4.4 Article

Mathematical modeling of monoclonal conversion in the colonic crypt

期刊

JOURNAL OF THEORETICAL BIOLOGY
卷 300, 期 -, 页码 118-133

出版社

ACADEMIC PRESS LTD- ELSEVIER SCIENCE LTD
DOI: 10.1016/j.jtbi.2012.01.021

关键词

Crypt; Stem cells; Monoclonal conversion; Cancer

资金

  1. Integrative Biology programme [GR/572023/01]
  2. OCISB [BB/D020190/1]
  3. EPRSC [EP/1017909/1]
  4. Microsoft Research, Cambridge
  5. BBSRC [BB/D020190/1] Funding Source: UKRI
  6. EPSRC [EP/I017909/1] Funding Source: UKRI
  7. Biotechnology and Biological Sciences Research Council [BB/D020190/1] Funding Source: researchfish
  8. Engineering and Physical Sciences Research Council [EP/I017909/1] Funding Source: researchfish

向作者/读者索取更多资源

A novel spatial multiscale model of a colonic crypt is described, which couples the cell cycle (including cell division) with the mechanics of cell movement. The model is used to investigate the process of monoclonal conversion under two hypotheses concerning stem cell behavior. Under the first hypothesis, 'stem-ness' is an intrinsic cell property, and the stem cell population is maintained through asymmetric division. Under the second hypothesis, the proliferative behavior of each cell is governed by its microenvironment through a biochemical signalling cue, and all cell division is symmetric. Under each hypothesis, the model is used to run virtual experiments, in which a harmless labeling mutation is bestowed upon a single cell in the crypt and the mutant clonal population is tracked over time to check if and when the crypt becomes monoclonal. It is shown that under the first hypothesis, a stable structured cell population is not possible without some form of population-dependent feedback; in contrast, under the second hypothesis, a stable crypt architecture arises naturally. Through comparison with an existing spatial crypt model and a non-spatial stochastic population model, it is shown that the spatial structure of the crypt has a significant effect on the time scale over which a crypt becomes monoclonal. (C) 2012 Elsevier Ltd. All rights reserved.

