halt cell cycle temporarily or permanently. In this work, we analyze the time evolution of p21 and p53 from two single cell datasets of retinal pigment epithelial cells exposed to several levels of radiation, and in particular, the effect of radiation on cell cycle arrest. Employing various quantification methods from signal processing, we show how p21 levels, and to a lesser extent p53 levels, dictate whether the cells are arrested in their cell cycle and how frequently these mitosis events are likely to occur. We observed that single cells exposed to the same dose of DNA damage exhibit heterogeneity in cellular outcomes and that the frequency of cell division is a more accurate monitor of cell damage rather than just radiation level. Finally, we show how heterogeneity in DNA damage signaling is manifested early in the response to radiation exposure level and has potential to predict long-term fate.
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Affiliation(s)
- Anh Phong Tran
- Department of Medical Physics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Christopher J Tralie
- Department of Mathematics and Computer Science, Ursinus College, Collegeville, PA, USA
| | - José Reyes
- Cancer Biology and Genetics Program and Computational and Systems Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Department of Systems Biology, Harvard Medical School, Boston, MA, USA
| | - Caroline Moosmüller
- Department of Mathematics, University of California, San Diego, La Jolla, CA, USA
| | - Zehor Belkhatir
- School of Engineering and Sustainable Development, De Montfort University, Leicester, UK
| | - Ioannis G Kevrekidis
- Department of Chemical and Biological Engineering, Johns Hopkins University, Baltimore, MD, USA
| | - Arnold J Levine
- Simons Center for Systems Biology, Institute for Advanced Study, Princeton, NJ, USA
| | - Joseph O Deasy
- Department of Medical Physics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Allen R Tannenbaum
- Departments of Computer Science and Applied Mathematics & Statistics, Stony Brook University, Stony Brook, NY, USA.
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20
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Charan K, Giri A, Kar S. Elucidating the Implications of Diverse Dynamical Responses in p53 Protein. Chemphyschem 2023; 24:e202200537. [PMID: 36208026 DOI: 10.1002/cphc.202200537] [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: 07/24/2022] [Revised: 10/06/2022] [Indexed: 11/07/2022]
Abstract
p53 is a well-known tumor suppressor gene that acts as a transcription factor to exhibit a variety of dynamical responses by sensing different types and extent of stress conditions causing DNA damage in Mammalian cells. Mathematical modeling has played a crucial role to correlate cell fate decision-making with some of these dynamic p53 regulations. However, it is extremely challenging to explain the various cell-type and stimulus-specific p53 protein dynamics under different stress conditions by using a single mathematical model. In this article, we propose a simple mathematical model of p53 regulation based on a generic p53 regulatory network that elucidates a range of p53 dynamical responses. By employing bifurcation analysis along with deterministic and stochastic simulations, we explain an array of p53 dynamics by correlating it with the corresponding cell fate regulations in a cell type-specific and stimulus-dependent manner. Moreover, our model makes experimentally testable predictions to fine-tune p53 dynamics under various DNA damage conditions and can be systematically used and improved to analyze complex p53 dynamics in the future.
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Affiliation(s)
- Kajal Charan
- Department of Chemistry, IIT Bombay, Powai, Mumbai, 400076, India
| | - Amitava Giri
- Department of Chemistry, IIT Bombay, Powai, Mumbai, 400076, India
| | - Sandip Kar
- Department of Chemistry, IIT Bombay, Powai, Mumbai, 400076, India
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21
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Wang P, Wang HY, Gao XJ, Zhu HX, Zhang XP, Liu F, Wang W. Encoding and Decoding of p53 Dynamics in Cellular Response to Stresses. Cells 2023; 12:cells12030490. [PMID: 36766831 PMCID: PMC9914463 DOI: 10.3390/cells12030490] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2022] [Revised: 01/20/2023] [Accepted: 01/29/2023] [Indexed: 02/05/2023] Open
Abstract
In the cellular response to stresses, the tumor suppressor p53 is activated to maintain genomic integrity and fidelity. As a transcription factor, p53 exhibits rich dynamics to allow for discrimination of the type and intensity of stresses and to direct the selective activation of target genes involved in different processes including cell cycle arrest and apoptosis. In this review, we focused on how stresses are encoded into p53 dynamics and how the dynamics are decoded into cellular outcomes. Theoretical modeling may provide a global view of signaling in the p53 network by coupling the encoding and decoding processes. We discussed the significance of modeling in revealing the mechanisms of the transition between p53 dynamic modes. Moreover, we shed light on the crosstalk between the p53 network and other signaling networks. This review may advance the understanding of operating principles of the p53 signaling network comprehensively and provide insights into p53 dynamics-based cancer therapy.
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Affiliation(s)
- Ping Wang
- Kuang Yaming Honors School, Nanjing University, Nanjing 210023, China
- Key Laboratory of High Performance Scientific Computation, School of Science, Xihua University, Chengdu 610039, China
| | - Hang-Yu Wang
- Kuang Yaming Honors School, Nanjing University, Nanjing 210023, China
| | - Xing-Jie Gao
- Kuang Yaming Honors School, Nanjing University, Nanjing 210023, China
| | - Hua-Xia Zhu
- Kuang Yaming Honors School, Nanjing University, Nanjing 210023, China
| | - Xiao-Peng Zhang
- Kuang Yaming Honors School, Nanjing University, Nanjing 210023, China
- Institute of Brain Sciences, Nanjing University, Nanjing 210093, China
- Correspondence: (X.-P.Z.); (W.W.)
| | - Feng Liu
- Institute of Brain Sciences, Nanjing University, Nanjing 210093, China
- National Laboratory of Solid State Microstructure, Nanjing University, Nanjing 210093, China
- Department of Physics, Nanjing University, Nanjing 210093, China
| | - Wei Wang
- Institute of Brain Sciences, Nanjing University, Nanjing 210093, China
- National Laboratory of Solid State Microstructure, Nanjing University, Nanjing 210093, China
- Department of Physics, Nanjing University, Nanjing 210093, China
- Correspondence: (X.-P.Z.); (W.W.)
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22
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Formal verification confirms the role of p53 protein in cell fate decision mechanism. Theory Biosci 2023; 142:29-45. [PMID: 36510032 PMCID: PMC9925526 DOI: 10.1007/s12064-022-00381-x] [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: 03/29/2022] [Accepted: 11/14/2022] [Indexed: 12/15/2022]
Abstract
The bio-cell cycle is controlled by a complex biochemical network of signaling pathways. Modeling such challenging networks accurately is imperative for the understanding of their detailed dynamical behavior. In this paper, we construct, analyze, and verify a hybrid Petri net (HPN) model of a complex biochemical network that captures the role of an important protein (namely p53) in deciding the fate of the cell. We model the behavior of the cell nucleus and cytoplasm as two stochastic and continuous Petri nets, respectively, combined together into a single HPN. We use simulative model checking to verify three different properties that capture the dynamical behavior of p53 protein with respect to the intensity of the ionizing radiation (IR) to which the cell is exposed. For each IR dose, 1000 simulation runs are carried out to verify each property. Our verification results showed that the fluctuations in p53, which relies on IR intensity, are compatible with the findings of the preceding simulation studies that have previously examined the role of p53 in cell fate decision.
