Modelling the Impact of HIF on Metabolism and the Extracellular Matrix: Consequences for Tumour Growth and Invasion.

The extracellular matrix (ECM) is a complex structure involved in many biological processes with collagen being the most abundant protein. Density of collagen fibers in the matrix is a factor influencing cell motility and migration speed. In cancer, this affects the ability of cells to migrate and invade distant tissues which is relevant for designing new therapies.

A biomechanical model for cell sensing and migration.

We developed an original computational model for cell deformation and migration capable of accounting for the cell sensitivity to the environment and its appropriate adaptation. This cell model is ultimately intended to be used to address tissue morphogenesis. Hence it has been designed to comply with four requirements: (1) the cell should be able to probe and sense its environment and respond accordingly; (2) the model should be easy to parametrize to adapt to different cell types; (3) the model should be able to extend to 3D cases; (4) simulations should be fast enough to integrate many interacting cells.

Is Cancer Metabolism an Atavism?

The atavistic theory of cancer posits that cancer emerges and progresses through the reversion of cellular phenotypes to more ancestral types with genomic and epigenetic changes deactivating recently evolved genetic modules and activating ancient survival mechanisms. This theory aims at explaining the known cancer hallmarks and the paradox of cancer's predictable progression despite the randomness of genetic mutations. Lineweaver and colleagues recently proposed the Serial Atavism Model (SAM), an enhanced version of the atavistic theory, which suggests that cancer progression involves multiple atavistic reversions where cells regress through evolutionary stages, losing recently evolved traits first and reactivating primitive ones later.

On the Importance of Acidity in Cancer Cells and Therapy.

Cancer cells are associated with high glycolytic activity, which results in acidification of the tumor microenvironment. The occurrence of this stressful condition fosters tumor aggressiveness, with the outcome of invasiveness and metastasis that are linked to a poor clinical prognosis. Acidosis can be both the cause or consequence of alterations in the functions and expressions of transporters involved in intracellular acidity regulation.

Characterization of the Intracellular Acidity Regulation of Brain Tumor Cells and Consequences for Therapeutic Optimization of Temozolomide.

A well-known feature of tumor cells is high glycolytic activity, leading to acidification of the tumor microenvironment through extensive lactate production. This acidosis promotes processes such as metastasis, aggressiveness, and invasiveness, which have been associated with a worse clinical prognosis. Moreover, the function and expression of transporters involved in regulation of intracellular pH might be altered.

Generalization of the Ratiometric Method to Extend pH Range Measurements of the BCECF Probe.

There is a variety of fluorescent probes for pH measurements and which are mainly used for biological systems. In general, they can be classified into two groups. The first group includes fluorescent pH probes which exhibit a single fluorescence emission peak.

A reduced model of cell metabolism to revisit the glycolysis-OXPHOS relationship in the deregulated tumor microenvironment.

Cancer cells metabolism focuses the interest of the cancer research community. Although this process is intensely studied experimentally, there are very few theoretical models that address this issue. One of the main reasons is the extraordinary complexity of the metabolism that involves numerous interdependent regulatory networks which makes the computational recreation of this complexity illusory.

Searching for the Metabolic Signature of Cancer: A Review from Warburg's Time to Now.

This review focuses on the evolving understanding that we have of tumor cell metabolism, particularly glycolytic and oxidative metabolism, and traces back its evolution through time. This understanding has developed since the pioneering work of Otto Warburg, but the understanding of tumor cell metabolism continues to be hampered by misinterpretation of his work. This has contributed to the use of the new concepts of and ， that are out of step with reality.

Metabolic Reprogramming, Questioning, and Implications for Cancer.

The expression "metabolic reprogramming" has been encountered more and more in the literature since the mid-1990s. It seems to encompass several notions depending on the author, but the lack of a clear definition allows it to be used as a "catch-all" expression. Our first intention is to point out the inconsistencies in the use of the reprogramming terminology for cancer metabolism.

pH as a potential therapeutic target to improve temozolomide antitumor efficacy : A mechanistic modeling study.