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Owen, A. Prior, I Saunders, L. Crilly, J. McKeon, H. K. Ubhi, I Ashworth, L. Nelson, D. Ratnasingham, A. Adeogun, R. Carr, C. Davison, S. Devalia, A. Hayat, R. B. Karsan, C. Osborne, C. Weegenaar, M. Wijeyaratne, M. Curran, C. Horner, F. Babatunde, E. Barnor-Ahiaku, P. Chitsabesan, O. Dixon, N. Hall, N. Ilenkovan, T. Mackrell, N. Nithianandasivam, J. Orr, F. Palazzo, M. Saad, L. Sandland-Taylor, J. Sherlock, T. Ashdown, S. Chandler, T. Garsaa, J. Lloyd, S. Y. Loh, S. Ng, C. Perkins, R. Underhill, T. Arthur, J. Ng, M. Kovacevic, S. Delibegovic, M. Karamanliev, T. Ivanov, T. Yotsov, I. Ilieva, A. Akisheva, M. Shoshkova, E. Nawaz, M. Swamad, V Neykov, R. Zebrak, R. Paramasivam, A. Martensen Hm Larsen Hm Larsen, L. Radeker, P. E. Frey, A. Kechagias, A. Turunen, J. Katunin, M. Niskakangas, A. Ojakaar, A. Venara, P. LeNaoures, E. Duchalais, T. Vignaud, S. Frey, C. Ricolleau, A. Ioannidis, M. Konstantinidis, F. Antonakopoulos, A. Mathioulaki, P. Chrysoheris, P. G. Athanasopoulos, C. Koutserimpas, S. M. Tenconi, S. Rausei, D. Maioli, V Marchionini, S. Pasquali, A. Simioni, V Farina, M. Podda, L. Lorenzon, F. Tirelli, V Fico, F. Santullo, F. Belia, V Schaeff, A. Otto, M. Jakubauskas, E. Poskus, D. Danys, M. Kryzauskas, S. Mikalauskas, R. Rackauskas, M. Drungilas, T. Poskus, V Jotautas, K. Strupas, M. Petrulionis, T. R. van Elst, Z. Abdulrahman, M. Chu, P. V. B. Fagan, C. Wells, A. Alagoa Joao, D. J. Aparicio, M. Fragoso, J. Guimaraes, G. Cruz, J. Ribeiro, I. Borges da Ponte, S. Almeida, A. R. Martins, J. Juloski, V. V. Cuk, R. Radulovic, K. Milosevic, J. Bojicic, M. Gencic, U. Jankovic, M. Jovanovic, Y. El Kasmy El Kasmi, M. J. Gomez Jurado, P. Alberti Delgado, A. Bordanova Reverter, A. Gomez del Pulgar, J. F. Belzunce-Capo, M. Verdaguer Tremolosa, Q. Lin, S. Perez-Ajates, N. Ramayo Diaz, I. Gonzalez Caraballo, T. Pascual Vicente, M. Orue-Echebarria, L. Sanchez-Calvo, D. Wang, C. Trueba-Collado, J. T. Morales Bernaldo de Quiros, O. Anabitarte Bautista, A. Yebes, E. Espin-Basany, D. Clerc, G. Mignon, A. Vanoni, A. Henkens, G. Jarrar, M. Odovic, M. Willemin, O. Milliet, D. Hahnloser, N. Demartines, P. Curchod, C. Ciubotaru, S. Popescu, S. S. Popescu, K. Piras, C. Ciubotaru, A. Yanishev, R. Luzan, E. Lutovinova, A. Gavrilina, A. Barkovskaya, N. Kudelkina, D. Topchubaev, B. B. Ozkan, A. Yagiz Sen, M. K. Aktas, N. Aykun, M. H. Agca, C. Bilen, I Kilinc, C. Atar, V Kilic, C. Aktuna, M. Aba, I. C. Eray, B. E. Baki, E. Arslan, G. Alemdag, M. Ulusahin, E. B. Gul, R. Yildirim, A. Semiz, G. Bektur, K. Tomas, S. Bodur, B. Yuksek, H. Serin, H. Erdonmez, F. Gursoy, H. Kara, U. Onsal, M. Ozbek, P. A. Kasar, A. Ipor, M. F. Cetin, R. A. Khaw, E. Mills, L. R. Manley, K. Vutipongsatorn, N. Thakral, M. Adra, S. M. Khan, A. Badran, A. Ramjeeawon, H. L. Tan, D. S. Rye, N. Rajaraman, J. G. Norman, G. Solomou, D. M. Baker, B. D. Brandao, B. Stainer, O. O. Onafowokan, A. Gharooni, N. Dabab, S. Carlton-Carew, G. Kungwengwe, M. Gabriel, E. Sewart, P. Pockney, A. Chrimes, A. Agarwal, J. Zhao, J. M. S. N. Jayalath, P. Liebenberg, S. Khor, T. Muddasani, A. Dawson, N. Taylor, C. Stevenson, A. Drane, U. Pahalawatta, L. T. Lai, A. Debiasio, M. Jung, C. D. Brumfitt, Y. Z. Beh, N. N. Dudi-Venkata, Y. D. Lee, P. Stewart, V Thirugnanasundralingam, K. Muir, B. Ng, D. M. Mendis, P. M. Robb, H. J. Lee, A. A. B. Wyche, L. T. Davis, J. K. Luong, ,

Summary: This study validates a prognostic model for acute kidney injury (AKI) after major gastrointestinal surgery. The model shows good predictive accuracy in two multicentre cohort studies.

BJS OPEN (2022)

Article Mathematics, Applied

A spectral analysis of the nonlinear Schr?dinger equation in the co-exploding frame

S. J. Chapman, M. Kavousanakis, E. G. Charalampidis, I. G. Kevrekidis, P. G. Kevrekidis

Summary: The present study examines the spectral characteristics of the linearized problem associated with the nonlinear Schrodinger model. The study identifies the eigenvalue pairs related to symmetries and the properties of the continuous spectrum, and approximates their values through asymptotic and numerical approaches. The findings highlight the physical significance of these eigenvalues.