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23
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Luo L, Liu H, Yan F. Dynamic behavior of P53-Mdm2-Wip1 gene regulatory network under the influence of time delay and noise. MATHEMATICAL BIOSCIENCES AND ENGINEERING : MBE 2023; 20:2321-2347. [PMID: 36899536 DOI: 10.3934/mbe.2023109] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
The tumor suppressor protein P53 can regulate the cell cycle, thereby preventing cell abnormalities. In this paper, we study the dynamic characteristics of the P53 network under the influence of time delay and noise, including stability and bifurcation. In order to study the influence of several factors on the concentration of P53, bifurcation analysis on several important parameters is conducted; the results show that the important parameters could induce P53 oscillations within an appropriate range. Then we study the stability of the system and the existing conditions of Hopf bifurcation by using Hopf bifurcation theory with time delays as the bifurcation parameter. It is found that time delay plays a key role in inducing Hopf bifurcation and regulating the period and amplitude of system oscillation. Meanwhile, the combination of time delays can not only promote the oscillation of the system but it also provides good robustness. Changing the parameter values appropriately can change the bifurcation critical point and even the stable state of the system. In addition, due to the low copy number of the molecules and the environmental fluctuations, the influence of noise on the system is also considered. Through numerical simulation, it is found that noise not only promotes system oscillation but it also induces system state switching. The above results may help us to further understand the regulation mechanism of the P53-Mdm2-Wip1 network in the cell cycle.
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Affiliation(s)
- LanJiang Luo
- Department of Mathematics, Yunnan Normal University, Kunming 650500, China
- Key Laboratory of Complex System Modeling and Application for Universities in Yunnan, Kunming 650500, China
| | - Haihong Liu
- Department of Mathematics, Yunnan Normal University, Kunming 650500, China
- Key Laboratory of Complex System Modeling and Application for Universities in Yunnan, Kunming 650500, China
| | - Fang Yan
- Department of Mathematics, Yunnan Normal University, Kunming 650500, China
- Key Laboratory of Complex System Modeling and Application for Universities in Yunnan, Kunming 650500, China
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24
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Konrath F, Loewer A, Wolf J. Resolving Crosstalk Between Signaling Pathways Using Mathematical Modeling and Time-Resolved Single Cell Data. Methods Mol Biol 2023; 2634:267-284. [PMID: 37074583 DOI: 10.1007/978-1-0716-3008-2_12] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/20/2023]
Abstract
Crosstalk between signaling pathways can modulate the cellular response to stimuli and is therefore an important part of signal transduction. For a comprehensive understanding of cellular responses, identifying points of interaction between the underlying molecular networks is essential. Here, we present an approach that allows the systematic prediction of such interactions by perturbing one pathway and quantifying the concomitant alterations in the response of a second pathway. As the observed alterations contain information about the crosstalk, we use an ordinary differential equation-based model to extract this information by linking altered dynamics to individual processes. Consequently, we can predict the interaction points between two pathways. As an example, we employed our approach to investigate the crosstalk between the NF-κB and p53 signaling pathway. We monitored the response of p53 to genotoxic stress using time-resolved single cell data and perturbed NF-κB signaling by inhibiting the kinase IKK2. Employing a subpopulation-based modeling approach enabled us to identify multiple interaction points that are simultaneously affected by perturbation of NF-κB signaling. Hence, our approach can be used to analyze crosstalk between two signaling pathways in a systematic manner.
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Affiliation(s)
- Fabian Konrath
- Mathematical Modelling of Cellular Processes, Max Delbrueck Center for Molecular Medicine, Berlin, Germany
| | - Alexander Loewer
- Systems Biology of the Stress Response, Department of Biology, Technische Universität Darmstadt, Darmstadt, Germany
| | - Jana Wolf
- Mathematical Modelling of Cellular Processes, Max Delbrueck Center for Molecular Medicine, Berlin, Germany.
- Mathematical Modelling of Cellular Processes, Department of Mathematics and Computer Science, Free University Berlin, Berlin, Germany.
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25
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Heltberg MS, Lucchetti A, Hsieh FS, Minh Nguyen DP, Chen SH, Jensen MH. Enhanced DNA repair through droplet formation and p53 oscillations. Cell 2022; 185:4394-4408.e10. [PMID: 36368307 DOI: 10.1016/j.cell.2022.10.004] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2022] [Revised: 08/23/2022] [Accepted: 10/05/2022] [Indexed: 11/11/2022]
Abstract
Living organisms are constantly exposed to DNA damage, and optimal repair is therefore crucial. A characteristic hallmark of the response is the formation of sub-compartments around the site of damage, known as foci. Following multiple DNA breaks, the transcription factor p53 exhibits oscillations in its nuclear concentration, but how this dynamics can affect the repair remains unknown. Here, we formulate a theory for foci formation through droplet condensation and discover how oscillations in p53, with its specific periodicity and amplitude, optimize the repair process by preventing Ostwald ripening and distributing protein material in space and time. Based on the theory predictions, we reveal experimentally that the oscillatory dynamics of p53 does enhance the repair efficiency. These results connect the dynamical signaling of p53 with the microscopic repair process and create a new paradigm for the interplay of complex dynamics and phase transitions in biology.
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Affiliation(s)
- Mathias S Heltberg
- Niels Bohr Institute, University of Copenhagen, Copenhagen, 2100, Denmark.
| | | | - Feng-Shu Hsieh
- Lab for Cell Dynamics, Institute of Molecular Biology, Academia Sinica, Taipei, 115, Taiwan
| | - Duy Pham Minh Nguyen
- Lab for Cell Dynamics, Institute of Molecular Biology, Academia Sinica, Taipei, 115, Taiwan
| | - Sheng-Hong Chen
- Lab for Cell Dynamics, Institute of Molecular Biology, Academia Sinica, Taipei, 115, Taiwan; National Center for Theoretical Sciences, Physics Division, Complex Systems, Taipei, 10617, Taiwan
| | - Mogens H Jensen
- Niels Bohr Institute, University of Copenhagen, Copenhagen, 2100, Denmark.
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26
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Abuetabh Y, Wu HH, Chai C, Al Yousef H, Persad S, Sergi CM, Leng R. DNA damage response revisited: the p53 family and its regulators provide endless cancer therapy opportunities. Exp Mol Med 2022; 54:1658-1669. [PMID: 36207426 PMCID: PMC9636249 DOI: 10.1038/s12276-022-00863-4] [Citation(s) in RCA: 80] [Impact Index Per Article: 26.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2022] [Revised: 07/22/2022] [Accepted: 08/01/2022] [Indexed: 12/29/2022] Open
Abstract
Antitumor therapeutic strategies that fundamentally rely on the induction of DNA damage to eradicate and inhibit the growth of cancer cells are integral approaches to cancer therapy. Although DNA-damaging therapies advance the battle with cancer, resistance, and recurrence following treatment are common. Thus, searching for vulnerabilities that facilitate the action of DNA-damaging agents by sensitizing cancer cells is an active research area. Therefore, it is crucial to decipher the detailed molecular events involved in DNA damage responses (DDRs) to DNA-damaging agents in cancer. The tumor suppressor p53 is active at the hub of the DDR. Researchers have identified an increasing number of genes regulated by p53 transcriptional functions that have been shown to be critical direct or indirect mediators of cell fate, cell cycle regulation, and DNA repair. Posttranslational modifications (PTMs) primarily orchestrate and direct the activity of p53 in response to DNA damage. Many molecules mediating PTMs on p53 have been identified. The anticancer potential realized by targeting these molecules has been shown through experiments and clinical trials to sensitize cancer cells to DNA-damaging agents. This review briefly acknowledges the complexity of DDR pathways/networks. We specifically focus on p53 regulators, protein kinases, and E3/E4 ubiquitin ligases and their anticancer potential.
