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Stoll G, Naldi A, Noël V, Viara E, Barillot E, Kroemer G, Thieffry D, Calzone L. UPMaBoSS: A Novel Framework for Dynamic Cell Population Modeling. Front Mol Biosci 2022; 9:800152. [PMID: 35309516 PMCID: PMC8924294 DOI: 10.3389/fmolb.2022.800152] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2021] [Accepted: 01/21/2022] [Indexed: 11/13/2022] Open
Abstract
Mathematical modeling aims at understanding the effects of biological perturbations, suggesting ways to intervene and to reestablish proper cell functioning in diseases such as cancer or in autoimmune disorders. This is a difficult task for obvious reasons: the level of details needed to describe the intra-cellular processes involved, the numerous interactions between cells and cell types, and the complex dynamical properties of such populations where cells die, divide and interact constantly, to cite a few. Another important difficulty comes from the spatial distribution of these cells, their diffusion and motility. All of these aspects cannot be easily resolved in a unique mathematical model or with a unique formalism. To cope with some of these issues, we introduce here a novel framework, UPMaBoSS (for Update Population MaBoSS), dedicated to modeling dynamic populations of interacting cells. We rely on the preexisting tool MaBoSS, which enables probabilistic simulations of cellular networks. A novel software layer is added to account for cell interactions and population dynamics, but without considering the spatial dimension. This modeling approach can be seen as an intermediate step towards more complex spatial descriptions. We illustrate our methodology by means of a case study dealing with TNF-induced cell death. Interestingly, the simulation of cell population dynamics with UPMaBoSS reveals a mechanism of resistance triggered by TNF treatment. Relatively easy to encode, UPMaBoSS simulations require only moderate computational power and execution time. To ease the reproduction of simulations, we provide several Jupyter notebooks that can be accessed within the CoLoMoTo Docker image, which contains all software and models used for this study.
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Affiliation(s)
- Gautier Stoll
- Equipe Labellisée Par La Ligue Contre Le Cancer, Université de Paris, Sorbonne Université, INSERM UMR1138, Centre de Recherche des Cordeliers, Paris, France
- Metabolomics and Cell Biology Platforms, Gustave Roussy Cancer Campus, Université Paris Saclay, Villejuif, France
| | - Aurélien Naldi
- Institut de Biologie de L’ENS (IBENS), Ecole Normale Supérieure, CNRS, INSERM, Université PSL, Paris, France
- Lifeware Group, Inria Saclay-Ile de France, Palaiseau, France
| | - Vincent Noël
- Institut Curie, PSL Research University, Paris, France
- INSERM U900, Paris, France
- MINES ParisTech, CBIO-Centre for Computational Biology, PSL Research University, Paris, France
| | | | - Emmanuel Barillot
- Institut Curie, PSL Research University, Paris, France
- INSERM U900, Paris, France
- MINES ParisTech, CBIO-Centre for Computational Biology, PSL Research University, Paris, France
| | - Guido Kroemer
- Equipe Labellisée Par La Ligue Contre Le Cancer, Université de Paris, Sorbonne Université, INSERM UMR1138, Centre de Recherche des Cordeliers, Paris, France
- Metabolomics and Cell Biology Platforms, Gustave Roussy Cancer Campus, Université Paris Saclay, Villejuif, France
- Pôle de Biologie, Hôpital européen Georges Pompidou, AP-HP, Paris, France
| | - Denis Thieffry
- Institut de Biologie de L’ENS (IBENS), Ecole Normale Supérieure, CNRS, INSERM, Université PSL, Paris, France
- Lifeware Group, Inria Saclay-Ile de France, Palaiseau, France
| | - Laurence Calzone
- Institut Curie, PSL Research University, Paris, France
- INSERM U900, Paris, France
- MINES ParisTech, CBIO-Centre for Computational Biology, PSL Research University, Paris, France
- *Correspondence: Laurence Calzone,
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Rajendran S, Barbon S, Pucciarelli S. Spotlight on Circadian Genes and Colorectal Cancer Crosstalk. Endocr Metab Immune Disord Drug Targets 2020; 21:4-11. [PMID: 32579510 DOI: 10.2174/1871530320666200624192517] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/16/2019] [Revised: 01/19/2020] [Accepted: 04/22/2020] [Indexed: 11/22/2022]
Abstract
Mammalian physiology is regulated by circadian clock through oscillating feedback loops controlling cellular processes and behaviors. Recent findings have led to an interesting connection between circadian disruption and colorectal cancer progression and incidence through controlling the hallmarks of cancer, namely cell cycle, cell metabolism and cell death. Deeper understanding of the circadian mechanisms that define the colorectal cancer pathophysiology is the need of the hour to define a chronotherapy for improving colorectal cancer patient survival. This review identifies the key areas in which circadian genes interact with cellular pathways to modify the outcome with respect to colorectal cancer incidence and progression.