PHYSICA D-NONLINEAR PHENOMENA (2022)

Article Electrochemistry

Nonlinear Electrochemical Impedance Spectroscopy for Lithium-Ion Battery Model Parameterization

Toby L. Kirk, Adam Lewis-Douglas, David Howey, Colin P. Please, S. J. Jon Chapman

Summary: In this work, the local nonlinear electrochemical impedance spectroscopy (NLEIS) response of a lithium-ion battery is analyzed and model parameters are estimated from measured NLEIS data. The analysis assumes a single-particle model that includes nonlinear diffusion of lithium within the electrode particles and asymmetric charge transfer kinetics at their surface. Analytical formulae for the impedances up to the second harmonic response are systematically derived, allowing the interpretation of each contribution in terms of physical processes and nonlinearities in the model. The validation of the model is demonstrated by predicting time-domain voltage response using the parameterized model, showing excellent agreement with measured voltage time-series data (11.1 mV RMSE).

JOURNAL OF THE ELECTROCHEMICAL SOCIETY (2023)

Article Materials Science, Multidisciplinary

A mechanical model for reinforced, expanding spirally-wound layered materials

Robert Timms, Steven Psaltis, Colin P. Please, S. Jon Chapman

Summary: This paper investigates the mechanical deformations of a spirally-wound elastic material with a thin inextensible reinforcing material, considering its application in batteries. The study reveals simple behaviors in the bulk of the spiral, but identifies boundary layers near the inner and outer windings, as well as finer-structure boundary layers at the beginning and end of the spiral. The paper provides analytical solutions for the deformations and tension in the inextensible layer, and compares them with finite-element solutions.

JOURNAL OF THE MECHANICS AND PHYSICS OF SOLIDS (2023)

Article Multidisciplinary Sciences

Derivation of a macroscopic model for Brownian hard needles

Maria Bruna, Stephen J. Chapman, Markus Schmidtchen

Summary: We investigate the impact of anisotropic steric interactions on hard Brownian needles in a two-dimensional system. Despite lacking volume, non-overlapping needles exclude volume in configuration space, influencing the macroscopic behavior of the system. By utilizing the method of matched asymptotic expansions and conformal mapping, we derive a nonlinear non-local partial differential equation describing the evolution of population density in position and orientation. We focus on the regime of high rotational diffusion, which yields an equation for spatial density enabling comparison between the effective excluded volumes of hard-needle and hard-sphere systems. Furthermore, we examine spatially homogeneous solutions and observe an isotropic to nematic transition as density increases, consistent with Onsager's theory.

PROCEEDINGS OF THE ROYAL SOCIETY A-MATHEMATICAL PHYSICAL AND ENGINEERING SCIENCES (2023)

Article Biology

ChemChaste: Simulating spatially inhomogeneous biochemical reaction-diffusion systems for modeling cell-environment feedbacks

Connah G. M. Johnson, Alexander G. Fletcher, Orkun S. Soyer

Summary: In this study, the authors introduce ChemChaste, an extension that enables spatial simulation of multicellular and bulk biochemistry. ChemChaste allows for the simulation of an arbitrary number of spatially diffusing chemicals, spatially heterogeneous chemical diffusion coefficients, and the inclusion of both bulk and intracellular biochemical reactions and their coupling. ChemChaste also introduces a file-based interface for defining parameters without direct interaction with Chaste's core C++ code.

GIGASCIENCE (2022)

Article Mathematics, Applied

MODELING ELECTRODE HETEROGENEITY IN LITHIUM-ION BATTERIES: UNIMODAL AND BIMODAL PARTICLE-SIZE DISTRIBUTIONS

Toby L. Kirk, Jack Evans, Colin P. Please, S. Jonathan Chapman

Summary: In this study, mathematical models were used to simulate the heterogeneous porous electrodes in lithium-ion batteries by considering the particle size distribution. The results showed that the single-particle model (SPM) could approximate the cell dynamics for a unimodal distribution, while a double-particle model (DPM) was needed for a bimodal distribution. Additionally, the study demonstrated an efficient method for computing the internal states of the electrode particles after simulation.