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Affiliation(s)
- Yasser Abuetabh
- 370 Heritage Medical Research Center, Department of Laboratory Medicine and Pathology, University of Alberta, Edmonton, Alberta, T6G 2S2, Canada
| | - H Helena Wu
- 370 Heritage Medical Research Center, Department of Laboratory Medicine and Pathology, University of Alberta, Edmonton, Alberta, T6G 2S2, Canada
| | - Chengsen Chai
- 370 Heritage Medical Research Center, Department of Laboratory Medicine and Pathology, University of Alberta, Edmonton, Alberta, T6G 2S2, Canada
- College of Laboratory Medicine, Chongqing Medical University, Chongqing, 400016, China
| | - Habib Al Yousef
- 370 Heritage Medical Research Center, Department of Laboratory Medicine and Pathology, University of Alberta, Edmonton, Alberta, T6G 2S2, Canada
| | - Sujata Persad
- Department of Pediatrics, University of Alberta, Edmonton, AB, T6G 2E1, Canada
| | - Consolato M Sergi
- Division of Anatomical Pathology, Children's Hospital of Eastern Ontario (CHEO), University of Ottawa, Ottawa, ON, K1H 8L1, Canada
| | - Roger Leng
- 370 Heritage Medical Research Center, Department of Laboratory Medicine and Pathology, University of Alberta, Edmonton, Alberta, T6G 2S2, Canada.
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27
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Xiong L, Garfinkel A. A common pathway to cancer: Oncogenic mutations abolish p53 oscillations. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2022; 174:28-40. [PMID: 35752348 DOI: 10.1016/j.pbiomolbio.2022.06.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Revised: 06/13/2022] [Accepted: 06/20/2022] [Indexed: 06/15/2023]
Abstract
The tumor suppressor p53 oscillates in response to DNA double-strand breaks, a behavior that has been suggested to be essential to its anti-cancer function. Nearly all human cancers have genetic alterations in the p53 pathway; a number of these alterations have been shown to be oncogenic by experiment. These alterations include somatic mutations and copy number variations as well as germline polymorphisms. Intriguingly, they exhibit a mixed pattern of interactions in tumors, such as co-occurrence, mutual exclusivity, and paradoxically, mutual antagonism. Using a differential equation model of p53-Mdm2 dynamics, we employ Hopf bifurcation analysis to show that these alterations have a common mode of action, to abolish the oscillatory competence of p53, thereby, we suggest, impairing its tumor suppressive function. In this analysis, diverse genetic alterations, widely associated with human cancers clinically, have a unified mechanistic explanation of their role in oncogenesis.
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Affiliation(s)
- Lingyun Xiong
- Department of Stem Cell Biology and Regenerative Medicine, University of Southern California, Los Angeles, CA 90007 USA; Department of Quantitative and Computational Biology, University of Southern California, Los Angeles, CA, 90007, USA; Ludwig Institute for Cancer Research, University of Oxford, Oxford, OX3 7DQ, UK
| | - Alan Garfinkel
- Departments of Medicine (Cardiology) and Integrative Biology and Physiology, University of California, Los Angeles, CA, 90095, USA; Newton-Abraham Visiting Professor (2019-2020), Lincoln College and Department of Computer Science, University of Oxford, Oxford, OX1 3DR, UK.
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28
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Computational-Model-Based Biopharmaceutics for p53 Pathway Using Modern Control Techniques for Cancer Treatment. APPLIED SCIENCES-BASEL 2022. [DOI: 10.3390/app12115748] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
The p53 pathway has been the focus of many researchers in the last few decades owing to its pivotal role as a frontline cancer suppressant protein. It plays a vital role in maintaining cell cycle checkpoints and cell apoptosis in response to a broken DNA strand. This is why it is found in the mutated form in more than 50% of malignant tumors. To overcome this, various drugs have been proposed to revive the p53 pathway in cancer patients. Small-molecule-based drugs, such as Nutlin 3a, which are capable of performing this stimulation, are at the fore of advanced clinical trials. However, the calculation of their dosage is a challenge. In this work, a method to determine the dosage of Nutlin 3a is investigated. A control-systems-based model is developed to study the response of the wild-type p53 protein to this drug. The proposed strategy regulates the p53 protein along with negative and positive feedback loops mediated by the MDM2 and MDM2 mRNA, respectively, along with the reversible repression of MDM2 caused by Nutlin 3a. For a broader perspective, the reported PBK dynamics of Nutlin 3a are also incorporated. It has been reported that p53 responds to stresses in two ways in terms of concentration to this drug: either it is a sustained (constant) or an oscillatory response. The claimed dosage strategy turned out to be appropriate for sustained p53 response. However, for the induction of oscillations, inhibition of MDM2 is not enough; rather, anti-repression of the p53–MDM2 complex is also needed, which opens new horizons for a new drug design paradigm.
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29
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Sampadi B, Mullenders LHF, Vrieling H. Low and high doses of ionizing radiation evoke discrete global (phospho)proteome responses. DNA Repair (Amst) 2022; 113:103305. [PMID: 35255311 DOI: 10.1016/j.dnarep.2022.103305] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2021] [Revised: 02/02/2022] [Accepted: 02/22/2022] [Indexed: 12/16/2022]
Abstract
BACKGROUND Although cancer risk is assumed to be linear with ionizing radiation (IR) dose, it is unclear to what extent low doses (LD) of IR from medical and occupational exposures pose a cancer risk for humans. Improved mechanistic understanding of the signaling responses to LD may help to clarify this uncertainty. Here, we performed quantitative mass spectrometry-based proteomics and phosphoproteomics experiments, using mouse embryonic stem cells, at 0.5 h and 4 h after exposure to LD (0.1 Gy) and high doses (HD; 1 Gy) of IR. RESULTS The proteome remained relatively stable (29; 0.5% proteins responded), whereas the phosphoproteome changed dynamically (819; 7% phosphosites changed) upon irradiation. Dose-dependent alterations of 25 IR-responsive proteins were identified, with only four in common between LD and HD. Mitochondrial metabolic proteins and pathways responded to LD, whereas transporter proteins and mitochondrial uncoupling pathways responded to HD. Congruently, mitochondrial respiration increased after LD exposure but decreased after HD exposure. While the bulk of the phosphoproteome response to LD (76%) occurred already at 0.5 h, an equivalent proportion of the phosphosites responded to HD at both time points. Motif, kinome/phosphatome, kinase-substrate, and pathway analyses revealed a robust DNA damage response (DDR) activation after HD exposure but not after LD exposure. Instead, LD-irradiation induced (de)phosphorylation of kinases, kinase-substrates and phosphatases that predominantly respond to reactive oxygen species (ROS) production. CONCLUSION Our analyses identify discrete global proteome and phosphoproteome responses after LD and HD, uncovering novel proteins and protein (de)phosphorylation events involved in the dose-dependent ionizing radiation responses.
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Affiliation(s)
- Bharath Sampadi
- Department of Human Genetics, Leiden University Medical Center, Einthovenweg 20, 2333ZC Leiden, The Netherlands.
| | - Leon H F Mullenders
- Department of Human Genetics, Leiden University Medical Center, Einthovenweg 20, 2333ZC Leiden, The Netherlands; Department of Genetics, Research Institute of Environmental Medicine (RIeM), Nagoya University, Nagoya, Japan
| | - Harry Vrieling
- Department of Human Genetics, Leiden University Medical Center, Einthovenweg 20, 2333ZC Leiden, The Netherlands.