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Affiliation(s)
| | - Silvia Barbon
- Department of Neurosciences, University of Padova, Padua, Italy
| | - Salvatore Pucciarelli
- Department of Surgery Oncology and Gastroenterology, University of Padova, Padua, Italy
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Shafi AA, Knudsen KE. Cancer and the Circadian Clock. Cancer Res 2019; 79:3806-3814. [PMID: 31300477 DOI: 10.1158/0008-5472.can-19-0566] [Citation(s) in RCA: 114] [Impact Index Per Article: 22.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2019] [Revised: 04/05/2019] [Accepted: 04/24/2019] [Indexed: 12/31/2022]
Abstract
The circadian clock is a master regulator of mammalian physiology, regulating daily oscillations of crucial biological processes and behaviors. Notably, circadian disruption has recently been identified as an independent risk factor for cancer and classified as a carcinogen. As such, it is imperative to discern the underpinning mechanisms by which circadian disruption alters cancer risk. Emergent data, reviewed herein, demonstrate that circadian regulatory functions play critical roles in several hallmarks of cancer, including control of cell proliferation, cell death, DNA repair, and metabolic alteration. Developing a deeper understanding of circadian-cancer regulation cross-talk holds promise for developing new strategies for cancer interception, prevention, and management.
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Affiliation(s)
- Ayesha A Shafi
- Department of Cancer Biology, Thomas Jefferson University, Philadelphia, Pennsylvania.,Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, Pennsylvania
| | - Karen E Knudsen
- Department of Cancer Biology, Thomas Jefferson University, Philadelphia, Pennsylvania. .,Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, Pennsylvania.,Department of Medical Oncology, Thomas Jefferson University, Philadelphia, Pennsylvania.,Department of Urology, Thomas Jefferson University, Philadelphia, Pennsylvania.,Department of Radiation Oncology, Thomas Jefferson University, Philadelphia, Pennsylvania
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Rigatos GG. Fixed-point bifurcation analysis in biological models using interval polynomials theory. BIOLOGICAL CYBERNETICS 2014; 108:365-380. [PMID: 24817437 DOI: 10.1007/s00422-014-0605-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/27/2013] [Accepted: 04/15/2014] [Indexed: 06/03/2023]
Abstract
The paper proposes a systematic method for fixed-point bifurcation analysis in circadian cells and similar biological models using interval polynomials theory. The stages for performing fixed-point bifurcation analysis in such biological systems comprise (i) the computation of fixed points as functions of the bifurcation parameter and (ii) the evaluation of the type of stability for each fixed point through the computation of the eigenvalues of the Jacobian matrix that is associated with the system's nonlinear dynamics model. Stage (ii) requires the computation of the roots of the characteristic polynomial of the Jacobian matrix. This problem is nontrivial since the coefficients of the characteristic polynomial are functions of the bifurcation parameter and the latter varies within intervals. To obtain a clear view about the values of the roots of the characteristic polynomial and about the stability features they provide to the system, the use of interval polynomials theory and particularly of Kharitonov's stability theorem is proposed. In this approach, the study of the stability of a characteristic polynomial with coefficients that vary in intervals is equivalent to the study of the stability of four polynomials with crisp coefficients computed from the boundaries of the aforementioned intervals. The efficiency of the proposed approach for the analysis of fixed-point bifurcations in nonlinear models of biological neurons is tested through numerical and simulation experiments.
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Affiliation(s)
- Gerasimos G Rigatos
- Unit of Industrial Automation, Industrial Systems Institute, Stadiou str, 26504, Rion Patras, Greece,
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Jolma IW, Laerum OD, Lillo C, Ruoff P. Circadian oscillators in eukaryotes. WILEY INTERDISCIPLINARY REVIEWS-SYSTEMS BIOLOGY AND MEDICINE 2011; 2:533-549. [PMID: 20836046 DOI: 10.1002/wsbm.81] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The biological clock, present in nearly all eukaryotes, has evolved such that organisms can adapt to our planet's rotation in order to anticipate the coming day or night as well as unfavorable seasons. As all modern high-precision chronometers, the biological clock uses oscillation as a timekeeping element. In this review, we describe briefly the discovery, historical development, and general properties of circadian oscillators. The issue of temperature compensation (TC) is discussed, and our present understanding of the underlying genetic and biochemical mechanisms in circadian oscillators are described with special emphasis on Neurospora crassa, mammals, and plants.
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Affiliation(s)
- Ingunn W Jolma
- Centre of Organelle Research, Faculty of Science and Technology, University of Stavanger, Stavanger, Norway
| | - Ole Didrik Laerum
- The Gade Institute, Department of Pathology, Haukeland University Hospital, N-5021 Bergen, Norway
| | - Cathrine Lillo
- Centre of Organelle Research, Faculty of Science and Technology, University of Stavanger, Stavanger, Norway
| | - Peter Ruoff
- Centre of Organelle Research, Faculty of Science and Technology, University of Stavanger, Stavanger, Norway
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