Chaste: an open source C++ library for computational physiology and biology

Chaste - Cancer, Heart And Soft Tissue Environment - is an open source C++ library for the computational simulation of mathematical models developed for physiology and biology. Code development has been driven by two initial applications: cardiac electrophysiology and cancer development. A large number of cardiac electrophysiology studies have been enabled and performed, including high performance computational investigations of defibrillation on realistic human cardiac geometries. New models for the initiation and growth of tumours have been developed. In particular, cell-based simulations have provided novel insight into the role of stem cells in the colorectal crypt. Chaste is constantly evolving and is now being applied to a far wider range of problems. The code provides modules for handling common scientific computing components, such as meshes and solvers for ordinary and partial differential equations (ODEs/PDEs). Re-use of these components avoids the need for researchers to "re-invent the wheel" with each new project, accelerating the rate of progress in new applications. Chaste is developed using industrially-derived techniques, in particular test-driven development, to ensure code quality, re-use and reliability. In this article we provide examples that illustrate the types of problems Chaste can be used to solve, which can be run on a desktop computer. We highlight some scientific studies that have used or are using Chaste, and the insights they have provided. The source code, both for specific releases and the development version, is available to download under an open source Berkeley Software Distribution (BSD) licence at http://www.cs.ox.ac.uk/chaste, together with details of a mailing list and links to documentation and tutorials

An agent-based model of anoikis in the colon crypt displays novel emergent behaviour consistent with biological observations

Colorectal cancer (CRC) is a major cause of cancer mortality. Colon crypts are multi-cellular flask-shaped invaginations of the colonic epithelium, with stem cells at their base which support the continual turnover of the epithelium with loss of cells by anoikis from the flat mucosa. Mutations in these stem cells can become embedded in the crypts, a process that is strongly implicated in CRC initiation. We describe a computational model which includes novel features, including an accurate representation of the geometry of the crypt mouth. Model simulations yield previously unseen emergent phenomena, such as localization of cell death to a small region of the crypt mouth which corresponds with that observed in vivo. A mechanism emerges in the model for regulation of crypt cellularity in response to changes in either cell proliferation rates or membrane adhesion strengths. We show that cell shape assumptions influence this behaviour, with cylinders recapitulating biology better than spheres. Potential applications of the model include determination of roles of mutations in neoplasia and exploring factors for altered crypt morphodynamics

Homogenization Model for Aberrant Crypt Foci

Several explanations can be found in the literature about the origin of colorectal cancer. There is however some agreement on the fact that the carcinogenic process is a result of several genetic mutations of normal cells. The colon epithelium is characterized by millions of invaginations, very small cavities, called crypts, where most of the cellular activity occurs. It is consensual in the medical community, that a potential first manifestation of the carcinogenic process, observed in conventional colonoscopy images, is the appearance of Aberrant Crypt Foci (ACF). These are clusters of abnormal crypts, morphologically characterized by an atypical behavior of the cells that populate the crypts. In this work an homogenization model is proposed, for representing the cellular dynamics in the colon epithelium. The goal is to simulate and predict, in silico, the spread and evolution of ACF, as it can be observed in colonoscopy images. By assuming that the colon is an heterogeneous media, exhibiting a periodic distribution of crypts, we start this work by describing a periodic model, that represents the ACF cell-dynamics in a two-dimensional setting. Then, homogenization techniques are applied to this periodic model, to find a simpler model, whose solution symbolizes the averaged behavior of ACF at the tissue level. Some theoretical results concerning the existence of solution of the homogenized model are proven, applying a fixed point theorem. Numerical results showing the convergence of the periodic model to the homogenized model are presented.Comment: 26 pages, 4 figure

Investigating the Origins of Cancer in the Intestinal Crypt with a Gene Network Agent Based Hybrid Model

