Biology subjects

Maini, P. K.

Publications and source records attributed to Maini, P. K..

28 records · Page 2Linked to original sources

bioRxiv2019

Head Mesoderm Tissue Growth, Dynamics and Neural Crest Cell Migration

Vertebrate head morphogenesis involves orchestrated cell growth and tissue movements of the mesoderm and neural crest to form the distinct craniofacial pattern. To better understand structural birth defects, it is important that we learn how these processes are controlled. Here, we examine this question during chick head morphogenesis using time-lapse imaging, computational modeling, and experiment. We find that head mesodermal cells are inherently dynamic in culture and alter cell behaviors in the presence of either ectoderm or neural crest cells. Mesodermal cells in vivo display large-scale whirling motions that rapidly transition to lateral, directed movements after neural crest cells emerge. Computer model simulations predict distinct changes in neural crest migration as the spatio-temporal growth profile of the mesoderm is varied. BrdU-labeling and photoconversion combined with cell density measurements then reveal non-uniform mesoderm growth in space and time. Chemical inhibition of head mesoderm proliferation or ablation of premigratory neural crest alters mesoderm growth and neural crest migration, implying a dynamic feedback between tissue growth and neural crest cell signaling to confer robustness to the system.\n\nSummary StatementDynamic feedback between tissue growth and neural crest cell migration ensures robust neural crest stream formation and head morphogenesis shown by time-lapse microscopy, mathematical modeling and embryo perturbations.

developmental biology↗

bioRxiv2019

Neural crest cells bulldoze through the microenvironment using Aquaporin-1 to stabilize filopodia

Neural crest migration requires cells to move through an environment filled with dense extracellular matrix and mesoderm to reach targets throughout the vertebrate embryo. Here, we use high-resolution microscopy, computational modeling, and in vitro and in vivo cell invasion assays to investigate the function of Aquaporin-1 (AQP-1) signaling. We find that migrating lead cranial neural crest cells express AQP-1 mRNA and protein, implicating a biological role for water channel protein function during invasion. Differential AQP-1 levels affect neural crest cell speed, direction, and the length and stability of cell filopodia. Further, AQP-1 enhances matrix metalloprotease (MMP) activity and colocalizes with phosphorylated focal adhesion kinases (pFAK). Co-localization of AQP-1 expression with EphB guidance receptors in the same migrating neural crest cells raises novel implications for the concept of guided bulldozing by lead cells during migration.

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↗

bioRxiv2019

Age-structure as key to delayed logistic proliferation of scratch assays

Scratch assays are in-vitro methods for studying cell migration. In these experiments, a scratch is made on a cell monolayer and recolonisation of the scratched region is imaged to quantify cell migration rates. Typically, scratch assays are modelled by reaction diffusion equations depicting cell migration by Fickian diffusion and modelling proliferation by a logistic term. In a recent paper (Jin, W. et al. Bull Math Biol (2017)), the authors observed experimentally that during the early stage of the recolonisation process, there is a disturbance phase where proliferation is not logistic, and this is followed by a growth phase where proliferation appears to be logistic. The authors did not identify the precise mechanism that causes the disturbance phase but showed that ignoring it can lead to incorrect parameter estimates. The aim of this work is to show that a non-linear age-structured population model can account for the two phases of proliferation in scratch assays. The model consists of an age-structured cell cycle model of a cell population, coupled with an ordinary differential equation describing the resource concentration dynamics in the substrate. The model assumes a resource-dependent cell cycle threshold age, above which cells are able to proliferate. By studying the dynamics of the full system in terms of the subpopulations of cells that can proliferate and the ones that can not, we are able to find conditions under which the model captures the two-phase behaviour. Through numerical simulations we are able to show that the resource concentration in the substrate regulates the biphasic dynamics.

cell biology↗

bioRxiv2018

Inferring Tumour Proliferative Organisation from Phylogenetic Tree Measures in a Computational Model

We use a computational modelling approach to explore whether it is possible to infer a tumours cell proliferative hierarchy, under the assumptions of the cancer stem cell hypothesis and neutral evolution. We focus on inferring the symmetric division probability for cancer stem cells in our model, as this is believed to be a key driving parameter of tumour progression and therapeutic response. Given the advent of multi-region sampling, and the opportunities offered by them to understand tumour evolutionary history, we focus on a suite of statistical measures of the phylogenetic trees resulting from the tumours evolution in different regions of parameter space and through time. We find strikingly different patterns in these measures for changing symmetric division probability which hinge on the inclusion of spatial constraints. These results give us a starting point to begin stratifying tumours by this biological parameter and also generate a number of actionable clinical and biological hypotheses including changes during therapy, and through tumour evolution.