Despite intensive treatments including temozolomide (TMZ) administration, glioblastoma patient prognosis remains dismal and innovative therapeutic strategies are urgently needed. A systems pharmacology approach was undertaken to investigate TMZ pharmacokinetics-pharmacodynamics (PK-PD) incorporating the effect of local pH, tumor spatial configuration and micro-environment. A hybrid mathematical framework was designed coupling ordinary differential equations describing the intracellular reactions, with a spatial cellular automaton to individualize the cells.

Systems Biology, Systems Medicine, Systems Pharmacology: The What and The Why.

Systems biology is today such a widespread discipline that it becomes difficult to propose a clear definition of what it really is. For some, it remains restricted to the genomic field. For many, it designates the integrated approach or the corpus of computational methods employed to handle the vast amount of biological or medical data and investigate the complexity of the living.

Towards the Design of a Patient-Specific Virtual Tumour.

The design of a patient-specific virtual tumour is an important step towards Personalized Medicine. However this requires to capture the description of many key events of tumour development, including angiogenesis, matrix remodelling, hypoxia, and cell state heterogeneity that will all influence the tumour growth kinetics and degree of tumour invasiveness. To that end, an integrated hybrid and multiscale approach has been developed based on data acquired on a preclinical mouse model as a proof of concept.

Role of compartmentalization on HiF-1α degradation dynamics during changing oxygen conditions: a computational approach.

HiF-1α is the central protein driving the cellular response to hypoxia. Its accumulation in cancer cells is linked to the appearance of chemoresistant and aggressive tumor phenotypes. As a consequence, understanding the regulation of HiF-1α dynamics is a major issue to design new anti-cancer therapies.

On the importance of the submicrovascular network in a computational model of tumour growth.

A computational model is potentially a powerful tool to apprehend complex phenomena like solid tumour growth and to predict the outcome of therapies. To that end, the confrontation of the model with experiments is essential to validate this tool. In this study, we develop a computational model specifically dedicated to the interpretation of tumour growth as observed in a mouse model with a dorsal skinfold chamber.

Mathematical modelling and numerical simulations of actin dynamics in the eukaryotic cell.

The aim of this article is to study cell deformation and cell movement by considering both the mechanical and biochemical properties of the cortical network of actin filaments and its concentration. Actin is a polymer that can exist either in filamentous form (F-actin) or in monometric form (G-actin) (Chen et al. in Trends Biochem Sci 25:19-23, 2000) and the filamentous form is arranged in a paired helix of two protofilaments (Ananthakrishnan et al.

A computational model of cell migration coupling the growth of focal adhesions with oscillatory cell protrusions.

Cell migration is a highly integrated process where actin turnover, actomyosin contractility, and adhesion dynamics are all closely linked. In this paper, we propose a computational model investigating the coupling of these fundamental processes within the context of spontaneous (i.e.

The motility of normal and cancer cells in response to the combined influence of the substrate rigidity and anisotropic microstructure.

Cell adhesion and migration are strongly influenced by extracellular matrix (ECM) architecture and rigidity, but little is known about the concomitant influence of such environmental signals to cell responses, especially when considering cells of similar origin and morphology, but exhibiting a normal or cancerous phenotype. Using micropatterned polydimethylsiloxane substrates (PDMS) with tunable stiffness (500 kPa, 750 kPa, 2000 kPa) and topography (lines, pillars or unpatterned), we systematically analyse the differential response of normal (3T3) and cancer (SaI/N) fibroblastic cells. Our results demonstrate that both cells exhibit differential morphology and motility responses to changes in substrate rigidity and microtopography.

Spatiotemporal dynamics of actin-rich adhesion microdomains: influence of substrate flexibility.

In this study we analyse the formation and dynamics of specific actin-rich structures called podosomes. Podosomes are very dynamic punctual adhesion sites tightly linked to the actin cytoskeleton. Mechanical properties of substrates are emerging as important physical modulators of anchorage-dependent processes involved in the cellular response.

Cytomechanics of cell deformations and migration: from models to experiments.

A cytomechanical model bas been proposed to analyse cell-cell interactions and cell migration through chemotaxis. We consider as the leading assumption that the cell cortical tension is locally modified by the protrusive activity of neighbour cells and binding of chemoattractant molecules to membrane receptors respectively. The model derives from the one initially proposed by Alt and Tranquillo (1995), which successfully describes experimentally observed cyclic autonomous cell shape changes.