Colorectal cancer (CRC) is the second most common tumour in the world (Bray, 2018). It has been proposed that morbidity and mortality could be mitigated by screening methods that identify key genetic mutations in the DNA of a patient’s biosample (Traverso, 2002). However, for this to work, a theoretical understanding of the most likely mutations that initiate malignant transformation, and how they affect subsequent microevolution, is needed. Specifically, we hypothesise that there is a CRC-proliferative mutation that is more likely to be initially fixated in the crypt. To investigate this, we developed an agent-based model of cells in the colon crypt that shows emergent biological homeostasis at the tissue level from the cellular and molecular interactions. We equipped each of the cells with a molecular gene network which, in their wildtype state, regulates homeostasis in the crypt and recapitulates known behaviour. We identified and modelled key genes implicated in CRC which, when mutated, alter the rate of death and division of cells. We used this model to study the biological first principles of the fixation of mutations, offering key spatial and temporal understanding of this process. We discuss the impact and clinical relevance of proliferative genetic mutations in isolation, pointing to the KRAS gene as a likely mutation to be initially fixed in the crypt

Molecular investigation of tight junction proteins related to the small intestines

The intestines are an integral part of homeostasis and vital functions that occur throughout the body via the mechanisms of the epithelial barrier. Deficiencies in the intestinal epithelial barrier corresponds with intestinal pathologies and mental disorders. Interestingly, the effectiveness of the barrier function is correlated with a family of transmembrane proteins known as claudin. Alterations of expression of claudin-3 and -23, which are known barrier-forming proteins, occur during the presentation of intestinal pathologies. Investigating how these proteins act using experimental methods presents many difficulties. Therefore, we will be using advances in computational modeling to study the assembly of claudin-3 and -23. By analyzing, the behavior of these proteins we can gain new insight on the mechanisms of transports and communication in the gut and to the rest of the body as wells as understand the molecular origins of intestinal disorders

Wnt/PCP controls spreading of Wnt/β-catenin signals by cytonemes in vertebrates

This is the author accepted manuscript.The final version is available from eLife Sciences Publications via the DOI in this record.Signaling filopodia, termed cytonemes, are dynamic actin-based membrane structures that regulate the exchange of signaling molecules and their receptors within tissues. However, how cytoneme formation is regulated remains unclear. Here, we show that Wnt/PCP autocrine signaling controls the emergence of cytonemes, and that cytonemes subsequently control paracrine Wnt/β-catenin signal activation. Upon binding of the Wnt family member Wnt8a, the receptor tyrosine kinase Ror2 gets activated. Ror2/PCP signaling leads to induction of cytonemes, which mediate transport of Wnt8a to neighboring cells. In the Wnt receiving cells, Wnt8a on cytonemes triggers Wnt/β-catenin-dependent gene transcription and proliferation. We show that cytoneme-based Wnt transport operates in diverse processes, including zebrafish development, the murine intestinal crypt, and human cancer organoids, demonstrating that Wnt transport by cytonemes and its control via the Ror2 pathway is highly conserved in vertebrates.This project was funded by the Living Systems Institute, the University of Exeter and the Boehringer Ingelheim Foundation to SS. Studies in the DMV lab are supported by the National Research Foundation of Singapore and National Medical Research Council under its STAR Award Program. JR and AS were supported by the Impuls- und Vernetzungsfond of the Helmholtz Association. GUN was funded by the Deutsche Forschungsgemeinschaft (SFB 1324, projects A6 and Z2, GRK2039) and Helmholtz Association Program STN

Modeling Biochemical Gradients In Vitro to Control Cell Compartmentalization in a Microengineered 3D Model of the Intestinal Epithelium