SIAM JOURNAL ON APPLIED MATHEMATICS (2022)

Article Medicine, Research & Experimental

Seven challenges in the multiscale modeling of multicellular tissues

Alexander G. Fletcher, James M. Osborne

Summary: The growth and dynamics of multicellular tissues involve complex cellular behaviors at multiple scales, and computational modeling approaches are crucial for understanding these processes. However, such models face technical and computational challenges.

WIRES MECHANISMS OF DISEASE (2022)

Article Physics, Fluids & Plasmas

Normal form for the onset of collapse: The prototypical example of the nonlinear Schrodinger equation

S. J. Chapman, M. Kavousanakis, I. G. Kevrekidis, P. G. Kevrekidis

Summary: The study of nonlinear waves that collapse in finite time is of universal interest in various disciplines. In this study, a normal form for the emergence of radially symmetric blowup solutions from stationary ones in the nonlinear Schrodinger equation is systematically derived. This normal form, based on asymptotics beyond all algebraic orders, shows good agreement with numerics in both leading and higher-order effects, and is applicable to both infinite and finite domains in critical and supercritical regimes.

PHYSICAL REVIEW E (2021)

Article Mathematics, Applied

ASYMPTOTIC REDUCTION OF A LITHIUM-ION POUCH CELL MODEL

Robert Timms, Scott G. Marquis, Valentin Sulzer, Colin P. Please, S. Jonathan Chapman

Summary: A three-dimensional model of a single-layer lithium-ion pouch cell was proposed in this study. Asymptotic analysis was used to reveal important characteristics of the model, simplifying computational complexity by coupling one-dimensional models with two-dimensional problems. This approach offers insights into the electrochemical and thermal behavior of lithium-ion pouch cells.

SIAM JOURNAL ON APPLIED MATHEMATICS (2021)

Article Mathematics, Applied

HOMOGENIZATION OF FLOW THROUGH PERIODIC NETWORKS

S. Jonathan Chapman, Zachary M. Wilmott

Summary: This study homogenizes the problem of fluid flow through a periodic network of one-dimensional channels to Darcy flow using a discrete version of the method of multiple scales. The effective permeability in terms of channel conductances is obtained through a simple, low-dimensional linear algebra problem. The research investigates the statistical properties of effective permeability for various random networks and evaluates the correlation between permeability and network tortuosity.

SIAM JOURNAL ON APPLIED MATHEMATICS (2021)

Article Biology

A framework for relating natural movement to length and quality of life in human and non-human animals

Iain Hunter, Raz Leib

Summary: Natural movement is related to health, but it is difficult to measure. Existing methods cannot capture the full range of natural movement. Comparing movement across different species helps identify common biomechanical and computational principles. Developing a system to quantify movement in freely moving animals in natural environments and relating it to life quality is crucial. This study proposes a theoretical framework based on movement ability and validates it in Drosophila.

JOURNAL OF THEORETICAL BIOLOGY (2024)

Article Biology

A geometric approach to the evolution of altruism

Andy Gardner

Summary: Fisher's geometric model is a useful tool for predicting key properties of Darwinian adaptation, and here it is applied to predict differences between the evolution of altruistic versus nonsocial phenotypes. The results suggest that the effect size maximizing probability of fixation is smaller in the context of altruism and larger in the context of nonsocial phenotypes, leading to lower overall probability of fixation for altruism and higher overall probability of fixation for nonsocial phenotypes.

JOURNAL OF THEORETICAL BIOLOGY (2024)

Article Biology

A mathematical framework for the emergence of winners and losers in cell competition

Thomas F. Pak, Joe Pitt-Francis, Ruth E. Baker

Summary: Cell competition is a process where cells interact in multicellular organisms to determine a winner or loser status, with loser cells being eliminated through programmed cell death. The winner cells then populate the tissue. The outcome of cell competition is context-dependent, as the same cell type can win or lose depending on the competing cell type. This paper proposes a mathematical framework to study the emergence of winner or loser status, highlighting the role of active cell death and identifying the factors that drive cell competition in a cell-based modeling context.

