Biology subjects

Pitt-Francis, J. M.

Publications and source records attributed to Pitt-Francis, J. M..

6 recordsLinked to original sources

bioRxiv2024

Characterising cancer cell responses to cyclic hypoxia using mathematical modelling

In vivo observations show that oxygen levels in tumours can fluctuate on fast and slow timescales. As a result, cancer cells can be periodically exposed to pathologically low oxygen levels; a phenomenon known as cyclic hypoxia. Yet, little is known about the response and adaptation of cancer cells to cyclic, rather than, constant hypoxia. Further, existing in vitro models of cyclic hypoxia fail to capture the complex and heterogeneous oxygen dynamics of tumours growing in vivo. Mathematical models can help to overcome current experimental limitations and, in so doing, offer new insights into the biology of tumour cyclic hypoxia by predicting cell responses to a wide range of cyclic dynamics. We develop an individual-based model to investigate how cell cycle progression and cell fate determination of cancer cells are altered following exposure to cyclic hypoxia. Our model can simulate standard in vitro experiments, such as clonogenic assays and cell cycle experiments, allowing for efficient screening of cell responses under a wide range of cyclic hypoxia conditions. Simulation results show that the same cell line can exhibit markedly different responses to cyclic hypoxia depending on the dynamics of the oxygen fluctuations. We also use our model to investigate the impact of changes to cell cycle checkpoint activation and damage repair on cell responses to cyclic hypoxia. Our simulations suggest that cyclic hypoxia can promote heterogeneity in cellular damage repair activity within vascular tumours.

systems biology↗

bioRxiv2023

Enhanced perfusion following exposure to radiotherapy: a theoretical investigation

Tumour angiogenesis leads to the formation of blood vessels that are structurally and spatially heterogeneous. Poor blood perfusion, in conjunction with increased hypoxia and oxygen heterogeneity, impairs a tumours response to radiotherapy. The optimal strategy for enhancing tumour perfusion remains unclear, preventing its regular deployment in combination therapies. In this work, we first identify vascular architectural features that correlate with enhanced perfusion following radiotherapy, using in vivo imaging data from vascular tumours. Then, we present a novel computational model to determine the relationship between these architectural features, blood perfusion, and tumour response to radiotherapy in silico. If perfusion is defined to be the proportion of vessels that support blood flow, we find that vascular networks with small mean diameters and large numbers of angiogenic sprouts show the largest increases in perfusion post-irradiation for both biological and synthetic tumours. We also identify cases where perfusion increases due to the pruning of hypoperfused vessels, rather than blood being rerouted. These results indicate the importance of considering network composition when determining the optimal irradiation strategy. In the future, we aim to use our findings to identify tumours that are good candidates for perfusion enhancement and to improve the efficacy of combination therapies. Author summaryDysregulated tumour vasculature often contains hypoperfused blood vessels which inhibit the delivery of blood-borne anticancer therapies. Radiotherapy, used to treat more than half of all cancer patients, causes DNA damage to vascular endothelial cells, preferentially impacting smaller vessels, leading to their death and vessel pruning. At the same time, experiments measuring changes in tumour perfusion post-irradiation produce varying outcomes and, therefore, the impact of irradiation-induced vessel pruning on network-scale perfusion remains unclear. In this study, we use recent (in vivo) imaging data to identify features of tumour vascular architectures that impact perfusion change post-irradiation. We then use a newly-developed computational framework, directly informed by the experimental observations, to elucidate the relationship between the vascular geometry and topology prior to radiotherapy and the irradiation-induced changes to network perfusion. We find that perfusion increases most significantly for networks of blood vessels with small mean diameters and large numbers of angiogenic sprouts. Our results also distinguish different mechanisms of perfusion increase and we identify cases where rerouting of blood flow causes previously hypoperfused vessels to become perfused. Our study sheds more light on the impact of radiotherapy on tumour blood flow; these insights could be useful for improving anti-cancer treatments.

systems biology↗

bioRxiv2023

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

Cell competition is a process in multicellular organisms where cells interact with their neighbours to determine a "winner" or "loser" status. The loser cells are eliminated through programmed cell death, leaving only the winner cells to populate the tissue. Cell competition is context-dependent; the same cell type can win or lose depending on the cell type it is competing against. Hence, winner/loser status is an emergent property. A key question in cell competition is: how do cells acquire their winner/loser status? In this paper, we propose a mathematical framework for studying the emergence of winner/loser status based on a set of quantitative criteria that distinguishes competitive from non-competitive outcomes. We apply this framework in a cell-based modelling context, to both highlight the crucial role of active cell death in cell competition and identify the factors that drive cell competition. HighlightsO_LIEmergent winner/loser status tests for competitive outcomes in cell-based models C_LIO_LIDifferences in biomechanical properties alone are not sufficient for cell competition C_LIO_LIWinners have both higher tolerance and higher emission of death signals than losers C_LI

developmental biology↗

bioRxiv2019

Abnormal morphology biases haematocrit distribution in tumour vasculature and contributes to heterogeneity in tissue oxygenation