Gradients of signaling pathways within the intestinal stem cell (ISC) niche are instrumental for cellular compartmentalization and tissue function, yet how are they sensed by the epithelium is still not fully understood. Here a new in vitro model of the small intestine based on primary epithelial cells (i), apically accessible (ii), with native tissue mechanical properties and controlled mesh size (iii), 3D villus-like architecture (iv), and precisely controlled biomolecular gradients of the ISC niche (v) is presented. Biochemical gradients are formed through hydrogel-based scaffolds by free diffusion from a source to a sink chamber. To confirm the establishment of spatiotemporally controlled gradients, light-sheet fluorescence microscopy and in-silico modeling are employed. The ISC niche biochemical gradients coming from the stroma and applied along the villus axis lead to the in vivo-like compartmentalization of the proliferative and differentiated cells, while changing the composition and concentration of the biochemical factors affects the cellular organization along the villus axis. This novel 3D in vitro intestinal model derived from organoids recapitulates both the villus-like architecture and the gradients of ISC biochemical factors, thus opening the possibility to study in vitro the nature of such gradients and the resulting cellular response.© 2022 The Authors. Advanced Healthcare Materials published by Wiley-VCH GmbH

A Multi-Scale Agent Based Model of Colon Carcinogenesis

Colorectal cancer (CRC) is a major cause of cancer mortality and there remain aspects of its formation which are not understood. The colon contains an epithelium punctuated by flask shaped invaginations called the crypts of Lieberkühn. These crypts are monoclonal in nature while adenomas are thought to be polyclonal, suggesting that multiple crypts are involved in carcinogenesis. It has been reported that fields of mutated tissue surround adenomas but the causes and growth of these fields are not well understood. There are two competing hypotheses regarding growth, the first being that mutated cells from one crypt invade neighbouring crypts, and the second that mutated crypts replicate themselves more often than wild-type crypts. To investigate these processes two agent based models were developed. The first model represents cells as agents and is similar to previous models in the field, but is novel in including the geometry of the crypt mouth. This is necessary to model multiple interacting crypts. This model is the first in the literature to be used to represent multiple crypts and is used to investigate invasion of neighbour crypts by mutated cells. The second model represents whole crypts as agents, which allows the entire colon to be simulated for multiple decades of biological time, as far as we are aware this is the first such model. The cell scale model predicts that crypt invasion does not occur, but that mutated cells can invade the flat mucosa above neighbouring crypts. Analysis of in-vivo data is consistent with this prediction. The crypt as agent model predicts fields of ~41,000 crypts, in agreement with data in the literature, this corresponds to a field ~23mm in diameter. This project models pre-cancerous fields for the first time over a variety of scales, making specific novel predictions which are in agreement with in-vivo data where such data exist. Two agent based models were created to study the development of precancerous fields, one a model with cells as agents to study cell scale phenomena and the other with crypts as agents to allow processes to be studied on larger spatial and temporal scales. These models could potentially be used to refine clinic practice by predicting the required frequency of post-intervention monitoring of patients or the necessity of further intervention

Investigation of Colonic Regeneration via Precise Damage Application Using Femtosecond Laser-Based Nanosurgery

Organoids represent the cellular composition of natural tissue. So called colonoids, organoids derived from colon tissue, are a good model for understanding regeneration. However, next to the cellular composition, the surrounding matrix, the cell–cell interactions, and environmental factors have to be considered. This requires new approaches for the manipulation of a colonoid. Of key interest is the precise application of localized damage and the following cellular reaction. We have established multiphoton imaging in combination with femtosecond laser-based cellular nanosurgery in colonoids to ablate single cells in the colonoids’ crypts, the proliferative zones, and the differentiated zones. We observed that half of the colonoids recovered within six hours after manipulation. An invagination of the damaged cell and closing of the structure was observed. In about a third of the cases of targeted crypt damage, it caused a stop in crypt proliferation. In the majority of colonoids ablated in the crypt, the damage led to an increase in Wnt signalling, indicated via a fluorescent lentiviral biosensor. qRT-PCR analysis showed increased expression of various proliferation and Wnt-associated genes in response to damage. Our new model of probing colonoid regeneration paves the way to better understand organoid dynamics on a single cell level. © 2022 by the authors. Licensee MDPI, Basel, Switzerland