JOURNAL OF THEORETICAL BIOLOGY (2024)

Article Biology

The eco-evolutionary dynamics of Batesian mimicry

Haruto Tomizuka, Yuuya Tachiki

Summary: Batesian mimicry is a strategy in which palatable prey species resemble unpalatable prey species to avoid predation. The evolution of this mimicry plays a crucial role in protecting the unpalatable species from extinction.

JOURNAL OF THEORETICAL BIOLOGY (2024)

Article Biology

Gene drives for the extinction of wild metapopulations

Jason W. Olejarz, Martin A. Nowak

Summary: Gene drive technology shows potential for population control, but its release may have unpredictable consequences. The study suggests that the failure of suppression is a natural outcome, and there are complex dynamics among wild populations.

JOURNAL OF THEORETICAL BIOLOGY (2024)

Article Biology

Intelligent phenotype-detection and gene expression profile generation with generative adversarial networks

Hamid Ravaee, Mohammad Hossein Manshaei, Mehran Safayani, Javad Salimi Sartakhti

Summary: Gene expression analysis is valuable for cancer classification and phenotype identification. IP3G, based on Generative Adversarial Networks, enhances gene expression data and discovers phenotypes in an unsupervised manner. By converting gene expression profiles into images and utilizing IP3G, new phenotype profiles can be generated, improving classification accuracy.

JOURNAL OF THEORETICAL BIOLOGY (2024)

Article Biology

Network-based uncertainty quantification for mathematical models in epidemiology

Beatrix Rahnsch, Leila Taghizadeh

Summary: This study forecasts the evolution of the COVID-19 pandemic in Germany using a network-based inference method and compares it with other approaches. The results show that the network-inference based approach outperforms other methods in short-to mid-term predictions, even with limited information about the new disease. Furthermore, predictions based on the estimation of the reproduction number in Germany can yield more reliable results with increasing data availability, but still cannot surpass the network-inference based algorithm.

JOURNAL OF THEORETICAL BIOLOGY (2024)

Article Biology

Dynamics of cell-type transition mediated by epigenetic modifications

Rongsheng Huang, Qiaojun Situ, Jinzhi Lei

Summary: Maintaining tissue homeostasis requires appropriate regulation of stem cell differentiation. Random inheritance of epigenetic states plays a pivotal role in stem cell differentiation. This computational model provides valuable insights into the intricate mechanism governing stem cell differentiation and cell reprogramming, offering a promising path for enhancing the field of regenerative medicine.

JOURNAL OF THEORETICAL BIOLOGY (2024)

Article Biology

Comparative analysis of kinetic realizations of insulin signaling

Patrick Vincent N. Lubenia, Eduardo R. Mendoza, Angelyn R. Lao

Summary: This study compares insulin signaling in healthy and type 2 diabetes states using reaction network analysis. The results show similarities and differences between the two conditions, providing insights into the mechanisms of insulin resistance, including the involvement of other complexes, less restrictive interplay between species, and loss of concentration robustness in GLUT4.

JOURNAL OF THEORETICAL BIOLOGY (2024)

Article Biology

Simulating tumor volume dynamics in response to radiotherapy: Implications of model selection

Nuverah Mohsin, Heiko Enderling, Renee Brady-Nicholls, Mohammad U. Zahid

Summary: Mathematical modeling is crucial in understanding radiobiology and designing treatment approaches in radiotherapy for cancer. This study compares three tumor volume dynamics models and analyzes the implications of model selection. A new metric, the point of maximum reduction of tumor volume (MRV), is introduced to quantify the impact of radiotherapy. The results emphasize the importance of caution in selecting models of response to radiotherapy due to the artifacts imposed by each model.

JOURNAL OF THEORETICAL BIOLOGY (2024)

Article Biology

Pillars of theoretical biology: Biochemical systems analysis, I, II and III

Armindo Salvador

Summary: Michael Savageau's Biochemical Systems Analysis papers have had a significant impact on Systems Biology, generating core concepts and tools. This article provides a brief summary of these papers and discusses the most relevant developments in Biochemical Systems Theory since their publication.

JOURNAL OF THEORETICAL BIOLOGY (2024)