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30
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Xie J, Zhang L, Liu B, Liang X, Shi J. Single-cell analysis of p53 transitional dynamics unravels stimulus- and cell type-dependent signaling output motifs. BMC Biol 2022; 20:85. [PMID: 35410287 PMCID: PMC9004066 DOI: 10.1186/s12915-022-01290-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2021] [Accepted: 03/31/2022] [Indexed: 11/19/2022] Open
Abstract
Background To understand functional changes of complex biological networks, mathematical modeling of network topologies provides a quantitative measure of the way biological systems adapt to external stimuli. However, systemic network topology-based analysis often generates conflicting evidence depending on specific experimental conditions, leading to a limited mechanistic understanding of signaling networks and their differential dynamic outputs, an example of which is the regulation of p53 pathway responses to different stress stimuli and in variable mammalian cell types. Here, we employ a network motif approach to dissect key regulatory units of the p53 pathway and elucidate how network activities at the motif level generate context-specific dynamic responses. Results By combining single-cell imaging and mathematical modeling of dose-dependent p53 dynamics induced by three chemotherapeutics of distinct mechanism-of-actions, including Etoposide, Nutlin-3a and 5-fluorouracil, and in five cancer cell types, we uncovered novel and highly variable p53 dynamic responses, in particular p53 transitional dynamics induced at intermediate drug concentrations, and identified the functional roles of distinct positive and negative feedback motifs of the p53 pathway in modulating the central p53-Mdm2 negative feedback to generate stimulus- and cell type-specific signaling responses. The mechanistic understanding of p53 network dynamics also revealed previously unknown mediators of anticancer drug actions and phenotypic variations in cancer cells that impact drug sensitivity. Conclusions Our results demonstrate that transitional dynamics of signaling proteins such as p53, activated at intermediate stimulus levels, vary the most between the dynamic outputs of different generic network motifs and can be employed as novel quantitative readouts to uncover and elucidate the key building blocks of large signaling networks. Our findings also provide new insight on drug mediators and phenotypic heterogeneity that underlie differential drug responses. Supplementary Information The online version contains supplementary material available at 10.1186/s12915-022-01290-7.
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Affiliation(s)
- Jun Xie
- Center for Quantitative Systems Biology, Department of Physics and Department of Biology, Hong Kong Baptist University, 224 Waterloo Road, Kowloon Tong, Kowloon, Hong Kong, China
| | - Lichun Zhang
- Center for Quantitative Systems Biology, Department of Physics and Department of Biology, Hong Kong Baptist University, 224 Waterloo Road, Kowloon Tong, Kowloon, Hong Kong, China
| | - Bodong Liu
- Center for Quantitative Systems Biology, Department of Physics and Department of Biology, Hong Kong Baptist University, 224 Waterloo Road, Kowloon Tong, Kowloon, Hong Kong, China
| | - Xiao Liang
- Center for Quantitative Systems Biology, Department of Physics and Department of Biology, Hong Kong Baptist University, 224 Waterloo Road, Kowloon Tong, Kowloon, Hong Kong, China
| | - Jue Shi
- Center for Quantitative Systems Biology, Department of Physics and Department of Biology, Hong Kong Baptist University, 224 Waterloo Road, Kowloon Tong, Kowloon, Hong Kong, China.
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31
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Jiménez A, Lu D, Kalocsay M, Berberich MJ, Balbi P, Jambhekar A, Lahav G. Time‐series transcriptomics and proteomics reveal alternative modes to decode p53 oscillations. Mol Syst Biol 2022; 18:e10588. [PMID: 35285572 PMCID: PMC8919251 DOI: 10.15252/msb.202110588] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2021] [Revised: 02/16/2022] [Accepted: 02/19/2022] [Indexed: 12/21/2022] Open
Affiliation(s)
- Alba Jiménez
- Department of Systems Biology Blavatnik Institute at Harvard Medical School Boston MA USA
| | - Dan Lu
- Department of Systems Biology Blavatnik Institute at Harvard Medical School Boston MA USA
| | - Marian Kalocsay
- Department of Systems Biology Blavatnik Institute at Harvard Medical School Boston MA USA
- Laboratory of Systems Pharmacology Blavatnik Institute at Harvard Medical School Boston MA USA
| | - Matthew J Berberich
- Laboratory of Systems Pharmacology Blavatnik Institute at Harvard Medical School Boston MA USA
- Center for Protein Degradation Dana‐Farber Cancer Institute Boston MA USA
| | - Petra Balbi
- Department of Systems Biology Blavatnik Institute at Harvard Medical School Boston MA USA
| | - Ashwini Jambhekar
- Department of Systems Biology Blavatnik Institute at Harvard Medical School Boston MA USA
- Ludwig Center at Harvard Medical School Boston MA USA
| | - Galit Lahav
- Department of Systems Biology Blavatnik Institute at Harvard Medical School Boston MA USA
- Ludwig Center at Harvard Medical School Boston MA USA
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32
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Chen M, Liu H, Wang R. Dynamical behaviors of quorum sensing network mediated by combinatorial perturbation. MATHEMATICAL BIOSCIENCES AND ENGINEERING : MBE 2022; 19:4812-4840. [PMID: 35430842 DOI: 10.3934/mbe.2022225] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
The dynamical behaviors of the quorum sensing (QS) system are closely related to the release drugs and control the PH value in microorganisms and plants. However, the effect of the main molecules AiiA, LuxI, H$ _2 $O$ _2 $, and time delayed individual and combinatorial perturbation on the QS system dynamics and the above-mentioned biological phenomena is still unclear, which are seen as a key consideration in our paper. This paper formulates a QS computational model by incorporating these several substances. First, for the protein production time delay, a critical value is given by Hopf bifurcation theory. It is found that a larger time delay can lead to a larger amplitude and a longer period. This indicates that the length of time for protein synthesis has a regulatory effect on the release of drugs from the bacterial population. Second, hen the concentrations of AiiA, LuxI, and H$ _2 $O$ _2 $ is modulated individually, the QS system undergoes periodic oscillation and bistable state. Meanwhile, oscillatory and bistable regions can be significantly affected by simultaneously perturbing any two parameters related to AiiA, LuxI, and H$ _2 $O$ _2 $. This means that the individual or simultaneous changes of the three intrinsic molecular concentrations can effectively control the drugs release and the PH value in microorganisms and plants. Finally, the sensitivity relationship between the critical value of the delay and AiiA, LuxI, H$ _2 $O$ _2 $ parameters is analyzed.
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Affiliation(s)
- Menghan Chen
- Department of Mathematics, Shanghai University, Shanghai 200444, China
| | - Haihong Liu
- Department of Mathematics, Yunnan Normal University, Kunming 650500, China
| | - Ruiqi Wang
- Department of Mathematics, Shanghai University, Shanghai 200444, China
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microRNA-Mediated Encoding and Decoding of Time-Dependent Signals in Tumorigenesis. Biomolecules 2022; 12:biom12020213. [PMID: 35204714 PMCID: PMC8961662 DOI: 10.3390/biom12020213] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2021] [Revised: 01/13/2022] [Accepted: 01/21/2022] [Indexed: 02/01/2023] Open
Abstract
microRNAs, pivotal post-transcriptional regulators of gene expression, in the past decades have caught the attention of researchers for their involvement in different biological processes, ranging from cell development to cancer. Although lots of effort has been devoted to elucidate the topological features and the equilibrium properties of microRNA-mediated motifs, little is known about how the information encoded in frequency, amplitude, duration, and other features of their regulatory signals can affect the resulting gene expression patterns. Here, we review the current knowledge about microRNA-mediated gene regulatory networks characterized by time-dependent input signals, such as pulses, transient inputs, and oscillations. First, we identify the general characteristic of the main motifs underlying temporal patterns. Then, we analyze their impact on two commonly studied oncogenic networks, showing how their dysfunction can lead to tumorigenesis.
