An in-silico study of cancer cell survival and spatial distribution within a 3D microenvironment

Abstract

3D cell cultures are in-vitro models representing a significant improvement with respect to traditional monolayers. Their diffusion and applicability, however, are hampered by the complexity of 3D systems, that add new physical variables for experimental analyses. In order to account for these additional features and improve the study of 3D cultures, we here present SALSA (ScAffoLd SimulAtor), a general purpose computational tool that can simulate the behavior of a population of cells cultured in a 3D scaffold. This software allows for the complete customization of both the polymeric template structure and the cell population behavior and characteristics. In the following the technical description of SALSA will be presented, together with its validation and an example of how it could be used to optimize the experimental analysis of two breast cancer cell lines cultured in collagen scaffolds. This work contributes to the growing field of integrated in-silico/in-vitro analysis of biological systems, which have great potential for the study of complex cell population behaviours and could lead to improve and facilitate the effectiveness and diffusion of 3D cell culture models. Cell culture is currently experiencing a fundamental shift from traditional 2D to 3D systems, that are more realistic representations of a biological tissue. These novel approaches, that integrate important aspects of cellular habitat, such as a non-uniform microenvironment, more complex diffusion processes and cell interactions with local physical features of the synthetic extracellular matrix (ECM), are bound to provide fundamental insights into cell biology, generating a closer approximation of reality as shown in 1-4. However, in order for 3D systems to become the standard in-vitro cell culturing technique, several issues still need to be addressed. In fact, the increased complexity in structural properties is, at the same time, the added value of these experimental systems and the limitation in optimising biological assays and protocols originally standardised for cells grown on 2D plastic surfaces. This complicates experimental design and data collection. While innovative 3D native assays are being developed 5,6 , computational models can complement the wet-lab experimental activity and help to address some of the limitations of 3D culture settings 7-9. The mathematical formalization of complex behaviours, however, is often maintained separate from the experimental analysis. As an example there are multiple models describing cancer-related cellular processes 10-17 and the effect of antineoplastic therapies 18-24 but most of them are presented as theoretical frameworks that do not aim at driving the experimental activity. To integrate this important functionality we developed a general purpose scaffold simulator named SALSA that can be programmed to reproduce the behaviour of a population of arbitrary cells, grown in 3D scaffolds of tunable size and material. It relies on a custom hybrid continuous/discrete framework that is particularly b...

Perfusion Flow Enhances Viability and Migratory Phenotype in 3D-Cultured Breast Cancer Cells

“…While a hypoxic core occurring in 3D culturing systems in standard static condition results in a non-uniform cell distribution within the 3D structure and could affect cell viability in inner regions, 13 , 19 , 33 in our system, perfusion also determines a more homogenous distribution of cells, as shown in Fig. 4 .…”

“…In this respect, culture conditions largely differ from 2D culture, where all the cells have uniform access to oxygen, nutrients and soluble molecules, such as drugs or cytokines. Indeed, multiple studies 13 , 19 , 33 have shown a non-uniform cell distribution and biological behavior within a 3D scaffold, that often suffers impeded diffusion of oxygen and nutrients inside its structure. Perfusion bioreactor systems have been used to improve medium transport within a scaffold that can contribute to reproduce physiological in vivo conditions, as suggested by many examples published by our or other research groups.…”

In Vitro/Ex Vivo Models for the Study of Ischemia Reperfusion Injury during Kidney Perfusion

“…Another interest is the compatibility of these in vitro perfusion systems with a computational tool to model cell-cell, cell-surface, and cell-medium interactions in an in silico mathematical model. This in silico study by computational tool is compatible with single-cell population cultures, co-culture model [87], or 3D microenvironment [88]. Indeed, to comprehend and predict such complex cell culture phenomena, and in designing of optimised cell culture conditions, mathematical modelling and numerical simulations are effective strategies [89].…”

Navigating Multi-Scale Cancer Systems Biology Towards Model-Driven Clinical Oncology and Its Applications in Personalized Therapeutics

“…To model cell population-level behavior in cancer, researchers are increasingly developing innovative cell lines in silico models which can complement in vivo wet-lab experiments, while overcoming wet-lab limitations ( 206 ) ( Figure 2F ). Such models are employed to investigate cell-to-cell interactions as well as evaluate physical features of the synthetic extracellular matrix (ECM) ( 206 ), etc ( 175 , 207 ). Amongst initial attempts at developing in silico cell line models, in 1989, Shackney et al ( 175 ) proposed an in silico cancer cell model to study tumor evolution.…”