Oxygen heterogeneity in solid tumours is recognised as a limiting factor for therapeutic efficacy. This heterogeneity arises from the abnormal vascular structure of the tumour, but the precise mechanisms linking abnormal structure and compromised oxygen transport are only partially understood. In this paper, we investigate the role that RBC transport plays in establishing oxygen heterogeneity in tumour tissue. We focus on heterogeneity driven by network effects, which are challenging to observe experimentally due to the reduced fields of view typically considered. Motivated by our findings of abnormal vascular patterns linked to deviations from current RBC transport theory, we calculate average vessel lengths [Formula] and diameters [Formula] from tumour allografts of three cancer cell lines and observe a substantial reduction in the ratio [Formula] compared to physiological conditions. Mathematical modelling reveals that small values of the ratio{lambda} (i.e. {lambda} < 6) can bias haematocrit distribution in tumour vascular networks and drive heterogeneous oxygenation of tumour tissue. Finally, we show an increase in the value of{lambda} in tumour vascular networks following treatment with the anti-angiogenic cancer agent DC101. Based on our findings, we propose{lambda} as an effective way of monitoring the efficacy of antiangiogenic agents and as a proxy measure of perfusion and oxygenation in tumour tissue undergoing anti-angiogenic treatment. Significance statementOxygen heterogeneity in solid tumours is recognised as a limiting factor for therapeutic efficacy. This heterogeneity arises from the abnormal tumour vascular structure. We investigate the role that anomalies in RBC transport play in establishing oxygen heterogeneity in tumour tissue. We introduce a metric to characterise tumour vasculature (mean vessel length-to-diameter ratio,{lambda} ) and demonstrate how it predicts tissue oxygen heterogeneity. We also report an increase in{lambda} following treatment with the antiangiogenic agent DC101. Together, we propose{lambda} as an effective way of monitoring the action of anti-angiogenic agents and a proxy measure of oxygen heterogeneity in tumour tissue. Unravelling the causal relationship between tumour vascular structure and tissue oxygenation will pave the way for new personalised therapeutic approaches.

cancer biology↗

bioRxiv2017

The importance of geometry in the corneal micropocket assay

The corneal micropocket angiogenesis assay is an experimental protocol for studying vessel network formation, or neovascularization, in vivo. The assay is attractive due to the ease with which the developing vessel network can be observed in the same animal over time. Measurements from the assay have been used in combination with mathematical modeling to gain insights into the mechanisms of angiogenesis. While previous modeling studies have adopted planar domains to represent the assay, the hemispherical shape of the cornea and asymmetric positioning of the angiogenic source can be seen to affect vascular patterning in experimental images. As such, we aim to better understand: i) how the geometry of the assay influences vessel network formation and ii) how to relate observations from planar domains to those in the hemispherical cornea. To do so, we develop a three-dimensional, off-lattice mathematical model of neovascularization in the cornea, using a spatially resolved representation of the assay for the first time. Relative to the detailed model, we predict that the adoption of planar geometries has a noticeable impact on vascular patterning, leading to increased vessel merging, or anastomosis, in particular when circular geometries are adopted. Significant differences in the dynamics of diffusible aniogenesis simulators are also predicted between different domains. In terms of comparing predictions across domains, the distance of the vascular front to the limbus metric is found to have low sensitivity to domain choice, while metrics such as densities of tip cells and vessels and vascularized fraction are sensitive to domain choice. Given the widespread adoption and attractive simplicity of planar tissue domains, both in silico and in vitro, the differences identified in the present study should prove useful in relating the results of previous and future theoretical studies of neovascularization to in vivo observations in the cornea.\n\nAuthor summaryNeovascularization, or the formation of new blood vessels, is an important process in development, wound healing and cancer. The corneal micropocket assay is used to better understand the process and, in the case of cancer, how it can be controlled with drug therapies for improved patient outcomes. In the assay, the hemispherical shape of the cornea can influence the way the vessel network forms. This makes it difficult to directly compare results from experiments with the predictions of mathematical models or cell culture experiments, which are typically performed on flat substrates or planar matrices. In this study, we use mathematical modeling to investigate how the hemispherical shape of the cornea affects vessel formation and to identify how sensitive different measurements of neovascularization are to geometry.

physiology↗

bioRxiv2017

Microvessel Chaste: An Open Library for Spatial Modelling of Vascularized Tissues

Spatial models of vascularized tissues are widely used in computational physiology, to study for example, tumour growth, angiogenesis, osteogenesis, coronary perfusion and oxygen delivery. Composition of such models is time-consuming, with many researchers writing custom software for this purpose. Recent advances in imaging have produced detailed three-dimensional (3D) datasets of vascularized tissues at the scale of individual cells. To fully exploit such data there is an increasing need for software that allows user-friendly composition of efficient, 3D models of vascularized tissue growth, and comparison of predictions with in vivo or in vitro experiments and other models. Microvessel Chaste is a new open-source library for building spatial models of vascularized tissue growth. It can be used to simulate vessel growth and adaptation in response to mechanical and chemical stimuli, intra- and extra-vascular transport of nutrient, growth factor and drugs, and cell proliferation in complex 3D geometries. The library provides a comprehensive Python interface to solvers implemented in C++, allowing user-friendly model composition, and integration with experimental data. Such integration is facilitated by interoperability with a growing collection of scientific Python software for image processing, statistical analysis, model annotation and visualization. The library is available under an open-source Berkeley Software Distribution (BSD) licence at https://jmsgrogan.github.io/MicrovesselChaste. This article links to two reproducible example problems, showing how the library can be used to model tumour growth and angiogenesis with realistic vessel networks.

systems biology↗