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34
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Bano S, Azam MR, Uppal AA, Javed SB, Bhatti AI. Robust p53 recovery using chattering free sliding mode control and a gain-scheduled modified Utkin observer. J Theor Biol 2022; 532:110914. [PMID: 34582825 DOI: 10.1016/j.jtbi.2021.110914] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2021] [Revised: 09/15/2021] [Accepted: 09/20/2021] [Indexed: 11/16/2022]
Abstract
p53 protein plays an essential role in protecting the genomic integrity of mammalian cells. A drastic decrease in the amount of p53 protein has been observed in cancerous cells. By using Nutlin-based small molecule drugs, the concentration of p53 can be restored to the desired level. This paper presents the drug-dosage design for p53 pathway, based on a control-oriented nonlinear model. A chattering free sliding mode control (CFSMC) strategy is employed to track the desired trajectory of p53 concentration for both of its dynamic behaviors, i.e., sustained and oscillatory responses. A gain-scheduled modified Utkin observer (GSMUO) is designed for robust state reconstruction and disturbance estimation. The simulation results show that CFSMC and GSMUO exhibit desired robustness and performance properties in the presence of parametric variations, an input disturbance and measurement noise. Moreover, a comprehensive simulation study, along with a detailed quantitative analysis is performed to compare CFSMC-GSMUO with four different techniques: a sliding mode control (SMC) with an equivalent control based sliding mode observer (SMO) and GSMUO, respectively, and a dynamic sliding mode control (DSMC) with SMO and GSMUO, respectively. The analysis demonstrates that the tracking error and utilization of the control energy is the least in the case of CFSMC-GSMUO as compared to its counterparts.
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Affiliation(s)
- Sheher Bano
- Electrical Engineering Department, Abasyn University, Islamabad, Pakistan
| | | | - Ali Arshad Uppal
- Department of Electrical Engineering, COMSATS University, Islamabad, Pakistan
| | - Syed Bilal Javed
- Department of Electrical Engineering, COMSATS University, Islamabad, Pakistan
| | - Aamer Iqbal Bhatti
- Department of Electronics Engineering, Capital University of Science & Technology, Islamabad, Pakistan
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35
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Targeting Post-Translational Regulation of p53 in Colorectal Cancer by Exploiting Vulnerabilities in the p53-MDM2 Axis. Cancers (Basel) 2022; 14:cancers14010219. [PMID: 35008383 PMCID: PMC8750794 DOI: 10.3390/cancers14010219] [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: 11/24/2021] [Revised: 12/23/2021] [Accepted: 12/30/2021] [Indexed: 02/05/2023] Open
Abstract
The role played by the key tumor suppressor gene p53 and the implications of p53 mutations for the development and progression of neoplasia continue to expand. This review focuses on colorectal cancer and the regulators of p53 expression and activity identified over the past decade. These newly recognized regulatory mechanisms include (1) direct regulation of mouse double minute 2 homolog (MDM2), an E3 ubiquitin-protein ligase; (2) modulation of the MDM2-p53 interaction; (3) MDM2-independent p53 degradation; and (4) inhibition of p53 nuclear translocation. We positioned these regulatory mechanisms in the context of p53 missense mutations, which not only evade canonical p53 degradation machinery but also exhibit gain-of-function phenotypes that enhance tumor survival and metastasis. Lastly, we discuss current and potential therapeutic strategies directed against p53 mutant-bearing tumors.
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36
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Androulakis IP. Teaching computational systems biology with an eye on quantitative systems pharmacology at the undergraduate level: Why do it, who would take it, and what should we teach? FRONTIERS IN SYSTEMS BIOLOGY 2022; 2:1044281. [PMID: 36866242 PMCID: PMC9977321 DOI: 10.3389/fsysb.2022.1044281] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
Computational systems biology (CSB) is a field that emerged primarily as the product of research activities. As such, it grew in several directions in a distributed and uncoordinated manner making the area appealing and fascinating. The idea of not having to follow a specific path but instead creating one fueled innovation. As the field matured, several interdisciplinary graduate programs emerged attempting to educate future generations of computational systems biologists. These educational initiatives coordinated the dissemination of information across student populations that had already decided to specialize in this field. However, we are now entering an era where CSB, having established itself as a valuable research discipline, is attempting the next major step: Entering undergraduate curricula. As interesting as this endeavor may sound, it has several difficulties, mainly because the field is not uniformly defined. In this manuscript, we argue that this diversity is a significant advantage and that several incarnations of an undergraduate-level CSB biology course could, and should, be developed tailored to programmatic needs. In this manuscript, we share our experiences creating a course as part of a Biomedical Engineering program.
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Affiliation(s)
- Ioannis P Androulakis
- Biomedical Engineering Department, New Brunswick, NJ, United States.,Chemical and Biochemical Engineering Department, Rutgers University, New Brunswick, NJ, United States
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37
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Jung Y, Kraikivski P, Shafiekhani S, Terhune SS, Dash RK. Crosstalk between Plk1, p53, cell cycle, and G2/M DNA damage checkpoint regulation in cancer: computational modeling and analysis. NPJ Syst Biol Appl 2021; 7:46. [PMID: 34887439 PMCID: PMC8660825 DOI: 10.1038/s41540-021-00203-8] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2020] [Accepted: 11/03/2021] [Indexed: 12/21/2022] Open
Abstract
Different cancer cell lines can have varying responses to the same perturbations or stressful conditions. Cancer cells that have DNA damage checkpoint-related mutations are often more sensitive to gene perturbations including altered Plk1 and p53 activities than cancer cells without these mutations. The perturbations often induce a cell cycle arrest in the former cancer, whereas they only delay the cell cycle progression in the latter cancer. To study crosstalk between Plk1, p53, and G2/M DNA damage checkpoint leading to differential cell cycle regulations, we developed a computational model by extending our recently developed model of mitotic cell cycle and including these key interactions. We have used the model to analyze the cancer cell cycle progression under various gene perturbations including Plk1-depletion conditions. We also analyzed mutations and perturbations in approximately 1800 different cell lines available in the Cancer Dependency Map and grouped lines by genes that are represented in our model. Our model successfully explained phenotypes of various cancer cell lines under different gene perturbations. Several sensitivity analysis approaches were used to identify the range of key parameter values that lead to the cell cycle arrest in cancer cells. Our resulting model can be used to predict the effect of potential treatments targeting key mitotic and DNA damage checkpoint regulators on cell cycle progression of different types of cancer cells.
