This article is part of the supplement: Research from the Eleventh International Workshop on Network Tools and Applications in Biology (NETTAB 2011)
Modelling non-homogeneous stochastic reaction-diffusion systems: the case study of gemcitabine-treated non-small cell lung cancer growth
The Microsoft Research - University of Trento Centre for Computational and Systems Biology, Rovereto, Italy
BMC Bioinformatics 2012, 13(Suppl 14):S14 doi:10.1186/1471-2105-13-S14-S14Published: 7 September 2012
Reaction-diffusion based models have been widely used in the literature for modeling the growth of solid tumors. Many of the current models treat both diffusion/consumption of nutrients and cell proliferation. The majority of these models use classical transport/mass conservation equations for describing the distribution of molecular species in tumor spheroids, and the Fick's law for describing the flux of uncharged molecules (i.e oxygen, glucose). Commonly, the equations for the cell movement and proliferation are first order differential equations describing the rate of change of the velocity of the cells with respect to the spatial coordinates as a function of the nutrient's gradient. Several modifications of these equations have been developed in the last decade to explicitly indicate that the tumor includes cells, interstitial fluids and extracellular matrix: these variants provided a model of tumor as a multiphase material with these as the different phases. Most of the current reaction-diffusion tumor models are deterministic and do not model the diffusion as a local state-dependent process in a non-homogeneous medium at the micro- and meso-scale of the intra- and inter-cellular processes, respectively. Furthermore, a stochastic reaction-diffusion model in which diffusive transport of the molecular species of nutrients and chemotherapy drugs as well as the interactions of the tumor cells with these species is a novel approach. The application of this approach to he scase of non-small cell lung cancer treated with gemcitabine is also novel.
We present a stochastic reaction-diffusion model of non-small cell lung cancer growth in the specification formalism of the tool Redi, we recently developed for simulating reaction-diffusion systems. We also describe how a spatial gradient of nutrients and oncological drugs affects the tumor progression. Our model is based on a generalization of the Fick's first diffusion law that allows to model diffusive transport in non-homogeneous media. The diffusion coefficient is explicitly expressed as a function depending on the local conditions of the medium, such as the concentration of molecular species, the viscosity of the medium and the temperature. We incorporated this generalized law in a reaction-based stochastic simulation framework implementing an efficient version of Gillespie algorithm for modeling the dynamics of the interactions between tumor cell, nutrients and gemcitabine in a spatial domain expressing a nutrient and drug concentration gradient.
Using the mathematical framework of model we simulated the spatial growth of a 2D spheroidal tumor model in response to a treatment with gemcitabine and a dynamic gradient of oxygen and glucose. The parameters of the model have been taken from recet literature and also inferred from real tumor shrinkage curves measured in patients suffering from non-small cell lung cancer. The simulations qualitatively reproduce the time evolution of the morphologies of these tumors as well as the morphological patterns follow the growth curves observed in patients.
s This model is able to reproduce the observed increment/decrement of tumor size in response to the pharmacological treatment with gemcitabine. The formal specification of the model in Redi can be easily extended in an incremental way to include other relevant biophysical processes, such as local extracellular matrix remodelling, active cell migration and traction, and reshaping of host tissue vasculature, in order to be even more relevant to support the experimental investigation of cancer.