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

The evolution of tumour composition during fractionated radiotherapy: implications for outcome

Current protocols for delivering radiotherapy are based primarily on tumour stage and nodal and metastases status, even though it is well known that tumours and their microenvironments are highly heterogeneous. It is well established that the local oxygen tension plays an important role in radiation-induced cell death, with hypoxic tumour regions responding poorly to irradiation. Therefore, to improve radiation response, it is important to understand more fully the spatiotemporal distribution of oxygen within a growing tumour before and during fractionated radiation. To this end, we have extended a spatially-resolved mathematical model of tumour growth first proposed by Greenspan (Stud. Appl. Math., 1972) to investigate the effects of oxygen heterogeneity on radiation-induced cell death. In more detail, cell death due to radiation at each location in the tumour, as determined by the well-known linear-quadratic model, is assumed also to depend on the local oxygen concentration. The oxygen concentration is governed by a reaction-diffusion equation that is coupled to an integro-differential equation that determines the size of the assumed spherically-symmetric tumour. We combine numerical and analytical techniques to investigate radiation response of tumours with different intra-tumoral oxygen distribution profiles. Model simulations reveal a rapid transient increase in hypoxia upon re-growth of the tumour spheroid post-irradiation. We investigate the response to different radiation fractionation schedules and identify a tumour-specific relationship between inter-fraction time and dose per fraction to achieve cure. The rich dynamics exhibited by the model suggest that spatial heterogeneity may be important for predicting tumour response to radiotherapy for clinical applications.

cancer biology↗

bioRxiv2017

Recasting the cancer stem cell hypothesis: unification using a continuum model of microenvironmental forces

Since the first evidence for cancer stem cells in leukemia, experimentalists have sought to identify tumorigenic subpopulations in solid tumors. In parallel, scientists have argued over the implications of the existence of this subpopulation. On one side, the cancer stem cell hypothesis posits that a small subset of cells within a tumor are responsible for tumorigenesis and are capable of recapitulating the entire tumor on their own. Under this hypothesis, a tumor may be conceptualized as a series of coupled compartments, representing populations of progressively differentiated cell types, starting from stem cells. The allure of this model is that it elegantly explains our therapeutic failures: we have been targeting the wrong cells. Alternatively, the stochastic model states that all cells in a tumor can have stem-like properties, and have an equally small capability of forming a tumor. As tumors are, by nature, heterogeneous, there is ample evidence to support both hypotheses. We propose a mechanistic mathematical description that integrates these two theories, settling the dissonance between the schools of thought and providing a road map for integrating disparate experimental results into a single theoretical framework. We present experimental results from clonogenic assays that demonstrate the importance of defining this novel formulation, and the clarity that is provided when interpreting these results through the lens of this formulation.

cancer biology↗

bioRxiv2017

Semblance Of Heterogeneity In Collective Cell Migration

Cell population heterogeneity is increasingly a focus of inquiry in biological research. For example, cell migration studies have investigated the heterogeneity of invasiveness and taxis in development, wound healing, and cancer. However, relatively little effort has been devoted to explore when heterogeneity is mechanistically relevant and how to reliably measure it. Statistical methods from the animal movement literature offer the potential to analyse heterogeneity in collections of cell tracking data. A popular measure of heterogeneity, which we use here as an example, is the distribution of delays in directional cross-correlation. Using a suitably generic, yet minimal, model of collective cell movement in three dimensions, we show how using such measures to quantify heterogeneity in tracking data can result in the inference of heterogeneity where there is none. Our study highlights a potential pitfall in the statistical analysis of cell population heterogeneity, and we argue this can be mitigated by the appropriate choice of null models.\n\nHighlightsO_LIgroups of identical cells appear heterogeneous due to limited sampling and experimental repeatability\nC_LIO_LIheterogeneity bias increases with attraction/repulsion between cells\nC_LIO_LImovement in confined environments decreases apparent heterogeneity\nC_LIO_LIhypothetical applications in neural crest and in vitro cancer systems\nC_LI\n\nIn BriefWe use a mathematical model to show how cell populations can appear heterogeneous in their migratory characteristics, even though they are made up of identically-behaving individual cells. This has important consequences for the study of collective cell migration in areas such as embryo development or cancer invasion.

systems biology↗

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↗