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Affiliation(s)
- Yongwoon Jung
- grid.30760.320000 0001 2111 8460Department of Biomedical Engineering, Medical College of Wisconsin, Milwaukee, WI 53226 USA
| | - Pavel Kraikivski
- Academy of Integrated Science, Division of Systems Biology, Virginia Tech, Blacksburg, VA, 24061, USA.
| | - Sajad Shafiekhani
- grid.411705.60000 0001 0166 0922Department of Biomedical Engineering, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | - Scott S. Terhune
- grid.30760.320000 0001 2111 8460Departments of Microbiology and Immunology, Medical College of Wisconsin, Milwaukee, WI 53226 USA ,grid.30760.320000 0001 2111 8460Center of Systems and Molecular Medicine, Medical College of Wisconsin, Milwaukee, WI 53226 USA
| | - Ranjan K. Dash
- grid.30760.320000 0001 2111 8460Department of Biomedical Engineering, Medical College of Wisconsin, Milwaukee, WI 53226 USA ,grid.30760.320000 0001 2111 8460Center of Systems and Molecular Medicine, Medical College of Wisconsin, Milwaukee, WI 53226 USA ,grid.30760.320000 0001 2111 8460Department of Physiology, Medical College of Wisconsin, Milwaukee, WI 53226 USA
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Progress and challenges in understanding the regulation and function of p53 dynamics. Biochem Soc Trans 2021; 49:2123-2131. [PMID: 34495325 PMCID: PMC8765192 DOI: 10.1042/bst20210148] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Revised: 08/20/2021] [Accepted: 08/23/2021] [Indexed: 02/01/2023]
Abstract
The dynamics of p53 expression provide a mechanism to increase differentiation between cellular stresses and specificity in appropriate responses. Here, we review recent advances in our understanding of the molecular mechanisms regulating p53 dynamics and the functions of the dynamics in the regulation of p53-dependent cell stress responses. We also compare dynamic encoding in the p53 system with that found in other important cell signaling systems, many of which can interact with the p53 network. Finally, we highlight some of the current challenges in understanding dynamic cell signaling within a larger cellular network context.
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Mathematical Modelling of p53 Signalling during DNA Damage Response: A Survey. Int J Mol Sci 2021; 22:ijms221910590. [PMID: 34638930 PMCID: PMC8508851 DOI: 10.3390/ijms221910590] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Revised: 09/14/2021] [Accepted: 09/26/2021] [Indexed: 02/05/2023] Open
Abstract
No gene has garnered more interest than p53 since its discovery over 40 years ago. In the last two decades, thanks to seminal work from Uri Alon and Ghalit Lahav, p53 has defined a truly synergistic topic in the field of mathematical biology, with a rich body of research connecting mathematic endeavour with experimental design and data. In this review we survey and distill the extensive literature of mathematical models of p53. Specifically, we focus on models which seek to reproduce the oscillatory dynamics of p53 in response to DNA damage. We review the standard modelling approaches used in the field categorising them into three types: time delay models, spatial models and coupled negative-positive feedback models, providing sample model equations and simulation results which show clear oscillatory dynamics. We discuss the interplay between mathematics and biology and show how one informs the other; the deep connections between the two disciplines has helped to develop our understanding of this complex gene and paint a picture of its dynamical response. Although yet more is to be elucidated, we offer the current state-of-the-art understanding of p53 response to DNA damage.
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Molinaro C, Martoriati A, Cailliau K. Proteins from the DNA Damage Response: Regulation, Dysfunction, and Anticancer Strategies. Cancers (Basel) 2021; 13:3819. [PMID: 34359720 PMCID: PMC8345162 DOI: 10.3390/cancers13153819] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2021] [Revised: 07/22/2021] [Accepted: 07/26/2021] [Indexed: 12/21/2022] Open
Abstract
Cells respond to genotoxic stress through a series of complex protein pathways called DNA damage response (DDR). These monitoring mechanisms ensure the maintenance and the transfer of a correct genome to daughter cells through a selection of DNA repair, cell cycle regulation, and programmed cell death processes. Canonical or non-canonical DDRs are highly organized and controlled to play crucial roles in genome stability and diversity. When altered or mutated, the proteins in these complex networks lead to many diseases that share common features, and to tumor formation. In recent years, technological advances have made it possible to benefit from the principles and mechanisms of DDR to target and eliminate cancer cells. These new types of treatments are adapted to the different types of tumor sensitivity and could benefit from a combination of therapies to ensure maximal efficiency.
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Affiliation(s)
| | | | - Katia Cailliau
- Univ. Lille, CNRS, UMR 8576-UGSF-Unité de Glycobiologie Structurale et Fonctionnelle, F-59000 Lille, France; (C.M.); (A.M.)
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42
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Ye L, Song Z, Li C. Landscape and flux quantify the stochastic transition dynamics for p53 cell fate decision. J Chem Phys 2021; 154:025101. [PMID: 33445890 DOI: 10.1063/5.0030558] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The p53 transcription factor is a key mediator in cellular responses to various stress signals including DNA repair, cell cycle arrest, and apoptosis. In this work, we employ landscape and flux theory to investigate underlying mechanisms of p53-regulated cell fate decisions. Based on a p53 regulatory network, we quantified the potential landscape and probabilistic flux for the p53 system. The landscape topography unifies and quantifies three cell fate states, including the limit cycle oscillations (representing cell cycle arrest), high p53 state (characterizing apoptosis), and low p53 state (characterizing the normal proliferative state). Landscape and flux results provide a quantitative explanation for the biphasic dynamics of the p53 system. In the oscillatory phase (first phase), the landscape attracts the system into the ring valley and flux drives the system cyclically moving, leading to cell cycle arrest. In the fate decision-making phase (second phase), the ring valley shape of the landscape provides an efficient way for cells to return to the normal proliferative state once DNA damage is repaired. If the damage is unrepairable with larger flux, the system may cross the barrier between two states and switch to the apoptotic state with a high p53 level. By landscape-flux decomposition, we revealed a trade-off between stability (guaranteed by landscape) and function (driven by flux) in cellular systems. Cells need to keep a balance between appropriate speed to repair DNA damage and appropriate stability to survive. This is further supported by flux landscape analysis showing that flux may provide the dynamical origin of phase transition in a non-equilibrium system by changing landscape topography.
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Affiliation(s)
- Leijun Ye
- Institute of Science and Technology for Brain-Inspired Intelligence, Fudan University, Shanghai, China
| | - Zhuoqing Song
- Shanghai Center for Mathematical Sciences, Fudan University, Shanghai, China
| | - Chunhe Li
- Institute of Science and Technology for Brain-Inspired Intelligence, Fudan University, Shanghai, China
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43
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Phan LM, Rezaeian AH. ATM: Main Features, Signaling Pathways, and Its Diverse Roles in DNA Damage Response, Tumor Suppression, and Cancer Development. Genes (Basel) 2021; 12:845. [PMID: 34070860 PMCID: PMC8228802 DOI: 10.3390/genes12060845] [Citation(s) in RCA: 50] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2021] [Revised: 05/26/2021] [Accepted: 05/27/2021] [Indexed: 11/30/2022] Open
Abstract
ATM is among of the most critical initiators and coordinators of the DNA-damage response. ATM canonical and non-canonical signaling pathways involve hundreds of downstream targets that control many important cellular processes such as DNA damage repair, apoptosis, cell cycle arrest, metabolism, proliferation, oxidative sensing, among others. Of note, ATM is often considered a major tumor suppressor because of its ability to induce apoptosis and cell cycle arrest. However, in some advanced stage tumor cells, ATM signaling is increased and confers remarkable advantages for cancer cell survival, resistance to radiation and chemotherapy, biosynthesis, proliferation, and metastasis. This review focuses on addressing major characteristics, signaling pathways and especially the diverse roles of ATM in cellular homeostasis and cancer development.
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Affiliation(s)
- Liem Minh Phan
- Department of Molecular & Cellular Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Abdol-Hossein Rezaeian
- Department of Drug Discovery & Biomedical Sciences, College of Pharmacy, The University of South Carolina, Columbia, SC 29208, USA
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44
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The p53-caspase-2 axis in the cell cycle and DNA damage response. Exp Mol Med 2021; 53:517-527. [PMID: 33854186 PMCID: PMC8102494 DOI: 10.1038/s12276-021-00590-2] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2021] [Revised: 02/15/2021] [Accepted: 02/16/2021] [Indexed: 02/08/2023] Open
Abstract
Caspase-2 was discovered almost three decades ago. It was one of the first two mammalian homologs of CED-3, the other being interleukin 1β-converting enzyme (ICE/caspase-1). Despite high similarity with CED-3 and its fly and mammalian counterparts (DRONC and caspase-9, respectively), the function of caspase-2 in apoptosis has remained enigmatic. A number of recent studies suggest that caspase-2 plays an important role in the regulation of p53 in response to cellular stress and DNA damage to prevent the proliferation and accumulation of damaged or aberrant cells. Here, we review these recent observations and their implications in caspase-2-mediated cellular death, senescence, and tumor suppression.
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45
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Regulation of cardiomyocyte DNA damage and cell death by the type 2A protein phosphatase regulatory protein alpha4. Sci Rep 2021; 11:6293. [PMID: 33737606 PMCID: PMC7973735 DOI: 10.1038/s41598-021-85616-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2020] [Accepted: 02/03/2021] [Indexed: 12/05/2022] Open
Abstract
The type 2A protein phosphatase regulatory protein alpha4 (α4) constitutes an anti-apoptotic protein in non-cardiac tissue, however it’s anti-apoptotic properties in the heart are poorly defined. To this end, we knocked down α4 protein expression (α4 KD) using siRNA in cultured H9c2 cardiomyocytes and confirmed the lack of DNA damage/cell death by TUNEL staining and MTT assay. However, α4 KD did increase the phosphorylation of p53 and ATM/ATR substrates, decreased the expression of poly ADP-ribose polymerase and associated fragments. Expression of anti-apoptotic proteins Bcl-2 and Bcl-xL was reduced, whereas expression of pro-apoptotic BAX protein did not change. Alpha4 KD reduced basal H2AX Ser139 phosphorylation, whereas adenoviral-mediated re-expression of α4 protein following α4 KD, restored basal H2AX phosphorylation at Ser139. The sensitivity of H9c2 cardiomyocytes to doxorubicin-induced DNA damage and cytotoxicity was augmented by α4 KD. Adenoviral-mediated overexpression of α4 protein in ARVM increased PP2AC expression and augmented H2AX Ser139 phosphorylation in response to doxorubicin. Furthermore, pressure overload-induced heart failure was associated with reduced α4 protein expression, increased ATM/ATR protein kinase activity, increased H2AX expression and Ser139 phosphorylation. Hence, this study describes the significance of altered α4 protein expression in the regulation of DNA damage, cardiomyocyte cell death and heart failure.
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46
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Fedak EA, Adler FR, Abegglen LM, Schiffman JD. ATM and ATR Activation Through Crosstalk Between DNA Damage Response Pathways. Bull Math Biol 2021; 83:38. [PMID: 33704589 DOI: 10.1007/s11538-021-00868-6] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Accepted: 02/10/2021] [Indexed: 11/28/2022]
Abstract
Cells losing the ability to self-regulate in response to damage are a hallmark of cancer. When a cell encounters damage, regulatory pathways estimate the severity of damage and promote repair, cell cycle arrest, or apoptosis. This decision-making process would be remarkable if it were based on the total amount of damage in the cell, but because damage detection pathways vary in the rate and intensity with which they promote pro-apoptotic factors, the cell's real challenge is to reconcile dissimilar signals. Crosstalk between repair pathways, crosstalk between pro-apoptotic signaling kinases, and signals induced by damage by-products complicate the process further. The cell's response to [Formula: see text] and UV radiation neatly illustrates this concept. While these forms of radiation produce lesions associated with two different pro-apoptotic signaling kinases, ATM and ATR, recent experiments show that ATM and ATR react to both forms of radiation. To simulate the pro-apoptotic signal induced by [Formula: see text] and UV radiation, we construct a mathematical model that includes three modes of crosstalk between ATM and ATR signaling pathways: positive feedback between ATM/ATR and repair proteins, ATM and ATR mutual upregulation, and changes in lesion topology induced by replication stress or repair. We calibrate the model to agree with 21 experimental claims about ATM and ATR crosstalk. We alter the model by adding or removing specific processes and then examine the effects of each process on ATM/ATR crosstalk by recording which claims the altered model violates. Not only is this the first mathematical model of ATM/ATR crosstalk, it provides a strong argument for treating pro-apoptotic signaling as a holistic effort rather than attributing it to a single dominant kinase.
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Affiliation(s)
- Elizabeth A Fedak
- Department of Mathematics, The University of Utah, 155 Presidents Circle, Salt Lake City, UT, 84112, USA. .,Department of Oncological Sciences, Huntsman Cancer Institute, The University of Utah, 2000 Cir of Hope Dr, Salt Lake City, UT, 84112, USA.
| | - Frederick R Adler
- Department of Mathematics, The University of Utah, 155 Presidents Circle, Salt Lake City, UT, 84112, USA.,Department of Biology, The University of Utah, 257 Presidents Circle, Salt Lake City, UT, 84112, USA
| | - Lisa M Abegglen
- Department of Oncological Sciences, Huntsman Cancer Institute, The University of Utah, 2000 Cir of Hope Dr, Salt Lake City, UT, 84112, USA.,Department of Pediatrics, The University of Utah, 295 Chipeta Way, Salt Lake City, UT, 84108, USA.,PEEL Therapeutics, Inc., Salt Lake City, UT, 84108, USA
| | - Joshua D Schiffman
- Department of Oncological Sciences, Huntsman Cancer Institute, The University of Utah, 2000 Cir of Hope Dr, Salt Lake City, UT, 84112, USA.,Department of Pediatrics, The University of Utah, 295 Chipeta Way, Salt Lake City, UT, 84108, USA.,PEEL Therapeutics, Inc., Salt Lake City, UT, 84108, USA
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De S, Campbell C, Venkitaraman AR, Esposito A. Pulsatile MAPK Signaling Modulates p53 Activity to Control Cell Fate Decisions at the G2 Checkpoint for DNA Damage. Cell Rep 2021; 30:2083-2093.e5. [PMID: 32075732 PMCID: PMC7029415 DOI: 10.1016/j.celrep.2020.01.074] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2019] [Revised: 12/04/2019] [Accepted: 01/22/2020] [Indexed: 01/01/2023] Open
Abstract
Cell-autonomous changes in p53 expression govern the duration and outcome of cell-cycle arrest at the G2 checkpoint for DNA damage. Here, we report that mitogen-activated protein kinase (MAPK) signaling integrates extracellular cues with p53 dynamics to determine cell fate at the G2 checkpoint. Optogenetic tools and quantitative cell biochemistry reveal transient oscillations in MAPK activity dependent on ataxia-telangiectasia-mutated kinase after DNA damage. MAPK inhibition alters p53 dynamics and p53-dependent gene expression after checkpoint enforcement, prolonging G2 arrest. In contrast, sustained MAPK signaling induces the phosphorylation of CDC25C, and consequently, the accumulation of pro-mitotic kinases, thereby relaxing checkpoint stringency and permitting cells to evade prolonged G2 arrest and senescence induction. We propose a model in which this MAPK-mediated mechanism integrates extracellular cues with cell-autonomous p53-mediated signals, to safeguard genomic integrity during tissue proliferation. Early steps in oncogene-driven carcinogenesis may imbalance this tumor-suppressive mechanism to trigger genome instability.
DNA damage elicits opposing pro-survival and pro-arrest responses via MAPK and p53 MAPK pulsations modulate p53-dependent transcription to determine cell fate MAPK/p53 signal dynamics control the stringency of the G2 DNA damage checkpoint MAPK/p53 integrate extracellular and intracellular cues to protect genome integrity
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Affiliation(s)
- Siddharth De
- Medical Research Council Cancer Unit, University of Cambridge, Hills Road, Cambridge CB2 0XZ, UK
| | - Callum Campbell
- Medical Research Council Cancer Unit, University of Cambridge, Hills Road, Cambridge CB2 0XZ, UK
| | - Ashok R Venkitaraman
- Medical Research Council Cancer Unit, University of Cambridge, Hills Road, Cambridge CB2 0XZ, UK.
| | - Alessandro Esposito
- Medical Research Council Cancer Unit, University of Cambridge, Hills Road, Cambridge CB2 0XZ, UK.
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Philippe GJB, Mittermeier A, Lawrence N, Huang YH, Condon ND, Loewer A, Craik DJ, Henriques ST. Angler Peptides: Macrocyclic Conjugates Inhibit p53:MDM2/X Interactions and Activate Apoptosis in Cancer Cells. ACS Chem Biol 2021; 16:414-428. [PMID: 33533253 DOI: 10.1021/acschembio.0c00988] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Peptides are being developed as targeted anticancer drugs to modulate cytosolic protein-protein interactions involved in cancer progression. However, their use as therapeutics is often limited by their low cell membrane permeation and/or inability to reach cytosolic targets. Conjugation to cell penetrating peptides has been successfully used to improve the cytosolic delivery of high affinity binder peptides, but cellular uptake does not always result in modulation of the targeted pathway. To overcome this limitation, we developed "angler peptides" by conjugating KD3, a noncell permeable but potent and specific peptide inhibitor of p53:MDM2 and p53:MDMX interactions, with a set of cyclic cell-penetrating peptides. We examined their binding affinity for MDM2 and MDMX, the cell entry mechanism, and role in reactivation of the p53 pathway. We identified two angler peptides, cTAT-KD3 and cR10-KD3, able to activate the p53 pathway in cancer cells. cTAT-KD3 entered cells via endocytic pathways, escaped endosomes, and activated the p53 pathway in breast (MCF7), lung (A549), and colon (HCT116) cancer cell lines at concentrations in the range of 1-12 μM. cR10-KD3 reached the cytosol via direct membrane translocation and activated the p53 pathway at 1 μM in all the tested cell lines. Our work demonstrates that nonpermeable anticancer peptides can be delivered into the cytosol and inhibit intracellular cancer pathways when they are conjugated with stable cell penetrating peptides. The mechanistic studies suggest that direct translocation leads to less toxicity, higher cytosol delivery at lower concentrations, and lower dependencies on the membrane of the tested cell line than occurs for an endocytic pathway with endosomal escape. The angler strategy can rescue high affinity peptide binders identified from high throughput screening and convert them into targeted anticancer therapeutics, but investigation of their cellular uptake and cell death mechanisms is essential to confirming modulation of the targeted cancer pathways.
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Affiliation(s)
- Grégoire J.-B. Philippe
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4072, Australia
- Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Queensland, Brisbane, Queensland 4072, Australia
| | | | - Nicole Lawrence
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4072, Australia
- Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Yen-Hua Huang
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4072, Australia
- Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Nicholas D. Condon
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4072, Australia
| | | | - David J. Craik
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4072, Australia
- Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Sónia T. Henriques
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4072, Australia
- Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Queensland, Brisbane, Queensland 4072, Australia
- Queensland University of Technology, School of Biomedical Sciences, Institute of Health & Biomedical Innovation and Translational Research Institute, Brisbane, Queensland 4102, Australia
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49
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Jangid A, Malik MZ, Ramaswamy R, Singh RKB. Transition and identification of pathological states in p53 dynamics for therapeutic intervention. Sci Rep 2021; 11:2349. [PMID: 33504910 PMCID: PMC7840995 DOI: 10.1038/s41598-021-82054-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2020] [Accepted: 01/11/2021] [Indexed: 01/30/2023] Open
Abstract
We study a minimal model of the stress-driven p53 regulatory network that includes competition between active and mutant forms of the tumor-suppressor gene p53. Depending on the nature and level of the external stress signal, four distinct dynamical states of p53 are observed. These states can be distinguished by different dynamical properties which associate to active, apoptotic, pre-malignant and cancer states. Transitions between any two states, active, apoptotic, and cancer, are found to be unidirectional and irreversible if the stress signal is either oscillatory or constant. When the signal decays exponentially, the apoptotic state vanishes, and for low stress the pre-malignant state is bounded by two critical points, allowing the system to transition reversibly from the active to the pre-malignant state. For significantly large stress, the range of the pre-malignant state expands, and the system moves to irreversible cancerous state, which is a stable attractor. This suggests that identification of the pre-malignant state may be important both for therapeutic intervention as well as for drug delivery.
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Affiliation(s)
- Amit Jangid
- School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Delhi, 110067, India
- Department of Chemistry, Indian Institute of Technology Delhi, New Delhi, 110016, India
| | - Md Zubbair Malik
- School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Delhi, 110067, India.
| | - Ram Ramaswamy
- Department of Chemistry, Indian Institute of Technology Delhi, New Delhi, 110016, India.
| | - R K Brojen Singh
- School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Delhi, 110067, India.
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50
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Nathans JF, Cornwell JA, Afifi MM, Paul D, Cappell SD. Cell cycle inertia underlies a bifurcation in cell fates after DNA damage. SCIENCE ADVANCES 2021; 7:7/3/eabe3882. [PMID: 33523889 PMCID: PMC7806216 DOI: 10.1126/sciadv.abe3882] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/18/2020] [Accepted: 11/18/2020] [Indexed: 05/29/2023]
Abstract
The G1-S checkpoint is thought to prevent cells with damaged DNA from entering S phase and replicating their DNA and efficiently arrests cells at the G1-S transition. Here, using time-lapse imaging and single-cell tracking, we instead find that DNA damage leads to highly variable and divergent fate outcomes. Contrary to the textbook model that cells arrest at the G1-S transition, cells triggering the DNA damage checkpoint in G1 phase route back to quiescence, and this cellular rerouting can be initiated at any point in G1 phase. Furthermore, we find that most of the cells receiving damage in G1 phase actually fail to arrest and proceed through the G1-S transition due to persistent cyclin-dependent kinase (CDK) activity in the interval between DNA damage and induction of the CDK inhibitor p21. These observations necessitate a revised model of DNA damage response in G1 phase and indicate that cells have a G1 checkpoint.
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Affiliation(s)
- Jenny F Nathans
- Laboratory of Cancer Biology and Genetics, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA
| | - James A Cornwell
- Laboratory of Cancer Biology and Genetics, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA
| | - Marwa M Afifi
- Laboratory of Cancer Biology and Genetics, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA
| | - Debasish Paul
- Laboratory of Cancer Biology and Genetics, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA
| | - Steven D Cappell
- Laboratory of Cancer Biology and Genetics, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA.
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